Run	Bins	Run Details	Motif	Z-score	Known Match	Match details	Pos. Bias	Best Domain	Best Domain pval	Domain Overlap Z-score	Best GO term	Motif-Motif Interaction?	Mutual information (MI)	Robustness
protein_40_YPR119W	2	CLB2:  B-type cyclin involved in cell cycle progression; activates Cdc28p to promote the transition from G2 to M phase; accumulates during G2 and M, then targeted via a destruction box motif for ubiquitin-mediated degradation by the proteasome	SP.[RK]	312	SP.[RK]	CDK kinase substrate motif	Y	Pkinase	1.E-04	-3.5	cell cycle (1e-16)	Y	0.055	10
protein_40_YBR160W	2	CDC28:  Catalytic subunit of the main cell cycle cyclin-dependent kinase (CDK); alternately associates with G1 cyclins (CLNs) and G2/M cyclins (CLBs) which direct the CDK to specific substrates	SP.[RK]	295	SP.[RK]	CDK kinase substrate motif	Y	Pkinase	1.E-04	-3.5	cell cycle (1e-17)	Y	0.053	10
yeast-256_GO-0016462	2	pyrophosphatase activity	G.GK[TS]	227	SG.G	Glycosaminoglycan attachment site		ABC_tran	1.E-19	4.5	nucleoside-triphosphatase activity (1e-11)	Y	0.047	10
yeast-238_GO-0017111	2	nucleoside-triphosphatase activity	G.GK[ST]	221	SG.G	Glycosaminoglycan attachment site		AAA	1.E-18	5.5	nucleoside-triphosphatase activity (1e-11)	Y	0.048	10
yeast-335_GO-0016772	2	transferase activity, transferring phosphorus-containing groups	[KVY][LIY].DFG	205				Pkinase	1.E-85	8.1	protein kinase activity (1e-85)		0.046	10
yeast-335_GO-0016772	2	transferase activity, transferring phosphorus-containing groups	H.D[LIC]K	197				Pkinase	1.E-09	8.5	protein kinase activity (1e-09)		0.044	10
yeast-335_GO-0016772	2	transferase activity, transferring phosphorus-containing groups	H[RCW]D[ILMV]	168				Pkinase	1.E-90	8.3	protein kinase activity (1e-90)	Y	0.038	10
protein_40_YAR019C	2	CDC15:  Protein kinase of the Mitotic Exit Network that is localized to the spindle pole bodies at late anaphase; promotes mitotic exit by directly switching on the kinase activity of Dbf2p	H[RQS]D[ILM]K	167			Y	Pkinase	1.E-29	5.4	protein kinase activity (1e-24)	Y	0.018	10
protein_40_YDL153C	2	SAS10:  Component of the small (ribosomal) subunit (SSU) processosome required for pre-18S rRNa processing; essential nucleolar protein that, when overproduced, disrupts silencing	H[RCS]D[ILV]K	165				Pkinase	1.E-27	4.8	protein kinase activity (1e-24)		0.017	10
protein_40_YNL272C	2	SEC2:  Guanyl-nucleotide exchange factor for the small G-protein Sec4p, located on cytoplasmic vesicles; essential for post-Golgi vesicle transport	[HVY]RD[LIM]K	154				Pkinase	1.E-30	5	protein kinase activity (1e-31)	Y	0.017	10
yeast-1974_GO-0005634	2	nucleus	K[KRP].K	154	K[KR].[KR]	Nuclear localization motif		Zn_clus	1.E-07	6.4	nuclear lumen (1e-10)		0.032	10
yeast-685_GO-0016740	2	transferase activity	H[RCG]D[ILMV]K	151				Pkinase	1.E-09	8.7	protein kinase activity (1e-97)		0.033	10
protein_40_YAR019C	2	CDC15:  Protein kinase of the Mitotic Exit Network that is localized to the spindle pole bodies at late anaphase; promotes mitotic exit by directly switching on the kinase activity of Dbf2p	[KLY][ILY].DFG	148			Y	Pkinase	1.E-28	4.9	protein kinase activity (1e-28)		0.015	10
yeast-685_GO-0016740	2	transferase activity	[KVY][LIV].DFG	148				Pkinase	1.E-89	8	protein kinase activity (1e-88)		0.033	10
yeast-238_GO-0017111	2	nucleoside-triphosphatase activity	[WFL]D..GQ[EDP]	136	D..G	motif that binds phosphate in GDP and GTP binding proteins		Ras	1.E-37	2.7	GTPase activity (1e-38)		0.020	10
protein_40_YNL272C	2	SEC2:  Guanyl-nucleotide exchange factor for the small G-protein Sec4p, located on cytoplasmic vesicles; essential for post-Golgi vesicle transport	[KVE][ILV].DFG	136				Pkinase	1.E-28	4.5	protein kinase activity (1e-29)		0.014	10
yeast-335_GO-0016772	2	transferase activity, transferring phosphorus-containing groups	Y.[ASG]PE	132	E.Y.[QSG]	Protease TEV		Pkinase	1.E-89	7.4	protein kinase activity (1e-85)	Y	0.030	10
yeast-335_GO-0016772	2	transferase activity, transferring phosphorus-containing groups	D[ILMV]W[SAQ]	132	PWDLW	LIG_Clathr_ClatBox_2		Pkinase	1.E-85	8	protein kinase activity (1e-88)	Y	0.029	10
protein_40_YDL153C	2	SAS10:  Component of the small (ribosomal) subunit (SSU) processosome required for pre-18S rRNa processing; essential nucleolar protein that, when overproduced, disrupts silencing	DFG[LSF][ACV]	131				Pkinase	1.E-23	4.4	protein kinase activity (1e-23)		0.014	10
yeast-1074_GO-0044428	2	nuclear part	DE[EDK][ED]	131	YDE[PDV]	SH2 ligand for Nck1 and Nck2 (Tyr must be phosphorylated)	Y				nuclear lumen (1e-09)	Y	0.026	10
protein_40_YNL186W	2	UBP10:  Ubiquitin-specific protease that deubiquitinates ubiquitin-protein moieties; may regulate silencing by acting on Sir4p; involved in posttranscriptionally regulating Gap1p and possibly other transporters; primarily located in the nucleus	[RSL]D[LIV]KP	129	DALDL	14-3-3 binding motif in ExoS		Pkinase	1.E-28	3.9	protein kinase activity (1e-25)		0.014	10
yeast-335_GO-0016772	2	transferase activity, transferring phosphorus-containing groups	[ILMV]K..N[ILV]L	129				Pkinase	1.E-83	7.9	protein kinase activity (1e-85)	Y	0.029	10
yeast-335_GO-0016772	2	transferase activity, transferring phosphorus-containing groups	KP.N[IVL][LMF]	128				Pkinase	1.E-72	6.6	protein kinase activity (1e-68)		0.028	10
ubiquitin_peng2003	2	ubiquitin_peng2003	L..[LDS]A	125			Y	IBN_N	1.E-05	-0.4	Golgi apparatus (1e-08)		0.021	10
yeast-1433_GO-0006139	2	nucleobase, nucleoside, nucleotide and nucleic acid metabolism	K[KRH].K	124	K[KR].[KR]	Nuclear localization motif		Helicase_C	1.E-06	-1.9	DNA metabolism (1e-11)	Y	0.027	10
protein_40_YNL186W	2	UBP10:  Ubiquitin-specific protease that deubiquitinates ubiquitin-protein moieties; may regulate silencing by acting on Sir4p; involved in posttranscriptionally regulating Gap1p and possibly other transporters; primarily located in the nucleus	KP.N[LIV][LM]	123			Y	Pkinase	1.E-25	3.8	protein kinase activity (1e-22)	Y	0.012	10
protein_40_YJR059W	2	PTK2:  Putative serine/threonine protein kinase involved in regulation of ion transport across plasma membrane; enhances spermine uptake	RR.[SHP]	122	[KR]R	CLV_PCSK_KEX2_1					phosphotransferase activity, alcohol group as acceptor (0.01)		0.022	10
protein_40_YDL153C	2	SAS10:  Component of the small (ribosomal) subunit (SSU) processosome required for pre-18S rRNa processing; essential nucleolar protein that, when overproduced, disrupts silencing	K[LIV].D[FW]G	121				Pkinase	1.E-23	4.2	protein kinase activity (1e-20)	Y	0.013	10
protein_40_YNL186W	2	UBP10:  Ubiquitin-specific protease that deubiquitinates ubiquitin-protein moieties; may regulate silencing by acting on Sir4p; involved in posttranscriptionally regulating Gap1p and possibly other transporters; primarily located in the nucleus	K..D[FWP]G	121				Pkinase	1.E-27	4.9	protein kinase activity (1e-23)	Y	0.013	10
matsuyama_nucleolus	2	matsuyama_nucleolus	KK.[KR][KRS]	119	K[KR].[KR]	Nuclear localization motif		Helicase_C	1.E-03	-1.2	nucleolus (1e-98)		0.029	10
yeast-335_GO-0016772	2	transferase activity, transferring phosphorus-containing groups	W[SAQ].G[CVI]	117			Y	Pkinase	1.E-79	7.4	protein kinase activity (1e-75)	Y	0.027	10
yeast-661_GO-0050789	2	regulation of biological process	N[NSE]N[SNV]	111				Zn_clus	1.E-06	-1.1	regulation of metabolism (1e-09)		0.023	10
yeast-335_GO-0016772	2	transferase activity, transferring phosphorus-containing groups	W[SA][LVC]G	111	WA.G[SH][LF]M	BOMBESIN PATTERN		Pkinase	1.E-68	7.2	protein kinase activity (1e-62)	Y	0.025	10
yeast-335_GO-0016772	2	transferase activity, transferring phosphorus-containing groups	RD[LIV][KT]	111	MR[DE][IL]	TUBULIN_B_AUTOREG PATTERN		Pkinase	1.E-86	7.8	kinase activity (1e-85)	Y	0.024	10
protein_40_YDL153C	2	SAS10:  Component of the small (ribosomal) subunit (SSU) processosome required for pre-18S rRNa processing; essential nucleolar protein that, when overproduced, disrupts silencing	W[SAG].G[ICV]	109				Pkinase	1.E-25	4.4	protein kinase activity (1e-25)		0.012	10
yeast-593_GO-0031981	2	nuclear lumen	DE[DEK][DEI]	107	YDE[PDV]	SH2 ligand for Nck1 and Nck2 (Tyr must be phosphorylated)	Y				nuclear lumen (1e-18)		0.022	10
yeast-648_GO-0050791	2	regulation of physiological process	N[SNE]N[SNV]	105				Zn_clus	1.E-06	-1.1	regulation of metabolism (1e-09)		0.022	10
protein_40_YAR019C	2	CDC15:  Protein kinase of the Mitotic Exit Network that is localized to the spindle pole bodies at late anaphase; promotes mitotic exit by directly switching on the kinase activity of Dbf2p	W[SAG][LCI]G	104				Pkinase	1.E-26	5.1	protein kinase activity (1e-24)	Y	0.012	10
protein_40_YDL153C	2	SAS10:  Component of the small (ribosomal) subunit (SSU) processosome required for pre-18S rRNa processing; essential nucleolar protein that, when overproduced, disrupts silencing	Y[RMA][AS]PE	103	SP	ERK1, ERK2 Kinase substrate motif	Y	Pkinase	1.E-19	3.6	kinase activity (1e-17)	Y	0.012	10
protein_40_YGL105W	2	ARC1:  Protein that binds tRNA and methionyl- and glutamyl-tRNA synthetases (Mes1p and Gus1p), delivering tRNA to them, stimulating catalysis, and ensuring their localization to the cytoplasm; also binds quadruplex nucleic acids	K[ILV].[DCG]FG	103				Pkinase	1.E-20	4.7	protein kinase activity (1e-20)	Y	0.010	10
yeast-256_GO-0016462	2	pyrophosphatase activity	TA.Q[ERV][RED]	101			Y	Ras	1.E-30	2.5	GTPase activity (1e-26)	Y	0.014	10
protein_40_YGL245W	2	GUS1:  Glutamyl-tRNA synthetase (GluRS), forms a complex with methionyl-tRNA synthetase (Mes1p) and Arc1p; complex formation increases the catalytic efficiency of both tRNA synthetases and ensures their correct localization to the cytoplasm	[HYA]RD[ILMV]K	101	[AG]R	Protease matriptase protease site		Pkinase	1.E-29	5.4	protein kinase activity (1e-26)		0.013	10
yeast-1074_GO-0044428	2	nuclear part	[KRN]KR[KSR]	99	KR	CLV_PCSK_PC1ET2_1		Bromodomain	1.E-03	-1.1	nuclear lumen (1e-91)	Y	0.021	10
yeast-752_GO-0016787	2	hydrolase activity	G.GK[TSH]	99	SG.G	Glycosaminoglycan attachment site		AAA	1.E-19	5.5	nucleoside-triphosphatase activity (1e-10)	Y	0.021	10
yeast-335_GO-0016772	2	transferase activity, transferring phosphorus-containing groups	[IVW]W..G[VCI]	99	[FW]W	EH(3) EF hand domain binding motif of EPS15, Class II		Pkinase	1.E-56	6.9	protein kinase activity (1e-53)	Y	0.022	10
yeast-1547_GO-0043283	2	biopolymer metabolism	K[KRN].K	98	K[KR].[KR]	Nuclear localization motif		Helicase_C	1.E-05	-1.8	DNA metabolism (1e-12)		0.020	10
protein_40_YAR019C	2	CDC15:  Protein kinase of the Mitotic Exit Network that is localized to the spindle pole bodies at late anaphase; promotes mitotic exit by directly switching on the kinase activity of Dbf2p	GT..[WY][MRI]A	98	[ST]FCGT.[ED]Y	PDK1 phosphorylation motif		Pkinase	1.E-13	4.2	kinase activity (1e-11)		0.011	10
protein_40_YNL272C	2	SEC2:  Guanyl-nucleotide exchange factor for the small G-protein Sec4p, located on cytoplasmic vesicles; essential for post-Golgi vesicle transport	[KN]P.N[LIF]L	97				Pkinase	1.E-18	3.9	protein kinase activity (1e-18)	Y	0.011	10
protein_40_YAR019C	2	CDC15:  Protein kinase of the Mitotic Exit Network that is localized to the spindle pole bodies at late anaphase; promotes mitotic exit by directly switching on the kinase activity of Dbf2p	Y.[ASF]PE	96	E.Y.[QSG]	Protease TEV		Pkinase	1.E-25	4	protein kinase activity (1e-23)		0.012	10
protein_40_YJL164C	2	TPK1:  cAMP-dependent protein kinase catalytic subunit; promotes vegetative growth in response to nutrients via the Ras-cAMP signaling pathway; inhibited by regulatory subunit Bcy1p in the absence of cAMP; partially redundant with Tpk2p and Tpk3p	R[RK].S	96	R[KER].S	PKC epsilon kinase substrate motif						Y	0.017	10
protein_40_YNL272C	2	SEC2:  Guanyl-nucleotide exchange factor for the small G-protein Sec4p, located on cytoplasmic vesicles; essential for post-Golgi vesicle transport	[LIM]K..N[ILF]L	95				Pkinase	1.E-25	4.6	protein kinase activity (1e-25)	Y	0.012	10
yeast-685_GO-0016740	2	transferase activity	Y.[ASQ]PE	95	E.Y.[QSG]	Protease TEV		Pkinase	1.E-81	7.3	protein kinase activity (1e-77)	Y	0.021	10
protein_40_YAR019C	2	CDC15:  Protein kinase of the Mitotic Exit Network that is localized to the spindle pole bodies at late anaphase; promotes mitotic exit by directly switching on the kinase activity of Dbf2p	[ILA]K..N[IVC]L	94				Pkinase	1.E-20	4	protein kinase activity (1e-15)		0.010	10
yeast-462_GO-0019222	2	regulation of metabolism	N[NEI]N	93				Zn_clus	1.E-09	-1.4	regulation of metabolism (1e-27)	Y	0.020	10
matsuyama_ER	2	matsuyama_ER	FF[TLG]	93	[FYWS][RK].GFF.R	INTEGRIN_ALPHA PATTERN		MFS_1	1.E-03	0.4	endoplasmic reticulum part (1e-31)	Y	0.023	10
yeast-299_GO-0005730	2	nucleolus	[KVA]K..K[KRH]	92	KR	CLV_PCSK_PC1ET2_1		Helicase_C	1.E-02	-1	nucleolus (1e-11)	Y	0.019	10
protein_40_YFR024C-A	2	LSB3:  Protein containing a C-terminal SH3 domain; binds Las17p, which is a homolog of human Wiskott-Aldrich Syndrome protein involved in actin patch assembly and actin polymerization	[PQ]P..P[PTM]R	92	P..P	SH3 general ligand,					actin cytoskeleton organization and biogenesis (1e-05)		0.010	10
protein_40_YNL272C	2	SEC2:  Guanyl-nucleotide exchange factor for the small G-protein Sec4p, located on cytoplasmic vesicles; essential for post-Golgi vesicle transport	W[SGA].G[CVI]	91				Pkinase	1.E-25	4.3	protein kinase activity (1e-25)		0.011	10
protein_40_YNL186W	2	UBP10:  Ubiquitin-specific protease that deubiquitinates ubiquitin-protein moieties; may regulate silencing by acting on Sir4p; involved in posttranscriptionally regulating Gap1p and possibly other transporters; primarily located in the nucleus	W[SA].G[CVI]	91				Pkinase	1.E-25	4.4	protein kinase activity (1e-25)		0.011	10
yeast-335_GO-0016772	2	transferase activity, transferring phosphorus-containing groups	[GA][LVG].YLH	91	Y[LI]	SH2 ligand for PLCgamma1 N-term.)group 3(phospho-peptide)		Pkinase	1.E-24	4.5	protein kinase activity (1e-24)		0.015	10
protein_40_YGL105W	2	ARC1:  Protein that binds tRNA and methionyl- and glutamyl-tRNA synthetases (Mes1p and Gus1p), delivering tRNA to them, stimulating catalysis, and ensuring their localization to the cytoplasm; also binds quadruplex nucleic acids	[HYE]RD[ILM]K	90				Pkinase	1.E-22	4.7	protein kinase activity (1e-20)	Y	0.010	10
protein_40_YPL093W	2	NOG1:  Putative GTPase that associates with free 60S ribosomal subunits in the nucleolus and is required for 60S ribosomal subunit biogenesis; constituent of 66S pre-ribosomal particles; member of the ODN family of nucleolar G-proteins	GR..[RKA][AGL]G	89	[AG]R	Protease matriptase protease site		DEAD	1.E-08	-1.6	RNA helicase activity (1e-07)		0.009	10
yeast-436_GO-0031323	2	regulation of cellular metabolism	N[NEI]N	89				Zn_clus	1.E-08	-1.3	regulation of cellular metabolism (1e-26)	Y	0.020	10
yeast-1062_GO-0016020	2	membrane	L[LAF]G	89	LLG	Beta2-Integrin binding motif		Mito_carr	1.E-06	0.3	intrinsic to membrane (1e-67)	Y	0.018	10
protein_40_YAR019C	2	CDC15:  Protein kinase of the Mitotic Exit Network that is localized to the spindle pole bodies at late anaphase; promotes mitotic exit by directly switching on the kinase activity of Dbf2p	[MRI][AM]PE	89				Pkinase	1.E-20	4.5	protein kinase activity (1e-17)		0.010	9
yeast-685_GO-0016740	2	transferase activity	D[ILMV]W[SAQ]	89	PWDLW	LIG_Clathr_ClatBox_2		Pkinase	1.E-76	7.8	protein kinase activity (1e-79)	Y	0.019	10
yeast-470_GO-0006259	2	DNA metabolism	KR.[KRM]	87	KR	CLV_PCSK_PC1ET2_1		BRCT	1.E-02	-1.4	DNA metabolism (1e-23)		0.018	10
yeast-335_GO-0016772	2	transferase activity, transferring phosphorus-containing groups	Y[CY]..G[DSE]L	87				Pkinase	1.E-13	3	protein kinase activity (1e-13)		0.011	10
protein_40_YAR019C	2	CDC15:  Protein kinase of the Mitotic Exit Network that is localized to the spindle pole bodies at late anaphase; promotes mitotic exit by directly switching on the kinase activity of Dbf2p	D[IL]..EN[VIL]	87	KEN	LIG_APCC_KENbox_2		Pkinase	1.E-15	3.7	kinase activity (1e-12)	Y	0.008	10
yeast-685_GO-0016740	2	transferase activity	W[SAQ].G[CVI]	87			Y	Pkinase	1.E-75	7.6	protein kinase activity (1e-72)	Y	0.019	10
yeast-462_GO-0019222	2	regulation of metabolism	[SAQ]S..[NSP]S	86	S..[ST]	Casein Kinase I consensus phosphorylation site (N-term Ser must first be phosphorylated)		Zn_clus	1.E-09	-0.9	regulation of metabolism (1e-19)		0.017	10
yeast-335_GO-0016772	2	transferase activity, transferring phosphorus-containing groups	G[TSN]..Y[ILMV]A	86	Y[VLTFIC]	LIG_SH2_STAT5		Pkinase	1.E-34	5.3	protein kinase activity (1e-34)		0.017	10
yeast-255_GO-0007028	2	cytoplasm organization and biogenesis	[KVQ]K..K[KRH]	85	KR	CLV_PCSK_PC1ET2_1		DEAD	1.E-03	-0.9	cytoplasm organization and biogenesis (1e-10)	Y	0.018	10
yeast-255_GO-0042254	2	ribosome biogenesis and assembly	[KVQ]K..K[KRH]	85	KR	CLV_PCSK_PC1ET2_1		DEAD	1.E-03	-0.8	cytoplasm organization and biogenesis (1e-10)	Y	0.018	10
yeast-376_GO-0019219	2	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism	N[NEI]N	84				Zn_clus	1.E-08	-1.4	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism (1e-24)	Y	0.017	10
yeast-217_GO-0007046	2	ribosome biogenesis	[KVQ]K..K[KRH]	84	KR	CLV_PCSK_PC1ET2_1		DEAD	1.E-04	-1.2	ribosome biogenesis (1e-10)	Y	0.018	10
protein_40_YAR019C	2	CDC15:  Protein kinase of the Mitotic Exit Network that is localized to the spindle pole bodies at late anaphase; promotes mitotic exit by directly switching on the kinase activity of Dbf2p	KP[EQA]N[IVF]	84	FKPY	TLA binding motif in Brinker transcription factor for binding TLA domain in Groucho		Pkinase	1.E-16	3.4	kinase activity (1e-13)	Y	0.009	10
protein_40_YKL014C	2	URB1:  Nucleolar protein required for the normal accumulation of 25S and 5.8S rRNAs, associated with the 27SA2 pre-ribosomal particle; proposed to be involved in the biogenesis of the 60S ribosomal subunit	[TEA]RE[LH]A	84	[AG]R	Protease matriptase protease site	Y	DEAD	1.E-06	3.5	ATP-dependent RNA helicase activity (1e-07)	Y	0.009	10
oshea_nucleolus	2	oshea_nucleolus	[KAV]K..K[KRH]	84	KR	CLV_PCSK_PC1ET2_1					nucleolus (1e-76)		0.017	10
matsuyama_ER	2	matsuyama_ER	I..[FLT]F	84	D..SII.FF	CK I delta kinase phosphorylation site (peptide screen)					endoplasmic reticulum part (1e-33)	Y	0.020	10
protein_40_YPR119W	2	CLB2:  B-type cyclin involved in cell cycle progression; activates Cdc28p to promote the transition from G2 to M phase; accumulates during G2 and M, then targeted via a destruction box motif for ubiquitin-mediated degradation by the proteasome	E.E[DKY]	83	Y.E.E	Src phosphorylation site		PH	1.E-03	-1.2	cell cycle (1e-15)		0.015	10
protein_40_YNL186W	2	UBP10:  Ubiquitin-specific protease that deubiquitinates ubiquitin-protein moieties; may regulate silencing by acting on Sir4p; involved in posttranscriptionally regulating Gap1p and possibly other transporters; primarily located in the nucleus	[ILMV]W..G[VCI]	82				Pkinase	1.E-23	4.4	protein kinase activity (1e-23)	Y	0.009	10
protein_40_YIL035C	2	CKA1:  Alpha catalytic subunit of casein kinase 2, a Ser/Thr protein kinase with roles in cell growth and proliferation; the holoenzyme also contains CKA2, CKB1 and CKB2, the many substrates include transcription factors and all RNA polymerases	ED..[EVK][EDQ]	82							nuclear lumen (1e-11)		0.015	10
yeast-335_GO-0016772	2	transferase activity, transferring phosphorus-containing groups	[LIR]K.[EQW]N	81	[VILAFP]K.E	Motif recognized for modification by SUMO-1		Pkinase	1.E-58	6.2	transferase activity, transferring phosphorus-containing groups (1e-86)	Y	0.017	10
yeast-685_GO-0016740	2	transferase activity	[LIM]K..N[ILV]L	81			Y	Pkinase	1.E-76	8	protein kinase activity (1e-77)	Y	0.018	10
yeast-661_GO-0050789	2	regulation of biological process	Q[QHD]Q	80	GQDQTKQQI	43_KD_POSTSYNAPTIC PATTERN		zf-C2H2	1.E-04	0	regulation of metabolism (1e-09)		0.017	10
matsuyama_ER	2	matsuyama_ER	L..F[LFI]	80				MFS_1	1.E-03	0.9	endoplasmic reticulum part (1e-31)	Y	0.020	10
protein_40_YBR160W	2	CDC28:  Catalytic subunit of the main cell cycle cyclin-dependent kinase (CDK); alternately associates with G1 cyclins (CLNs) and G2/M cyclins (CLBs) which direct the CDK to specific substrates	E.E[KDY]	79	Y.E.E	Src phosphorylation site		Pkinase	1.E-03	0	cell cycle (1e-19)	Y	0.014	10
matsuyama_ER	2	matsuyama_ER	I...[LFY]F	79	L...I...[IL]	Corepressor nuclear box motif binds to nuclear receptors		MFS_1	1.E-06	1.4	endoplasmic reticulum part (1e-17)	Y	0.019	10
protein_40_YBR160W	2	CDC28:  Catalytic subunit of the main cell cycle cyclin-dependent kinase (CDK); alternately associates with G1 cyclins (CLNs) and G2/M cyclins (CLBs) which direct the CDK to specific substrates	V..[TSP]P	78	[ST]P	LIG_WW_4		Pkinase	1.E-05	-1.7	site of polarized growth (1e-11)	Y	0.014	10
yeast-341_GO-0045449	2	regulation of transcription	N[NEI]N	78				Zn_clus	1.E-09	-1.3	regulation of transcription (1e-23)	Y	0.016	10
yeast-238_GO-0017111	2	nucleoside-triphosphatase activity	TA..E[RED][FY]	78				Ras	1.E-33	2.6	GTPase activity (1e-30)	Y	0.012	10
protein_40_YDL153C	2	SAS10:  Component of the small (ribosomal) subunit (SSU) processosome required for pre-18S rRNa processing; essential nucleolar protein that, when overproduced, disrupts silencing	K[PV].N.L	78				Pkinase	1.E-17	3.6	protein kinase activity (1e-14)		0.010	10
yeast-335_GO-0016772	2	transferase activity, transferring phosphorus-containing groups	[ILV]G.G[SAT]F	78	G[GA]G[ASC][FY]S.K[DE]	ADOMET_SYNTHETASE_2 PATTERN	Y	Pkinase	1.E-36	5.2	protein kinase activity (1e-36)		0.016	10
yeast-335_GO-0016772	2	transferase activity, transferring phosphorus-containing groups	[YW][RMI].PE	78	[IVL].Y[FM].P	SHP2 N-terminal SH2 domain binding motif		Pkinase	1.E-65	6.7	protein kinase activity (1e-59)	Y	0.018	10
yeast-504_GO-0006350	2	transcription	N[NTP]N[NAP]	77	PNAY	CrkII motif in C-terminal SH3 domain required for Abl activation	Y	Zn_clus	1.E-03	-0.7	transcription (1e-10)		0.016	10
yeast-312_GO-0006414	2	translational elongation	D[VM].F[GQ]	77			Y	Ribosomal_60s	1.E-11	1.6	translational elongation (1e-21)	Y	0.010	10
yeast-685_GO-0016740	2	transferase activity	K[PTA].N[ILMV]L	77				Pkinase	1.E-62	7.3	protein kinase activity (1e-65)	Y	0.017	10
yeast-1939_GO-0003824	2	catalytic activity	HRD[ILMV][KIP]	77	[LIVMF]PCHR[LIVMF][LIVMF]	MGMT PATTERN		Pkinase	1.E-82	7.8	protein kinase activity (1e-83)		0.016	10
protein_40_YOR061W	2	CKA2:  Alpha' catalytic subunit of casein kinase 2, a Ser/Thr protein kinase with roles in cell growth and proliferation; the holoenzyme also contains CKA1, CKB1 and CKB2, the many substrates include transcription factors and all RNA polymerases	D[EDC][ESH]D	77	DEHD	Protease Caspase 1 /ICE					RNA elongation from RNA polymerase II promoter (1e-09)		0.015	10
yeast-1115_GO-0006996	2	organelle organization and biogenesis	EE[DRN][EDI]	76	EED	Ankyrin B C-terminal motif that binds internal Ankyrin repeats		Helicase_C	1.E-03	-0.7	chromosome organization and biogenesis (1e-51)		0.016	10
yeast-256_GO-0016462	2	pyrophosphatase activity	I[LWF]D[ETM]A	76				Ras	1.E-12	1.7	nucleoside-triphosphatase activity (1e-26)	Y	0.013	10
protein_40_YLL008W	2	DRS1:  Nucleolar DEAD-box protein required for ribosome assembly and function, including synthesis of 60S ribosomal subunits; constituent of 66S pre-ribosomal particles	KP.N[LFV][LMK]	76				Pkinase	1.E-15	3.4	protein kinase activity (1e-15)		0.008	10
yeast-335_GO-0016772	2	transferase activity, transferring phosphorus-containing groups	[YWQ][RMI]AP	76				Pkinase	1.E-46	6.4	protein kinase activity (1e-44)	Y	0.017	10
yeast-685_GO-0016740	2	transferase activity	[ILMV]W..G[VCI]	76				Pkinase	1.E-67	7.2	protein kinase activity (1e-63)	Y	0.016	10
protein_40_YER125W	2	RSP5:  Ubiquitin-protein ligase involved in ubiquitin-mediated protein degradation; functions in multivesicular body sorting, heat shock response and ubiquitylation of arrested RNAPII; contains a hect (homologous to E6-AP carboxyl terminus) domain	PP.Y	76	PP.Y	LIG_WW_1						Y	0.014	10
protein_40_YBL007C	2	SLA1:  Cytoskeletal protein binding protein required for assembly of the cortical actin cytoskeleton; interacts with proteins regulating actin dynamics and proteins required for endocytosis; found in the nucleus and cell cortex; has 3 SH3 domains	[PQR]PP[LRI]P	76	PPLP	LIG_WW_2	Y				actin cortical patch (1e-05)		0.008	10
oshea_spindle_pole	2	oshea_spindle_pole	L[LGP]..[SMR]LR	76							spindle (1e-13)		0.008	10
yeast-1216_GO-0009058	2	biosynthesis	N.[SNY]S	75	N.[TS]	N-linked glycosylation site	Y	Pkinase	1.E-03	-3.4	transcription (1e-14)		0.016	10
yeast-942_GO-0043232	2	intracellular non-membrane-bound organelle	[KSA]K..K[KRV]	75	KR	CLV_PCSK_PC1ET2_1		DEAD	1.E-03	-2	nucleolus (1e-70)	Y	0.015	10
yeast-942_GO-0043228	2	non-membrane-bound organelle	[KSA]K..K[KRV]	75	KR	CLV_PCSK_PC1ET2_1		DEAD	1.E-03	-2	nucleolus (1e-70)	Y	0.015	10
yeast-376_GO-0019219	2	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism	[SAP]S..[NSP]S	75	S..[ST]	Casein Kinase I consensus phosphorylation site (N-term Ser must first be phosphorylated)		zf-C2H2	1.E-09	-1.5	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism (1e-18)	Y	0.015	10
yeast-248_GO-0016072	2	rRNA metabolism	[AKV]K..K[RKH]	75	KR	CLV_PCSK_PC1ET2_1		Helicase_C	1.E-02	-1.1	rRNA metabolism (1e-09)		0.016	10
yeast-1062_GO-0016020	2	membrane	V[GFA].F	75	F.FP	LIG_MAPK_2		MFS_1	1.E-04	1	transporter activity (1e-45)	Y	0.015	10
protein_40_YGL245W	2	GUS1:  Glutamyl-tRNA synthetase (GluRS), forms a complex with methionyl-tRNA synthetase (Mes1p) and Arc1p; complex formation increases the catalytic efficiency of both tRNA synthetases and ensures their correct localization to the cytoplasm	DFG[LMS][ACE]	75				Pkinase	1.E-16	3.7	protein kinase activity (1e-15)	Y	0.008	10
protein_40_YOR206W	2	NOC2:  Protein that forms a nucleolar complex with Mak21p that binds to 90S and 66S pre-ribosomes, as well as a nuclear complex with Noc3p that binds to 66S pre-ribosomes; both complexes mediate intranuclear transport of ribosomal precursors	R[VAL]G[RQC]T	75			Y	Helicase_C	1.E-07	7.8	RNA helicase activity (1e-08)		0.008	10
protein_40_YPR119W	2	CLB2:  B-type cyclin involved in cell cycle progression; activates Cdc28p to promote the transition from G2 to M phase; accumulates during G2 and M, then targeted via a destruction box motif for ubiquitin-mediated degradation by the proteasome	L..SP	74	SP	ERK1, ERK2 Kinase substrate motif		Pkinase	1.E-03	-1.4	bud neck (1e-06)		0.013	10
yeast-238_GO-0017111	2	nucleoside-triphosphatase activity	[LFI][YHD].PPG	74				AAA	1.E-18	4.4	ATPase activity (1e-15)		0.009	10
yeast-200_GO-0006519	2	amino acid and derivative metabolism	KM[SW][KA]S	74							amino acid activation (1e-16)	Y	0.009	10
protein_40_YMR290C	2	HAS1:  ATP-dependent RNA helicase; localizes to both the nuclear periphery and nucleolus; highly enriched in nuclear pore complex fractions; constituent of 66S pre-ribosomal particles	K[KVM]..K[KRE]	74	KR	CLV_PCSK_PC1ET2_1					cytoplasm organization and biogenesis (1e-29)	Y	0.013	10
protein_40_YOR063W	2	RPL3:  Protein component of the large (60S) ribosomal subunit, has similarity to E. coli L3 and rat L3 ribosomal proteins; involved in the replication and maintenance of killer double stranded RNA virus	DV[AV]A[RKQ]	73				DEAD	1.E-04	-1.2	nucleolus (1e-06)		0.008	9
protein_40_YGL120C	2	PRP43:  RNA helicase in the DEAH-box family, functions in both RNA polymerase I and polymerase II transcript metabolism, involved in release of the lariat-intron from the spliceosome	[KDA]K.[KVA]K	73	P.[ST]PKK.KK	Cdc2 like protein kinase substrate motif		Helicase_C	1.E-02	-0.9	nucleolus (1e-33)	Y	0.013	10
matsuyama_periphery	2	matsuyama_periphery	S[LSF]..[VGK]S	73	S[ST]	MDC1 BRCT domain binding motif	Y	Pkinase	1.E-04	-0.7	barrier septum (1e-53)	Y	0.018	10
oshea_bud_neck	2	oshea_bud_neck	S[STV][SVK]S	73	S[ST]	MDC1 BRCT domain binding motif		RhoGAP	1.E-04	0.2	site of polarized growth (1e-55)	Y	0.014	10
yeast-299_GO-0005730	2	nucleolus	DE[ADE][DSE]	73	YDE[PDV]	SH2 ligand for Nck1 and Nck2 (Tyr must be phosphorylated)	Y	DEAD	1.E-08	2.5	nucleolus (1e-12)	Y	0.016	10
protein_40_YAR019C	2	CDC15:  Protein kinase of the Mitotic Exit Network that is localized to the spindle pole bodies at late anaphase; promotes mitotic exit by directly switching on the kinase activity of Dbf2p	HP[NWP][IVF]	73	HPQ	Biotin binding motif in streptavidin	Y	Pkinase	1.E-19	3.2	kinase activity (1e-17)	Y	0.008	10
protein_40_YDL153C	2	SAS10:  Component of the small (ribosomal) subunit (SSU) processosome required for pre-18S rRNa processing; essential nucleolar protein that, when overproduced, disrupts silencing	KP[EDQ]N[ILF]	73	FKPY	TLA binding motif in Brinker transcription factor for binding TLA domain in Groucho		Pkinase	1.E-14	3.6	kinase activity (1e-12)		0.008	10
protein_40_YPL093W	2	NOG1:  Putative GTPase that associates with free 60S ribosomal subunits in the nucleolus and is required for 60S ribosomal subunit biogenesis; constituent of 66S pre-ribosomal particles; member of the ODN family of nucleolar G-proteins	[PET][TSE]REL	73	RE..E	Iron binding motif in ferritin L-chain and yeast Iron transport protein	Y	DEAD	1.E-10	4.5	ribosome assembly (1e-12)	Y	0.008	9
yeast-685_GO-0016740	2	transferase activity	W[SAG][LVC]G	73				Pkinase	1.E-65	6.9	protein kinase activity (1e-62)	Y	0.016	10
yeast-222_GO-0009308	2	amine metabolism	[KD]MS[KAI]S	73	YMPMS	PI3 Kinase p85 SH2 domain binding motif					amino acid activation (1e-19)	Y	0.009	10
protein_40_YMR047C	2	NUP116:  Subunit of the nuclear pore complex (NPC) that is localized to both sides of the pore; contains a repetitive GLFG motif that interacts with mRNA export factor Mex67p and with karyopherin Kap95p; homologous to Nup100p	[AGE]FSF[GHK]	73	F.F	WASP Homology 1 binding motif					rRNA export from nucleus (1e-17)	Y	0.008	10
yeast-413_GO-0005215	2	transporter activity	IA..[FIG][GFA]	72				Mito_carr	1.E-07	1.6	transporter activity (1e-74)	Y	0.015	10
protein_40_YDR060W	2	MAK21:  Constituent of 66S pre-ribosomal particles, required for large (60S) ribosomal subunit biogenesis; involved in nuclear export of pre-ribosomes; required for maintenance of dsRNA virus; homolog of human CAATT-binding protein	P[TLG]R[EQF]L	72	[AG]R	Protease matriptase protease site		DEAD	1.E-06	3.5	ATP-dependent RNA helicase activity (1e-07)		0.007	10
protein_40_YAR019C	2	CDC15:  Protein kinase of the Mitotic Exit Network that is localized to the spindle pole bodies at late anaphase; promotes mitotic exit by directly switching on the kinase activity of Dbf2p	G[ILMV]..[LMY]H	72				Pkinase	1.E-20	4.8	protein kinase activity (1e-17)	Y	0.010	10
yeast-335_GO-0016772	2	transferase activity, transferring phosphorus-containing groups	[MRI]APE	72	P[TS]AP	LIG_PTAP		Pkinase	1.E-55	6.5	protein kinase activity (1e-49)	Y	0.016	10
yeast-565_GO-0006464	2	protein modification	HRD[ILMV][KLS]	72	[LIVMF]PCHR[LIVMF][LIVMF]	MGMT PATTERN		Pkinase	1.E-55	6.7	protein amino acid phosphorylation (1e-63)		0.016	10
protein_40_YMR139W	2	RIM11:  Protein kinase required for signal transduction during entry into meiosis; promotes the formation of the Ime1p-Ume6p complex by phosphorylating Ime1p and Ume6p; shares similarity with mammalian glycogen synthase kinase 3-beta	[GSQ]S..[ANV]SP	72	SP	ERK1, ERK2 Kinase substrate motif							0.008	10
protein_40_YBR017C	2	KAP104:  Transportin, cytosolic karyopherin beta 2 involved in delivery of heterogeneous nuclear ribonucleoproteins to the nucleoplasm, binds rg-nuclear localization signals on Nab2p and Hrp1p, plays a role in cell-cycle progression	GG.[FGT]G[NSK]	72							nuclear organization and biogenesis (1e-06)		0.008	10
yeast-217_GO-0007046	2	ribosome biogenesis	[HFV]R.GR[TSA]	71	[AG]R	Protease matriptase protease site		DEAD	1.E-20	-2.2	ATP-dependent RNA helicase activity (1e-23)	Y	0.011	10
yeast-413_GO-0005215	2	transporter activity	[VGI]GI[VGA]	71				MFS_1	1.E-07	1.2	transporter activity (1e-76)	Y	0.015	10
yeast-238_GO-0017111	2	nucleoside-triphosphatase activity	LDE[PCH][TS]	71				ABC_tran	1.E-12	3.4	nucleoside-triphosphatase activity (1e-13)		0.009	10
protein_40_YGL105W	2	ARC1:  Protein that binds tRNA and methionyl- and glutamyl-tRNA synthetases (Mes1p and Gus1p), delivering tRNA to them, stimulating catalysis, and ensuring their localization to the cytoplasm; also binds quadruplex nucleic acids	K[PAS].N[ILF]L	71				Pkinase	1.E-19	4.3	protein kinase activity (1e-18)	Y	0.008	10
yeast-248_GO-0016072	2	rRNA metabolism	[HFG]R.GR[TRS]	71	[AG]R	Protease matriptase protease site		Helicase_C	1.E-19	9.1	ATP-dependent RNA helicase activity (1e-23)		0.012	10
yeast-462_GO-0019222	2	regulation of metabolism	QQ[QIP]	70	S[QT]Q	ATM phosphorylation of this motif on Chk2		zf-C2H2	1.E-03	-1.6	regulation of metabolism (1e-15)	Y	0.015	10
yeast-341_GO-0045449	2	regulation of transcription	[SAP]S..[NSP]S	70	S..[ST]	Casein Kinase I consensus phosphorylation site (N-term Ser must first be phosphorylated)		Zn_clus	1.E-09	-1.1	regulation of transcription (1e-17)	Y	0.014	10
protein_40_YPR119W	2	CLB2:  B-type cyclin involved in cell cycle progression; activates Cdc28p to promote the transition from G2 to M phase; accumulates during G2 and M, then targeted via a destruction box motif for ubiquitin-mediated degradation by the proteasome	[EPA]K.R	70	F.F.LK...K.R	Phosphatidylserine binding motif in PKC	Y	Pkinase	1.E-07	-1	cell cycle (1e-11)	Y	0.013	10
yeast-1062_GO-0016020	2	membrane	I[FIW]..V	70				Adaptin_N	1.E-03	0.6	transporter activity (1e-40)	Y	0.015	10
protein_40_YGR252W	2	GCN5:  Histone acetyltransferase, acetylates N-terminal lysines on histones H2B and H3; catalytic subunit of the ADA and SAGA histone acetyltransferase complexes; founding member of the Gcn5p-related N-acetyltransferase superfamily	RL.[RIY][RGL]G	70	RGG	Alternative integrin binding site in FMDV virus		Histone	1.E-06	1.6	nuclear nucleosome (1e-05)		0.007	10
protein_40_YNL186W	2	UBP10:  Ubiquitin-specific protease that deubiquitinates ubiquitin-protein moieties; may regulate silencing by acting on Sir4p; involved in posttranscriptionally regulating Gap1p and possibly other transporters; primarily located in the nucleus	[TAI]D[FW]G	70			Y	Pkinase	1.E-21	4.1	protein kinase activity (1e-18)	Y	0.008	10
protein_40_YAR019C	2	CDC15:  Protein kinase of the Mitotic Exit Network that is localized to the spindle pole bodies at late anaphase; promotes mitotic exit by directly switching on the kinase activity of Dbf2p	[YWD][MLR].PE	70	[VIL].Y[MLF].P	SHP1, SHP2 SH2 domain binding motif	Y	Pkinase	1.E-24	4.4	protein kinase activity (1e-22)	Y	0.011	10
protein_40_YOL012C	2	HTZ1:  Histone variant H2AZ, exchanged for histone H2A in nucleosomes by the SWR1 complex; involved in transcriptional regulation through prevention of the spread of silent heterochromatin	[VQ]LE[YFR]L	70									0.007	10
protein_40_YFR034C	2	PHO4:  Basic helix-loop-helix (bHLH) transcription factor of the myc-family; binds cooperatively with Pho2p to the PHO5 promoter; function is regulated by phosphorylation at multiple sites and by phosphate availability	A[AGT]R[KYW]A	70	[AG]R	Protease matriptase protease site					ribosome (1e-04)		0.007	10
protein_40_YER110C	2	KAP123:  Karyopherin beta, mediates nuclear import of ribosomal proteins prior to assembly into ribosomes and import of histones H3 and H4; localizes to the nuclear pore, nucleus, and cytoplasm; exhibits genetic interactions with RAI1	GG.F[GWV][SRL]	70	GGQ	N-methylation motif in E. coli, Gln residue in methylated, mimics CCA motif at the end of tRNA molecule	Y				snRNP protein import into nucleus (1e-04)	Y	0.008	10
oshea_nuclear_periphery	2	oshea_nuclear_periphery	F[GDT].K[PHD]A	70							nuclear pore (1e-12)		0.009	10
yeast-217_GO-0007046	2	ribosome biogenesis	E[EDS]D[EID]	69	E[ST]D	Ankyrin G binding motif in KNCQ2 and KNCQ3 potaqssium channels		Helicase_C	1.E-03	-1	ribosome biogenesis (1e-11)	Y	0.015	10
yeast-413_GO-0005215	2	transporter activity	L[FYG].G[LIT]	69				Mito_carr	1.E-16	1.5	transporter activity (1e-90)	Y	0.015	10
protein_40_YNL186W	2	UBP10:  Ubiquitin-specific protease that deubiquitinates ubiquitin-protein moieties; may regulate silencing by acting on Sir4p; involved in posttranscriptionally regulating Gap1p and possibly other transporters; primarily located in the nucleus	Y[RMT].P[EK]	69	Y..P	SH2 ligand group 1B-Crk, SH2 binding motif for ITK, Nck and RasGAP to Doc-R (needs to be Tyr phosphorylated)		Pkinase	1.E-23	3.5	protein kinase activity (1e-20)		0.009	10
protein_40_YLL008W	2	DRS1:  Nucleolar DEAD-box protein required for ribosome assembly and function, including synthesis of 60S ribosomal subunits; constituent of 66S pre-ribosomal particles	DFG[MFL][ATV]	69				Pkinase	1.E-15	3.7	protein kinase activity (1e-14)		0.007	10
yeast-324_GO-0030528	2	transcription regulator activity	R.[RPK]K	69				Zn_clus	1.E-16	13.5	transcription regulator activity (1e-19)	Y	0.014	10
protein_40_YOR174W	2	MED4:  Subunit of the RNA polymerase II mediator complex; associates with core polymerase subunits to form the RNA polymerase II holoenzyme; essential for transcriptional regulation	M[QMV][QRI]Q	69							RNA polymerase II transcription mediator activity (1e-11)		0.007	10
protein_40_YHR196W	2	UTP9:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	DE..[NAI]E[KGY]	69							snoRNA binding (1e-08)		0.007	10
protein_40_YPL093W	2	NOG1:  Putative GTPase that associates with free 60S ribosomal subunits in the nucleolus and is required for 60S ribosomal subunit biogenesis; constituent of 66S pre-ribosomal particles; member of the ODN family of nucleolar G-proteins	GR[TEF][AGK]R	68	[AG]R	Protease matriptase protease site		DEAD	1.E-11	-1.7	RNA helicase activity (1e-11)		0.007	10
yeast-504_GO-0006350	2	transcription	Q[QNH]Q	68				zf-C2H2	1.E-11	-0.9	transcription (1e-14)		0.014	10
oshea_nucleolus	2	oshea_nucleolus	[VSE][LES]DE	68	SEDEE	CKII kinase phosphorylation site (peptide screen)	Y	DEAD	1.E-06	1.3	nucleolus (1e-72)		0.013	10
yeast-413_GO-0005215	2	transporter activity	A[LVI]..G[LFV]	68				Mito_carr	1.E-10	1.4	transporter activity (1e-82)	Y	0.014	10
yeast-1062_GO-0016020	2	membrane	I..[LFV]I	68			Y	MFS_1	1.E-08	1.5	intrinsic to membrane (1e-61)	Y	0.014	10
yeast-312_GO-0006414	2	translational elongation	D[DGN][DKQ]M	68			Y	Ribosomal_60s	1.E-11	1.6	translational elongation (1e-21)	Y	0.008	9
protein_40_YKL014C	2	URB1:  Nucleolar protein required for the normal accumulation of 25S and 5.8S rRNAs, associated with the 27SA2 pre-ribosomal particle; proposed to be involved in the biogenesis of the 60S ribosomal subunit	T[GHW]..[KGH]TL	68	PTL	Motif in Fos for proteosome degredation		DEAD	1.E-10	2.9	ATP-dependent RNA helicase activity (1e-10)		0.007	10
yeast-1939_GO-0003824	2	catalytic activity	T..Y	68	[ST]FCGT.[ED]Y	PDK1 phosphorylation motif	Y	Pkinase	1.E-19	3.6	transferase activity, transferring phosphorus-containing groups (1e-61)	Y	0.015	10
protein_40_YNL272C	2	SEC2:  Guanyl-nucleotide exchange factor for the small G-protein Sec4p, located on cytoplasmic vesicles; essential for post-Golgi vesicle transport	[LKM]G..H[RDP]	68				Pkinase	1.E-12	3.7	protein kinase activity (1e-12)	Y	0.008	10
yeast-255_GO-0042254	2	ribosome biogenesis and assembly	E[EDK]..E[EKD]	67				WD40	1.E-02	-2.3	cytoplasm organization and biogenesis (1e-12)		0.014	10
yeast-255_GO-0007028	2	cytoplasm organization and biogenesis	E[EDK]..E[EKD]	67				WD40	1.E-02	-2.3	cytoplasm organization and biogenesis (1e-12)		0.014	10
protein_40_YOR272W	2	YTM1:  Constituent of 66S pre-ribosomal particles, required for maturation of the large ribosomal subunit	[RGT]R.[AGY]RA	67	[AG]R	Protease matriptase protease site		DEAD	1.E-04	-1.1	ribosomal large subunit assembly and maintenance (1e-05)	Y	0.007	10
yeast-1974_GO-0005634	2	nucleus	LK	67	F.F.LK...K.R	Phosphatidylserine binding motif in PKC		WD40	1.E-07	-0.4	nuclear lumen (1e-19)		0.014	10
yeast-1721_GO-0016043	2	cell organization and biogenesis	Q.L[LSQ]	67				HEAT	1.E-06	1.4	cellular localization (1e-74)		0.013	10
yeast-312_GO-0006414	2	translational elongation	AA.G[DG]A	67				Ribosomal_60s	1.E-08	1.5	translational elongation (1e-12)		0.009	9
yeast-335_GO-0016772	2	transferase activity, transferring phosphorus-containing groups	[ILG]G.G	67	LG.GD	Aspartyl protease active site in Presenilin also a YD motif		Pkinase	1.E-64	6	transferase activity, transferring phosphorus-containing groups (1e-16)	Y	0.014	10
yeast-685_GO-0016740	2	transferase activity	[ILH]G.G	67	LG.GD	Aspartyl protease active site in Presenilin also a YD motif	Y	Pkinase	1.E-48	6.8	transferase activity, transferring phosphorus-containing groups (1e-94)	Y	0.014	10
yeast-799_GO-0043233	2	organelle lumen	K[KRE][REH]K	67	KR	CLV_PCSK_PC1ET2_1	Y				nuclear lumen (1e-10)		0.014	10
yeast-799_GO-0031974	2	membrane-enclosed lumen	K[KRE][REH]K	67	KR	CLV_PCSK_PC1ET2_1	Y				nuclear lumen (1e-10)		0.014	10
yeast-240_GO-0006807	2	nitrogen compound metabolism	[KD]MS[KAI]S	67	YMPMS	PI3 Kinase p85 SH2 domain binding motif					amino acid activation (1e-19)	Y	0.009	10
protein_40_YPL131W	2	RPL5:  Protein component of the large (60S) ribosomal subunit with similarity to E. coli L18 and rat L5 ribosomal proteins; binds 5S rRNA and is required for 60S subunit assembly	[DAK]E.[EGW]DA	67							ribosome assembly (0.01)		0.006	9
protein_40_YIL094C	2	LYS12:  Homo-isocitrate dehydrogenase, an NAD-linked mitochondrial enzyme required for the fourth step in the biosynthesis of lysine, in which homo-isocitrate is oxidatively decarboxylated to alpha-ketoadipate	[SYK]V..AL[NLA]	67								Y	0.007	10
protein_40_YHR135C	2	YCK1:  Palmitoylated, plasma membrane-bound casein kinase I isoform; shares redundant functions with Yck2p in morphogenesis, proper septin assembly, endocytic trafficking; provides an essential function overlapping with that of Yck2p	[SEN]D.D[SDE]	67	D.D	Ribose moiety of UDP and manganese binding site in glucuronyl transferase							0.012	10
protein_40_YGL180W	2	ATG1:  Protein serine/threonine kinase, required for vesicle formation during autophagy and the cytoplasm-to-vacuole targeting (Cvt) pathway; structurally required for pre-autophagosome formation; forms a complex with Atg13p and Atg17p	[SNG]D..S	67									0.012	10
yeast-235_GO-0009653	2	morphogenesis	[STL]S..[SAD]S	66	S..[ST]	Casein Kinase I consensus phosphorylation site (N-term Ser must first be phosphorylated)		Pkinase	1.E-02	-4.6	cellular morphogenesis (1e-15)		0.014	10
yeast-235_GO-0000902	2	cellular morphogenesis	[STL]S..[SAD]S	66	S..[ST]	Casein Kinase I consensus phosphorylation site (N-term Ser must first be phosphorylated)		Pkinase	1.E-02	-4.6	cellular morphogenesis (1e-15)		0.014	10
protein_40_YPR119W	2	CLB2:  B-type cyclin involved in cell cycle progression; activates Cdc28p to promote the transition from G2 to M phase; accumulates during G2 and M, then targeted via a destruction box motif for ubiquitin-mediated degradation by the proteasome	L..T[QPD]	66				Pkinase	1.E-02	-2.1	mitotic cell cycle (1e-08)		0.012	10
protein_40_YDR145W	2	TAF12:  Subunit (61/68 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation and in chromatin modification, similar to histone H2A	NN[VNI][ELG]E	66				Bromodomain	1.E-02	-0.6	transcription factor TFIID complex (1e-07)		0.007	10
yeast-413_GO-0005215	2	transporter activity	I[IFG].[LAI]V	66				AA_permease	1.E-05	0.5	transporter activity (1e-81)		0.014	10
yeast-1974_GO-0005634	2	nucleus	Q[QEK]Q	66				Helicase_C	1.E-04	0.5	transcription (1e-51)	Y	0.013	10
protein_40_YLL008W	2	DRS1:  Nucleolar DEAD-box protein required for ribosome assembly and function, including synthesis of 60S ribosomal subunits; constituent of 66S pre-ribosomal particles	EN..[LKG][DKG]K	66			Y	Pkinase	1.E-03	2.5	cytoplasm organization and biogenesis (0.001)		0.007	10
protein_40_YGL135W	2	RPL1B:  N-terminally acetylated protein component of the large (60S) ribosomal subunit, nearly identical to Rpl1Ap and has similarity to E. coli L1 and rat L10a ribosomal proteins; rpl1a rpl1b double null mutation is lethal	[TEA]RE[LAT]A	66	[AG]R	Protease matriptase protease site	Y	DEAD	1.E-04	3	RNA helicase activity (0.001)		0.007	10
protein_40_YDL153C	2	SAS10:  Component of the small (ribosomal) subunit (SSU) processosome required for pre-18S rRNa processing; essential nucleolar protein that, when overproduced, disrupts silencing	[LIA]K..N.L	66			Y	Pkinase	1.E-24	4.2	protein kinase activity (1e-22)	Y	0.012	10
yeast-335_GO-0016772	2	transferase activity, transferring phosphorus-containing groups	PE[VNR][ILMV]	66			Y	Pkinase	1.E-51	5.7	transferase activity, transferring phosphorus-containing groups (1e-74)	Y	0.014	10
yeast-544_GO-0016070	2	RNA metabolism	[KQG]K.[KSQ]K	66	P.[ST]PKK.KK	Cdc2 like protein kinase substrate motif					RNA metabolism (1e-12)	Y	0.014	10
protein_40_YMR047C	2	NUP116:  Subunit of the nuclear pore complex (NPC) that is localized to both sides of the pore; contains a repetitive GLFG motif that interacts with mRNA export factor Mex67p and with karyopherin Kap95p; homologous to Nup100p	KP..[STG][FTH]G	66	KP..[QK]	LIG_SH3_4	Y				snRNP protein import into nucleus (1e-15)		0.007	10
protein_40_YML007W	2	YAP1:  Basic leucine zipper (bZIP) transcription factor required for oxidative stress tolerance; activated by H2O2 through the multistep formation of disulfide bonds and transit from the cytoplasm to the nucleus; mediates resistance to cadmium	QQ..M[QIV][QTA]	66							general RNA polymerase II transcription factor activity (1e-06)		0.008	10
protein_40_YDR510W	2	SMT3:  Ubiquitin-like protein of the SUMO family, conjugated to lysine residues of target proteins; regulates chromatid cohesion, chromosome segregation, APC-mediated proteolysis, DNA replication and septin ring dynamics	A[DVA]A	66	FED[LV]IA[DE][PA]	CAVEOLIN PATTERN	Y				carboxylic acid metabolism (1e-07)		0.012	10
protein_40_YBR106W	2	PHO88:  Probable membrane protein, involved in phosphate transport; pho88 pho86 double null mutant exhibits enhanced synthesis of repressible acid phosphatase at high inorganic phosphate concentrations	VS.L[VW][LCW]	66									0.007	10
protein_40_YKL021C	2	MAK11:  Protein involved in an early, nucleolar step of 60S ribosomal subunit biogenesis; essential for cell growth and replication of killer M1 dsRNA virus; contains four beta-transducin repeats	H[RM].G[RDC]	65			Y	DEAD	1.E-07	-1.4	rRNA processing (1e-10)		0.007	10
protein_40_YKL014C	2	URB1:  Nucleolar protein required for the normal accumulation of 25S and 5.8S rRNAs, associated with the 27SA2 pre-ribosomal particle; proposed to be involved in the biogenesis of the 60S ribosomal subunit	T[GQ].[GRE]KT	65				Helicase_C	1.E-10	-1	ATP-dependent RNA helicase activity (1e-13)	Y	0.007	9
protein_40_YNL061W	2	NOP2:  Probable RNA m(5)C methyltransferase, essential for processing and maturation of 27S pre-rRNA and large ribosomal subunit biogenesis; localized to the nucleolus; constituent of 66S pre-ribosomal particles	K[KPV]..K[KRA]	65	P.[ST]PKK.KK	Cdc2 like protein kinase substrate motif		DEAD	1.E-05	-0.8	cytoplasm organization and biogenesis (1e-28)	Y	0.012	10
yeast-437_GO-0044429	2	mitochondrial part	D[ESD]D	65	D[SGDN]D[PE][LIVMF]D[LIVMGAC]	PPASE PATTERN		HEAT	1.E-02	0	cell cycle (1e-12)		0.014	10
oshea_microtubule	2	oshea_microtubule	DL.[GSF]S[EPQ]	65	DLL	Binding motif for clathrin heavy chain ear	Y	Kinesin	1.E-07	2.2	microtubule (1e-10)		0.009	10
yeast-685_GO-0016740	2	transferase activity	[KMN]P.[NVY]I	65			Y	Pkinase	1.E-31	4.5	transferase activity, transferring phosphorus-containing groups (1e-40)	Y	0.014	10
protein_40_YNL272C	2	SEC2:  Guanyl-nucleotide exchange factor for the small G-protein Sec4p, located on cytoplasmic vesicles; essential for post-Golgi vesicle transport	[AS]PE[ILMV]	65	SP	ERK1, ERK2 Kinase substrate motif		Pkinase	1.E-25	4.8	protein kinase activity (1e-26)	Y	0.012	10
protein_40_YJR002W	2	MPP10:  Component of the SSU processome, which is required for pre-18S rRNA processing, interacts with and controls the stability of Imp3p and Imp4p, essential for viability; similar to human Mpp10p	LE..D[EQA][EDY]	65							processing of 20S pre-rRNA (1e-12)		0.007	9
protein_40_YHR135C	2	YCK1:  Palmitoylated, plasma membrane-bound casein kinase I isoform; shares redundant functions with Yck2p in morphogenesis, proper septin assembly, endocytic trafficking; provides an essential function overlapping with that of Yck2p	S.[SEV]D	65	HSTSDD	Branched chain alpha-ketoacid dehydrogenase kinase substrate motif							0.012	10
protein_40_YDL213C	2	NOP6:  Putative RNA-binding protein implicated in ribosome biogenesis; contains an RNA recognition motif (RRM) and has similarity to hydrophilins; NOP6 may be a fungal-specific gene as no homologs have been yet identified in higher eukaryotes	[GPE]G..RG[GEI]	65	RGG	Alternative integrin binding site in FMDV virus	Y				rRNA processing (0.01)	Y	0.007	10
yeast-388_GO-0007275	2	development	S[SGF]S[SRN]	64	S[ST]	MDC1 BRCT domain binding motif		Pkinase	1.E-05	-2.2	multicellular organismal development (1e-16)		0.013	10
yeast-251_GO-0005886	2	plasma membrane	TA[GSI]	64	[LIVM][ST]A[STAG]HC	TRYPSIN_HIS PATTERN		MFS_1	1.E-05	-0.5	plasma membrane (1e-15)	Y	0.013	10
matsuyama_nuclear_envelope_or_dots	2	matsuyama_nuclear_envelope_or_dots	S..[PDA]S	64	S...S	WD40 binding motif, Ser residues must be phosphorylated		IBN_N	1.E-03	0.3	nuclear envelope (1e-41)		0.015	10
yeast-312_GO-0006414	2	translational elongation	G[FTR]..[FQA]D	64	R..[PA]DG	LIG_TNKBM	Y	Ribosomal_60s	1.E-11	1.6	translational elongation (1e-24)	Y	0.008	10
yeast-238_GO-0017111	2	nucleoside-triphosphatase activity	[AVC]G...L	64				Ras	1.E-19	1.7	nucleoside-triphosphatase activity (1e-12)	Y	0.013	10
yeast-238_GO-0017111	2	nucleoside-triphosphatase activity	A[GDC]Q[ECM]	64			Y	Ras	1.E-32	2.6	nucleoside-triphosphatase activity (1e-34)	Y	0.014	10
yeast-706_GO-0043412	2	biopolymer modification	HRD[ILMV][KLS]	64	[LIVMF]PCHR[LIVMF][LIVMF]	MGMT PATTERN		Pkinase	1.E-53	6.9	protein amino acid phosphorylation (1e-61)		0.014	10
yeast-685_GO-0016740	2	transferase activity	[DW][LI]KP	64	FKPY	TLA binding motif in Brinker transcription factor for binding TLA domain in Groucho	Y	Pkinase	1.E-65	7	protein kinase activity (1e-64)	Y	0.014	10
yeast-335_GO-0016772	2	transferase activity, transferring phosphorus-containing groups	[ER]A..FK[LRP]	64	KR	CLV_PCSK_PC1ET2_1	Y				transferase activity, transferring phosphorus-containing groups (1e-10)		0.008	10
protein_40_YMR117C	2	SPC24:  Component of the evolutionarily conserved kinetochore-associated Ndc80 complex (Ndc80p-Nuf2p-Spc24p-Spc25p); involved in chromosome segregation, spindle checkpoint activity and kinetochore clustering	EI.N[KSR][EVQ]	64									0.006	9
protein_40_YLL011W	2	SOF1:  Essential protein required for biogenesis of 40S (small) ribosomal subunit; has similarity to the beta subunit of trimeric G-proteins and the splicing factor Prp4p	[SDL][KCQ].KNI	64							nucleolus (1e-07)		0.007	10
protein_40_YER177W	2	BMH1:  14-3-3 protein, major isoform; controls proteome at post-transcriptional level, binds proteins and DNA, involved in regulation of many processes including exocytosis, vesicle transport, Ras/MAPK signaling, and rapamycin-sensitive signaling	[DFK]NNS[NHM]	64								Y	0.007	10
yeast-388_GO-0007275	2	development	T..[SQP]N	63	T..[SA]	FHA of KAPP binding motif, Thr must be phosphorylated		SH3_1	1.E-02	-1.2	multicellular organismal development (1e-18)	Y	0.013	10
yeast-436_GO-0031323	2	regulation of cellular metabolism	Q.Q	63	GQDQTKQQI	43_KD_POSTSYNAPTIC PATTERN		zf-C2H2	1.E-08	-0.8	regulation of cellular metabolism (10)		0.013	10
yeast-1134_GO-0044249	2	cellular biosynthesis	N.[SNY]S	63	N.[TS]	N-linked glycosylation site		PH	1.E-04	-0.8	transcription (1e-13)		0.013	10
oshea_actin	2	oshea_actin	PPP.[PHY]	63	[DE]FPPP	EVH binding motif of Mena	Y	SH3_1	1.E-04	-0.7	actin cortical patch (1e-14)		0.007	10
protein_40_YHR052W	2	CIC1:  Essential protein that interacts with proteasome components and has a potential role in proteasome substrate specificity; also copurifies with 66S pre-ribosomal particles	[VKY]K..K[KRH]	63	KR	CLV_PCSK_PC1ET2_1		Helicase_C	1.E-04	0.2	cytoplasm organization and biogenesis (1e-29)	Y	0.012	10
protein_40_YER148W	2	SPT15:  TATA-binding protein, general transcription factor that interacts with other factors to form the preinitiation complex at promoters, essential for viability	R[LAH].R[RYI]G	63	R.[RK]R	CLV_PCSK_FUR_1		Histone	1.E-03	1.4	nuclear nucleosome (0.01)		0.007	10
protein_40_YBL002W	2	HTB2:  One of two nearly identical (see HTB1) histone H2B subtypes required for chromatin assembly and chromosome function; Rad6p-Bre1p-Lge1p mediated ubiquitination regulates transcriptional activation, meiotic DSB formation and H3 methylation	RL.[RLT][RAP]G	63				Histone	1.E-08	1.8	nuclear nucleosome (1e-08)	Y	0.007	10
yeast-238_GO-0017111	2	nucleoside-triphosphatase activity	NK.[DM][LVR]	63	NK.D	Motif for specificity of guanine in purine binding proteins		Ras	1.E-14	2.4	nucleoside-triphosphatase activity (1e-50)	Y	0.014	10
protein_40_YHR030C	2	SLT2:  Serine/threonine MAP kinase involved in regulating the maintenance of cell wall integrity and progression through the cell cycle; regulated by the PKC1-mediated signaling pathway	V[DWP].W[SAQ]	63	VP	Interleukin converting enzyme protease		Pkinase	1.E-07	3.8	transferase activity, transferring phosphorus-containing groups (1e-08)		0.007	10
yeast-335_GO-0016772	2	transferase activity, transferring phosphorus-containing groups	HP[NFW][ILT]	63	HPQ	Biotin binding motif in streptavidin		Pkinase	1.E-30	4.6	transferase activity, transferring phosphorus-containing groups (1e-42)	Y	0.014	10
yeast-799_GO-0043233	2	organelle lumen	EED[EAK][DGL]	63	EED	Ankyrin B C-terminal motif that binds internal Ankyrin repeats					nuclear lumen (1e-39)		0.013	10
yeast-799_GO-0031974	2	membrane-enclosed lumen	EED[EAK][DGL]	63	EED	Ankyrin B C-terminal motif that binds internal Ankyrin repeats					nuclear lumen (1e-39)		0.013	10
protein_40_YLR175W	2	CBF5:  Pseudouridine synthase catalytic subunit of box H/ACA small nucleolar ribonucleoprotein particles (snoRNPs), acts on both large and small rRNAs and on snRNA U2	RGG[SAK][RSE]	63	GGRGG	Arginine methyl transferease substrate motif (PRMT1)					nuclear lumen (1e-04)		0.006	10
protein_40_YHR099W	2	TRA1:  Subunit of SAGA and NuA4 histone acetyltransferase complexes; interacts with acidic activators (e.g., Gal4p) which leads to transcription activation; similar to human TRRAP, which is a cofactor for c-Myc mediated oncogenic transformation	[LGF]L..Q[QFS]Q	63	SQ	ATM kinase substrate motif					histone acetylation (1e-08)		0.007	8
yeast-792_GO-0006412	2	protein biosynthesis	N.[NSY]S	62	N.[TS]	N-linked glycosylation site	Y	Zn_clus	1.E-04	-2.1	transcription regulator activity (1e-15)		0.013	10
oshea_bud_neck	2	oshea_bud_neck	S..N[SRF]	62			Y	RhoGAP	1.E-06	-0.6	site of polarized growth (1e-68)	Y	0.012	10
yeast-376_GO-0019219	2	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism	QQ..[LPN]	62				zf-C2H2	1.E-10	-0.5	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism (1e-14)	Y	0.013	10
protein_40_YOL069W	2	NUF2:  Component of the evolutionarily conserved kinetochore-associated Ndc80 complex (Ndc80p-Nuf2p-Spc24p-Spc25p); involved in chromosome segregation, spindle checkpoint activity and kinetochore clustering	K[LQM]N[DNE]	62	KEN	LIG_APCC_KENbox_2		SMC_N	1.E-03	0.2	microtubule cytoskeleton (1e-06)		0.012	10
yeast-1062_GO-0016020	2	membrane	AF..[LGS]	62	F..LF	Androgen receptor motif that interacts with AF2	Y	MFS_1	1.E-11	0.9	endomembrane system (1e-43)	Y	0.013	10
protein_40_YLR340W	2	RPP0:  Conserved ribosomal protein P0 similar to rat P0, human P0, and E. coli L10e; shown to be phosphorylated on serine 302	SD[DGS][DVK]M	62				Ribosomal_60s	1.E-07	0.9	translational elongation (1e-05)		0.007	8
yeast-312_GO-0006414	2	translational elongation	EE..DD[MV]	62	EED	Ankyrin B C-terminal motif that binds internal Ankyrin repeats		Ribosomal_60s	1.E-12	1.6	translational elongation (1e-12)	Y	0.008	10
protein_40_YGR252W	2	GCN5:  Histone acetyltransferase, acetylates N-terminal lysines on histones H2B and H3; catalytic subunit of the ADA and SAGA histone acetyltransferase complexes; founding member of the Gcn5p-related N-acetyltransferase superfamily	V[LYG]EY[LY]	62	[DE]YY	Tyr phosphorylated in activation loop of Jak		Histone	1.E-03	1.6	SAGA complex (0.01)		0.007	10
protein_40_YPL031C	2	PHO85:  Cyclin-dependent kinase, with ten cyclin partners; involved in regulating the cellular response to nutrient levels and environmental conditions and progression through the cell cycle	[RHN]D..P[ELW]N	62				Pkinase	1.E-07	3.4	protein kinase activity (1e-07)		0.007	9
yeast-207_GO-0003677	2	DNA binding	KR[KRA]	62	KR	CLV_PCSK_PC1ET2_1		Zn_clus	1.E-09	6.5	DNA binding (1e-17)	Y	0.013	10
protein_40_YMR229C	2	RRP5:  Protein required for the synthesis of both 18S and 5.8S rRNA; C-terminal region is crucial for the formation of 18S rRNA and N-terminal region is required for the 5.8S rRNA; component of small ribosomal subunit (SSU) processosome	KK[SDL][KRA]	62	KKSRGDYMTMQIG	Insulin receptor kinase substrate motif					nucleolus (1e-28)		0.011	10
protein_40_YGL180W	2	ATG1:  Protein serine/threonine kinase, required for vesicle formation during autophagy and the cytoplasm-to-vacuole targeting (Cvt) pathway; structurally required for pre-autophagosome formation; forms a complex with Atg13p and Atg17p	KK[KRS]	62	KKKKKK[ST]	TGF beta receptor kinase substrate motif					rRNA processing (0.01)		0.011	10
protein_40_YGL120C	2	PRP43:  RNA helicase in the DEAH-box family, functions in both RNA polymerase I and polymerase II transcript metabolism, involved in release of the lariat-intron from the spliceosome	E[EDV].E[EDK]	62	SEDEE	CKII kinase phosphorylation site (peptide screen)					nucleolus (1e-30)		0.011	10
protein_40_YGL059W	2	PKP2:  Mitochondrial protein kinase that negatively regulates activity of the pyruvate dehydrogenase complex by phosphorylating the ser-133 residue of the Pda1p subunit; acts in concert with kinase Pkp1p and phosphatases Ptc5p and Ptc6p	R[RQK][ARK]S	62	R[KER].S	PKC epsilon kinase substrate motif							0.012	10
protein_40_YGL030W	2	RPL30:  Protein component of the large (60S) ribosomal subunit, has similarity to rat L30 ribosomal protein; involved in pre-rRNA processing in the nucleolus; autoregulates splicing of its transcript	NK.[KQR][KFN]V	62			Y				nucleolus (0.01)	Y	0.007	10
oshea_mitochondrion	2	oshea_mitochondrion	[DNEQ]EE[DCS]	61	EED	Ankyrin B C-terminal motif that binds internal Ankyrin repeats		HEAT	1.E-02	-1.1	nuclear lumen (1e-13)		0.012	10
yeast-1721_GO-0016043	2	cell organization and biogenesis	NK..[ERK][LSA]	61	K[KR].[KR]	Nuclear localization motif		PI3_PI4_kinase	1.E-02	-0.8	cellular localization (1e-19)	Y	0.012	10
protein_40_YPR119W	2	CLB2:  B-type cyclin involved in cell cycle progression; activates Cdc28p to promote the transition from G2 to M phase; accumulates during G2 and M, then targeted via a destruction box motif for ubiquitin-mediated degradation by the proteasome	E...D[LSI]	61				Pkinase	1.E-04	-0.3	cell cycle (1e-15)	Y	0.011	10
protein_40_YOR063W	2	RPL3:  Protein component of the large (60S) ribosomal subunit, has similarity to E. coli L3 and rat L3 ribosomal proteins; involved in the replication and maintenance of killer double stranded RNA virus	K..[AKR]A	61	K[KR].[KR]	Nuclear localization motif		DEAD	1.E-02	0.2	cytosolic ribosome (sensu Eukaryota) (1e-35)	Y	0.011	10
yeast-312_GO-0006414	2	translational elongation	[FRG]G.F[DN]	61	GCF	Motif for covalent cholesterol attachment at Cys	Y	Ribosomal_60s	1.E-11	1.6	translational elongation (1e-18)	Y	0.007	10
protein_40_YNL031C	2	HHT2:  One of two identical histone H3 proteins (see also HHT1); core histone required for chromatin assembly, involved in heterochromatin-mediated telomeric and HM silencing; regulated by acetylation, methylation, and mitotic phosphorylation	R[LST].[RLV]RG	61	[KR]R	CLV_PCSK_KEX2_1		Histone	1.E-06	1.6	nuclear chromatin (1e-05)	Y	0.007	8
yeast-248_GO-0031966	2	mitochondrial membrane	[LFV]D..[KR]TR	61			Y	Mito_carr	1.E-26	1.9	mitochondrial membrane (1e-15)		0.010	10
protein_40_YML073C	2	RPL6A:  N-terminally acetylated protein component of the large (60S) ribosomal subunit, has similarity to Rpl6Bp and to rat L6 ribosomal protein; binds to 5.8S rRNA	TRE[LTV][AQK]	61				DEAD	1.E-04	2.9	RNA helicase activity (1e-04)		0.006	10
protein_40_YGR128C	2	UTP8:  Nucleolar protein required for export of tRNAs from the nucleus; also copurifies with the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	[IMP]K.W[DNP]	61				WD40	1.E-07	3.1	small nucleolar ribonucleoprotein complex (1e-11)	Y	0.006	10
protein_40_YDL153C	2	SAS10:  Component of the small (ribosomal) subunit (SSU) processosome required for pre-18S rRNa processing; essential nucleolar protein that, when overproduced, disrupts silencing	[IWF]K.EN[VCI]	61	[VILAFP]K.E	Motif recognized for modification by SUMO-1		Pkinase	1.E-08	3.2	kinase activity (1e-06)		0.007	9
protein_40_YGL105W	2	ARC1:  Protein that binds tRNA and methionyl- and glutamyl-tRNA synthetases (Mes1p and Gus1p), delivering tRNA to them, stimulating catalysis, and ensuring their localization to the cytoplasm; also binds quadruplex nucleic acids	W[SA].G[ICV]	61				Pkinase	1.E-20	4.5	protein kinase activity (1e-20)	Y	0.008	10
protein_40_YPL153C	2	RAD53:  Protein kinase, required for cell-cycle arrest in response to DNA damage; activated by trans autophosphorylation when interacting with hyperphosphorylated Rad9p; also interacts with ARS1 and plays a role in initiation of DNA replication	[NIT]SN[NRA]	61			Y					Y	0.011	10
matsuyama_vacuole	2	matsuyama_vacuole	LY.[LAD]F[TID]	61	[IVL]Y..[PF]	ABL phosphorylation site					vacuole (1e-12)		0.009	8
protein_40_YBR160W	2	CDC28:  Catalytic subunit of the main cell cycle cyclin-dependent kinase (CDK); alternately associates with G1 cyclins (CLNs) and G2/M cyclins (CLBs) which direct the CDK to specific substrates	I[NDM][EY]LG	60							 		0.007	9
yeast-256_GO-0016462	2	pyrophosphatase activity	[DGE]K..T[LAH]T	60	K..[ST]	PKA kinase substrate motif		E1-E2_ATPase	1.E-09	-1.2	nucleoside-triphosphatase activity (1e-16)		0.009	10
protein_40_YPL131W	2	RPL5:  Protein component of the large (60S) ribosomal subunit with similarity to E. coli L18 and rat L5 ribosomal proteins; binds 5S rRNA and is required for 60S subunit assembly	R[GST].[DAQ]IP	60				DEAD	1.E-05	-1.1	ribosome biogenesis (1e-08)		0.007	10
protein_40_YHR052W	2	CIC1:  Essential protein that interacts with proteasome components and has a potential role in proteasome substrate specificity; also copurifies with 66S pre-ribosomal particles	[ILR]A.P[GYQ]R	60				Helicase_C	1.E-08	-0.9	RNA helicase activity (1e-08)		0.006	10
yeast-251_GO-0005886	2	plasma membrane	F...F[AWC]	60	F..LF	Androgen receptor motif that interacts with AF2		Sugar_tr	1.E-05	1	plasma membrane (1e-83)		0.013	10
protein_40_YDR303C	2	RSC3:  Component of the RSC chromatin remodeling complex; essential gene required for maintenance of proper ploidy and regulation of ribosomal protein genes and the cell wall/stress response; highly similar to Rsc30p	RL.R[RSQ][GQV]	60				Histone	1.E-03	1.4	nuclear nucleosome (0.001)		0.007	10
yeast-248_GO-0016072	2	rRNA metabolism	[DKS]E[AED]D	60	EED	Ankyrin B C-terminal motif that binds internal Ankyrin repeats	Y	DEAD	1.E-08	3.1	rRNA metabolism (1e-09)	Y	0.013	10
protein_40_YMR229C	2	RRP5:  Protein required for the synthesis of both 18S and 5.8S rRNA; C-terminal region is crucial for the formation of 18S rRNA and N-terminal region is required for the 5.8S rRNA; component of small ribosomal subunit (SSU) processosome	[REV]D.KP[EHQ]	60	P.[IV][ND]R..KP	SH3 binding motif for HBP STAM and GRB2		Pkinase	1.E-13	3.7	protein kinase activity (1e-13)		0.008	10
yeast-238_GO-0017111	2	nucleoside-triphosphatase activity	A[LIR]..P[GDI]R	60			Y	AAA	1.E-12	4.2	nucleoside-triphosphatase activity (1e-12)	Y	0.008	10
yeast-256_GO-0016462	2	pyrophosphatase activity	[AER][RHE]..DIP	60			Y	Helicase_C	1.E-07	4.4	ATPase activity (1e-12)		0.007	10
yeast-706_GO-0043412	2	biopolymer modification	[KYF]..DFG	60				Pkinase	1.E-48	6.7	protein amino acid phosphorylation (1e-65)		0.013	10
yeast-335_GO-0016772	2	transferase activity, transferring phosphorus-containing groups	D[IWV]..[LVC]G	60				Pkinase	1.E-54	6.9	phosphotransferase activity, alcohol group as acceptor (1e-57)	Y	0.013	10
yeast-324_GO-0030528	2	transcription regulator activity	C[NDA].C[GRQ]L	60	C..C	Motif on TIM mitochondrial translocation proteins		GATA	1.E-16	7.8	transcription regulator activity (1e-13)		0.010	10
protein_40_YMR236W	2	TAF9:  Subunit (17 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation and in chromatin modification, similar to histone H3	[QRE]Q..Q[GIT]Q	60			Y				SLIK (SAGA-like) complex (1e-07)		0.007	9
protein_40_YLR432W	2	IMD3:  Inosine monophosphate dehydrogenase, catalyzes the first step of GMP biosynthesis, member of a four-gene family in S. cerevisiae, constitutively expressed	[AIL][ESP]..AAE	60									0.006	9
protein_40_YIL094C	2	LYS12:  Homo-isocitrate dehydrogenase, an NAD-linked mitochondrial enzyme required for the fourth step in the biosynthesis of lysine, in which homo-isocitrate is oxidatively decarboxylated to alpha-ketoadipate	SE.[KHV]E[NAR]	60	[ST]E	G protein-coupled receptor kinase 1 substrate motif						Y	0.006	10
protein_40_YGL019W	2	CKB1:  Beta regulatory subunit of casein kinase 2, a Ser/Thr protein kinase with roles in cell growth and proliferation; the holoenzyme also contains CKA1, CKA2 and CKB2, the many substrates include transcription factors and all RNA polymerases	DE[ESA][DRT]	60	SEDEE	CKII kinase phosphorylation site (peptide screen)					RNA elongation from RNA polymerase II promoter (1e-12)		0.012	10
protein_40_YDL055C	2	PSA1:  GDP-mannose pyrophosphorylase (mannose-1-phosphate guanyltransferase), synthesizes GDP-mannose from GTP and mannose-1-phosphate in cell wall biosynthesis; required for normal cell wall structure	E[IGD]LD[LMA]	60			Y						0.007	9
protein_40_YBR106W	2	PHO88:  Probable membrane protein, involved in phosphate transport; pho88 pho86 double null mutant exhibits enhanced synthesis of repressible acid phosphatase at high inorganic phosphate concentrations	IL[YC]L[LTM]	60									0.006	8
yeast-630_GO-0051244	2	regulation of cellular physiological process	EE[DEI]	59	EE[DE]IYFFFF	CSK kinase substrate motif		Zn_clus	1.E-03	-1.1	regulation of metabolism (1e-19)		0.012	10
yeast-460_GO-0006351	2	transcription, DNA-dependent	N[NHP]..N[SDQ]	59				Zn_clus	1.E-04	-0.8	transcription, DNA-dependent (1e-91)		0.012	10
protein_40_YOR117W	2	RPT5:  One of six ATPases of the 19S regulatory particle of the 26S proteasome involved in the degradation of ubiquitinated substrates; recruited to the GAL1-10 promoter region upon induction of transcription	L[KID][NPG]DL	59	WDL	Binding motif for AP-2 and clathrin heavy chain ear		PCI	1.E-06	0.1	proteasome complex (sensu Eukaryota) (1e-10)		0.006	9
protein_40_YJL109C	2	UTP10:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	[LQR]LA[VIP]G	59				WD40	1.E-05	0.8	small nucleolar ribonucleoprotein complex (1e-06)		0.006	10
protein_40_YDL140C	2	RPO21:  RNA polymerase II largest subunit B220, part of central core; phosphorylation of C-terminal heptapeptide repeat domain regulates association with transcription and splicing factors; similar to bacterial beta-prime	[FLN]GL[AKL]R	59	[KR]R	CLV_PCSK_KEX2_1	Y	Pkinase	1.E-02	1.4	cyclin-dependent protein kinase activity (0.001)		0.006	9
yeast-256_GO-0016462	2	pyrophosphatase activity	[NTH]K.D[LQM]	59	[NT]K.D	Motif for binding guanine nucleotides	Y	Ras	1.E-18	2.5	pyrophosphatase activity (1e-56)	Y	0.013	10
protein_40_YGL245W	2	GUS1:  Glutamyl-tRNA synthetase (GluRS), forms a complex with methionyl-tRNA synthetase (Mes1p) and Arc1p; complex formation increases the catalytic efficiency of both tRNA synthetases and ensures their correct localization to the cytoplasm	W[SAR][LCM]G	59				Pkinase	1.E-15	4.4	protein kinase activity (1e-15)		0.008	9
yeast-1939_GO-0003824	2	catalytic activity	[WHV]S[LFV]G	59	RR.S[MILVFY]	PKA kinase substrate motif	Y	Pkinase	1.E-25	5.4	phosphotransferase activity, alcohol group as acceptor (1e-28)	Y	0.012	10
yeast-685_GO-0016740	2	transferase activity	[LIG]K.[EMA]N	59	[VILAFP]K.E	Motif recognized for modification by SUMO-1	Y	Pkinase	1.E-65	7.9	protein kinase activity (1e-66)	Y	0.012	10
yeast-504_GO-0006350	2	transcription	[CAF]R.[RKW]K	59	R.RKGSF	PKC delta kinase substrate motif	Y	Zn_clus	1.E-20	18.1	transcription (1e-57)		0.013	10
protein_40_YNL178W	2	RPS3:  Protein component of the small (40S) ribosomal subunit, has apurinic/apyrimidinic (AP) endonuclease activity; essential for viability; has similarity to E. coli S3 and rat S3 ribosomal proteins	A[PA]..K[VEG]V	59							ribosome (0.001)		0.006	10
protein_40_YMR047C	2	NUP116:  Subunit of the nuclear pore complex (NPC) that is localized to both sides of the pore; contains a repetitive GLFG motif that interacts with mRNA export factor Mex67p and with karyopherin Kap95p; homologous to Nup100p	FG..N[NKT][NM]	59	G[SA]LNK	GDP-mannose binding motif in transporter	Y				snRNP protein import into nucleus (1e-12)		0.007	10
protein_40_YJL187C	2	SWE1:  Protein kinase that regulates the G2/M transition by inhibition of Cdc28p kinase activity; localizes to the nucleus and to the daughter side of the mother-bud neck; homolog of S. pombe Wee1p; potential Cdc28p substrate	SD.[SDW][DSR]	59	D.D	Ribose moiety of UDP and manganese binding site in glucuronyl transferase							0.011	10
protein_40_YFR001W	2	LOC1:  Nuclear protein involved in asymmetric localization of ASH1 mRNA; binds double-stranded RNA in vitro; constituent of 66S pre-ribosomal particles	[KRT]K..K[EGA]Q	59	P.[ST]PKK.KK	Cdc2 like protein kinase substrate motif					cytoplasm organization and biogenesis (1e-08)		0.006	10
protein_40_YER177W	2	BMH1:  14-3-3 protein, major isoform; controls proteome at post-transcriptional level, binds proteins and DNA, involved in regulation of many processes including exocytosis, vesicle transport, Ras/MAPK signaling, and rapamycin-sensitive signaling	[SQP]S..T[SMF]N	59	S..[ST]	Casein Kinase I consensus phosphorylation site (N-term Ser must first be phosphorylated)						Y	0.006	10
protein_40_YDL083C	2	RPS16B:  Protein component of the small (40S) ribosomal subunit; identical to Rps16Ap and has similarity to E. coli S9 and rat S16 ribosomal proteins	[VMY][APL]KKR	59	KR	CLV_PCSK_PC1ET2_1					ribonucleoprotein complex (1e-04)	Y	0.006	10
protein_40_YDL014W	2	NOP1:  Nucleolar protein, component of the small subunit processome complex, which is required for processing of pre-18S rRNA; has similarity to mammalian fibrillarin	E[EDS]..E[ERD]	59	[ST]..E	Casien kinase II consensus phosphorylation site					nucleolus (1e-40)		0.011	10
protein_40_YLR029C	2	RPL15A:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl15Bp and has similarity to rat L15 ribosomal protein; binds to 5.8 S rRNA	GR..[RSV]A[GRA]	58	[AG]R	Protease matriptase protease site		DEAD	1.E-05	-1.3	RNA helicase activity (1e-04)		0.006	10
yeast-631_GO-0050794	2	regulation of cellular process	EE[DEI]	58	EE[DE]IYFFFF	CSK kinase substrate motif		Zn_clus	1.E-03	-1.1	regulation of metabolism (1e-19)		0.012	10
yeast-294_GO-0006366	2	transcription from RNA polymerase II promoter	N[DNS].[SNH]N	58				Zn_clus	1.E-03	-0.9	transcription from RNA polymerase II promoter (1e-10)		0.012	10
yeast-345_GO-0006396	2	RNA processing	[KNP]K.K[RKT]	58	P.[ST]PKK.KK	Cdc2 like protein kinase substrate motif		DEAD	1.E-03	-0.8	RNA processing (1e-12)		0.012	10
matsuyama_Golgi	2	matsuyama_Golgi	I..[LFV]F	58	D..SII.FF	CK I delta kinase phosphorylation site (peptide screen)		zf-DHHC	1.E-03	0	Golgi apparatus (1e-11)	Y	0.014	10
yeast-980_GO-0051179	2	localization	I..[LFW]I	58				MFS_1	1.E-09	0.8	cellular localization (1e-88)	Y	0.012	10
yeast-251_GO-0005886	2	plasma membrane	I[GAD]..[VFI]G	58				MFS_1	1.E-02	1.2	plasma membrane (1e-65)		0.012	10
protein_40_YNL031C	2	HHT2:  One of two identical histone H3 proteins (see also HHT1); core histone required for chromatin assembly, involved in heterochromatin-mediated telomeric and HM silencing; regulated by acetylation, methylation, and mitotic phosphorylation	I[RIS].[DIE]DE	58	SEDEE	CKII kinase phosphorylation site (peptide screen)		Histone	1.E-03	1.6	establishment and/or maintenance of chromatin architecture (0.001)	Y	0.006	9
protein_40_YPL211W	2	NIP7:  Nucleolar protein required for 60S ribosome subunit biogenesis, constituent of 66S pre-ribosomal particles; physically interacts with Nop8p and the exosome subunit Rrp43p	K[TIR]AA[FLS]	58	KR	CLV_PCSK_PC1ET2_1		DEAD	1.E-02	2.8	cytoplasm organization and biogenesis (1e-06)		0.006	10
protein_40_YBL007C	2	SLA1:  Cytoskeletal protein binding protein required for assembly of the cortical actin cytoskeleton; interacts with proteins regulating actin dynamics and proteins required for endocytosis; found in the nucleus and cell cortex; has 3 SH3 domains	[HMT]RD[LIM]K	58				Pkinase	1.E-13	3.8	protein kinase activity (1e-13)		0.007	10
protein_40_YGL245W	2	GUS1:  Glutamyl-tRNA synthetase (GluRS), forms a complex with methionyl-tRNA synthetase (Mes1p) and Arc1p; complex formation increases the catalytic efficiency of both tRNA synthetases and ensures their correct localization to the cytoplasm	D[FW]G[LMF]	58	[GD][FYWA]G[LIVM][LIVMFYD]G[KN][NHW]	CAP_GLY_1 PATTERN		Pkinase	1.E-19	4	protein kinase activity (1e-18)		0.008	10
protein_40_YNL272C	2	SEC2:  Guanyl-nucleotide exchange factor for the small G-protein Sec4p, located on cytoplasmic vesicles; essential for post-Golgi vesicle transport	[VFM]A[IVQ]K	58			Y	Pkinase	1.E-19	4.4	protein kinase activity (1e-19)	Y	0.010	10
protein_40_YOR181W	2	LAS17:  Actin assembly factor, activates the Arp2/3 protein complex that nucleates branched actin filaments; localizes with the Arp2/3 complex to actin patches; homolog of the human Wiskott-Aldrich syndrome protein (WASP)	[FI][PC].NYV	58				SH3_1	1.E-14	5.2			0.007	10
yeast-685_GO-0016740	2	transferase activity	[VAC]D.WS	58				Pkinase	1.E-37	5.6	protein kinase activity (1e-31)		0.013	10
yeast-565_GO-0006464	2	protein modification	K[ILY].[DSP]FG	58				Pkinase	1.E-47	6.4	protein amino acid phosphorylation (1e-56)		0.013	10
yeast-1939_GO-0003824	2	catalytic activity	W[SAD].G[CVL]	58			Y	Pkinase	1.E-50	6.4	protein kinase activity (1e-50)		0.012	10
protein_40_YER165W	2	PAB1:  Poly(A) binding protein, part of the 3'-end RNA-processing complex, mediates interactions between the 5' cap structure and the 3' mRNA poly(A) tail, involved in control of poly(A) tail length, interacts with translation factor eIF-4G	ST..G[GQA][LSM]	58	S[ST]	MDC1 BRCT domain binding motif					protein export from nucleus (1e-06)		0.007	7
protein_40_YEL063C	2	CAN1:  Plasma membrane arginine permease, requires phosphatidyl ethanolamine (PE) for localization, exclusively associated with lipid rafts; mutation confers canavanine resistance	I[TAM][YMC]N	58							endoplasmic reticulum (0.01)		0.006	10
oshea_ambiguous	2	oshea_ambiguous	SS.[SEF][STA]	58	S[ST]	MDC1 BRCT domain binding motif					bud (1e-07)	Y	0.011	10
protein_40_YPL211W	2	NIP7:  Nucleolar protein required for 60S ribosome subunit biogenesis, constituent of 66S pre-ribosomal particles; physically interacts with Nop8p and the exosome subunit Rrp43p	R[GS].[DAQ]IP	57				DEAD	1.E-06	-1.1	ribosome biogenesis (1e-06)	Y	0.007	9
yeast-661_GO-0050789	2	regulation of biological process	EE[DIE]	57	EE[DE]IYFFFF	CSK kinase substrate motif		Zn_clus	1.E-02	-1	regulation of metabolism (1e-19)		0.012	10
protein_40_YLR029C	2	RPL15A:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl15Bp and has similarity to rat L15 ribosomal protein; binds to 5.8 S rRNA	DV[AVE]A[RKP]	57				DEAD	1.E-02	-1	nucleolus (0.001)		0.006	10
yeast-324_GO-0030528	2	transcription regulator activity	[SNV]P.T[TNM]	57	[ST]P	LIG_WW_4		zf-C2H2	1.E-04	-0.9	transcription regulator activity (1e-58)		0.012	10
protein_40_YLR293C	2	GSP1:  GTP binding protein (mammalian Ranp homolog) involved in the maintenance of nuclear organization, RNA processing and transport; regulated by Prp20p, Rna1p, Yrb1p, Yrb2p, Yrp4p, Yrb30p, Cse1p and Kap95p; yeast Gsp2p homolog	F[LYH]S[QKA]L	57	SQ	ATM kinase substrate motif		HEAT	1.E-02	-0.8	protein carrier activity (1e-05)		0.006	10
protein_40_YGR275W	2	RTT102:  Component of both the SWI/SNF and RSC chromatin remodeling complexes, suggested role in chromosome maintenance; possible weak regulator of Ty1 transposition	L[QSK]..[QDT]QQ	57				Bromodomain	1.E-04	-0.8	chromatin remodeling complex (1e-13)		0.006	9
protein_40_YDR224C	2	HTB1:  One of two nearly identical (see HTB2) histone H2B subtypes required for chromatin assembly and chromosome function; Rad6p-Bre1p-Lge1p mediated ubiquitination regulates transcriptional activation, meiotic DSB formation and H3 methylation	[LER]T..LE[YVA]	57	T..[IL]	FHA2 binding motif, Thr must be phosphorylated		Histone	1.E-03	1.5	nuclear chromatin (0.001)	Y	0.006	10
yeast-312_GO-0006414	2	translational elongation	M[GP]..L[FC]	57	M...L	PMSA motif for internalization	Y	Ribosomal_60s	1.E-12	1.6	translational elongation (1e-15)	Y	0.008	10
protein_40_YDL213C	2	NOP6:  Putative RNA-binding protein implicated in ribosome biogenesis; contains an RNA recognition motif (RRM) and has similarity to hydrophilins; NOP6 may be a fungal-specific gene as no homologs have been yet identified in higher eukaryotes	DG[TKR][VKI]R	57	[KR]R	CLV_PCSK_KEX2_1	Y	WD40	1.E-02	2.4	ribosome biogenesis (0.001)		0.006	9
protein_40_YOR181W	2	LAS17:  Actin assembly factor, activates the Arp2/3 protein complex that nucleates branched actin filaments; localizes with the Arp2/3 complex to actin patches; homolog of the human Wiskott-Aldrich syndrome protein (WASP)	[LAG]Q.S[DSL]I	57	S[ST]	MDC1 BRCT domain binding motif		SH3_1	1.E-05	2.5	cell cortex (0.001)		0.006	9
yeast-248_GO-0016072	2	rRNA metabolism	P[TGY]RE[LTQ]	57	[AG]R	Protease matriptase protease site		DEAD	1.E-11	3.9	ATP-dependent RNA helicase activity (1e-15)	Y	0.008	9
matsuyama_Cytosol	2	matsuyama_Cytosol	D[FSV].L[SAM]	57				Pkinase	1.E-08	4.1	phosphotransferase activity, alcohol group as acceptor (1e-11)		0.014	10
protein_40_YHR052W	2	CIC1:  Essential protein that interacts with proteasome components and has a potential role in proteasome substrate specificity; also copurifies with 66S pre-ribosomal particles	[DQG]EAD[RLS]	57	[LIVMF][LIVMF]DEAD[RKEN].[LIVMFYGSTN]	DEAD_ATP_HELICASE PATTERN		DEAD	1.E-09	4.2	RNA helicase activity (1e-08)		0.006	10
yeast-685_GO-0016740	2	transferase activity	KP[EQW][NR]	57	[WFY][KR]P[WFY]	LIG_WRPW_2		Pkinase	1.E-47	5.8	protein kinase activity (1e-49)	Y	0.012	10
yeast-256_GO-0016462	2	pyrophosphatase activity	R[GLT].DI[PN]	57				Helicase_C	1.E-09	5.9	ATPase activity (1e-13)	Y	0.008	10
yeast-648_GO-0050791	2	regulation of physiological process	E[DNEQ][EDN]E	57	[KRHQSA][DENQ]EL	ER_TARGET PATTERN					regulation of metabolism (1e-09)		0.012	10
yeast-304_GO-0019752	2	carboxylic acid metabolism	[KD]MS[KAI]S	57	YMPMS	PI3 Kinase p85 SH2 domain binding motif					amino acid activation (1e-19)	Y	0.008	10
yeast-304_GO-0006082	2	organic acid metabolism	[KD]MS[KAI]S	57	YMPMS	PI3 Kinase p85 SH2 domain binding motif					amino acid activation (1e-19)	Y	0.008	10
yeast-262_GO-0031224	2	intrinsic to membrane	L[LIF]I[LFI]	57	L[IVLMF].[IVLMF][DE]	LIG_Clathr_ClatBox_1	Y				intrinsic to membrane (1e-88)		0.012	10
yeast-256_GO-0016021	2	integral to membrane	L[LIF]I[LFI]	57	L[IVLMF].[IVLMF][DE]	LIG_Clathr_ClatBox_1	Y				integral to membrane (1e-88)		0.012	10
protein_40_YPL153C	2	RAD53:  Protein kinase, required for cell-cycle arrest in response to DNA damage; activated by trans autophosphorylation when interacting with hyperphosphorylated Rad9p; also interacts with ARS1 and plays a role in initiation of DNA replication	E[DQ]I[GIM]E	57							heterochromatin formation (0.001)	Y	0.006	9
protein_40_YOL127W	2	RPL25:  Primary rRNA-binding ribosomal protein component of the large (60S) ribosomal subunit, has similarity to E. coli L23 and rat L23a ribosomal proteins; binds to 26S rRNA via a conserved C-terminal motif	N[KNV].[KQM]KV	57							nucleolus (0.001)		0.006	8
protein_40_YOL120C	2	RPL18A:  Protein component of the large (60S) ribosomal subunit, identical to Rpl18Bp and has similarity to rat L18 ribosomal protein; intron of RPL18A pre-mRNA forms stem-loop structures that are a target for Rnt1p cleavage leading to degradation	QK..[LAY]S[LKI]	57									0.006	10
protein_40_YMR308C	2	PSE1:  Karyopherin/importin that interacts with the nuclear pore complex; acts as the nuclear import receptor for specific proteins, including Pdr1p, Yap1p, Ste12p, and Aft1p	FG.K[PHV][ALV]	57							snRNP protein import into nucleus (1e-09)		0.006	9
protein_40_YJL092W	2	SRS2:  DNA helicase and DNA-dependent ATPase involved in DNA repair, needed for proper timing of commitment to meiotic recombination and transition from Meiosis I to II; affects genome stability by suppressing unscheduled homologous recombination	N[VRA][LCE]AS	57	YASI	SHP2 phosphatase substrate motif						Y	0.006	10
protein_40_YER133W	2	GLC7:  Catalytic subunit of type 1 serine/threonine protein phosphatase, involved in many processes including glycogen metabolism, sporulation, and mitosis; interacts with multiple regulatory subunits; predominantly isolated with Sds22p	P[SIM]..RS[RK]	57								Y	0.006	9
protein_40_YDR477W	2	SNF1:  AMP-activated serine/threonine protein kinase found in a complex containing Snf4p and members of the Sip1p/Sip2p/Gal83p family; required for transcription of glucose-repressed genes, thermotolerance, sporulation, and peroxisome biogenesis	[SLV]S[SND]S	57									0.010	10
protein_40_YDR145W	2	TAF12:  Subunit (61/68 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation and in chromatin modification, similar to histone H2A	L[ADW]..[RND]AK	57			Y						0.006	9
protein_40_YDL055C	2	PSA1:  GDP-mannose pyrophosphorylase (mannose-1-phosphate guanyltransferase), synthesizes GDP-mannose from GTP and mannose-1-phosphate in cell wall biosynthesis; required for normal cell wall structure	A[DAV]..LL[DEH]	57	[DE]..LL	Di-Leu acidic motif for receptor endocytosis (recognized by VHS domain of GGA proteins)							0.006	10
protein_40_YBR247C	2	ENP1:  Protein associated with U3 and U14 snoRNAs, required for pre-rRNA processing and 40S ribosomal subunit synthesis; localized in the nucleus and concentrated in the nucleolus	[LEW]KV[LPI]K	57	VP	Interleukin converting enzyme protease					35S primary transcript processing (0.001)		0.007	10
oshea_vacuole	2	oshea_vacuole	V[FGY].[LAT]VG	57							storage vacuole (0.001)		0.007	10
ucsf_loc_k_means_G6	6	Sub-cellular localization, 6 clusters	K[KRP].K	57	K[KR].[KR]	Nuclear localization motif		PHD	1.E-04	-1.3	nuclear lumen (1e-70)		0.035	10
protein_40_YPL211W	2	NIP7:  Nucleolar protein required for 60S ribosome subunit biogenesis, constituent of 66S pre-ribosomal particles; physically interacts with Nop8p and the exosome subunit Rrp43p	KK..[KNH][KEV]	56	RKK.[ST]	ZIP kinase phosphorylation motif		DEAD	1.E-04	-1.5	cytoplasm organization and biogenesis (1e-29)		0.010	10
protein_40_YOR310C	2	NOP58:  Protein involved in pre-rRNA processing, 18S rRNA synthesis, and snoRNA synthesis; component of the small subunit processome complex, which is required for processing of pre-18S rRNA	[GS]F..[RKH]GG	56	RGG	Alternative integrin binding site in FMDV virus		RRM_1	1.E-02	-1.4	nucleolus (0.01)		0.006	7
protein_40_YPL043W	2	NOP4:  Nucleolar protein, essential for processing and maturation of 27S pre-rRNA and large ribosomal subunit biogenesis; constituent of 66S pre-ribosomal particles; contains four RNA recognition motifs (RRMs)	K[EKS]K[KIR]	56	[KR][LIM]K[DE]K[LIM]PG	DEHYDRIN_2 PATTERN		DEAD	1.E-02	-1.3	nucleolus (1e-23)	Y	0.011	10
yeast-436_GO-0031323	2	regulation of cellular metabolism	ND.[KDF]	56	D.D	Ribose moiety of UDP and manganese binding site in glucuronyl transferase		zf-C2H2	1.E-04	-1.1	regulation of cellular metabolism (1e-22)	Y	0.012	10
protein_40_YOR272W	2	YTM1:  Constituent of 66S pre-ribosomal particles, required for maturation of the large ribosomal subunit	R[GPT].[DQF]IP	56			Y	DEAD	1.E-05	-1.1	ribosome biogenesis (1e-08)	Y	0.007	10
protein_40_YNL061W	2	NOP2:  Probable RNA m(5)C methyltransferase, essential for processing and maturation of 27S pre-rRNA and large ribosomal subunit biogenesis; localized to the nucleolus; constituent of 66S pre-ribosomal particles	R[GST].[DQF]IP	56			Y	DEAD	1.E-05	-1.1	ribosome biogenesis (1e-08)		0.006	10
protein_40_YKR081C	2	RPF2:  Essential protein involved in the processing of pre-rRNA and the assembly of the 60S ribosomal subunit; interacts with ribosomal protein L11; localizes predominantly to the nucleolus; constituent of 66S pre-ribosomal particles	[KVH]K..K[KES]	56	P.[ST]PKK.KK	Cdc2 like protein kinase substrate motif		Helicase_C	1.E-03	-0.9	cytoplasm organization and biogenesis (1e-23)		0.010	10
yeast-1721_GO-0016043	2	cell organization and biogenesis	L[ETN]..L[EKV]	56	L..LL	Motif for interaction with nuclear receptors, docking motif for p300 on p53 to promote acetylation		IBN_N	1.E-03	-0.8	cellular localization (1e-37)	Y	0.012	10
yeast-216_GO-0006325	2	establishment and/or maintenance of chromatin architecture	KR.[KLG]	56	KR	CLV_PCSK_PC1ET2_1		Bromodomain	1.E-04	-0.3	establishment and/or maintenance of chromatin architecture (1e-18)		0.012	10
yeast-216_GO-0006323	2	DNA packaging	KR.[KLG]	56	KR	CLV_PCSK_PC1ET2_1		Bromodomain	1.E-04	-0.3	establishment and/or maintenance of chromatin architecture (1e-18)		0.012	10
protein_40_YHR148W	2	IMP3:  Component of the SSU processome, which is required for pre-18S rRNA processing, essential protein that interacts with Mpp10p and mediates interactions of Imp4p and Mpp10p with U3 snoRNA	[LQK]LA[VIA]G	56				WD40	1.E-04	1	nucleolus (1e-07)		0.006	9
yeast-251_GO-0005886	2	plasma membrane	I..F[LAF]	56	D..SII.FF	CK I delta kinase phosphorylation site (peptide screen)		MFS_1	1.E-07	1.1	plasma membrane (1e-13)		0.012	10
yeast-251_GO-0005886	2	plasma membrane	LG.[VGC][LTA]	56				MFS_1	1.E-06	1.1	plasma membrane (1e-70)		0.012	10
yeast-312_GO-0006414	2	translational elongation	G[FMY]G[LEI]	56	SG.G	Glycosaminoglycan attachment site	Y	Ribosomal_60s	1.E-11	1.6	translational elongation (1e-21)		0.007	10
yeast-312_GO-0006414	2	translational elongation	[AGT]A.[PKG]A	56			Y	Ribosomal_60s	1.E-10	1.6	translational elongation (1e-33)	Y	0.010	10
yeast-284_GO-0005740	2	mitochondrial envelope	[DKP][VTC].KTR	56				Mito_carr	1.E-24	2	mitochondrial envelope (1e-17)		0.011	10
protein_40_YLR429W	2	CRN1:  Coronin, cortical actin cytoskeletal component that associates with the Arp2p/Arp3p complex to regulate its activity; plays a role in regulation of actin patch assembly	IG.[GRT][STI]F	56				Pkinase	1.E-06	2.4	protein serine/threonine kinase activity (1e-07)		0.006	10
yeast-256_GO-0016462	2	pyrophosphatase activity	IF..[EVF][IRQ]D	56				AAA	1.E-05	2.6	nucleoside-triphosphatase activity (1e-10)	Y	0.007	9
protein_40_YBR031W	2	RPL4A:  N-terminally acetylated protein component of the large (60S) ribosomal subunit, nearly identical to Rpl4Bp and has similarity to E. coli L4 and rat L4 ribosomal proteins	[GIK]KT[LIK]A	56	KTPAKEE	GSK-3, ERK1, ERK2, CDK5 substrate motif	Y	DEAD	1.E-04	3.1	nucleolus (1e-04)	Y	0.006	10
protein_40_YOL139C	2	CDC33:  Cytoplasmic mRNA cap binding protein; the eIF4E-cap complex is responsible for mediating cap-dependent mRNA translation via interactions with the translation initiation factor eIF4G (Tif4631p or Tif4632p)	RD..[PLS][EDV]N	56				Pkinase	1.E-13	4	protein kinase activity (1e-11)		0.006	8
yeast-685_GO-0016740	2	transferase activity	PE[VNL][ILMV]	56				Pkinase	1.E-58	6.5	transferase activity, transferring phosphorus-containing groups (1e-60)	Y	0.012	10
yeast-301_GO-0044451	2	nucleoplasm part	E[DRG].[DGN]E	56							nucleoplasm part (1e-89)		0.012	10
yeast-262_GO-0031224	2	intrinsic to membrane	FG.K[PH][AN]	56							rRNA export from nucleus (1e-12)		0.007	10
protein_40_YPR144C	2	NOC4:  Nucleolar protein, forms a complex with Nop14p that mediates maturation and nuclear export of 40S ribosomal subunits	KR..[ED][DEK]D	56	KR	CLV_PCSK_PC1ET2_1					small nucleolar ribonucleoprotein complex (1e-11)	Y	0.006	9
protein_40_YNL110C	2	NOP15:  Constituent of 66S pre-ribosomal particles, involved in 60S ribosomal subunit biogenesis; localizes to both nucleolus and cytoplasm	SEL[KGC][SMQ]	56	[ST]E	G protein-coupled receptor kinase 1 substrate motif					cytoplasm organization and biogenesis (1e-07)		0.006	9
protein_40_YMR093W	2	UTP15:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	[KPY]K.LL[RFG]	56	DLL	Binding motif for clathrin heavy chain ear					nucleolus (0.001)		0.006	9
protein_40_YLR002C	2	NOC3:  Protein that forms a nuclear complex with Noc2p that binds to 66S ribosomal precursors to mediate their intranuclear transport; also binds to chromatin to promote the association of DNA replication factors and replication initiation	[AGQ]T.KK[SDG]	56	RKK.[ST]	ZIP kinase phosphorylation motif							0.006	10
protein_40_YJL010C	2	NOP9:  Essential component of pre-40S ribosomes that is required for early cleavages of 35S pre-rRNA and hence formation of 18S rRNA; binds RNA in vitro and contains multiple pumilio-like repeats	[GS]GR[GSV]G	56	[AG]R	Protease matriptase protease site					rRNA processing (1e-05)		0.007	10
protein_40_YIL094C	2	LYS12:  Homo-isocitrate dehydrogenase, an NAD-linked mitochondrial enzyme required for the fourth step in the biosynthesis of lysine, in which homo-isocitrate is oxidatively decarboxylated to alpha-ketoadipate	[VGH][LC]GQ	56	GGQ	N-methylation motif in E. coli, Gln residue in methylated, mimics CCA motif at the end of tRNA molecule						Y	0.007	10
protein_40_YHR114W	2	BZZ1:  SH3 domain protein implicated in the regulation of actin polymerization, able to recruit actin polymerization machinery through its SH3 domains, colocalizes with cortical actin patches and Las17p, interacts with type I myosins	PPP[PIL][PGT]	56	[DE]FPPP	EVH binding motif of Mena					actin cortical patch (0.001)		0.006	10
protein_40_YBR142W	2	MAK5:  Essential nucleolar protein, putative DEAD-box RNA helicase required for maintenance of M1 dsRNA virus; involved in biogenesis of large (60S) ribosomal subunits	[AD]D.E[RE]L	56	D.E	Sec24p	Y				nucleolus (0.001)		0.006	9
protein_40_YBR106W	2	PHO88:  Probable membrane protein, involved in phosphate transport; pho88 pho86 double null mutant exhibits enhanced synthesis of repressible acid phosphatase at high inorganic phosphate concentrations	IG.[IAC][IVG]	56							transporter activity (1e-10)		0.011	10
protein_40_YBR017C	2	KAP104:  Transportin, cytosolic karyopherin beta 2 involved in delivery of heterogeneous nuclear ribonucleoproteins to the nucleoplasm, binds rg-nuclear localization signals on Nab2p and Hrp1p, plays a role in cell-cycle progression	LF..K[PSF][AEK]	56	LFG	Protease Papain substrate, a prototype cysteine proteinase					protein import into nucleus (1e-05)		0.006	9
protein_40_YBR160W	2	CDC28:  Catalytic subunit of the main cell cycle cyclin-dependent kinase (CDK); alternately associates with G1 cyclins (CLNs) and G2/M cyclins (CLBs) which direct the CDK to specific substrates	L..L[QEP]	55				Pkinase	1.E-06	0.3	cell cycle (1e-15)		0.010	10
protein_40_YKL021C	2	MAK11:  Protein involved in an early, nucleolar step of 60S ribosomal subunit biogenesis; essential for cell growth and replication of killer M1 dsRNA virus; contains four beta-transducin repeats	EE..[EKD][KEY]	55	EED	Ankyrin B C-terminal motif that binds internal Ankyrin repeats		DEAD	1.E-02	-1.8	nucleolus (1e-32)	Y	0.010	10
matsuyama_nucleolus	2	matsuyama_nucleolus	[RV][GP].DIP	55				DEAD	1.E-10	-1.6	ATP-dependent RNA helicase activity (1e-09)		0.008	10
yeast-256_GO-0016462	2	pyrophosphatase activity	DE[AVI][DHC]	55	YDE[PDV]	SH2 ligand for Nck1 and Nck2 (Tyr must be phosphorylated)	Y	Helicase_C	1.E-24	-1.5	ATPase activity (1e-64)	Y	0.012	10
yeast-248_GO-0016072	2	rRNA metabolism	DV[AQW]A[RQ]	55				DEAD	1.E-07	-1.5	ATP-dependent RNA helicase activity (1e-08)		0.007	10
protein_40_YOL127W	2	RPL25:  Primary rRNA-binding ribosomal protein component of the large (60S) ribosomal subunit, has similarity to E. coli L23 and rat L23a ribosomal proteins; binds to 26S rRNA via a conserved C-terminal motif	K..[RAK]A	55	K[KR].[KR]	Nuclear localization motif		Ribosomal_60s	1.E-02	-1.4	cytosolic ribosome (sensu Eukaryota) (1e-41)	Y	0.010	10
protein_40_YNL175C	2	NOP13:  Protein of unknown function, localizes to the nucleolus and nucleoplasm; contains an RNA recognition motif (RRM) and has similarity to Nop12p, which is required for processing of pre-18S rRNA	G[RLS]TA[RPG]	55	KSGST	eIF4 motif phosphorylation motif		DEAD	1.E-07	-1.2	RNA helicase activity (1e-06)		0.006	10
protein_40_YDR060W	2	MAK21:  Constituent of 66S pre-ribosomal particles, required for large (60S) ribosomal subunit biogenesis; involved in nuclear export of pre-ribosomes; required for maintenance of dsRNA virus; homolog of human CAATT-binding protein	DV..R[GAD][LVA]	55			Y	DEAD	1.E-05	-1.2	ATP-dependent RNA helicase activity (1e-05)		0.005	10
protein_40_YGL120C	2	PRP43:  RNA helicase in the DEAH-box family, functions in both RNA polymerase I and polymerase II transcript metabolism, involved in release of the lariat-intron from the spliceosome	KR..[EDK][DKE]	55	KR	CLV_PCSK_PC1ET2_1		Helicase_C	1.E-03	-0.9	nucleolus (1e-29)		0.010	10
yeast-856_GO-0009059	2	macromolecule biosynthesis	N.[SNY]S	55	N.[TS]	N-linked glycosylation site	Y	PH	1.E-05	-0.6	transcription regulator activity (1e-13)		0.011	10
protein_40_YPL129W	2	TAF14:  Subunit of TFIID, TFIIF, INO80, SWI/SNF, and NuA3 complexes, involved in RNA polymerase II transcription initiation and in chromatin modification; contains a YEATS domain	T[LPT].LE[SQN]	55	P.L	Motif in C-Fos for protein instability		Bromodomain	1.E-02	-0.4	nucleoplasm part (1e-05)		0.006	10
yeast-1547_GO-0043283	2	biopolymer metabolism	N.[LDF]K	55				Helicase_C	1.E-03	0.1	protein modification (1e-80)		0.012	10
protein_40_YJR002W	2	MPP10:  Component of the SSU processome, which is required for pre-18S rRNA processing, interacts with and controls the stability of Imp3p and Imp4p, essential for viability; similar to human Mpp10p	LNK[LEP][ATP]	55	G[SA]LNK	GDP-mannose binding motif in transporter		WD40	1.E-02	0.1	snoRNA binding (1e-14)		0.006	8
protein_40_YOL069W	2	NUF2:  Component of the evolutionarily conserved kinetochore-associated Ndc80 complex (Ndc80p-Nuf2p-Spc24p-Spc25p); involved in chromosome segregation, spindle checkpoint activity and kinetochore clustering	[KEV]L..E[VKF]E	55				SMC_N	1.E-02	0.2		Y	0.006	10
yeast-413_GO-0005215	2	transporter activity	FA[LVW][AVH]	55				MFS_1	1.E-06	0.8	transporter activity (1e-44)	Y	0.013	10
protein_40_YDR449C	2	UTP6:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	[LQK]LA[VIA]G	55				WD40	1.E-04	1	nucleolus (1e-07)		0.006	10
protein_40_YLR197W	2	SIK1:  Essential evolutionarily-conserved nucleolar protein component of the box C/D snoRNP complexes that direct 2'-O-methylation of pre-rRNA during its maturation; overexpression causes spindle orientation defects	K[ETM][KVL]K	55				WD40	1.E-02	1.7	nucleolus (1e-28)		0.010	10
yeast-752_GO-0016787	2	hydrolase activity	[WL]D..GQ[EDP]	55	D..G	motif that binds phosphate in GDP and GTP binding proteins		Ras	1.E-34	2.7	GTPase activity (1e-35)		0.013	10
protein_40_YKL021C	2	MAK11:  Protein involved in an early, nucleolar step of 60S ribosomal subunit biogenesis; essential for cell growth and replication of killer M1 dsRNA virus; contains four beta-transducin repeats	[GEI]K[TWK]LA	55				DEAD	1.E-02	2.7	nucleolus (1e-07)		0.006	10
protein_40_YLL008W	2	DRS1:  Nucleolar DEAD-box protein required for ribosome assembly and function, including synthesis of 60S ribosomal subunits; constituent of 66S pre-ribosomal particles	I[GQL].G[SHQ]F	55	GCF	Motif for covalent cholesterol attachment at Cys		Pkinase	1.E-04	3.3	protein kinase activity (0.001)	Y	0.006	9
protein_40_YJR066W	2	TOR1:  PIK-related protein kinase and rapamycin target; subunit of TORC1, a complex that controls growth in response to nutrients by regulating translation, transcription, ribosome biogenesis, nutrient transport and autophagy; involved in meiosis	LF.[KHF][LM]H	55	LFG	Protease Papain substrate, a prototype cysteine proteinase		GATA	1.E-06	7	regulation of nitrogen utilization (1e-07)		0.006	10
yeast-324_GO-0030528	2	transcription regulator activity	[ASG]C..C[RIQ]	55	C..C	Motif on TIM mitochondrial translocation proteins	Y	Zn_clus	1.E-36	20.7	transcription regulator activity (1e-33)		0.012	10
yeast-322_GO-0005654	2	nucleoplasm	ED[EAK][DEG]	55	SEDEE	CKII kinase phosphorylation site (peptide screen)	Y				nucleoplasm (1e-10)	Y	0.012	10
protein_40_YPR161C	2	SGV1:  Cyclin (Bur2p)-dependent protein kinase that functions in transcriptional regulation; phosphorylates the carboxy-terminal domain of Rpo21p, which is the largest subunit of RNA polymerase II; regulated by Cak1p	[EVA][ERD]..GDE	55	RGD	LIG_RGD					nucleolus (1e-06)		0.006	10
protein_40_YPR034W	2	ARP7:  Component of both the SWI/SNF and RSC chromatin remodeling complexes; actin-related protein involved in transcriptional regulation	L[QWG].[LTE]LK	55							SWI/SNF complex (1e-05)		0.006	9
protein_40_YPL204W	2	HRR25:  Protein kinase involved in regulating diverse events including vesicular trafficking, DNA repair, and chromosome segregation; binds the CTD of RNA pol II; homolog of mammalian casein kinase 1delta (CK1delta)	[KHY]V[KDP]KV	55	VP	Interleukin converting enzyme protease							0.006	10
protein_40_YPL153C	2	RAD53:  Protein kinase, required for cell-cycle arrest in response to DNA damage; activated by trans autophosphorylation when interacting with hyperphosphorylated Rad9p; also interacts with ARS1 and plays a role in initiation of DNA replication	EQ[KVQ]	55	[PG].[GS]C[GA]E[EQ].[LIVM]	ALPHA_2_MACROGLOBULIN PATTERN					DNA integrity checkpoint (0.001)	Y	0.010	10
protein_40_YPL153C	2	RAD53:  Protein kinase, required for cell-cycle arrest in response to DNA damage; activated by trans autophosphorylation when interacting with hyperphosphorylated Rad9p; also interacts with ARS1 and plays a role in initiation of DNA replication	NN[SQL][NQK]R	55	[KR]R	CLV_PCSK_KEX2_1						Y	0.006	8
protein_40_YPL093W	2	NOG1:  Putative GTPase that associates with free 60S ribosomal subunits in the nucleolus and is required for 60S ribosomal subunit biogenesis; constituent of 66S pre-ribosomal particles; member of the ODN family of nucleolar G-proteins	[KRH]K..K[EAR]	55	KR	CLV_PCSK_PC1ET2_1					cytoplasm organization and biogenesis (1e-30)		0.011	10
protein_40_YMR117C	2	SPC24:  Component of the evolutionarily conserved kinetochore-associated Ndc80 complex (Ndc80p-Nuf2p-Spc24p-Spc25p); involved in chromosome segregation, spindle checkpoint activity and kinetochore clustering	[DHW]K..K[DMK]I	55							cytoskeletal part (0.01)		0.006	8
protein_40_YML073C	2	RPL6A:  N-terminally acetylated protein component of the large (60S) ribosomal subunit, has similarity to Rpl6Bp and to rat L6 ribosomal protein; binds to 5.8S rRNA	VVV[VSE][GHY]	55	VEHD	Protease Caspase 6-stringent					cytosol (0.001)		0.005	9
protein_40_YML010W	2	SPT5:  Protein that forms a complex with Spt4p and mediates both activation and inhibition of transcription elongation; Spt4p-Spt5p complex also plays a role in pre-mRNA processing	[DGF]D..E[EDK]	55							nuclear lumen (1e-10)	Y	0.010	10
protein_40_YLR429W	2	CRN1:  Coronin, cortical actin cytoskeletal component that associates with the Arp2p/Arp3p complex to regulate its activity; plays a role in regulation of actin patch assembly	NK.[ELF][KCT]L	55									0.006	10
protein_40_YLR180W	2	SAM1:  S-adenosylmethionine synthetase, catalyzes transfer of the adenosyl group of ATP to the sulfur atom of methionine; one of two differentially regulated isozymes (Sam1p and Sam2p)	[IDF]LA[AWT]L	55								Y	0.006	9
protein_40_YIL144W	2	TID3:  Component of the evolutionarily conserved kinetochore-associated Ndc80 complex (Ndc80p-Nuf2p-Spc24p-Spc25p); conserved coiled-coil protein involved in chromosome segregation, spindle checkpoint activity, kinetochore assembly and clustering	[NPQ][EQL]..RLK	55							microtubule cytoskeleton (0.001)		0.006	8
protein_40_YGR218W	2	CRM1:  Major karyopherin, involved in export of proteins, RNAs, and ribosomal subunits from the nucleus	L[FHI].[NSI]NN	55							rRNA export from nucleus (0.001)	Y	0.006	9
protein_40_YGR086C	2	PIL1:  Primary component of eisosomes, which are large immobile cell cortex structures associated with endocytosis; null mutants show activation of Pkc1p/Ypk1p stress resistance pathways; detected in phosphorylated state in mitochondria	[LPR]N..[QSG]QQ	55	S[QT]Q	ATM phosphorylation of this motif on Chk2							0.006	9
protein_40_YFR034C	2	PHO4:  Basic helix-loop-helix (bHLH) transcription factor of the myc-family; binds cooperatively with Pho2p to the PHO5 promoter; function is regulated by phosphorylation at multiple sites and by phosphate availability	A[LT].RA[LVC]	55							cytosol (0.01)		0.006	10
protein_40_YER118C	2	SHO1:  Transmembrane osmosensor, participates in activation of both the Cdc42p- and MAP kinase-dependent filamentous growth pathway and the high-osmolarity glycerol response pathway	S[SFV]AS[RTG]	55	S[ST]	MDC1 BRCT domain binding motif							0.006	10
protein_40_YDR448W	2	ADA2:  Transcription coactivator, component of the ADA and SAGA transcriptional adaptor/HAT (histone acetyltransferase) complexes	L[LEK]..[QIV]QQ	55							SAGA complex (1e-09)		0.006	10
protein_40_YCR009C	2	RVS161:  Amphiphysin-like lipid raft protein; subunit of a complex (Rvs161p-Rvs167p) that regulates polarization of the actin cytoskeleton, endocytosis, cell polarity, cell fusion and viability following starvation or osmotic stress	P[PIT].P[PN]R	55	PPR	LIG_WW_3					actin cytoskeleton organization and biogenesis (0.01)		0.007	10
protein_40_YBR059C	2	AKL1:  Ser-Thr protein kinase, member (with Ark1p and Prk1p) of the Ark kinase family; involved in endocytosis and actin cytoskeleton organization	[SVI]S.DE[SWH]	55	S.D	CAMKII phosphorylation site							0.006	10
protein_40_YAR007C	2	RFA1:  Subunit of heterotrimeric Replication Protein A (RPA), which is a highly conserved single-stranded DNA binding protein involved in DNA replication, repair, and recombination	P[EKF]LV[PTL]	55	LVPRG	Protease Thrombin					replication fork (sensu Eukaryota) (0.01)		0.006	10
yeast-410_GO-0007049	2	cell cycle	[SYI]S...S	54	S...S	WD40 binding motif, Ser residues must be phosphorylated		Pkinase	1.E-04	-4.8	cell cycle (10)	Y	0.011	10
yeast-399_GO-0003723	2	RNA binding	RGG[FNQ][RFA]	54	GGRGG	Arginine methyl transferease substrate motif (PRMT1)	Y	RRM_1	1.E-07	-2.6	RNA binding (1e-09)		0.007	10
oshea_mitochondrion	2	oshea_mitochondrion	N.N[SEN]	54				Zn_clus	1.E-11	-2.3	transcription regulator activity (1e-18)		0.011	10
protein_40_YOL077C	2	BRX1:  Nucleolar protein, constituent of 66S pre-ribosomal particles; depletion leads to defects in rRNA processing and a block in the assembly of large ribosomal subunits; possesses a sigma(70)-like RNA-binding motif	KK.[SVR][KEG]	54	RKK.[ST]	ZIP kinase phosphorylation motif		Brix	1.E-02	-1.5	cytoplasm organization and biogenesis (1e-25)		0.010	10
yeast-410_GO-0007049	2	cell cycle	L[LSQ]Q	54	LSQE	ATM kinase substrate motif		Pkinase	1.E-04	-1.4	cell cycle (1e-25)	Y	0.011	10
protein_40_YKL014C	2	URB1:  Nucleolar protein required for the normal accumulation of 25S and 5.8S rRNAs, associated with the 27SA2 pre-ribosomal particle; proposed to be involved in the biogenesis of the 60S ribosomal subunit	KK..[KDF][KEH]	54	RKK.[ST]	ZIP kinase phosphorylation motif		Helicase_C	1.E-02	-1.3	cytoplasm organization and biogenesis (1e-26)		0.010	10
yeast-207_GO-0003677	2	DNA binding	N.N[TNF]	54				Zn_clus	1.E-08	-1.2	DNA binding (1e-15)	Y	0.011	10
yeast-1721_GO-0016043	2	cell organization and biogenesis	[KNV]K.S[KEN]	54	RKK.[ST]	ZIP kinase phosphorylation motif		Helicase_C	1.E-02	-1.1	chromosome organization and biogenesis (1e-30)	Y	0.011	10
protein_40_YLR002C	2	NOC3:  Protein that forms a nuclear complex with Noc2p that binds to 66S ribosomal precursors to mediate their intranuclear transport; also binds to chromatin to promote the association of DNA replication factors and replication initiation	[RVT]A[AG]R	54	[AG]R	Protease matriptase protease site		DEAD	1.E-03	-1.1	nucleolus (1e-06)		0.007	10
protein_40_YPL198W	2	RPL7B:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl7Ap and has similarity to E. coli L30 and rat L7 ribosomal proteins; contains a conserved C-terminal Nucleic acid Binding Domain (NDB2)	DVA[AQC][RTP]	54	DVAD	Protease Caspase 2 -stringent	Y	DEAD	1.E-02	-1	ribosomal large subunit assembly and maintenance (1e-05)	Y	0.006	9
protein_40_YOR181W	2	LAS17:  Actin assembly factor, activates the Arp2/3 protein complex that nucleates branched actin filaments; localizes with the Arp2/3 complex to actin patches; homolog of the human Wiskott-Aldrich syndrome protein (WASP)	[AVI]P..PP[AP]	54	P..P	SH3 general ligand,		SH3_1	1.E-05	-0.9	actin cortical patch (1e-05)	Y	0.006	9
yeast-661_GO-0050789	2	regulation of biological process	L.Q[DEP]	54	LSQE	ATM kinase substrate motif	Y	Zn_clus	1.E-02	-0.8	regulation of metabolism (1e-12)		0.011	10
protein_40_YOR206W	2	NOC2:  Protein that forms a nucleolar complex with Mak21p that binds to 90S and 66S pre-ribosomes, as well as a nuclear complex with Noc3p that binds to 66S pre-ribosomes; both complexes mediate intranuclear transport of ribosomal precursors	[TRI][GER].GKT	54				Helicase_C	1.E-09	-0.8	RNA helicase activity (1e-10)		0.006	10
yeast-312_GO-0006414	2	translational elongation	RGITI	54	FRGGT	Phosphoinositide binding motif in ATG18 and ATG21		GTP_EFTU_D2	1.E-08	-0.7	translation elongation factor activity (1e-08)		0.006	9
protein_40_YFL039C	2	ACT1:  Actin, structural protein involved in cell polarization, endocytosis, and other cytoskeletal functions	[SLD]KR[YAD]S	54	KR	CLV_PCSK_PC1ET2_1		SH3_1	1.E-02	-0.7	actin cytoskeleton organization and biogenesis (0.001)		0.006	10
matsuyama_periphery	2	matsuyama_periphery	A[SFD]S	54	C[SA]DSR[LIVM].[AP]	PROK_CO2_ANHYDRASE_1 PATTERN		PH	1.E-04	-0.7	barrier septum (1e-89)	Y	0.013	10
protein_40_YNL186W	2	UBP10:  Ubiquitin-specific protease that deubiquitinates ubiquitin-protein moieties; may regulate silencing by acting on Sir4p; involved in posttranscriptionally regulating Gap1p and possibly other transporters; primarily located in the nucleus	S[SI]PL[NKV]	54	SP	ERK1, ERK2 Kinase substrate motif		Pkinase	1.E-02	-0.6		Y	0.005	8
protein_40_YBR198C	2	TAF5:  Subunit (90 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation and in chromatin modification	NN[VNI]E[EV]	54				Bromodomain	1.E-02	-0.6	transcription factor TFIID complex (1e-07)		0.006	9
protein_40_YDR356W	2	SPC110:  Inner plaque spindle pole body (SPB) component, ortholog of human kendrin; involved in connecting nuclear microtubules to SPB; interacts with Tub4p-complex and calmodulin; phosphorylated by Mps1p in cell cycle-dependent manner	[DS]V..AL[KGP]	54			Y	Kinesin	1.E-02	0.3	spindle pole body (1e-04)	Y	0.006	10
protein_40_YNL186W	2	UBP10:  Ubiquitin-specific protease that deubiquitinates ubiquitin-protein moieties; may regulate silencing by acting on Sir4p; involved in posttranscriptionally regulating Gap1p and possibly other transporters; primarily located in the nucleus	N[PKF]..R[IPD]	54				Pkinase	1.E-10	0.9	protein kinase activity (1e-10)	Y	0.009	10
yeast-1062_GO-0016020	2	membrane	A..F[GLA]	54				MFS_1	1.E-06	1	plasma membrane (1e-53)	Y	0.011	10
yeast-304_GO-0019752	2	carboxylic acid metabolism	V.[STA]G	54				PALP	1.E-02	1.4	carboxylic acid metabolism (1e-15)		0.011	10
yeast-304_GO-0006082	2	organic acid metabolism	V.[STA]G	54				PALP	1.E-02	1.4	carboxylic acid metabolism (1e-15)		0.011	10
protein_40_YKR048C	2	NAP1:  Protein that interacts with mitotic cyclin Clb2p; required for the regulation of microtubule dynamics during mitosis; controls bud morphogenesis; involved in the transport of H2A and H2B histones to the nucleus; phosphorylated by CK2	YL..E[ILMV][LVM]	54	Y[LI]	SH2 ligand for PLCgamma1 N-term.)group 3(phospho-peptide)		Histone	1.E-03	1.5		Y	0.006	10
protein_40_YML069W	2	POB3:  Subunit of the heterodimeric FACT complex (Spt16p-Pob3p), which facilitates RNA Pol II transcription elongation through nucleosomes by destabilizing and then reassembling nucleosome structure; interacts with DNA polymerase alpha (Pol1p)	[RT]L.R[RGV]G	54	RGG	Alternative integrin binding site in FMDV virus		Histone	1.E-06	1.6	nuclear nucleosome (1e-06)		0.006	10
protein_40_YNL272C	2	SEC2:  Guanyl-nucleotide exchange factor for the small G-protein Sec4p, located on cytoplasmic vesicles; essential for post-Golgi vesicle transport	K[IHR][IVP]H	54	KR	CLV_PCSK_PC1ET2_1		Pkinase	1.E-09	1.9	protein kinase activity (1e-07)		0.007	10
protein_40_YPR137W	2	RRP9:  Protein involved in pre-rRNA processing, associated with U3 snRNP; component of small ribosomal subunit (SSU) processosome; ortholog of the human U3-55k protein	[IPM][KHG].WD	54	PWDLW	LIG_Clathr_ClatBox_2		WD40	1.E-05	2.1	small nucleolar ribonucleoprotein complex (1e-11)	Y	0.006	8
protein_40_YKL009W	2	MRT4:  Protein involved in mRNA turnover and ribosome assembly, localizes to the nucleolus	[GKR]K.AA[FMS]	54				DEAD	1.E-03	3.2	cytoplasm organization and biogenesis (1e-05)		0.006	9
protein_40_YKL021C	2	MAK11:  Protein involved in an early, nucleolar step of 60S ribosomal subunit biogenesis; essential for cell growth and replication of killer M1 dsRNA virus; contains four beta-transducin repeats	[PT][TDE]REL	54	RE..E	Iron binding motif in ferritin L-chain and yeast Iron transport protein	Y	DEAD	1.E-05	3.3	ATP-dependent RNA helicase activity (1e-06)	Y	0.007	10
yeast-256_GO-0016462	2	pyrophosphatase activity	PTR[EM][LIT]	54	P[ST]	DNA dependent Protein kinase substrate motif		DEAD	1.E-16	3.9	ATP-dependent RNA helicase activity (1e-18)	Y	0.008	10
protein_40_YAR019C	2	CDC15:  Protein kinase of the Mitotic Exit Network that is localized to the spindle pole bodies at late anaphase; promotes mitotic exit by directly switching on the kinase activity of Dbf2p	G[AST].G.V	54				Pkinase	1.E-20	4.5	protein kinase activity (1e-17)		0.008	9
yeast-628_GO-0043037	2	translation	[KWV]MS[KAE]S	54	WM	Substrate binding motif of barley alpha-amylase 1 (AMY1) enzyme					amino acid activation (1e-15)		0.009	10
protein_40_YOR326W	2	MYO2:  One of two type V myosin motors (along with MYO4) involved in actin-based transport of cargos; required for the polarized delivery of secretory vesicles, the vacuole, late Golgi elements, peroxisomes, and the mitotic spindle	[LM]EN[VAP]Q	54	KEN	LIG_APCC_KENbox_2						Y	0.007	9
protein_40_YOR039W	2	CKB2:  Beta' regulatory subunit of casein kinase 2, a Ser/Thr protein kinase with roles in cell growth and proliferation; the holoenzyme also contains CKA1, CKA2 and CKB1, the many substrates include transcription factors and all RNA polymerases	D[EDY]..DE[EDG]	54	YDE[PDV]	SH2 ligand for Nck1 and Nck2 (Tyr must be phosphorylated)					transcription elongation factor complex (1e-04)		0.008	10
protein_40_YOL120C	2	RPL18A:  Protein component of the large (60S) ribosomal subunit, identical to Rpl18Bp and has similarity to rat L18 ribosomal protein; intron of RPL18A pre-mRNA forms stem-loop structures that are a target for Rnt1p cleavage leading to degradation	[NIK]K.V[VMI]V	54							cytosolic large ribosomal subunit (sensu Eukaryota) (1e-04)		0.006	8
protein_40_YNL124W	2	NAF1:  Protein required for the assembly of box H/ACA snoRNPs and for pre-rRNA processing, forms a complex with Shq1p and interacts with H/ACA snoRNP components Nhp2p and Cbf5p; has similarity to Gar1p and other RNA-binding proteins	ET.[KAY][ED]E	54	T.Y	MEK phosphorylation of MAPK activation site							0.006	8
protein_40_YNL118C	2	DCP2:  Catalytic subunit of the Dcp1p-Dcp2p decapping enzyme complex, which removes the 5' cap structure from mRNAs prior to their degradation; member of the Nudix hydrolase family	D[DPK]..S[KQM]I	54	DDDD..S	Casein kinase 1 phosphorylation motif	Y					Y	0.006	9
protein_40_YMR093W	2	UTP15:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	[TIV]D.SK[RIY]	54	KR	CLV_PCSK_PC1ET2_1	Y				snoRNA binding (1e-08)	Y	0.006	7
protein_40_YLL011W	2	SOF1:  Essential protein required for biogenesis of 40S (small) ribosomal subunit; has similarity to the beta subunit of trimeric G-proteins and the splicing factor Prp4p	[LDG]E..D[EKL]E	54							rRNA processing (1e-11)		0.006	10
protein_40_YHR196W	2	UTP9:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	IS[KEC]A[SKR]	54							small nucleolar ribonucleoprotein complex (1e-04)	Y	0.006	9
protein_40_YGL173C	2	KEM1:  Evolutionarily-conserved 5'-3' exonuclease component of cytoplasmic processing (P) bodies involved in mRNA decay; plays a role in microtubule-mediated processes, filamentous growth, ribosomal RNA maturation, and telomere maintenance	[GRK][GT]RGG	54	RGG	Alternative integrin binding site in FMDV virus	Y						0.006	9
protein_40_YBR036C	2	CSG2:  Endoplasmic reticulum membrane protein, required for mannosylation of inositolphosphorylceramide and for growth at high calcium concentrations	GL..L[IFM][VRN]	54	L..L.L..L	Leucine rich repeat common in protein protein interactions. They are normally 24 amino acids long							0.006	8
protein_40_YAL024C	2	LTE1:  Putative GDP/GTP exchange factor required for mitotic exit at low temperatures; acts as a guanine nucleotide exchange factor (GEF) for Tem1p, which is a key regulator of mitotic exit; physically associates with Ras2p-GTP	KL[IP]D[EWG]	54	LPDEL	Motif in CBP for interaction with PPARg-LBD (secondary site)							0.006	8
yeast-1166_GO-0005488	2	binding	Q..[QVT]Q	53	[ST]Q	ATM kinase phosphorylation site		RRM_1	1.E-03	-3.2	protein binding (1e-58)		0.011	10
yeast-345_GO-0006396	2	RNA processing	H[RHL].G[RCL]T	53			Y	DEAD	1.E-19	-2	RNA helicase activity (1e-19)	Y	0.010	10
yeast-1547_GO-0043283	2	biopolymer metabolism	KL.[SEI]	53	NKLY	LIM3 domain in enigma binds to this site in Ret		BRCT	1.E-05	-1.8	DNA metabolism (1e-10)		0.011	10
protein_40_YDR496C	2	PUF6:  Pumilio-homology domain protein that binds ASH1 mRNA at PUF consensus sequences in the 3' UTR and represses its translation, resulting in proper asymmetric localization of ASH1 mRNA	KK.[SVR][KGE]	53	RKK.[ST]	ZIP kinase phosphorylation motif		Brix	1.E-02	-1.4	cytoplasm organization and biogenesis (1e-25)		0.010	10
yeast-648_GO-0050791	2	regulation of physiological process	L..[PNM]S	53			Y	Zn_clus	1.E-05	-1.2	regulation of metabolism (1e-15)		0.011	10
yeast-238_GO-0017111	2	nucleoside-triphosphatase activity	DE[AVI][DHR]	53	YDE[PDV]	SH2 ligand for Nck1 and Nck2 (Tyr must be phosphorylated)	Y	Helicase_C	1.E-14	-1.2	nucleoside-triphosphatase activity (1e-61)	Y	0.011	10
yeast-238_GO-0017111	2	nucleoside-triphosphatase activity	L[YIV]..P[GPT]	53	[PV]..P	LIG_SH3_3		Helicase_C	1.E-12	-1.2	nucleoside-triphosphatase activity (1e-53)	Y	0.012	10
protein_40_YOL127W	2	RPL25:  Primary rRNA-binding ribosomal protein component of the large (60S) ribosomal subunit, has similarity to E. coli L23 and rat L23a ribosomal proteins; binds to 26S rRNA via a conserved C-terminal motif	DV[AVE]A[RFK]	53			Y	DEAD	1.E-04	-1.2	RNA helicase activity (1e-04)		0.006	9
yeast-460_GO-0006351	2	transcription, DNA-dependent	Q[QNH]Q	53				zf-C2H2	1.E-09	-0.6	transcription, DNA-dependent (1e-13)		0.011	10
protein_40_YJR066W	2	TOR1:  PIK-related protein kinase and rapamycin target; subunit of TORC1, a complex that controls growth in response to nutrients by regulating translation, transcription, ribosome biogenesis, nutrient transport and autophagy; involved in meiosis	[SE]D..[GPE]TL	53	PTL	Motif in Fos for proteosome degredation		Cation_ATPase_N	1.E-02	-0.4	ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism (0.01)		0.006	7
yeast-1721_GO-0016043	2	cell organization and biogenesis	N[SGT].[STN]S	53				PH	1.E-02	-0.3	cellular morphogenesis (1e-33)	Y	0.011	10
protein_40_YNL272C	2	SEC2:  Guanyl-nucleotide exchange factor for the small G-protein Sec4p, located on cytoplasmic vesicles; essential for post-Golgi vesicle transport	Q[ITW][LHG]R	53	[AG]R	Protease matriptase protease site		Pkinase	1.E-13	0.5	protein kinase activity (1e-13)	Y	0.008	10
protein_40_YBR106W	2	PHO88:  Probable membrane protein, involved in phosphate transport; pho88 pho86 double null mutant exhibits enhanced synthesis of repressible acid phosphatase at high inorganic phosphate concentrations	I..[VIL]V	53				MFS_1	1.E-08	1.6	transporter activity (1e-13)		0.010	10
protein_40_YJR002W	2	MPP10:  Component of the SSU processome, which is required for pre-18S rRNA processing, interacts with and controls the stability of Imp3p and Imp4p, essential for viability; similar to human Mpp10p	[IMP][KH].WD	53	PWDLW	LIG_Clathr_ClatBox_2		WD40	1.E-07	1.9	small nucleolar ribonucleoprotein complex (1e-14)		0.006	9
protein_40_YAR019C	2	CDC15:  Protein kinase of the Mitotic Exit Network that is localized to the spindle pole bodies at late anaphase; promotes mitotic exit by directly switching on the kinase activity of Dbf2p	HP.[IV][VIC]	53	HPQ	Biotin binding motif in streptavidin		Pkinase	1.E-14	3.2	kinase activity (1e-12)		0.006	10
protein_40_YNL002C	2	RLP7:  Nucleolar protein with similarity to large ribosomal subunit L7 proteins; constituent of 66S pre-ribosomal particles; plays an essential role in processing of precursors to the large ribosomal subunit RNAs	GK[TQG][LAF]A	53				DEAD	1.E-05	3.3	ribosome biogenesis (1e-05)	Y	0.006	9
protein_40_YGL245W	2	GUS1:  Glutamyl-tRNA synthetase (GluRS), forms a complex with methionyl-tRNA synthetase (Mes1p) and Arc1p; complex formation increases the catalytic efficiency of both tRNA synthetases and ensures their correct localization to the cytoplasm	[VSM]D.W[SAR]	53				Pkinase	1.E-18	3.8	protein kinase activity (1e-17)		0.007	8
yeast-345_GO-0006396	2	RNA processing	[DY]EAD[RFQ]	53	YE	TPK-IIB/P38Syk kinase phosphorylation site (peptide screen)		DEAD	1.E-13	4.8	RNA helicase activity (1e-12)		0.009	9
yeast-685_GO-0016740	2	transferase activity	[LRM]AP[ECM]	53	P[TS]AP	LIG_PTAP		Pkinase	1.E-30	5.7	kinase activity (1e-30)	Y	0.011	10
yeast-685_GO-0016740	2	transferase activity	[MRH][AKS]PE	53	FP.[PAILSK]P	LIG_EVH1_I		Pkinase	1.E-33	5.8	kinase activity (1e-33)	Y	0.011	10
yeast-685_GO-0016740	2	transferase activity	D[ILC]..[EQA]N	53				Pkinase	1.E-71	8.2	kinase activity (1e-67)	Y	0.011	10
yeast-255_GO-0007028	2	cytoplasm organization and biogenesis	[HFG]R.GR[TER]	53	[AG]R	Protease matriptase protease site		Helicase_C	1.E-16	9.8	ribosome biogenesis (1e-19)		0.010	10
yeast-255_GO-0042254	2	ribosome biogenesis and assembly	[HFG]R.GR[TER]	53	[AG]R	Protease matriptase protease site		Helicase_C	1.E-16	9.9	ribosome biogenesis (1e-19)		0.010	10
yeast-336_GO-0005783	2	endoplasmic reticulum	L..[LIV]F	53							endoplasmic reticulum (1e-22)	Y	0.012	10
yeast-335_GO-0016772	2	transferase activity, transferring phosphorus-containing groups	[QRC]L..R[LE]P	53			Y				transferase activity, transferring phosphorus-containing groups (1e-07)		0.007	9
yeast-285_GO-0012505	2	endomembrane system	F[GQ].K[PHT]A	53							snRNP protein import into nucleus (1e-09)		0.007	9
yeast-256_GO-0016462	2	pyrophosphatase activity	DE..[ELM]T[AP]	53							pyrophosphatase activity (1e-07)		0.007	8
yeast-251_GO-0005886	2	plasma membrane	S[SCV].[AFM]S	53	S[ST]	MDC1 BRCT domain binding motif					plasma membrane (1e-86)	Y	0.011	10
yeast-234_GO-0006605	2	protein targeting	FG.K[PEH][AN]	53	KEN	LIG_APCC_KENbox_2					rRNA export from nucleus (1e-12)		0.006	8
protein_40_YPR119W	2	CLB2:  B-type cyclin involved in cell cycle progression; activates Cdc28p to promote the transition from G2 to M phase; accumulates during G2 and M, then targeted via a destruction box motif for ubiquitin-mediated degradation by the proteasome	L..D[ENT]	53			Y				cell cycle (1e-13)		0.009	10
protein_40_YPL240C	2	HSP82:  Hsp90 chaperone required for pheromone signaling and negative regulation of Hsf1p; docks with Tom70p for mitochondrial preprotein delivery; promotes telomerase DNA binding and nucleotide addition; interacts with Cns1p, Cpr6p, Cpr7p, Sti1p	L.G	53	LFG	Protease Papain substrate, a prototype cysteine proteinase						Y	0.009	10
protein_40_YPL153C	2	RAD53:  Protein kinase, required for cell-cycle arrest in response to DNA damage; activated by trans autophosphorylation when interacting with hyperphosphorylated Rad9p; also interacts with ARS1 and plays a role in initiation of DNA replication	[ATR]S...D	53							DNA damage response, signal transduction (0.001)	Y	0.010	10
protein_40_YPL153C	2	RAD53:  Protein kinase, required for cell-cycle arrest in response to DNA damage; activated by trans autophosphorylation when interacting with hyperphosphorylated Rad9p; also interacts with ARS1 and plays a role in initiation of DNA replication	[DES]E[DEK]E	53	EEEYF	EGFR kinase phosphorylation site (peptide screen)					regulation of gene expression, epigenetic (0.001)	Y	0.010	10
protein_40_YOL127W	2	RPL25:  Primary rRNA-binding ribosomal protein component of the large (60S) ribosomal subunit, has similarity to E. coli L23 and rat L23a ribosomal proteins; binds to 26S rRNA via a conserved C-terminal motif	G[KIR]KV[TAK]	53	G[KR][KR]	Amidation after cleavage after Gly (must be in secretory pathway)					cytosolic ribosome (sensu Eukaryota) (1e-07)		0.006	9
protein_40_YMR093W	2	UTP15:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	[LEM][LAV].KLS	53							nucleolus (1e-06)	Y	0.006	10
protein_40_YLR175W	2	CBF5:  Pseudouridine synthase catalytic subunit of box H/ACA small nucleolar ribonucleoprotein particles (snoRNPs), acts on both large and small rRNAs and on snRNA U2	EE..[KGP][DEK]	53	EED	Ankyrin B C-terminal motif that binds internal Ankyrin repeats					nucleolus (1e-13)		0.010	10
protein_40_YKL009W	2	MRT4:  Protein involved in mRNA turnover and ribosome assembly, localizes to the nucleolus	AR..[ASH]K[EIK]	53	[AG]R	Protease matriptase protease site							0.006	10
protein_40_YJR066W	2	TOR1:  PIK-related protein kinase and rapamycin target; subunit of TORC1, a complex that controls growth in response to nutrients by regulating translation, transcription, ribosome biogenesis, nutrient transport and autophagy; involved in meiosis	[DVF]I..F[DNG]D	53	DF.DF	EF hand in gamma-synergin binding motif					cellular morphogenesis (0.01)		0.006	10
protein_40_YJL095W	2	BCK1:  Mitogen-activated protein (MAP) kinase kinase kinase acting in the protein kinase C signaling pathway, which controls cell integrity; upon activation by Pkc1p phosphorylates downstream kinases Mkk1p and Mkk2p	K[LFA]..G[SQE]K	53	[LI][IVCAP]D.K[LIFY]E[FI]G	SAICAR_SYNTHETASE_2 PATTERN							0.005	9
protein_40_YHR169W	2	DBP8:  Putative ATP-dependent RNA helicase of the DEAD-box family involved in biogenesis of the 40S ribosomal subunit	[SMP]EV[DTP]A	53	[ST]E	G protein-coupled receptor kinase 1 substrate motif							0.006	10
protein_40_YGL173C	2	KEM1:  Evolutionarily-conserved 5'-3' exonuclease component of cytoplasmic processing (P) bodies involved in mRNA decay; plays a role in microtubule-mediated processes, filamentous growth, ribosomal RNA maturation, and telomere maintenance	[PKA]P.P[QKF]Q	53	P.P	motif in interleukin 5 receptor necessary for signaling							0.006	8
protein_40_YFL037W	2	TUB2:  Beta-tubulin; associates with alpha-tubulin (Tub1p and Tub3p) to form tubulin dimer, which polymerizes to form microtubules	VQ..[TDP][TFW]	53			Y						0.007	10
protein_40_YER082C	2	UTP7:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	ES..[DGR][ED]K	53	S..[ED]	Casein kinase II substrate motif					processing of 20S pre-rRNA (1e-05)		0.006	10
protein_40_YDR381W	2	YRA1:  Nuclear protein that binds to RNA and to Mex67p, required for export of poly(A)+ mRNA from the nucleus; member of the REF (RNA and export factor binding proteins) family; another family member, Yra2p, can substitute for Yra1p function	ED[EKD].E	53	SEDEE	CKII kinase phosphorylation site (peptide screen)					rRNA metabolism (1e-05)		0.010	10
protein_40_YDR303C	2	RSC3:  Component of the RSC chromatin remodeling complex; essential gene required for maintenance of proper ploidy and regulation of ribosomal protein genes and the cell wall/stress response; highly similar to Rsc30p	[FM]EV[LCM]	53									0.006	9
protein_40_YDR174W	2	HMO1:  Chromatin associated high mobility group (HMG) family member involved in genome maintenance; rDNA-binding component of the Pol I transcription system; associates with a 5'-3' DNA helicase and Fpr1p, a prolyl isomerase	[IQY]K..K[RMF]S	53	KR	CLV_PCSK_PC1ET2_1							0.005	9
protein_40_YDL148C	2	NOP14:  Nucleolar protein, forms a complex with Noc4p that mediates maturation and nuclear export of 40S ribosomal subunits; also present in the small subunit processome complex, which is required for processing of pre-18S rRNA	L[KAP]V[LWI]K	53							small nucleolar ribonucleoprotein complex (1e-04)		0.005	9
protein_40_YDL148C	2	NOP14:  Nucleolar protein, forms a complex with Noc4p that mediates maturation and nuclear export of 40S ribosomal subunits; also present in the small subunit processome complex, which is required for processing of pre-18S rRNA	L[NDA]K[LRV]A	53	G[SA]LNK	GDP-mannose binding motif in transporter					rRNA processing (1e-04)	Y	0.005	8
protein_40_YBR142W	2	MAK5:  Essential nucleolar protein, putative DEAD-box RNA helicase required for maintenance of M1 dsRNA virus; involved in biogenesis of large (60S) ribosomal subunits	[TVA]E.[EVF]ED	53	EED	Ankyrin B C-terminal motif that binds internal Ankyrin repeats					cytoplasm organization and biogenesis (0.01)		0.006	10
protein_40_YAL032C	2	PRP45:  Protein required for pre-mRNA splicing; associates with the spliceosome and interacts with splicing factors Prp22p and Prp46p; orthologous to human transcriptional coactivator SKIP and can activate transcription of a reporter gene	LE..S[IFL][SIR]	53									0.006	7
oshea_bud	2	oshea_bud	S[SVI][STR]S	53	S[ST]	MDC1 BRCT domain binding motif					bud (1e-27)		0.010	10
protein_40_YDL188C	2	PPH22:  Catalytic subunit of protein phosphatase 2A, functionally redundant with Pph21p; methylated at C terminus; forms alternate complexes with several regulatory subunits; involved in signal transduction and regulation of mitosis	SP.[GD]R[LYN]	52	SP	ERK1, ERK2 Kinase substrate motif		Proteasome	1.E-08	-3.7	proteasome core complex, alpha-subunit complex (sensu Eukaryota) (1e-10)		0.007	9
yeast-345_GO-0006396	2	RNA processing	E[EVD].E[KDI]	52	SEDEE	CKII kinase phosphorylation site (peptide screen)		DEAD	1.E-07	-2.1	RNA processing (1e-11)		0.011	10
protein_40_YML069W	2	POB3:  Subunit of the heterodimeric FACT complex (Spt16p-Pob3p), which facilitates RNA Pol II transcription elongation through nucleosomes by destabilizing and then reassembling nucleosome structure; interacts with DNA polymerase alpha (Pol1p)	K[ACQ].A[ERA]K	52				Histone	1.E-03	-1.9	establishment and/or maintenance of chromatin architecture (0.001)		0.006	9
yeast-460_GO-0006351	2	transcription, DNA-dependent	N.D[DST]	52				zf-C2H2	1.E-06	-1.5	transcription, DNA-dependent (1e-23)	Y	0.011	10
protein_40_YOL127W	2	RPL25:  Primary rRNA-binding ribosomal protein component of the large (60S) ribosomal subunit, has similarity to E. coli L23 and rat L23a ribosomal proteins; binds to 26S rRNA via a conserved C-terminal motif	[RMS][GSW].DIP	52	S.D	CAMKII phosphorylation site		DEAD	1.E-07	-1.3	RNA helicase activity (1e-06)		0.005	10
yeast-256_GO-0016021	2	integral to membrane	F.[FLY]L	52	YF.[FPLY]	SH2 ligand for PTPN6-N (Tyr must be phosphorylated)		ABC_tran	1.E-03	-1.2	integral to membrane (1e-15)		0.011	10
yeast-462_GO-0019222	2	regulation of metabolism	EE[DIT]	52	EE[END]Y[MF][MF][MFIE][MF]	Insulin receptor kinase substrate motif		Zn_clus	1.E-05	-0.9	regulation of metabolism (1e-26)		0.011	10
protein_40_YML085C	2	TUB1:  Alpha-tubulin; associates with beta-tubulin (Tub2p) to form tubulin dimer, which polymerizes to form microtubules	L[LIG].[NAP]VL	52				HEAT	1.E-02	-0.7			0.005	8
protein_40_YKR081C	2	RPF2:  Essential protein involved in the processing of pre-rRNA and the assembly of the 60S ribosomal subunit; interacts with ribosomal protein L11; localizes predominantly to the nucleolus; constituent of 66S pre-ribosomal particles	E[EKY]..[EDG]E	52				Helicase_C	1.E-02	-0.7	cytoplasm organization and biogenesis (1e-22)		0.009	10
protein_40_YMR236W	2	TAF9:  Subunit (17 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation and in chromatin modification, similar to histone H3	[ND]N[VNI]EE	52	Y[DE]N[IFV]	SH2 ligand for SYK-C (Tyr must be phosphorylated)		Bromodomain	1.E-02	-0.6	transcription factor TFIID complex (1e-10)	Y	0.006	10
yeast-942_GO-0043232	2	intracellular non-membrane-bound organelle	[KDQ]E[DNEQ]E	52	EEEYF	EGFR kinase phosphorylation site (peptide screen)	Y	HEAT	1.E-03	-0.5	nucleolus (1e-55)	Y	0.011	10
yeast-942_GO-0043228	2	non-membrane-bound organelle	[KDQ]E[DNEQ]E	52	EEEYF	EGFR kinase phosphorylation site (peptide screen)	Y	HEAT	1.E-03	-0.4	nucleolus (1e-55)	Y	0.011	10
yeast-376_GO-0019219	2	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism	N..D[DET]	52	NK.D	Motif for specificity of guanine in purine binding proteins		PUF	1.E-02	-0.2	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism (1e-20)		0.011	10
protein_40_YPL131W	2	RPL5:  Protein component of the large (60S) ribosomal subunit with similarity to E. coli L18 and rat L5 ribosomal proteins; binds 5S rRNA and is required for 60S subunit assembly	[NGK]K.K[NKP]	52	P.[ST]PKK.KK	Cdc2 like protein kinase substrate motif		Helicase_C	1.E-02	0.3	cytoplasm organization and biogenesis (1e-17)		0.010	10
yeast-939_GO-0051234	2	establishment of localization	LV..[LVF][ILMV]	52				MFS_1	1.E-05	0.4	transporter activity (1e-43)		0.011	10
yeast-312_GO-0006414	2	translational elongation	A[ES]..KE[EH]	52	KEN	LIG_APCC_KENbox_2		Ribosomal_60s	1.E-08	0.9	translational elongation (1e-12)		0.007	8
protein_40_YNL031C	2	HHT2:  One of two identical histone H3 proteins (see also HHT1); core histone required for chromatin assembly, involved in heterochromatin-mediated telomeric and HM silencing; regulated by acetylation, methylation, and mitotic phosphorylation	LE..[GRA][NI]A	52				Histone	1.E-04	1.6	establishment and/or maintenance of chromatin architecture (0.01)		0.006	10
yeast-200_GO-0006519	2	amino acid and derivative metabolism	[GAC]L...G	52				PALP	1.E-05	1.7	amino acid and derivative metabolism (1e-13)		0.011	10
yeast-413_GO-0005215	2	transporter activity	EG..[AGS]L[YFW]	52				Mito_carr	1.E-31	1.8	transporter activity (1e-16)	Y	0.010	10
yeast-379_GO-0031975	2	envelope	[DKP][VTC].KTR	52				Mito_carr	1.E-23	1.9	envelope (1e-17)		0.011	10
yeast-379_GO-0031967	2	organelle envelope	[DKP][VTC].KTR	52				Mito_carr	1.E-23	2	envelope (1e-17)		0.011	10
yeast-413_GO-0005215	2	transporter activity	[LFI]D..K[TVF]R	52			Y	Mito_carr	1.E-46	2.2	transporter activity (1e-22)	Y	0.012	10
yeast-1547_GO-0043283	2	biopolymer metabolism	V.[ELI]K	52	P.V.L	Shadow-Chromo domain binding motif		Pkinase	1.E-05	2.2	DNA metabolism (1e-65)		0.011	10
yeast-752_GO-0016787	2	hydrolase activity	G[KYI]..L[LAD]	52	Y..L	Motif for down regulation of the CD46 receptor	Y	ABC_tran	1.E-06	2.5	hydrolase activity, acting on acid anhydrides (1e-43)	Y	0.011	10
protein_40_YGL105W	2	ARC1:  Protein that binds tRNA and methionyl- and glutamyl-tRNA synthetases (Mes1p and Gus1p), delivering tRNA to them, stimulating catalysis, and ensuring their localization to the cytoplasm; also binds quadruplex nucleic acids	[LIA]K..N	52				Pkinase	1.E-18	2.9	protein kinase activity (1e-19)	Y	0.009	10
yeast-341_GO-0045449	2	regulation of transcription	KR...[KGE]	52	KR	CLV_PCSK_PC1ET2_1		Zn_clus	1.E-08	3.1	regulation of transcription (1e-19)	Y	0.011	10
protein_40_YDR496C	2	PUF6:  Pumilio-homology domain protein that binds ASH1 mRNA at PUF consensus sequences in the 3' UTR and represses its translation, resulting in proper asymmetric localization of ASH1 mRNA	[GVS]K.AA[FSG]	52				DEAD	1.E-03	3.1	nucleolus (1e-07)		0.006	8
protein_40_YER006W	2	NUG1:  GTPase that associates with nuclear 60S pre-ribosomes, required for export of 60S ribosomal subunits from the nucleus	DEA[DRA][RLS]	52				DEAD	1.E-02	3.2	ribosome biogenesis (1e-05)		0.005	8
protein_40_YML010W	2	SPT5:  Protein that forms a complex with Spt4p and mediates both activation and inhibition of transcription elongation; Spt4p-Spt5p complex also plays a role in pre-mRNA processing	[SIK]P..E[LCY]A	52	[ST]P	LIG_WW_4		DEAD	1.E-05	3.4	ATP-dependent RNA helicase activity (1e-05)		0.006	8
protein_40_YLL008W	2	DRS1:  Nucleolar DEAD-box protein required for ribosome assembly and function, including synthesis of 60S ribosomal subunits; constituent of 66S pre-ribosomal particles	[TRV]G.GK[TIY]	52	[SAG]GGTG[SA]G	TUBULIN PATTERN		DEAD	1.E-04	3.4	ribosomal large subunit assembly and maintenance (1e-05)		0.006	10
protein_40_YOL127W	2	RPL25:  Primary rRNA-binding ribosomal protein component of the large (60S) ribosomal subunit, has similarity to E. coli L23 and rat L23a ribosomal proteins; binds to 26S rRNA via a conserved C-terminal motif	[PTD][TES]REL	52	RE..E	Iron binding motif in ferritin L-chain and yeast Iron transport protein		DEAD	1.E-09	4.1	RNA helicase activity (1e-09)		0.005	10
yeast-468_GO-0051276	2	chromosome organization and biogenesis	D[EDG]..E[DNEQ]	52	Q[MLVI]DG..[DE]	CLV_TASPASE1					chromosome organization and biogenesis (1e-12)		0.011	10
yeast-343_GO-0005198	2	structural molecule activity	FG.[KR][PGH]A	52	G[KR][KR]	Amidation after cleavage after Gly (must be in secretory pathway)					snRNP protein import into nucleus (1e-09)		0.007	9
yeast-234_GO-0006605	2	protein targeting	[AGE]FSFG	52	F.F	WASP Homology 1 binding motif					rRNA export from nucleus (1e-15)		0.006	10
protein_40_YPR119W	2	CLB2:  B-type cyclin involved in cell cycle progression; activates Cdc28p to promote the transition from G2 to M phase; accumulates during G2 and M, then targeted via a destruction box motif for ubiquitin-mediated degradation by the proteasome	I..[QKC]R	52	[KR]R	CLV_PCSK_KEX2_1					cell cycle (1e-07)		0.009	10
protein_40_YPL209C	2	IPL1:  Aurora kinase involved in regulating kinetochore-microtubule attachments; helps maintain condensed chromosomes during anaphase and early telophase; associates with Sli15p, which promotes Ipl1p association with mitotic spindle	[EDT]K..[KNS]AA	52	K..[ST]	PKA kinase substrate motif						Y	0.006	10
protein_40_YOR310C	2	NOP58:  Protein involved in pre-rRNA processing, 18S rRNA synthesis, and snoRNA synthesis; component of the small subunit processome complex, which is required for processing of pre-18S rRNA	LE..D[EQA][EQD]	52							small nucleolar ribonucleoprotein complex (1e-11)		0.006	9
protein_40_YOL120C	2	RPL18A:  Protein component of the large (60S) ribosomal subunit, identical to Rpl18Bp and has similarity to rat L18 ribosomal protein; intron of RPL18A pre-mRNA forms stem-loop structures that are a target for Rnt1p cleavage leading to degradation	KK[VDQ][EVF]D	52							cytoplasm organization and biogenesis (0.001)		0.006	10
protein_40_YNL118C	2	DCP2:  Catalytic subunit of the Dcp1p-Dcp2p decapping enzyme complex, which removes the 5' cap structure from mRNAs prior to their degradation; member of the Nudix hydrolase family	L[SDT]..E[IEF]S	52	[ST]..E	Casien kinase II consensus phosphorylation site							0.006	7
protein_40_YNL110C	2	NOP15:  Constituent of 66S pre-ribosomal particles, involved in 60S ribosomal subunit biogenesis; localizes to both nucleolus and cytoplasm	[ELG]E..E[ENG]E	52							cytoplasm organization and biogenesis (1e-21)		0.009	10
protein_40_YNL002C	2	RLP7:  Nucleolar protein with similarity to large ribosomal subunit L7 proteins; constituent of 66S pre-ribosomal particles; plays an essential role in processing of precursors to the large ribosomal subunit RNAs	S[DSW].E[ESL]E	52	QPS..E	Phosphorylation motif in alpha 3A, alpha 6A, alpha 7A Integrin tails	Y				nucleolus (1e-13)		0.007	10
protein_40_YMR049C	2	ERB1:  Protein required for maturation of the 25S and 5.8S ribosomal RNAs; constituent of 66S pre-ribosomal particles; homologous to mammalian Bop1	AR..[ASP]K[EIV]	52	[AG]R	Protease matriptase protease site					nucleolus (0.001)		0.005	9
protein_40_YJL190C	2	RPS22A:  Protein component of the small (40S) ribosomal subunit; nearly identical to Rps22Bp and has similarity to E. coli S8 and rat S15a ribosomal proteins	AE..[AS]A[ENL]	52							ribonucleoprotein complex (0.001)		0.006	10
protein_40_YHR152W	2	SPO12:  Nucleolar protein of unknown function, positive regulator of mitotic exit; involved in regulating release of Cdc14p from the nucleolus in early anaphase, may play similar role in meiosis	D[QC].R[DSY]	52									0.005	8
protein_40_YHR114W	2	BZZ1:  SH3 domain protein implicated in the regulation of actin polymerization, able to recruit actin polymerization machinery through its SH3 domains, colocalizes with cortical actin patches and Las17p, interacts with type I myosins	[LF]R[TQM]LG	52	R.L	Cyclin A motif that binds cdk2 complexes							0.006	9
protein_40_YGL135W	2	RPL1B:  N-terminally acetylated protein component of the large (60S) ribosomal subunit, nearly identical to Rpl1Ap and has similarity to E. coli L1 and rat L10a ribosomal proteins; rpl1a rpl1b double null mutation is lethal	[KAP]GK[KLT]V	52	G[KR][KR]	Amidation after cleavage after Gly (must be in secretory pathway)					cytosolic ribosome (sensu Eukaryota) (1e-06)		0.005	10
protein_40_YGL019W	2	CKB1:  Beta regulatory subunit of casein kinase 2, a Ser/Thr protein kinase with roles in cell growth and proliferation; the holoenzyme also contains CKA1, CKA2 and CKB2, the many substrates include transcription factors and all RNA polymerases	[KGR]P..K[VHR]L	52	KP..[QK]	LIG_SH3_4							0.006	10
protein_40_YDR450W	2	RPS18A:  Protein component of the small (40S) ribosomal subunit; nearly identical to Rps18Bp and has similarity to E. coli S13 and rat S18 ribosomal proteins	[RPD]R.[AY]R	52	[AG]R	Protease matriptase protease site					cytosolic ribosome (sensu Eukaryota) (1e-05)		0.006	9
protein_40_YDR382W	2	RPP2B:  Ribosomal protein P2 beta, a component of the ribosomal stalk, which is involved in the interaction between translational elongation factors and the ribosome; regulates the accumulation of P1 (Rpp1Ap and Rpp1Bp) in the cytoplasm	KK..[FQG]T[KNG]	52							cytosolic ribosome (sensu Eukaryota) (0.01)		0.006	8
protein_40_YDR145W	2	TAF12:  Subunit (61/68 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation and in chromatin modification, similar to histone H2A	SVL[PFY][KNG]	52	LPKY	WW motif (non-conventional ) in spt23 for binding to WW domain of RSP5p, also for NEDD4 WW domain						Y	0.005	8
protein_40_YDL055C	2	PSA1:  GDP-mannose pyrophosphorylase (mannose-1-phosphate guanyltransferase), synthesizes GDP-mannose from GTP and mannose-1-phosphate in cell wall biosynthesis; required for normal cell wall structure	[FAR]D..P[EQ]D	52									0.006	9
protein_40_YDL014W	2	NOP1:  Nucleolar protein, component of the small subunit processome complex, which is required for processing of pre-18S rRNA; has similarity to mammalian fibrillarin	[SEA]D.D[SEN]	52	D.D	Ribose moiety of UDP and manganese binding site in glucuronyl transferase					nucleolus (1e-22)		0.010	10
protein_40_YBR017C	2	KAP104:  Transportin, cytosolic karyopherin beta 2 involved in delivery of heterogeneous nuclear ribonucleoproteins to the nucleoplasm, binds rg-nuclear localization signals on Nab2p and Hrp1p, plays a role in cell-cycle progression	LF.N[NAC][NKF]	52	LFG	Protease Papain substrate, a prototype cysteine proteinase					tRNA splicing (0.01)		0.006	8
oshea_nuclear_periphery	2	oshea_nuclear_periphery	[FLT]G..N[NT]N	52							snRNP protein import into nucleus (1e-09)		0.006	10
oshea_mitochondrion	2	oshea_mitochondrion	R[FYL].[SWT]T	52			Y				mitochondrial part (1e-16)	Y	0.010	10
genetic_YLR262C	2	YPT6: GTPase, Ras-like GTP binding protein involved in the secretory pathway, required for fusion of endosome-derived vesicles with the late Golgi, maturation of the vacuolar carboxypeptidase Y; has similarity to the human GTPase, Rab6	EN..[KDL][EAQ]	52							nucleoplasm part (1e-05)		0.009	10
yeast-217_GO-0007046	2	ribosome biogenesis	DV.[AS]R[GR]	51	[AG]R	Protease matriptase protease site		DEAD	1.E-14	-1.9	ATP-dependent RNA helicase activity (1e-16)		0.007	10
protein_40_YPL093W	2	NOG1:  Putative GTPase that associates with free 60S ribosomal subunits in the nucleolus and is required for 60S ribosomal subunit biogenesis; constituent of 66S pre-ribosomal particles; member of the ODN family of nucleolar G-proteins	RG.[DAQ][IL]P	51	RGD	LIG_RGD		DEAD	1.E-08	-1.3	ATP-dependent RNA helicase activity (1e-08)		0.006	10
protein_40_YGL111W	2	NSA1:  Constituent of 66S pre-ribosomal particles, involved in 60S ribosomal subunit biogenesis	HR.[GLE][RDC]	51	R.L	Cyclin A motif that binds cdk2 complexes		DEAD	1.E-06	-1.3	ribosomal large subunit assembly and maintenance (1e-09)	Y	0.006	9
yeast-262_GO-0031224	2	intrinsic to membrane	F.[FLY]L	51	YF.[FPLY]	SH2 ligand for PTPN6-N (Tyr must be phosphorylated)		ABC_tran	1.E-03	-1.2	intrinsic to membrane (1e-15)		0.011	10
protein_40_YHR052W	2	CIC1:  Essential protein that interacts with proteasome components and has a potential role in proteasome substrate specificity; also copurifies with 66S pre-ribosomal particles	[TR]G.[GMS]KT	51				Helicase_C	1.E-11	-1	RNA helicase activity (1e-12)		0.007	10
protein_40_YDR496C	2	PUF6:  Pumilio-homology domain protein that binds ASH1 mRNA at PUF consensus sequences in the 3' UTR and represses its translation, resulting in proper asymmetric localization of ASH1 mRNA	D[VML]AA[RLT]	51				DEAD	1.E-02	-1	cytoplasm organization and biogenesis (1e-05)		0.006	10
protein_40_YNL061W	2	NOP2:  Probable RNA m(5)C methyltransferase, essential for processing and maturation of 27S pre-rRNA and large ribosomal subunit biogenesis; localized to the nucleolus; constituent of 66S pre-ribosomal particles	[TRM]G.GK[TI]	51	[SAG]GGTG[SA]G	TUBULIN PATTERN		Helicase_C	1.E-10	-0.8	ATP-dependent RNA helicase activity (1e-10)		0.006	9
yeast-215_GO-0007010	2	cytoskeleton organization and biogenesis	PPP[LRH][PRQ]	51	[DE]FPPP	EVH binding motif of Mena		SH3_1	1.E-02	-0.6	cytoskeleton organization and biogenesis (1e-15)		0.009	10
yeast-1433_GO-0006139	2	nucleobase, nucleoside, nucleotide and nucleic acid metabolism	QQ...[QKH]	51				zf-C2H2	1.E-06	-0.1	transcription (1e-65)	Y	0.011	10
yeast-457_GO-0007001	2	chromosome organization and biogenesis (sensu Eukaryota)	KR[KPM]	51	KR	CLV_PCSK_PC1ET2_1		Bromodomain	1.E-02	0.2	chromosome organization and biogenesis (sensu Eukaryota) (1e-19)	Y	0.011	10
yeast-413_GO-0005215	2	transporter activity	[LAC]L..A[FVA]	51				Mito_carr	1.E-08	0.3	transporter activity (1e-78)	Y	0.011	10
yeast-1062_GO-0016020	2	membrane	F..Y	51			Y	Mito_carr	1.E-08	0.4	endomembrane system (1e-72)	Y	0.011	10
protein_40_YML085C	2	TUB1:  Alpha-tubulin; associates with beta-tubulin (Tub2p) to form tubulin dimer, which polymerizes to form microtubules	IV..[LPF][LRA]S	51				HEAT	1.E-04	0.5	protein carrier activity (0.001)		0.005	7
yeast-939_GO-0051234	2	establishment of localization	I..[LAI]I	51				MFS_1	1.E-06	0.6	establishment of cellular localization (1e-10)	Y	0.010	10
protein_40_YPL126W	2	NAN1:  U3 snoRNP protein, component of the small (ribosomal) subunit (SSU) processosome containing U3 snoRNA; required for the biogenesis of18S rRNA	LL[ACF][VIA]G	51	FIGQY	Ankryn G binding motif in neurofascin		WD40	1.E-04	0.7	nucleolus (1e-07)	Y	0.006	9
yeast-413_GO-0005215	2	transporter activity	VV.[LVF][LVY]	51				MFS_1	1.E-03	1.5	transporter activity (1e-65)	Y	0.011	10
protein_40_YBR031W	2	RPL4A:  N-terminally acetylated protein component of the large (60S) ribosomal subunit, nearly identical to Rpl4Bp and has similarity to E. coli L4 and rat L4 ribosomal proteins	[LQE]V..EA[DKT]	51	IEAD	Protease Caspase 10		DEAD	1.E-02	2.6			0.005	10
protein_40_YBR031W	2	RPL4A:  N-terminally acetylated protein component of the large (60S) ribosomal subunit, nearly identical to Rpl4Bp and has similarity to E. coli L4 and rat L4 ribosomal proteins	[PFS]T.E[LF]A	51				DEAD	1.E-07	3.2	RNA helicase activity (1e-06)	Y	0.005	10
protein_40_YGL207W	2	SPT16:  Subunit of the heterodimeric FACT complex (Spt16p-Pob3p), facilitates RNA Polymerase II transcription elongation through nucleosomes by destabilizing and then reassembling nucleosome structure	R[DRI].K[PIL]E	51				Pkinase	1.E-07	3.4	protein kinase activity (1e-07)	Y	0.006	10
protein_40_YPL217Cs	2	BMS1:  Essential conserved nucleolar GTP-binding protein required for synthesis of 40S ribosomal subunits and for processing of the 35S pre-rRNA at sites A0, A1, and A2; interacts with Rcl1p, has similarity to Tsr1p	E[YR]..GG[SFD]	51	G[FL]PGER..G	LIG_IBS_1		Pkinase	1.E-03	3.6	protein serine/threonine kinase activity (0.001)		0.006	9
protein_40_YGL207W	2	SPT16:  Subunit of the heterodimeric FACT complex (Spt16p-Pob3p), facilitates RNA Polymerase II transcription elongation through nucleosomes by destabilizing and then reassembling nucleosome structure	W[SA].G[ITC]	51				Pkinase	1.E-10	3.7	protein kinase activity (1e-09)		0.007	10
yeast-376_GO-0019219	2	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism	K[KPR].K	51	K[KR].[KR]	Nuclear localization motif		Zn_clus	1.E-06	3.8	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism (1e-26)		0.011	10
yeast-256_GO-0016462	2	pyrophosphatase activity	KT.[LTA][LAI]	51	DKTGT[LIVM][TI]	ATPASE_E1_E2 PATTERN	Y	AAA	1.E-10	3.8	nucleoside-triphosphatase activity (1e-79)	Y	0.011	10
protein_40_YMR229C	2	RRP5:  Protein required for the synthesis of both 18S and 5.8S rRNA; C-terminal region is crucial for the formation of 18S rRNA and N-terminal region is required for the 5.8S rRNA; component of small ribosomal subunit (SSU) processosome	R[DIE].K[PTL]	51	MR[DE][IL]	TUBULIN_B_AUTOREG PATTERN		Pkinase	1.E-15	3.9	protein kinase activity (1e-15)		0.010	10
yeast-504_GO-0006350	2	transcription	C..C[RGE]	51	C..C	Motif on TIM mitochondrial translocation proteins	Y	Zn_clus	1.E-24	19.8	transcription (1e-75)	Y	0.011	10
yeast-379_GO-0031975	2	envelope	[SHW][GMF]GLF	51							envelope (1e-08)		0.008	9
yeast-379_GO-0031967	2	organelle envelope	[SHW][GMF]GLF	51							envelope (1e-08)		0.008	9
yeast-256_GO-0016462	2	pyrophosphatase activity	EN.[LP]K[DT]	51							pyrophosphatase activity (1e-11)		0.007	9
yeast-213_GO-0009719	2	response to endogenous stimulus	K[KRI][RVP]K	51	KR	CLV_PCSK_PC1ET2_1					response to endogenous stimulus (1e-91)	Y	0.011	10
yeast-207_GO-0006974	2	response to DNA damage stimulus	K[RIK][VRP]K	51	KR	CLV_PCSK_PC1ET2_1					response to DNA damage stimulus (1e-91)	Y	0.011	10
protein_40_YPL153C	2	RAD53:  Protein kinase, required for cell-cycle arrest in response to DNA damage; activated by trans autophosphorylation when interacting with hyperphosphorylated Rad9p; also interacts with ARS1 and plays a role in initiation of DNA replication	G[TQN][TPI]TT	51	YTT[ILM]	Syk N-terminal SH2 domain binding motif							0.005	10
protein_40_YPL093W	2	NOG1:  Putative GTPase that associates with free 60S ribosomal subunits in the nucleolus and is required for 60S ribosomal subunit biogenesis; constituent of 66S pre-ribosomal particles; member of the ODN family of nucleolar G-proteins	DI..E[IA][ALG]	51							cytoplasm organization and biogenesis (1e-05)		0.006	10
protein_40_YMR047C	2	NUP116:  Subunit of the nuclear pore complex (NPC) that is localized to both sides of the pore; contains a repetitive GLFG motif that interacts with mRNA export factor Mex67p and with karyopherin Kap95p; homologous to Nup100p	A[ALI]K[PQV]S	51							mRNA export from nucleus (1e-07)		0.005	10
protein_40_YMR047C	2	NUP116:  Subunit of the nuclear pore complex (NPC) that is localized to both sides of the pore; contains a repetitive GLFG motif that interacts with mRNA export factor Mex67p and with karyopherin Kap95p; homologous to Nup100p	G[GN].FG[NSF]	51	LFG	Protease Papain substrate, a prototype cysteine proteinase					snRNP protein import into nucleus (1e-09)	Y	0.005	9
protein_40_YLR293C	2	GSP1:  GTP binding protein (mammalian Ranp homolog) involved in the maintenance of nuclear organization, RNA processing and transport; regulated by Prp20p, Rna1p, Yrb1p, Yrb2p, Yrp4p, Yrb30p, Cse1p and Kap95p; yeast Gsp2p homolog	L[EIG]LS[ANQ]	51	LSQE	ATM kinase substrate motif							0.005	8
protein_40_YLL034C	2	RIX7:  Putative ATPase of the AAA family, required for export of pre-ribosomal large subunits from the nucleus; distributed between the nucleolus, nucleoplasm, and nuclear periphery depending on growth conditions	E[DKA].E[DNA]E	51	SEDEE	CKII kinase phosphorylation site (peptide screen)					nucleolus (1e-07)		0.007	10
protein_40_YLL011W	2	SOF1:  Essential protein required for biogenesis of 40S (small) ribosomal subunit; has similarity to the beta subunit of trimeric G-proteins and the splicing factor Prp4p	[TVI]D.SK[RYI]	51	KR	CLV_PCSK_PC1ET2_1					snoRNA binding (1e-09)		0.005	10
protein_40_YKL065C	2	YET1:  Endoplasmic reticulum transmembrane protein; may interact with ribosomes, based on co-purification experiments; homolog of human BAP31 protein	V[SGL].L[VWI]L	51									0.006	10
protein_40_YJR145C	2	RPS4A:  Protein component of the small (40S) ribosomal subunit; mutation affects 20S pre-rRNA processing; identical to Rps4Bp and has similarity to rat S4 ribosomal protein	[KGR]E..E[KDI]T	51	RE..E	Iron binding motif in ferritin L-chain and yeast Iron transport protein						Y	0.005	10
protein_40_YHR099W	2	TRA1:  Subunit of SAGA and NuA4 histone acetyltransferase complexes; interacts with acidic activators (e.g., Gal4p) which leads to transcription activation; similar to human TRRAP, which is a cofactor for c-Myc mediated oncogenic transformation	VLE[YD][LV]	51							establishment and/or maintenance of chromatin architecture (0.01)		0.006	8
protein_40_YGR252W	2	GCN5:  Histone acetyltransferase, acetylates N-terminal lysines on histones H2B and H3; catalytic subunit of the ADA and SAGA histone acetyltransferase complexes; founding member of the Gcn5p-related N-acetyltransferase superfamily	NN.[TEP][NIG]T	51	N.[TS]	N-linked glycosylation site					SLIK (SAGA-like) complex (0.01)		0.005	8
protein_40_YEL037C	2	RAD23:  Protein with ubiquitin-like N terminus, recognizes and binds damaged DNA (with Rad4p) during nucleotide excision repair; regulates Rad4p levels, subunit of Nuclear Excision Repair Factor 2 (NEF2); homolog of human HR23A and HR23B proteins	K[TAY].[DQA]LL	51	DLL	Binding motif for clathrin heavy chain ear					proteasome complex (sensu Eukaryota) (1e-05)		0.005	8
protein_40_YDR382W	2	RPP2B:  Ribosomal protein P2 beta, a component of the ribosomal stalk, which is involved in the interaction between translational elongation factors and the ribosome; regulates the accumulation of P1 (Rpp1Ap and Rpp1Bp) in the cytoplasm	[KLA]G.KV[TVG]	51							cytosolic ribosome (sensu Eukaryota) (1e-06)		0.006	10
protein_40_YDL213C	2	NOP6:  Putative RNA-binding protein implicated in ribosome biogenesis; contains an RNA recognition motif (RRM) and has similarity to hydrophilins; NOP6 may be a fungal-specific gene as no homologs have been yet identified in higher eukaryotes	KL[DVW][SKY]F	51	NKLY	LIM3 domain in enigma binds to this site in Ret							0.005	10
protein_40_YDL148C	2	NOP14:  Nucleolar protein, forms a complex with Noc4p that mediates maturation and nuclear export of 40S ribosomal subunits; also present in the small subunit processome complex, which is required for processing of pre-18S rRNA	[LYD]Q[ECT]EE	51	EEEYF	EGFR kinase phosphorylation site (peptide screen)					cytoplasm organization and biogenesis (0.001)		0.006	10
protein_40_YDL147W	2	RPN5:  Essential, non-ATPase regulatory subunit of the 26S proteasome lid, similar to mammalian p55 subunit and to another S. cerevisiae regulatory subunit, Rpn7p	KG..L[YQN][GSV]	51									0.006	8
protein_40_YDL055C	2	PSA1:  GDP-mannose pyrophosphorylase (mannose-1-phosphate guanyltransferase), synthesizes GDP-mannose from GTP and mannose-1-phosphate in cell wall biosynthesis; required for normal cell wall structure	[QAD]E..[EAK]A	51							translation (0.01)	Y	0.010	10
protein_40_YBR200W	2	BEM1:  Protein containing SH3-domains, involved in establishing cell polarity and morphogenesis; functions as a scaffold protein for complexes that include Cdc24p, Ste5p, Ste20p, and Rsr1p	K[SRG]A[SK]S	51	KR	CLV_PCSK_PC1ET2_1					incipient bud site (0.001)		0.006	9
protein_40_YBR198C	2	TAF5:  Subunit (90 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation and in chromatin modification	[EVM]DE[DNV]E	51	S[DE][DE]E	BARD1 BRCT domain binding motif					transcription factor complex (1e-13)		0.006	9
protein_40_YBR059C	2	AKL1:  Ser-Thr protein kinase, member (with Ark1p and Prk1p) of the Ark kinase family; involved in endocytosis and actin cytoskeleton organization	QQQ[PDK][QAP]	51							endocytosis (1e-04)		0.006	9
genetic_YPL055C	2	LGE1: Protein of unknown function; null mutant forms abnormally large cells, and homozygous diploid null mutant displays delayed premeiotic DNA synthesis and reduced efficiency of meiotic nuclear division	D[NLQ].N	51							chromosome organization and biogenesis (sensu Eukaryota) (1e-16)	Y	0.009	10
genetic_YPL055C	2	LGE1: Protein of unknown function; null mutant forms abnormally large cells, and homozygous diploid null mutant displays delayed premeiotic DNA synthesis and reduced efficiency of meiotic nuclear division	L..E[LEF]	51	S[LW]LD[DE]EL[LM]	TRG_LysEnd_GGAAcLL_2	Y				chromosome organization and biogenesis (sensu Eukaryota) (1e-21)	Y	0.009	10
protein_40_YPR103W	2	PRE2:  Beta 5 subunit of the 20S proteasome, responsible for the chymotryptic activity of the proteasome	S[PG].G[RNK]L	50	SG.G	Glycosaminoglycan attachment site	Y	Proteasome	1.E-08	-3.9	proteasome core complex, alpha-subunit complex (sensu Eukaryota) (1e-10)		0.006	9
protein_40_YLR197W	2	SIK1:  Essential evolutionarily-conserved nucleolar protein component of the box C/D snoRNP complexes that direct 2'-O-methylation of pre-rRNA during its maturation; overexpression causes spindle orientation defects	E...[ELP]E	50			Y	WD40	1.E-05	-2.2	nucleolus (1e-43)		0.009	10
yeast-410_GO-0007049	2	cell cycle	K[KRL]..[TPI]S	50	K[KR].[KR]	Nuclear localization motif		Pkinase	1.E-02	-1.3	cell cycle (1e-10)		0.010	10
protein_40_YMR049C	2	ERB1:  Protein required for maturation of the 25S and 5.8S ribosomal RNAs; constituent of 66S pre-ribosomal particles; homologous to mammalian Bop1	K[KSV]K	50	P.[ST]PKK.KK	Cdc2 like protein kinase substrate motif		Brix	1.E-03	-1.3	cytoplasm organization and biogenesis (1e-31)		0.009	10
protein_40_YJR145C	2	RPS4A:  Protein component of the small (40S) ribosomal subunit; mutation affects 20S pre-rRNA processing; identical to Rps4Bp and has similarity to rat S4 ribosomal protein	G[LQN]DIP	50			Y	DEAD	1.E-02	-1.2	ribosome biogenesis (0.01)	Y	0.006	9
yeast-238_GO-0017111	2	nucleoside-triphosphatase activity	[LVD]I.[DFN]EA	50				Helicase_C	1.E-05	-0.8	ATPase activity (1e-18)	Y	0.008	10
protein_40_YHR052W	2	CIC1:  Essential protein that interacts with proteasome components and has a potential role in proteasome substrate specificity; also copurifies with 66S pre-ribosomal particles	L[DGV].A[DLI]R	50				Helicase_C	1.E-03	-0.8	helicase activity (1e-04)		0.006	9
protein_40_YER006W	2	NUG1:  GTPase that associates with nuclear 60S pre-ribosomes, required for export of 60S ribosomal subunits from the nucleus	[TRK]G.G[KNF]T	50	[SAG]GGTG[SA]G	TUBULIN PATTERN	Y	Helicase_C	1.E-05	-0.7	ATP-dependent RNA helicase activity (1e-07)		0.006	7
protein_40_YGR128C	2	UTP8:  Nucleolar protein required for export of tRNAs from the nucleus; also copurifies with the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	[LQR]LA[VI]G	50				WD40	1.E-06	-0.6	snoRNA binding (1e-07)	Y	0.006	10
protein_40_YGL112C	2	TAF6:  Subunit (60 kDa) of TFIID and SAGA complexes, involved in transcription initiation of RNA polymerase II and in chromatin modification, similar to histone H4	NN[VNL][ES]E	50	[ST]E	G protein-coupled receptor kinase 1 substrate motif	Y	Bromodomain	1.E-02	-0.6	G1-specific transcription in mitotic cell cycle (1e-08)		0.005	10
protein_40_YDR167W	2	TAF10:  Subunit (145 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation and in chromatin modification	[NV]N[VNL]EE	50	Y[IV]N[ILV]	SH2 ligand for Grb2 (Tyr must be phosphorylated)	Y	Bromodomain	1.E-02	-0.6	G1-specific transcription in mitotic cell cycle (1e-08)	Y	0.006	10
yeast-468_GO-0051276	2	chromosome organization and biogenesis	K[KRN][RPV]K	50	KR	CLV_PCSK_PC1ET2_1	Y	Bromodomain	1.E-04	-0.2	chromosome organization and biogenesis (1e-10)		0.011	10
yeast-921_GO-0006810	2	transport	I..[LAI]I	50				MFS_1	1.E-07	0.3	intracellular transport (1e-10)	Y	0.010	10
protein_40_YLR180W	2	SAM1:  S-adenosylmethionine synthetase, catalyzes transfer of the adenosyl group of ATP to the sulfur atom of methionine; one of two differentially regulated isozymes (Sam1p and Sam2p)	AR.[ADG]	50	[AG]R	Protease matriptase protease site		GATase	1.E-02	1.2	carboxylic acid metabolism (1e-06)	Y	0.010	10
protein_40_YML010W	2	SPT5:  Protein that forms a complex with Spt4p and mediates both activation and inhibition of transcription elongation; Spt4p-Spt5p complex also plays a role in pre-mRNA processing	[KHL]K..VV[DIS]	50				DEAD	1.E-02	1.3	ATP-dependent RNA helicase activity (1e-04)	Y	0.006	9
protein_40_YBL002W	2	HTB2:  One of two nearly identical (see HTB1) histone H2B subtypes required for chromatin assembly and chromosome function; Rad6p-Bre1p-Lge1p mediated ubiquitination regulates transcriptional activation, meiotic DSB formation and H3 methylation	L[ED]..GN[ALG]	50	D..G	motif that binds phosphate in GDP and GTP binding proteins	Y	Histone	1.E-04	1.5			0.005	9
protein_40_YPL211W	2	NIP7:  Nucleolar protein required for 60S ribosome subunit biogenesis, constituent of 66S pre-ribosomal particles; physically interacts with Nop8p and the exosome subunit Rrp43p	[DQH]EAD	50	[LIVMF][LIVMF]DEAD[RKEN].[LIVMFYGSTN]	DEAD_ATP_HELICASE PATTERN	Y	DEAD	1.E-04	3.6	ribosome biogenesis (1e-06)		0.005	8
protein_40_YLL045C	2	RPL8B:  Ribosomal protein L4 of the large (60S) ribosomal subunit, nearly identical to Rpl8Ap and has similarity to rat L7a ribosomal protein; mutation results in decreased amounts of free 60S subunits	IA[TR]P[GNI]	50	[ST]P	LIG_WW_4	Y	DEAD	1.E-05	3.6	RNA helicase activity (1e-04)		0.005	8
protein_40_YNL186W	2	UBP10:  Ubiquitin-specific protease that deubiquitinates ubiquitin-protein moieties; may regulate silencing by acting on Sir4p; involved in posttranscriptionally regulating Gap1p and possibly other transporters; primarily located in the nucleus	[MRE][ASK]PE	50	FP.[PAILSK]P	LIG_EVH1_I		Pkinase	1.E-18	3.7	protein kinase activity (1e-18)	Y	0.009	10
protein_40_YPL211W	2	NIP7:  Nucleolar protein required for 60S ribosome subunit biogenesis, constituent of 66S pre-ribosomal particles; physically interacts with Nop8p and the exosome subunit Rrp43p	[TR]G.[GMS]KT	50				DEAD	1.E-08	3.9	ATP-dependent RNA helicase activity (1e-08)		0.005	10
protein_40_YHR052W	2	CIC1:  Essential protein that interacts with proteasome components and has a potential role in proteasome substrate specificity; also copurifies with 66S pre-ribosomal particles	IA[TR][PM]G	50				DEAD	1.E-08	3.9	RNA helicase activity (1e-06)		0.006	8
yeast-630_GO-0051244	2	regulation of cellular physiological process	[ASV]C..C[RDV]	50	C..C	Motif on TIM mitochondrial translocation proteins		Zn_clus	1.E-27	19.7	regulation of cellular metabolism (1e-21)		0.011	10
yeast-631_GO-0050794	2	regulation of cellular process	[ASV]C..C[RDV]	50	C..C	Motif on TIM mitochondrial translocation proteins		Zn_clus	1.E-27	19.9	regulation of cellular metabolism (1e-21)		0.011	10
yeast-1062_GO-0016020	2	membrane	W..[AIW]I	50	W..[WFY]	AP1 binding site for endosomal trafficking					plasma membrane (1e-24)		0.010	10
protein_40_YPL153C	2	RAD53:  Protein kinase, required for cell-cycle arrest in response to DNA damage; activated by trans autophosphorylation when interacting with hyperphosphorylated Rad9p; also interacts with ARS1 and plays a role in initiation of DNA replication	A...Q[PEY]	50							cell cortex part (0.01)	Y	0.009	10
protein_40_YPL153C	2	RAD53:  Protein kinase, required for cell-cycle arrest in response to DNA damage; activated by trans autophosphorylation when interacting with hyperphosphorylated Rad9p; also interacts with ARS1 and plays a role in initiation of DNA replication	TN[VMT]	50	CP[ST]N[ILV]GT	GUANIDO_KINASE PATTERN	Y				DNA integrity checkpoint (0.001)	Y	0.009	10
protein_40_YOR016C	2	ERP4:  Protein with similarity to Emp24p and Erv25p, member of the p24 family involved in ER to Golgi transport	G[LMD]..L[IYC]V	50							integral to membrane (1e-04)	Y	0.006	10
protein_40_YNL308C	2	KRI1:  Essential nucleolar protein required for 40S ribosome biogenesis; physically and functionally interacts with Krr1p	E[EQS].K[KHI]A	50	KEESEK	14-3-3 gamma, epsilon nonphosphorylated binding motif in Ammodytoxin C, not confirmed							0.005	10
protein_40_YNL298W	2	CLA4:  Cdc42p activated signal transducing kinase of the PAK (p21-activated kinase) family, involved in septin ring assembly and cytokinesis; directly phosphorylates septins Cdc3p and Cdc10p; other yeast PAK family members are Ste20p and Skm1p	[AKP]KK[RTQ]L	50	KKKKKK[ST]	TGF beta receptor kinase substrate motif	Y						0.005	9
protein_40_YNL298W	2	CLA4:  Cdc42p activated signal transducing kinase of the PAK (p21-activated kinase) family, involved in septin ring assembly and cytokinesis; directly phosphorylates septins Cdc3p and Cdc10p; other yeast PAK family members are Ste20p and Skm1p	SS..[KSQ][SRT]D	50	S[ST]	MDC1 BRCT domain binding motif					establishment of cell polarity (sensu Fungi) (0.01)		0.006	10
protein_40_YMR186W	2	HSC82:  Cytoplasmic chaperone of the Hsp90 family, redundant in function and nearly identical with Hsp82p, and together they are essential; expressed constitutively at 10-fold higher basal levels than HSP82 and induced 2-3 fold by heat shock	[NEV]I[KTM]LS	50									0.006	8
protein_40_YMR047C	2	NUP116:  Subunit of the nuclear pore complex (NPC) that is localized to both sides of the pore; contains a repetitive GLFG motif that interacts with mRNA export factor Mex67p and with karyopherin Kap95p; homologous to Nup100p	[DAK]I.[LEV]KA	50								Y	0.005	8
protein_40_YML069W	2	POB3:  Subunit of the heterodimeric FACT complex (Spt16p-Pob3p), which facilitates RNA Pol II transcription elongation through nucleosomes by destabilizing and then reassembling nucleosome structure; interacts with DNA polymerase alpha (Pol1p)	[TC][KCM].AI	50							RNA elongation from RNA polymerase II promoter (0.001)		0.005	8
protein_40_YLR423C	2	ATG17:  Scaffold potein responsible for pre-autophagosomal structure organization; interacts with and is required for activation of Apg1p protein kinase; involved in autophagy but not in the Cvt (cytoplasm to vacuole targeting) pathway	[RQY]RLS[ILW]	50	R.S	PKA kinase substrate motif							0.006	9
protein_40_YLR180W	2	SAM1:  S-adenosylmethionine synthetase, catalyzes transfer of the adenosyl group of ATP to the sulfur atom of methionine; one of two differentially regulated isozymes (Sam1p and Sam2p)	A[GSF].[VLC]K	50								Y	0.010	10
protein_40_YLR175W	2	CBF5:  Pseudouridine synthase catalytic subunit of box H/ACA small nucleolar ribonucleoprotein particles (snoRNPs), acts on both large and small rRNAs and on snRNA U2	[KSF]K..K[KHN]	50	P.[ST]PKK.KK	Cdc2 like protein kinase substrate motif	Y				nucleolus (1e-13)		0.009	10
protein_40_YKR081C	2	RPF2:  Essential protein involved in the processing of pre-rRNA and the assembly of the 60S ribosomal subunit; interacts with ribosomal protein L11; localizes predominantly to the nucleolus; constituent of 66S pre-ribosomal particles	[KHM]E[LAH]LS	50									0.005	9
protein_40_YKR001C	2	VPS1:  Dynamin-like GTPase required for vacuolar sorting; also involved in actin cytoskeleton organization, late Golgi-retention of some proteins, regulating peroxisome biogenesis	ND..E[DRN][DTI]	50			Y						0.005	9
protein_40_YJR145C	2	RPS4A:  Protein component of the small (40S) ribosomal subunit; mutation affects 20S pre-rRNA processing; identical to Rps4Bp and has similarity to rat S4 ribosomal protein	A.K[AGF]	50	ARKGSLRQ	PKC alpha kinase substrate motif					ribonucleoprotein complex (1e-24)	Y	0.009	10
protein_40_YJR022W	2	LSM8:  Lsm (Like Sm) protein; forms heteroheptameric complex (with Lsm2p, Lsm3p, Lsm4p, Lsm5p, Lsm6p, and Lsm7p) that is part of spliceosomal U6 snRNP and is also implicated in processing of pre-tRNA, pre-snoRNA, and pre-rRNA	A[KCP]..KV[LMT]	50							U4/U6 x U5 tri-snRNP complex (0.01)		0.006	9
protein_40_YJL164C	2	TPK1:  cAMP-dependent protein kinase catalytic subunit; promotes vegetative growth in response to nutrients via the Ras-cAMP signaling pathway; inhibited by regulatory subunit Bcy1p in the absence of cAMP; partially redundant with Tpk2p and Tpk3p	EK..[KSQ]	50	K..[ST]	PKA kinase substrate motif	Y				RNA binding (0.01)		0.009	10
protein_40_YJL033W	2	HCA4:  Putative nucleolar DEAD box RNA helicase; high-copy number suppression of a U14 snoRNA processing mutant suggests an involvement in 18S rRNA synthesis	KK..[KSM]S[KDP]	50	RKK.[ST]	ZIP kinase phosphorylation motif					nuclear lumen (1e-05)		0.006	9
protein_40_YHR088W	2	RPF1:  Nucleolar protein involved in the assembly of the large ribosomal subunit; constituent of 66S pre-ribosomal particles; contains a sigma(70)-like motif, which is thought to bind RNA	[EDQ]E..A[KQR]K	50	WAQKW	Motif in Cet1 RNA triphosphosphatase for binding to RNA guanylyltransferase Ceg1					nucleolus (1e-07)		0.005	10
protein_40_YHR066W	2	SSF1:  Constituent of 66S pre-ribosomal particles, required for ribosomal large subunit maturation; functionally redundant with Ssf2p; member of the Brix family	QR..K[ELY][ETD]	50	R..K	SH3 binding motif for GADS SH3 recognizing slp-76 motif (nonconventional)					ribosome biogenesis (1e-04)		0.006	10
protein_40_YDR447C	2	RPS17B:  Ribosomal protein 51 (rp51) of the small (40s) subunit; nearly identical to Rps17Ap and has similarity to rat S17 ribosomal protein	AR..[AR]	50	AR..R[RK]RSFRR	PKC eta kinase substrate motif					cytosolic ribosome (sensu Eukaryota) (1e-32)	Y	0.009	10
protein_40_YDR145W	2	TAF12:  Subunit (61/68 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation and in chromatin modification, similar to histone H2A	LN.S[LDI][SKQ]	50	N.[TS]	N-linked glycosylation site							0.005	9
protein_40_YDR025W	2	RPS11A:  Protein component of the small (40S) ribosomal subunit; identical to Rps11Bp and has similarity to E. coli S17 and rat S11 ribosomal proteins	[RHL]R.[AGW]R	50	[AG]R	Protease matriptase protease site					cytosolic ribosome (sensu Eukaryota) (1e-04)		0.009	10
protein_40_YDL147W	2	RPN5:  Essential, non-ATPase regulatory subunit of the 26S proteasome lid, similar to mammalian p55 subunit and to another S. cerevisiae regulatory subunit, Rpn7p	L[QA].IN[DCS]	50			Y						0.005	10
protein_40_YDL147W	2	RPN5:  Essential, non-ATPase regulatory subunit of the 26S proteasome lid, similar to mammalian p55 subunit and to another S. cerevisiae regulatory subunit, Rpn7p	S[LEP][ATD]IS	50	SP	ERK1, ERK2 Kinase substrate motif							0.006	9
protein_40_YDL043C	2	PRP11:  Subunit of the SF3a splicing factor complex, required for spliceosome assembly	L[RY]..K[NDK]S	50	R..K	SH3 binding motif for GADS SH3 recognizing slp-76 motif (nonconventional)	Y						0.005	8
protein_40_YCR034W	2	FEN1:  Fatty acid elongase, involved in sphingolipid biosynthesis; acts on fatty acids of up to 24 carbons in length; mutations have regulatory effects on 1,3-beta-glucan synthase, vacuolar ATPase, and the secretory pathway	FI..[IE]I[SGV]	50			Y						0.006	9
protein_40_YCL059C	2	KRR1:  Essential nucleolar protein required for the synthesis of 18S rRNA and for the assembly of 40S ribosomal subunit	EE[SQK]S[GNH]	50	YEE[IV]	SH2 ligand group 1A, Src FGR SH2 domain (needs to be Tyr phosphorylated)					processing of 20S pre-rRNA (1e-05)		0.005	8
protein_40_YBR159W	2	IFA38: Microsomal beta-keto-reductase; contains oleate response element (ORE) sequence in the promoter region; mutants exhibit reduced VLCFA synthesis, accumulate high levels of dihydrosphingosine, phytosphingosine and medium-chain ceramides	VS.[LVT][VWI]L	50									0.005	10
protein_40_YBR009C	2	HHF1:  One of two identical histone H4 proteins (see also HHF2); core histone required for chromatin assembly and chromosome function; contributes to telomeric silencing; N-terminal domain involved in maintaining genomic integrity	KD..[SM]K[IT]	50									0.005	9
genetic_YNL153C	2	GIM3: Subunit of the heterohexameric cochaperone prefoldin complex which binds specifically to cytosolic chaperonin and transfers target proteins to it	KK[LTP]	50	KKKKKK[ST]	TGF beta receptor kinase substrate motif					cell cycle (1e-12)		0.009	10
yeast-341_GO-0045449	2	regulation of transcription	LP[SHP]	49	DLPPP	EVH1 binding motif		zf-C2H2	1.E-10	-2	regulation of transcription (1e-20)		0.010	10
protein_40_YPL153C	2	RAD53:  Protein kinase, required for cell-cycle arrest in response to DNA damage; activated by trans autophosphorylation when interacting with hyperphosphorylated Rad9p; also interacts with ARS1 and plays a role in initiation of DNA replication	[QKP]R..S	49	R..SFF	Phosphorylase kinase phosphorylation site (peptide screen)		PH	1.E-02	-1.3			0.009	10
protein_40_YGL111W	2	NSA1:  Constituent of 66S pre-ribosomal particles, involved in 60S ribosomal subunit biogenesis	[KRY]K..K[KER]	49	KR	CLV_PCSK_PC1ET2_1		DEAD	1.E-04	-1.3	cytoplasm organization and biogenesis (1e-29)	Y	0.009	10
yeast-410_GO-0007049	2	cell cycle	D[SKY]I	49				Pkinase	1.E-05	-1.2	cell cycle (1e-21)		0.010	10
protein_40_YNL175C	2	NOP13:  Protein of unknown function, localizes to the nucleolus and nucleoplasm; contains an RNA recognition motif (RRM) and has similarity to Nop12p, which is required for processing of pre-18S rRNA	[EAV]K..[AKT]K	49	K..[ST]	PKA kinase substrate motif		DEAD	1.E-02	-1.2	cytoplasm organization and biogenesis (1e-16)	Y	0.009	10
protein_40_YLR002C	2	NOC3:  Protein that forms a nuclear complex with Noc2p that binds to 66S ribosomal precursors to mediate their intranuclear transport; also binds to chromatin to promote the association of DNA replication factors and replication initiation	R[GC]..I[PMY]	49			Y	DEAD	1.E-04	-1.2	nucleolus (1e-05)	Y	0.005	8
yeast-238_GO-0017111	2	nucleoside-triphosphatase activity	V[AIM]..[DCP]G	49			Y	ABC_tran	1.E-03	-0.6	nucleoside-triphosphatase activity (1e-42)	Y	0.011	10
yeast-1433_GO-0006139	2	nucleobase, nucleoside, nucleotide and nucleic acid metabolism	L.[LEI]D	49				Helicase_C	1.E-05	-0.5	transcription (1e-09)		0.010	10
yeast-304_GO-0019752	2	carboxylic acid metabolism	[DEY]A..[AVR]G	49				GATase	1.E-02	0	carboxylic acid metabolism (1e-48)		0.011	10
yeast-304_GO-0006082	2	organic acid metabolism	[DEY]A..[AVR]G	49				GATase	1.E-02	0	carboxylic acid metabolism (1e-48)		0.011	10
protein_40_YGL105W	2	ARC1:  Protein that binds tRNA and methionyl- and glutamyl-tRNA synthetases (Mes1p and Gus1p), delivering tRNA to them, stimulating catalysis, and ensuring their localization to the cytoplasm; also binds quadruplex nucleic acids	S[DE]..LL[NCY]	49	[DE]..LL	Di-Leu acidic motif for receptor endocytosis (recognized by VHS domain of GGA proteins)	Y	Pkinase	1.E-07	0	protein kinase activity (1e-06)		0.005	7
protein_40_YMR049C	2	ERB1:  Protein required for maturation of the 25S and 5.8S ribosomal RNAs; constituent of 66S pre-ribosomal particles; homologous to mammalian Bop1	ED.[DIE][EDM]	49	YEDP	Fyn SH2 domain binding motif		Brix	1.E-02	0.1	cytoplasm organization and biogenesis (1e-19)		0.009	10
protein_40_YDR060W	2	MAK21:  Constituent of 66S pre-ribosomal particles, required for large (60S) ribosomal subunit biogenesis; involved in nuclear export of pre-ribosomes; required for maintenance of dsRNA virus; homolog of human CAATT-binding protein	[AVK]K.A[KTR]	49				DEAD	1.E-02	0.1	nucleolus (1e-18)		0.009	10
protein_40_YLR175W	2	CBF5:  Pseudouridine synthase catalytic subunit of box H/ACA small nucleolar ribonucleoprotein particles (snoRNPs), acts on both large and small rRNAs and on snRNA U2	R.[GVA]K	49	GR.A	Protease tPA proteolytic site		Ribosomal_L7Ae	1.E-02	0.2	cytoplasm organization and biogenesis (1e-10)		0.009	10
yeast-240_GO-0006807	2	nitrogen compound metabolism	GA.[IKV][VAI]	49				PALP	1.E-05	0.6	nitrogen compound metabolism (1e-62)	Y	0.010	10
protein_40_YLR222C	2	UTP13:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	[LQR]LA[VI]G	49				WD40	1.E-06	0.8	small nucleolar ribonucleoprotein complex (1e-07)	Y	0.006	9
matsuyama_ER	2	matsuyama_ER	F[VFL].[GAI]I	49				MFS_1	1.E-03	1.5	endoplasmic reticulum membrane (1e-13)	Y	0.012	10
protein_40_YGL207W	2	SPT16:  Subunit of the heterodimeric FACT complex (Spt16p-Pob3p), facilitates RNA Polymerase II transcription elongation through nucleosomes by destabilizing and then reassembling nucleosome structure	[RP]L.R[RGV]G	49	RGG	Alternative integrin binding site in FMDV virus		Histone	1.E-06	1.6	establishment and/or maintenance of chromatin architecture (1e-06)		0.005	9
yeast-320_GO-0006355	2	regulation of transcription, DNA-dependent	KR...[KGE]	49	KR	CLV_PCSK_PC1ET2_1		Zn_clus	1.E-06	2.3	regulation of transcription, DNA-dependent (1e-19)	Y	0.010	10
protein_40_YNL186W	2	UBP10:  Ubiquitin-specific protease that deubiquitinates ubiquitin-protein moieties; may regulate silencing by acting on Sir4p; involved in posttranscriptionally regulating Gap1p and possibly other transporters; primarily located in the nucleus	I[LAV]..LG[TNF]	49				Pkinase	1.E-08	2.4	protein kinase activity (1e-08)	Y	0.005	9
yeast-217_GO-0007046	2	ribosome biogenesis	PT.E[LH][AV]	49	P[ST]	DNA dependent Protein kinase substrate motif	Y	DEAD	1.E-17	4.2	RNA helicase activity (1e-16)	Y	0.007	10
protein_40_YGL245W	2	GUS1:  Glutamyl-tRNA synthetase (GluRS), forms a complex with methionyl-tRNA synthetase (Mes1p) and Arc1p; complex formation increases the catalytic efficiency of both tRNA synthetases and ensures their correct localization to the cytoplasm	K..DF[GHM]	49				Pkinase	1.E-16	4.3	protein kinase activity (1e-16)		0.007	10
protein_40_YGL245W	2	GUS1:  Glutamyl-tRNA synthetase (GluRS), forms a complex with methionyl-tRNA synthetase (Mes1p) and Arc1p; complex formation increases the catalytic efficiency of both tRNA synthetases and ensures their correct localization to the cytoplasm	W[SAG].G[CIV]	49				Pkinase	1.E-23	4.6	protein kinase activity (1e-23)		0.008	10
yeast-462_GO-0019222	2	regulation of metabolism	K.[DPF]S	49	[NT]K.D	Motif for binding guanine nucleotides		zf-C2H2	1.E-06	4.7	regulation of metabolism (1e-22)	Y	0.010	10
yeast-335_GO-0016772	2	transferase activity, transferring phosphorus-containing groups	[GNK][IVW]IH	49				Pkinase	1.E-31	4.8	transferase activity, transferring phosphorus-containing groups (1e-39)	Y	0.011	10
yeast-685_GO-0016740	2	transferase activity	[GKN][ICH]IH	49				Pkinase	1.E-24	4.9	protein kinase activity (1e-28)	Y	0.010	10
yeast-631_GO-0050794	2	regulation of cellular process	KR[KRE]	49	KR	CLV_PCSK_PC1ET2_1		Zn_clus	1.E-08	5.3	regulation of cellular metabolism (1e-16)		0.010	10
yeast-630_GO-0051244	2	regulation of cellular physiological process	KR[KRE]	49	KR	CLV_PCSK_PC1ET2_1		Zn_clus	1.E-08	5.4	regulation of cellular metabolism (1e-16)		0.011	10
yeast-238_GO-0017111	2	nucleoside-triphosphatase activity	FL.[ESM][PRY]T	49							nucleoside-triphosphatase activity (1e-09)	Y	0.006	8
protein_40_YPR137W	2	RRP9:  Protein involved in pre-rRNA processing, associated with U3 snRNP; component of small ribosomal subunit (SSU) processosome; ortholog of the human U3-55k protein	[LMS]E.[DSE]DE	49	SEDEE	CKII kinase phosphorylation site (peptide screen)					small nucleolar ribonucleoprotein complex (1e-09)		0.005	9
protein_40_YPR119W	2	CLB2:  B-type cyclin involved in cell cycle progression; activates Cdc28p to promote the transition from G2 to M phase; accumulates during G2 and M, then targeted via a destruction box motif for ubiquitin-mediated degradation by the proteasome	GK..[FEA][GIN]K	49			Y						0.006	10
protein_40_YPL240C	2	HSP82:  Hsp90 chaperone required for pheromone signaling and negative regulation of Hsf1p; docks with Tom70p for mitochondrial preprotein delivery; promotes telomerase DNA binding and nucleotide addition; interacts with Cns1p, Cpr6p, Cpr7p, Sti1p	[FMI]G..[IGE]PK	49	GP	Protease TTP cleavage site							0.007	10
protein_40_YOR310C	2	NOP58:  Protein involved in pre-rRNA processing, 18S rRNA synthesis, and snoRNA synthesis; component of the small subunit processome complex, which is required for processing of pre-18S rRNA	L[KGA]..G[LTN]T	49							processing of 20S pre-rRNA (1e-07)		0.005	7
protein_40_YNL308C	2	KRI1:  Essential nucleolar protein required for 40S ribosome biogenesis; physically and functionally interacts with Krr1p	[GN]G.RG[RGN]	49	RGG	Alternative integrin binding site in FMDV virus	Y				small nucleolar ribonucleoprotein complex (0.001)		0.005	9
protein_40_YMR236W	2	TAF9:  Subunit (17 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation and in chromatin modification, similar to histone H3	[ELP]FLE[RYA]	49	F.E	DNA binding motif in MutS					SLIK (SAGA-like) complex (1e-05)	Y	0.005	9
protein_40_YMR117C	2	SPC24:  Component of the evolutionarily conserved kinetochore-associated Ndc80 complex (Ndc80p-Nuf2p-Spc24p-Spc25p); involved in chromosome segregation, spindle checkpoint activity and kinetochore clustering	[LVE]E.F[NQV]K	49	EEEYF	EGFR kinase phosphorylation site (peptide screen)	Y						0.005	8
protein_40_YMR117C	2	SPC24:  Component of the evolutionarily conserved kinetochore-associated Ndc80 complex (Ndc80p-Nuf2p-Spc24p-Spc25p); involved in chromosome segregation, spindle checkpoint activity and kinetochore clustering	[QLD]EL[QEK]	49	[KRHQSA][DENQ]EL	ER_TARGET PATTERN					chromosome segregation (0.001)		0.009	10
protein_40_YML069W	2	POB3:  Subunit of the heterodimeric FACT complex (Spt16p-Pob3p), which facilitates RNA Pol II transcription elongation through nucleosomes by destabilizing and then reassembling nucleosome structure; interacts with DNA polymerase alpha (Pol1p)	[TDI][SAG]..GKK	49	G[KR][KR]	Amidation after cleavage after Gly (must be in secretory pathway)					DNA binding (0.01)		0.005	9
protein_40_YML010W	2	SPT5:  Protein that forms a complex with Spt4p and mediates both activation and inhibition of transcription elongation; Spt4p-Spt5p complex also plays a role in pre-mRNA processing	[SPE]T..AN[IGH]	49	T..[SA]	FHA of KAPP binding motif, Thr must be phosphorylated	Y						0.005	7
protein_40_YLR429W	2	CRN1:  Coronin, cortical actin cytoskeletal component that associates with the Arp2p/Arp3p complex to regulate its activity; plays a role in regulation of actin patch assembly	E[SFP].SE[PCR]	49	[ST]E	G protein-coupled receptor kinase 1 substrate motif							0.005	7
protein_40_YLR347C	2	KAP95:  Karyopherin beta, forms a dimeric complex with Srp1p (Kap60p) that mediates nuclear import of cargo proteins via a nuclear localization signal (NLS), interacts with nucleoporins to guide transport across the nuclear pore complex	FG[AW][NE]	49			Y				nuclear pore (1e-09)		0.006	10
protein_40_YKL101W	2	HSL1:  Nim1p-related protein kinase that regulates the morphogenesis and septin checkpoints; associates with the assembled septin filament; required along with Hsl7p for bud neck recruitment, phosphorylation, and degradation of Swe1p	[LRT]A..[IMG]ET	49									0.005	9
protein_40_YJL109C	2	UTP10:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	[KRE]A.KT[KHQ]	49			Y				cytoplasm organization and biogenesis (1e-04)		0.005	9
protein_40_YJL092W	2	SRS2:  DNA helicase and DNA-dependent ATPase involved in DNA repair, needed for proper timing of commitment to meiotic recombination and transition from Meiosis I to II; affects genome stability by suppressing unscheduled homologous recombination	E.[LPF]D	49								Y	0.009	10
protein_40_YJL033W	2	HCA4:  Putative nucleolar DEAD box RNA helicase; high-copy number suppression of a U14 snoRNA processing mutant suggests an involvement in 18S rRNA synthesis	[NEC]I.S[SEL]T	49	S[ST]	MDC1 BRCT domain binding motif					mRNA cleavage factor complex (1e-04)		0.005	8
protein_40_YHR197W	2	RIX1:  Essential component of the Rix1 complex (Rix1p, Ipi1p, Ipi3p) that is required for processing of ITS2 sequences from 35S pre-rRNA; Rix1 complex associates with Mdn1p in pre-60S ribosomal particles	[TFV][EN].EED	49	EED	Ankyrin B C-terminal motif that binds internal Ankyrin repeats	Y				ribosome biogenesis (0.01)		0.005	9
protein_40_YHR052W	2	CIC1:  Essential protein that interacts with proteasome components and has a potential role in proteasome substrate specificity; also copurifies with 66S pre-ribosomal particles	N[KNP].[KMI]KV	49							nucleolus (0.001)		0.005	9
protein_40_YHR052W	2	CIC1:  Essential protein that interacts with proteasome components and has a potential role in proteasome substrate specificity; also copurifies with 66S pre-ribosomal particles	SEL[KGM][SMQ]	49	[ST]E	G protein-coupled receptor kinase 1 substrate motif					cytoplasm organization and biogenesis (1e-07)	Y	0.005	9
protein_40_YFR037C	2	RSC8:  Component of the RSC chromatin remodeling complex; essential for viability and mitotic growth; homolog of SWI/SNF subunit Swi3p, but unlike Swi3p, does not activate transcription of reporters	[LD][IM]..GP	49	GP	Protease TTP cleavage site							0.005	7
protein_40_YFR037C	2	RSC8:  Component of the RSC chromatin remodeling complex; essential for viability and mitotic growth; homolog of SWI/SNF subunit Swi3p, but unlike Swi3p, does not activate transcription of reporters	I[DQN]..KD[TPA]	49									0.005	8
protein_40_YFR034C	2	PHO4:  Basic helix-loop-helix (bHLH) transcription factor of the myc-family; binds cooperatively with Pho2p to the PHO5 promoter; function is regulated by phosphorylation at multiple sites and by phosphate availability	G[FTG]G[GVE]R	49	GGRGG	Arginine methyl transferease substrate motif (PRMT1)						Y	0.005	9
protein_40_YFR031C-A	2	RPL2A:  Protein component of the large (60S) ribosomal subunit, identical to Rpl2Bp and has similarity to E. coli L2 and rat L8 ribosomal proteins	GL[RAN][IK]G	49									0.005	10
protein_40_YER082C	2	UTP7:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	SK.[KSC][NQF]I	49	KRKQISVR	Phosphorylase kinase substrate motif					small nucleolar ribonucleoprotein complex (1e-04)		0.005	10
protein_40_YDR496C	2	PUF6:  Pumilio-homology domain protein that binds ASH1 mRNA at PUF consensus sequences in the 3' UTR and represses its translation, resulting in proper asymmetric localization of ASH1 mRNA	DE.[EMT]I[EYW]	49	IY	cFGR and Csk kinase phosphorylation site (peptide screen)					nucleolus (1e-07)		0.005	10
protein_40_YDR448W	2	ADA2:  Transcription coactivator, component of the ADA and SAGA transcriptional adaptor/HAT (histone acetyltransferase) complexes	[YWM][DW]DV	49	Y[DQ]DV	SH2 ligand for Blnk (Tyr must be phosphorylated)	Y				SAGA complex (1e-04)		0.005	8
protein_40_YDR145W	2	TAF12:  Subunit (61/68 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation and in chromatin modification, similar to histone H2A	QK[KDS][RV]K	49									0.006	10
protein_40_YDL083C	2	RPS16B:  Protein component of the small (40S) ribosomal subunit; identical to Rps16Ap and has similarity to E. coli S9 and rat S16 ribosomal proteins	[RKV]V.RR	49	[KR]R	CLV_PCSK_KEX2_1					cytosolic ribosome (sensu Eukaryota) (1e-10)		0.006	9
protein_40_YDL055C	2	PSA1:  GDP-mannose pyrophosphorylase (mannose-1-phosphate guanyltransferase), synthesizes GDP-mannose from GTP and mannose-1-phosphate in cell wall biosynthesis; required for normal cell wall structure	[TYQ]K..EE[IAS]	49	YEEI	SH2 ligand group 1A (Src,Fyn,Lck) (phospho-peptide)						Y	0.005	9
protein_40_YDL031W	2	DBP10:  Putative ATP-dependent RNA helicase of the DEAD-box protein family, constituent of 66S pre-ribosomal particles; essential protein involved in ribosome biogenesis	K[RKD]..[VEK]E	49	K[KR].[KR]	Nuclear localization motif					cytoplasm organization and biogenesis (1e-20)		0.009	10
protein_40_YDL029W	2	ARP2:  Essential component of the Arp2/3 complex, which is a highly conserved actin nucleation center required for the motility and integrity of actin patches; involved in endocytosis and membrane growth and polarity	[AVW]L.[LRG]SD	49								Y	0.006	9
protein_40_YCR031C	2	RPS14A:  Ribosomal protein 59 of the small subunit, required for ribosome assembly and 20S pre-rRNA processing; mutations confer cryptopleurine resistance; nearly identical to Rps14Bp and similar to E. coli S11 and rat S14 ribosomal proteins	AR..A[KNM][KVS]	49	[AG]R	Protease matriptase protease site					cytosolic ribosome (sensu Eukaryota) (1e-04)		0.005	9
protein_40_YBR106W	2	PHO88:  Probable membrane protein, involved in phosphate transport; pho88 pho86 double null mutant exhibits enhanced synthesis of repressible acid phosphatase at high inorganic phosphate concentrations	[FLI]F..[FLI]I	49							transporter activity (1e-04)	Y	0.009	10
protein_40_YAL032C	2	PRP45:  Protein required for pre-mRNA splicing; associates with the spliceosome and interacts with splicing factors Prp22p and Prp46p; orthologous to human transcriptional coactivator SKIP and can activate transcription of a reporter gene	[LNA]S..N[VSY]F	49			Y					Y	0.005	9
protein_40_YAL032C	2	PRP45:  Protein required for pre-mRNA splicing; associates with the spliceosome and interacts with splicing factors Prp22p and Prp46p; orthologous to human transcriptional coactivator SKIP and can activate transcription of a reporter gene	E.[TES]Q	49	[ST]Q	ATM kinase phosphorylation site					nuclear mRNA splicing, via spliceosome (1e-11)	Y	0.009	10
oshea_vacuolar_membrane	2	oshea_vacuolar_membrane	S[ED]E[LTA]S	49	S[DE][DE][DE]	Casein Kinase II substrate motif	Y				vacuole (1e-06)		0.006	9
oshea_nuclear_periphery	2	oshea_nuclear_periphery	[SRM][AQF].GT	49	[SAG]GGTG[SA]G	TUBULIN PATTERN					nuclear pore (1e-19)	Y	0.009	10
oshea_cytoplasm	2	oshea_cytoplasm	P..[FVR]E	49	PP..F	LIG_EVH1_II						Y	0.009	10
oshea_cell_periphery	2	oshea_cell_periphery	[STH]SS[SAP]	49	S[ST]	MDC1 BRCT domain binding motif	Y				site of polarized growth (1e-19)		0.010	10
matsuyama_Cytosol	2	matsuyama_Cytosol	GK[VTY]	49	[GA]....GK[ST]	Purine nucleotide triphosphate binding motif	Y				purine nucleotide binding (1e-14)	Y	0.011	10
matsuyama_Cytosol	2	matsuyama_Cytosol	V[ESK]E	49	[ST]E	G protein-coupled receptor kinase 1 substrate motif					purine nucleotide binding (1e-05)	Y	0.012	10
genetic_YNL153C	2	GIM3: Subunit of the heterohexameric cochaperone prefoldin complex which binds specifically to cytosolic chaperonin and transfers target proteins to it	[QE]Q..[QIW]QT	49								Y	0.005	10
genetic_YNL153C	2	GIM3: Subunit of the heterohexameric cochaperone prefoldin complex which binds specifically to cytosolic chaperonin and transfers target proteins to it	NS[VNK]	49			Y				cell cycle (1e-16)	Y	0.009	10
yeast-1166_GO-0005488	2	binding	N.N[NAL]	48				RRM_1	1.E-09	-2.8	nucleic acid binding (1e-10)		0.010	10
protein_40_YGR252W	2	GCN5:  Histone acetyltransferase, acetylates N-terminal lysines on histones H2B and H3; catalytic subunit of the ADA and SAGA histone acetyltransferase complexes; founding member of the Gcn5p-related N-acetyltransferase superfamily	[EQR]K..AS[KVQ]	48	SQ	ATM kinase substrate motif		Histone	1.E-03	-1.9	establishment and/or maintenance of chromatin architecture (0.001)		0.005	9
protein_40_YDL153C	2	SAS10:  Component of the small (ribosomal) subunit (SSU) processosome required for pre-18S rRNa processing; essential nucleolar protein that, when overproduced, disrupts silencing	EDE[TEY][LYF]	48	SEDEE	CKII kinase phosphorylation site (peptide screen)		Pkinase	1.E-04	-1.7	protein serine/threonine kinase activity (1e-05)		0.006	10
yeast-661_GO-0050789	2	regulation of biological process	L.S[LDN]	48	WLNS	Lipid binding motif in C-terminus of Apolipoprotein AII		Zn_clus	1.E-06	-1.6	regulation of metabolism (1e-22)		0.010	10
protein_40_YER006W	2	NUG1:  GTPase that associates with nuclear 60S pre-ribosomes, required for export of 60S ribosomal subunits from the nucleus	[KVR]K..K[KEV]	48	P.[ST]PKK.KK	Cdc2 like protein kinase substrate motif		DEAD	1.E-02	-1.6	cytoplasm organization and biogenesis (1e-26)		0.009	10
protein_40_YML010W	2	SPT5:  Protein that forms a complex with Spt4p and mediates both activation and inhibition of transcription elongation; Spt4p-Spt5p complex also plays a role in pre-mRNA processing	K[KAY]K[SYA]	48	KKKKKK[ST]	TGF beta receptor kinase substrate motif		DEAD	1.E-03	-1.4	nuclear lumen (1e-08)	Y	0.009	10
protein_40_YPL211W	2	NIP7:  Nucleolar protein required for 60S ribosome subunit biogenesis, constituent of 66S pre-ribosomal particles; physically interacts with Nop8p and the exosome subunit Rrp43p	H[RM].G[RDC]	48			Y	DEAD	1.E-07	-1.3	rRNA processing (1e-09)		0.005	8
protein_40_YKL014C	2	URB1:  Nucleolar protein required for the normal accumulation of 25S and 5.8S rRNAs, associated with the 27SA2 pre-ribosomal particle; proposed to be involved in the biogenesis of the 60S ribosomal subunit	[RYM]G.DI[PNK]	48				DEAD	1.E-05	-1.3	nucleolus (1e-06)		0.005	8
protein_40_YPL093W	2	NOG1:  Putative GTPase that associates with free 60S ribosomal subunits in the nucleolus and is required for 60S ribosomal subunit biogenesis; constituent of 66S pre-ribosomal particles; member of the ODN family of nucleolar G-proteins	D[VMS]AA[RDA]	48				DEAD	1.E-04	-1.2	RNA helicase activity (1e-04)		0.005	7
protein_40_YPL043W	2	NOP4:  Nucleolar protein, essential for processing and maturation of 27S pre-rRNA and large ribosomal subunit biogenesis; constituent of 66S pre-ribosomal particles; contains four RNA recognition motifs (RRMs)	[PYD]S..[KER]KV	48				DEAD	1.E-03	-1	ribosome biogenesis (0.001)	Y	0.005	9
protein_40_YGR128C	2	UTP8:  Nucleolar protein required for export of tRNAs from the nucleus; also copurifies with the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	[WC]D..[STL]G	48	DH[YF]LGK[EQK]	G6P_DEHYDROGENASE PATTERN		WD40	1.E-10	-1	processing of 20S pre-rRNA (1e-07)		0.005	10
yeast-752_GO-0016787	2	hydrolase activity	D.L[EVF]	48	DLL	Binding motif for clathrin heavy chain ear		Helicase_C	1.E-05	-0.9	pyrophosphatase activity (1e-77)	Y	0.010	10
yeast-320_GO-0006355	2	regulation of transcription, DNA-dependent	QQ..[LSP]	48				Zn_clus	1.E-03	-0.9	regulation of transcription, DNA-dependent (1e-13)		0.010	10
protein_40_YNL002C	2	RLP7:  Nucleolar protein with similarity to large ribosomal subunit L7 proteins; constituent of 66S pre-ribosomal particles; plays an essential role in processing of precursors to the large ribosomal subunit RNAs	[KNG]K[SEG]K	48				MMR_HSR1	1.E-02	-0.9	cytoplasm organization and biogenesis (1e-30)		0.009	10
protein_40_YLR293C	2	GSP1:  GTP binding protein (mammalian Ranp homolog) involved in the maintenance of nuclear organization, RNA processing and transport; regulated by Prp20p, Rna1p, Yrb1p, Yrb2p, Yrp4p, Yrb30p, Cse1p and Kap95p; yeast Gsp2p homolog	[DRA]ISN[STA]	48			Y	IBN_N	1.E-02	-0.4	nucleocytoplasmic transport (0.001)		0.005	9
protein_40_YPL004C	2	LSP1:  Primary component of eisosomes, which are large immobile patch structures at the cell cortex associated with endocytosis, along with Pil1p and Sur7p; null mutants show activation of Pkc1p/Ypk1p stress resistance pathways	L[VKM]RA	48	[KR]R	CLV_PCSK_KEX2_1		Cpn60_TCP1	1.E-02	-0.1			0.006	9
protein_40_YGL048C	2	RPT6:  One of six ATPases of the 19S regulatory particle of the 26S proteasome involved in the degradation of ubiquitinated substrates; bound by ubiquitin-protein ligases Ubr1p and Ufd4p; localized mainly to the nucleus throughout the cell cycle	Q[PVY][QNW]E	48				PCI	1.E-03	0.4	proteasome complex (sensu Eukaryota) (1e-08)		0.007	10
protein_40_YDR328C	2	SKP1:  Evolutionarily conserved kinetochore protein that is part of multiple protein complexes, including the SCF ubiquitin ligase complex, the CBF3 complex that binds centromeric DNA, and the RAVE complex that regulates assembly of the V-ATPase	[VI]K.LT[GNI]	48			Y	ubiquitin	1.E-04	1.4	protein tag (0.001)		0.005	8
yeast-921_GO-0006810	2	transport	L..[GIM]L	48			Y	Mito_carr	1.E-13	1.5	intracellular transport (1e-14)	Y	0.010	10
yeast-413_GO-0005215	2	transporter activity	L.[WFV]A	48	PLARTLSVAGLP	Calmodulin-dependent protein kinase IV substrate motif	Y	MFS_1	1.E-13	1.6	transporter activity (1e-14)	Y	0.010	10
protein_40_YDR224C	2	HTB1:  One of two nearly identical (see HTB2) histone H2B subtypes required for chromatin assembly and chromosome function; Rad6p-Bre1p-Lge1p mediated ubiquitination regulates transcriptional activation, meiotic DSB formation and H3 methylation	LE..[GV][NI]A	48				Histone	1.E-04	1.6		Y	0.006	10
protein_40_YJL081C	2	ARP4:  Nuclear actin-related protein involved in chromatin remodeling, component of chromatin-remodeling enzyme complexes	[RQV]L.[RIY]RG	48	[KR]R	CLV_PCSK_KEX2_1		Histone	1.E-07	1.7	establishment and/or maintenance of chromatin architecture (1e-04)		0.006	8
protein_40_YLL008W	2	DRS1:  Nucleolar DEAD-box protein required for ribosome assembly and function, including synthesis of 60S ribosomal subunits; constituent of 66S pre-ribosomal particles	HR..[KRC][PTL]	48	R..K	SH3 binding motif for GADS SH3 recognizing slp-76 motif (nonconventional)		Pkinase	1.E-14	2.8	protein kinase activity (1e-14)		0.008	10
protein_40_YLL008W	2	DRS1:  Nucleolar DEAD-box protein required for ribosome assembly and function, including synthesis of 60S ribosomal subunits; constituent of 66S pre-ribosomal particles	R[DLI].K	48	L..RR..KK	ERK docking motif in RSK stringent	Y	Pkinase	1.E-12	2.9	cytoplasm organization and biogenesis (1e-20)		0.009	10
matsuyama_Cytosol	2	matsuyama_Cytosol	I..[RNE]D	48				Pkinase	1.E-02	3.4	purine nucleotide binding (1e-07)	Y	0.012	10
protein_40_YAR019C	2	CDC15:  Protein kinase of the Mitotic Exit Network that is localized to the spindle pole bodies at late anaphase; promotes mitotic exit by directly switching on the kinase activity of Dbf2p	W..G[CVI]	48			Y	Pkinase	1.E-26	4.5	protein kinase activity (1e-25)	Y	0.008	10
yeast-648_GO-0050791	2	regulation of physiological process	KR[KRE]	48	KR	CLV_PCSK_PC1ET2_1		Zn_clus	1.E-07	4.9	regulation of metabolism (1e-16)		0.010	10
protein_40_YOL133W	2	HRT1:  RING finger containing subunit of Skp1-Cullin-F-box ubiquitin protein ligases (SCF); required for Gic2p, Far1p, Sic1p and Cln2p degradation; may tether Cdc34p (a ubiquitin conjugating enzyme or E2) and Cdc53p (a cullin) subunits of SCF	LP.[EAT][IYA]	48	P.LP.K	SH3 binding motif, stringent Crk SH3 binding site (Class 2)		F-box	1.E-06	7.8	cellular protein catabolism (1e-07)		0.009	10
yeast-322_GO-0005654	2	nucleoplasm	[QIM]Q..Q	48							nucleoplasm (1e-11)		0.010	10
yeast-294_GO-0006366	2	transcription from RNA polymerase II promoter	Q[QNI].Q[QNH]	48							transcription from RNA polymerase II promoter (1e-70)		0.010	10
yeast-261_GO-0016491	2	oxidoreductase activity	SS.[SNQ][SNT]	48	S[ST]	MDC1 BRCT domain binding motif							0.010	10
yeast-235_GO-0009653	2	morphogenesis	[STY]ST[LNV]H	48	S[ST]	MDC1 BRCT domain binding motif					cellular morphogenesis (1e-13)		0.008	10
yeast-235_GO-0000902	2	cellular morphogenesis	[STY]ST[LNV]H	48	S[ST]	MDC1 BRCT domain binding motif					cellular morphogenesis (1e-13)		0.008	10
protein_40_YPR144C	2	NOC4:  Nucleolar protein, forms a complex with Nop14p that mediates maturation and nuclear export of 40S ribosomal subunits	[NQG][SDG]NKI	48	NK.D	Motif for specificity of guanine in purine binding proteins					small nucleolar ribonucleoprotein complex (0.001)	Y	0.005	9
protein_40_YPR119W	2	CLB2:  B-type cyclin involved in cell cycle progression; activates Cdc28p to promote the transition from G2 to M phase; accumulates during G2 and M, then targeted via a destruction box motif for ubiquitin-mediated degradation by the proteasome	KSK[RQY][SNM]	48	KR	CLV_PCSK_PC1ET2_1	Y						0.006	8
protein_40_YPL153C	2	RAD53:  Protein kinase, required for cell-cycle arrest in response to DNA damage; activated by trans autophosphorylation when interacting with hyperphosphorylated Rad9p; also interacts with ARS1 and plays a role in initiation of DNA replication	LD.[IET]S[TPI]	48	WLDLE	14-3-3 binding motif from peptide screen					DNA integrity checkpoint (0.01)	Y	0.005	10
protein_40_YPL042C	2	SSN3:  Cyclin-dependent protein kinase, component of RNA polymerase II holoenzyme; involved in phosphorylation of the RNA polymerase II C-terminal domain; involved in glucose repression	[QLR]Q[QST]QL	48	[ST]Q	ATM kinase phosphorylation site					transcription regulator activity (0.001)		0.006	10
protein_40_YOR181W	2	LAS17:  Actin assembly factor, activates the Arp2/3 protein complex that nucleates branched actin filaments; localizes with the Arp2/3 complex to actin patches; homolog of the human Wiskott-Aldrich syndrome protein (WASP)	[STV]LA[PVH]E	48								Y	0.005	8
protein_40_YOL013C	2	HRD1:  Ubiquitin-protein ligase required for endoplasmic reticulum-associated degradation (ERAD) of misfolded proteins; genetically linked to the unfolded protein response (UPR); regulated through association with Hrd3p; contains an H2 ring finger	[AYE]LAK[LGM]	48									0.005	9
protein_40_YOL001W	2	PHO80:  Cyclin, negatively regulates phosphate metabolism; Pho80p-Pho85p (cyclin-CDK complex) phosphorylates Pho4p and Swi5p; deletion of PHO80 leads to aminoglycoside supersensitivity; truncated form of PHO80 affects vacuole inheritance	K[AVY]..I[DTM]L	48	YIDL	SH2 ligand for Syp (also tyr is phosphorylated by the insulin receptor)							0.007	10
protein_40_YNL209W	2	SSB2:  Cytoplasmic ATPase that is a ribosome-associated molecular chaperone, functions with J-protein partner Zuo1p; may be involved in the folding of newly-synthesized polypeptide chains; member of the HSP70 family; homolog of SSB1	K[EPR].[LEV]YQ	48	[EDY]Y	TC-PTP phosphatase substrate motif	Y						0.006	8
protein_40_YNL110C	2	NOP15:  Constituent of 66S pre-ribosomal particles, involved in 60S ribosomal subunit biogenesis; localizes to both nucleolus and cytoplasm	[KVG]K..[KRE]K	48	K[KR].[KR]	Nuclear localization motif					cytoplasm organization and biogenesis (1e-25)		0.009	10
protein_40_YMR242C	2	RPL20A:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl20Bp and has similarity to rat L18a ribosomal protein	K..[AKR]A	48	K[KR].[KR]	Nuclear localization motif					cytosolic ribosome (sensu Eukaryota) (1e-38)	Y	0.009	10
protein_40_YMR001C	2	CDC5:  Polo-like kinase with similarity to Xenopus Plx1 and S. pombe Plo1p; found at bud neck, nucleus and SPBs; has multiple functions in mitosis and cytokinesis through phosphorylation of substrates; may be a Cdc28p substrate	L[DCF].N[GQA]N	48									0.006	10
protein_40_YML063W	2	RPS1B:  Ribosomal protein 10 (rp10) of the small (40S) subunit; nearly identical to Rps1Ap and has similarity to rat S3a ribosomal protein	IA.[SQ][RKM]R	48	[KR]R	CLV_PCSK_KEX2_1	Y				translation (1e-04)		0.005	9
protein_40_YLR180W	2	SAM1:  S-adenosylmethionine synthetase, catalyzes transfer of the adenosyl group of ATP to the sulfur atom of methionine; one of two differentially regulated isozymes (Sam1p and Sam2p)	EV..[AEF][TGN]	48			Y					Y	0.009	10
protein_40_YLR009W	2	RLP24:  Essential protein with similarity to Rpl24Ap and Rpl24Bp, associated with pre-60S ribosomal subunits and required for ribosomal large subunit biogenesis	EE..[EDK][EKM]	48	EED	Ankyrin B C-terminal motif that binds internal Ankyrin repeats					cytoplasm organization and biogenesis (1e-26)	Y	0.009	10
protein_40_YLL045C	2	RPL8B:  Ribosomal protein L4 of the large (60S) ribosomal subunit, nearly identical to Rpl8Ap and has similarity to rat L7a ribosomal protein; mutation results in decreased amounts of free 60S subunits	[ATG]R..A	48	[AG]R	Protease matriptase protease site					cytosolic ribosome (sensu Eukaryota) (1e-23)		0.009	10
protein_40_YKL014C	2	URB1:  Nucleolar protein required for the normal accumulation of 25S and 5.8S rRNAs, associated with the 27SA2 pre-ribosomal particle; proposed to be involved in the biogenesis of the 60S ribosomal subunit	[AFV]K[SWR]DE	48	KR	CLV_PCSK_PC1ET2_1							0.005	10
protein_40_YJR066W	2	TOR1:  PIK-related protein kinase and rapamycin target; subunit of TORC1, a complex that controls growth in response to nutrients by regulating translation, transcription, ribosome biogenesis, nutrient transport and autophagy; involved in meiosis	[LFM]L..N[LRV]G	48			Y						0.005	9
protein_40_YIL019W	2	FAF1:  Protein required for pre-rRNA processing and 40S ribosomal subunit assembly	[LNF]S.I[KFW]L	48							small nucleolar ribonucleoprotein complex (1e-09)		0.005	9
protein_40_YGL200C	2	EMP24:  Integral membrane component of endoplasmic reticulum-derived COPII-coated vesicles, which function in ER to Golgi transport	[AQ][AIL]..YG	48							secretory pathway (0.01)		0.007	9
protein_40_YFR052W	2	RPN12:  Subunit of the 19S regulatory particle of the 26S proteasome lid; synthetically lethal with RPT1, which is an ATPase component of the 19S regulatory particle; physically interacts with Nob1p and Rpn3p	[LPN]DIL[EFD]	48									0.005	10
protein_40_YFR028C	2	CDC14:  Protein phosphatase required for mitotic exit; located in the nucleolus until liberated by the FEAR and Mitotic Exit Network in anaphase, enabling it to act on key substrates to effect a decrease in CDK/B-cyclin activity and mitotic exit	RK.S[LKI][EPR]	48	RRK.[ST]	ZIP kinase phosphorylation motif					regulation of exit from mitosis (1e-04)		0.005	9
protein_40_YFL037W	2	TUB2:  Beta-tubulin; associates with alpha-tubulin (Tub1p and Tub3p) to form tubulin dimer, which polymerizes to form microtubules	E[TNR]K[EGL]K	48			Y					Y	0.005	8
protein_40_YDR427W	2	RPN9:  Non-ATPase regulatory subunit of the 26S proteasome, has similarity to putative proteasomal subunits in other species; null mutant is temperature sensitive and exhibits cell cycle and proteasome assembly defects	LA.[GLR][GDR]E	48							proteasome complex (sensu Eukaryota) (0.001)	Y	0.005	9
protein_40_YDR324C	2	UTP4:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	S[GWH]E[GVK]V	48	[ED]GSG[DE]	Glycosaminoglycan attachment site					snoRNA binding (1e-04)		0.005	8
protein_40_YDR225W	2	HTA1:  One of two nearly identical (see also HTA2) histone H2A subtypes; core histone required for chromatin assembly and chromosome function; DNA damage-dependent phosphorylation by Mec1p facilitates DNA repair; acetylated by Nat4p	DE.[EYT][ERG]E	48	E[ST][EA]REA[RK].[LI]	RIBOSOMAL_S28E PATTERN							0.007	10
protein_40_YDR174W	2	HMO1:  Chromatin associated high mobility group (HMG) family member involved in genome maintenance; rDNA-binding component of the Pol I transcription system; associates with a 5'-3' DNA helicase and Fpr1p, a prolyl isomerase	K[SNG]..N[DVY]S	48									0.005	8
protein_40_YDR172W	2	SUP35:  Translation termination factor eRF3; altered protein conformation creates the [PSI(+)] prion, a dominant cytoplasmically inherited protein aggregate that alters translational fidelity and creates a nonsense suppressor phenotype	V[LHK].[GE]GS	48	R.GSF	PKCdelta kinase phosphorylation site (peptide screen)	Y						0.006	10
protein_40_YDR145W	2	TAF12:  Subunit (61/68 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation and in chromatin modification, similar to histone H2A	E[ALP]K[EHA]L	48							SAGA complex (1e-04)		0.005	10
protein_40_YCR031C	2	RPS14A:  Ribosomal protein 59 of the small subunit, required for ribosome assembly and 20S pre-rRNA processing; mutations confer cryptopleurine resistance; nearly identical to Rps14Bp and similar to E. coli S11 and rat S14 ribosomal proteins	S[KGF].[LKV]RA	48	[KR]R	CLV_PCSK_KEX2_1					cytosolic ribosome (sensu Eukaryota) (1e-06)		0.005	7
protein_40_YCL059C	2	KRR1:  Essential nucleolar protein required for the synthesis of 18S rRNA and for the assembly of 40S ribosomal subunit	[SQT]L[DPT]AT	48	LP.TG	C-terminal sorting signal which targets surface proteins of Staphylococcus aureus to the cell wall peptidoglycan; Sortase cleaves between Thr and Gly and C-termini is used for crosslinking in cell wall					ribonucleoprotein complex (1e-05)		0.005	10
matsuyama_Cytosol	2	matsuyama_Cytosol	[SVH]L.D[LSP]	48	LFDLM	Binding motif in Clint for clathrin TD domain					regulation of cell cycle (0.01)		0.011	10
genetic_YNL153C	2	GIM3: Subunit of the heterohexameric cochaperone prefoldin complex which binds specifically to cytosolic chaperonin and transfers target proteins to it	N..[DMT]K	48							cytoskeletal part (1e-07)	Y	0.009	10
genetic_YER083C	2	GET2: Subunit of the GET complex; required for meiotic nuclear division and for the retrieval of HDEL proteins from the Golgi to the ER in an ERD2 dependent fashion; may be involved in cell wall function	L...[ILMV]E	48							chromosome organization and biogenesis (sensu Eukaryota) (1e-23)		0.009	10
protein_40_YBR160W	2	CDC28:  Catalytic subunit of the main cell cycle cyclin-dependent kinase (CDK); alternately associates with G1 cyclins (CLNs) and G2/M cyclins (CLBs) which direct the CDK to specific substrates	[QDY]Y..[ETP]LP	48	[EDY]Y	TC-PTP phosphatase substrate motif					 		0.006	10
protein_40_YGR252W	2	GCN5:  Histone acetyltransferase, acetylates N-terminal lysines on histones H2B and H3; catalytic subunit of the ADA and SAGA histone acetyltransferase complexes; founding member of the Gcn5p-related N-acetyltransferase superfamily	GK.[GRP][ARS]K	47	KTPAKEE	GSK-3, ERK1, ERK2, CDK5 substrate motif	Y	Histone	1.E-13	-3	nuclear nucleosome (1e-08)		0.005	9
matsuyama_nucleolus	2	matsuyama_nucleolus	[HM]R.[GKP]R	47	R.[RK]R	CLV_PCSK_FUR_1		DEAD	1.E-10	-1.8	nucleolus (1e-24)		0.013	10
yeast-324_GO-0030528	2	transcription regulator activity	HT.[EQS]K[PNY]	47				zf-C2H2	1.E-18	-1.4	transcription regulator activity (1e-13)		0.009	10
yeast-504_GO-0006350	2	transcription	T..N[DSR]	47				Zn_clus	1.E-11	-1.3	transcription (1e-20)		0.010	10
protein_40_YPL093W	2	NOG1:  Putative GTPase that associates with free 60S ribosomal subunits in the nucleolus and is required for 60S ribosomal subunit biogenesis; constituent of 66S pre-ribosomal particles; member of the ODN family of nucleolar G-proteins	T[DR].A[ASL]R	47	[AG]R	Protease matriptase protease site	Y	DEAD	1.E-07	-1.3	ribosomal large subunit assembly and maintenance (1e-08)		0.006	9
yeast-261_GO-0016491	2	oxidoreductase activity	G[PLY].[GV]L	47	GP	Protease TTP cleavage site		Ferric_reduct	1.E-05	-0.9	oxidoreductase activity (1e-52)		0.010	10
oshea_cytoplasm	2	oshea_cytoplasm	PQ[QEH]	47	HPQ	Biotin binding motif in streptavidin		zf-C2H2	1.E-02	-0.9	regulation of metabolism (1e-06)	Y	0.009	10
matsuyama_Golgi	2	matsuyama_Golgi	Y.L[GFY]	47				MFS_1	1.E-03	-0.9	Golgi apparatus (1e-09)	Y	0.011	10
yeast-413_GO-0005215	2	transporter activity	AV[VMG][TIA]	47				MFS_1	1.E-02	-0.5	transporter activity (1e-54)		0.010	10
protein_40_YOL133W	2	HRT1:  RING finger containing subunit of Skp1-Cullin-F-box ubiquitin protein ligases (SCF); required for Gic2p, Far1p, Sic1p and Cln2p degradation; may tether Cdc34p (a ubiquitin conjugating enzyme or E2) and Cdc53p (a cullin) subunits of SCF	E[LIF]..A[IAC]	47				F-box	1.E-02	-0.4	cullin-RING ubiquitin ligase complex (1e-04)	Y	0.009	10
protein_40_YAR019C	2	CDC15:  Protein kinase of the Mitotic Exit Network that is localized to the spindle pole bodies at late anaphase; promotes mitotic exit by directly switching on the kinase activity of Dbf2p	I[SPK][SRT]KS	47				Pkinase	1.E-02	-0.2	protein amino acid phosphorylation (0.01)		0.005	10
protein_40_YNL031C	2	HHT2:  One of two identical histone H3 proteins (see also HHT1); core histone required for chromatin assembly, involved in heterochromatin-mediated telomeric and HM silencing; regulated by acetylation, methylation, and mitotic phosphorylation	L[AEF]..A[ACS]R	47	[AG]R	Protease matriptase protease site		Histone	1.E-04	0.4	nuclear chromatin (0.001)	Y	0.005	8
yeast-222_GO-0009308	2	amine metabolism	GA.[IKV][VIA]	47				PALP	1.E-03	0.5	amine metabolism (1e-61)		0.010	10
protein_40_YJR002W	2	MPP10:  Component of the SSU processome, which is required for pre-18S rRNA processing, interacts with and controls the stability of Imp3p and Imp4p, essential for viability; similar to human Mpp10p	[LQR]LA[VI]G	47				WD40	1.E-06	0.7	small nucleolar ribonucleoprotein complex (1e-07)	Y	0.005	10
yeast-261_GO-0016491	2	oxidoreductase activity	VV.[GLV][AGP]	47				ADH_N	1.E-03	0.9	oxidoreductase activity (1e-60)		0.010	10
protein_40_YPR103W	2	PRE2:  Beta 5 subunit of the 20S proteasome, responsible for the chymotryptic activity of the proteasome	P[FPY]G[VAW]	47	LVPRG	Protease Thrombin	Y	Proteasome	1.E-12	1.5	proteasome complex (sensu Eukaryota) (1e-16)	Y	0.006	9
protein_40_YPR103W	2	PRE2:  Beta 5 subunit of the 20S proteasome, responsible for the chymotryptic activity of the proteasome	[ASG]G..[APG]D	47			Y	Proteasome	1.E-20	1.8	proteasome core complex (sensu Eukaryota) (1e-19)		0.008	10
protein_40_YML010W	2	SPT5:  Protein that forms a complex with Spt4p and mediates both activation and inhibition of transcription elongation; Spt4p-Spt5p complex also plays a role in pre-mRNA processing	[KEG]K.[IAL]A	47				DEAD	1.E-05	1.8	nuclear lumen (1e-11)	Y	0.009	10
protein_40_YAR019C	2	CDC15:  Protein kinase of the Mitotic Exit Network that is localized to the spindle pole bodies at late anaphase; promotes mitotic exit by directly switching on the kinase activity of Dbf2p	A[GRS]GS[VLF]	47	G[SA]LNK	GDP-mannose binding motif in transporter		Pkinase	1.E-05	2.6	protein kinase activity (0.01)		0.005	9
protein_40_YDR496C	2	PUF6:  Pumilio-homology domain protein that binds ASH1 mRNA at PUF consensus sequences in the 3' UTR and represses its translation, resulting in proper asymmetric localization of ASH1 mRNA	P[TGL]R[EFQ]L	47	[AG]R	Protease matriptase protease site		DEAD	1.E-07	3.6	ribosome assembly (1e-09)		0.005	10
yeast-685_GO-0016740	2	transferase activity	[ILV]G.G[STA]F	47	G[GA]G[ASC][FY]S.K[DE]	ADOMET_SYNTHETASE_2 PATTERN		Pkinase	1.E-28	4.8	protein kinase activity (1e-28)		0.011	10
protein_40_YJR066W	2	TOR1:  PIK-related protein kinase and rapamycin target; subunit of TORC1, a complex that controls growth in response to nutrients by regulating translation, transcription, ribosome biogenesis, nutrient transport and autophagy; involved in meiosis	[TYN]P..R[RVF]	47	P..R..KP	SH3 binding motif for GRB2 C-term		GATA	1.E-02	5.3	regulation of nitrogen utilization (1e-05)		0.008	10
yeast-706_GO-0043412	2	biopolymer modification	KP.N[ILF][LMG]	47				Pkinase	1.E-39	5.5	protein amino acid phosphorylation (1e-45)		0.011	10
yeast-238_GO-0017111	2	nucleoside-triphosphatase activity	[HGL]R.G[RYQ]	47	RGG	Alternative integrin binding site in FMDV virus	Y	Helicase_C	1.E-25	11.6	nucleoside-triphosphatase activity (1e-42)	Y	0.011	10
yeast-648_GO-0050791	2	regulation of physiological process	[AVY]C..C[RDE]	47	C..C	Motif on TIM mitochondrial translocation proteins		Zn_clus	1.E-19	17.4	regulation of cellular metabolism (1e-18)		0.010	10
yeast-388_GO-0007275	2	development	A[PH].[PSE]P	47	[ST]P	LIG_WW_4					multicellular organismal development (1e-38)		0.010	10
yeast-240_GO-0006807	2	nitrogen compound metabolism	A.[IEV]L	47	[FHYM].A[AV].[VAC]L[MV].[MI]	LIG_Sin3_2					nitrogen compound metabolism (1e-17)	Y	0.010	10
yeast-223_GO-0003735	2	structural constituent of ribosome	P..P[SIQ]	47	[RKY]..P..P	LIG_SH3_1							0.010	10
protein_40_YPR110C	2	RPC40:  RNA polymerase subunit, common to RNA polymerase I and III	T[LFA].IN[GKC]	47									0.005	9
protein_40_YPL204W	2	HRR25:  Protein kinase involved in regulating diverse events including vesicular trafficking, DNA repair, and chromosome segregation; binds the CTD of RNA pol II; homolog of mammalian casein kinase 1delta (CK1delta)	S[VQG]..[PLA]QN	47	SQ	ATM kinase substrate motif							0.005	9
protein_40_YPL076W	2	GPI2:  Protein involved in the synthesis of N-acetylglucosaminyl phosphatidylinositol (GlcNAc-PI), the first intermediate in the synthesis of glycosylphosphatidylinositol (GPI) anchors; homologous to the human PIG-C protein	[VIA]G.LI[IYT]	47	IY	cFGR and Csk kinase phosphorylation site (peptide screen)							0.005	8
protein_40_YOR326W	2	MYO2:  One of two type V myosin motors (along with MYO4) involved in actin-based transport of cargos; required for the polarized delivery of secretory vesicles, the vacuole, late Golgi elements, peroxisomes, and the mitotic spindle	[RIE]I[RWF]NL	47									0.005	8
protein_40_YOR326W	2	MYO2:  One of two type V myosin motors (along with MYO4) involved in actin-based transport of cargos; required for the polarized delivery of secretory vesicles, the vacuole, late Golgi elements, peroxisomes, and the mitotic spindle	E[LS].GI[DL]	47									0.006	10
protein_40_YMR242C	2	RPL20A:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl20Bp and has similarity to rat L18a ribosomal protein	N[KNI].[KQ]KV	47									0.005	8
protein_40_YLR372W	2	SUR4:  Elongase, involved in fatty acid and sphingolipid biosynthesis; synthesizes very long chain 20-26-carbon fatty acids from C18-CoA primers; involved in regulation of sphingolipid biosynthesis	V[SLK].LV[LIV]	47							endoplasmic reticulum (0.01)		0.005	9
protein_40_YLR186W	2	EMG1:  Protein required for the maturation of the 18S rRNA and for 40S ribosome production; associated with spindle/microtubules; nuclear localization depends on physical interaction with Nop14p; may bind snoRNAs	D[TAK]LL[TAI]	47	LLTP	WD40 domain of Cdc4 binding motif, Thr must be phosphorylated, CPD motif					small nucleolar ribonucleoprotein complex (1e-09)	Y	0.005	8
protein_40_YLR180W	2	SAM1:  S-adenosylmethionine synthetase, catalyzes transfer of the adenosyl group of ATP to the sulfur atom of methionine; one of two differentially regulated isozymes (Sam1p and Sam2p)	G[IKY].[DRI]EL	47								Y	0.005	10
protein_40_YKL021C	2	MAK11:  Protein involved in an early, nucleolar step of 60S ribosomal subunit biogenesis; essential for cell growth and replication of killer M1 dsRNA virus; contains four beta-transducin repeats	[KNR]K[SDE]K	47	[KR][LIM]K[DE]K[LIM]PG	DEHYDRIN_2 PATTERN					nucleolus (1e-28)	Y	0.009	10
protein_40_YJR145C	2	RPS4A:  Protein component of the small (40S) ribosomal subunit; mutation affects 20S pre-rRNA processing; identical to Rps4Bp and has similarity to rat S4 ribosomal protein	KA..[AEV]E[IVQ]	47							ribonucleoprotein complex (0.01)		0.006	9
protein_40_YJL138C	2	TIF2:  Translation initiation factor eIF4A, identical to Tif1p; DEA(D/H)-box RNA helicase that couples ATPase activity to RNA binding and unwinding; forms a dumbbell structure of two compact domains connected by a linker; interacts with eIF4G	[SCT][NTE]IDE	47									0.006	10
protein_40_YJL081C	2	ARP4:  Nuclear actin-related protein involved in chromatin remodeling, component of chromatin-remodeling enzyme complexes	[NPL]EN[DES]E	47	[ST]E	G protein-coupled receptor kinase 1 substrate motif					nucleoplasm part (0.01)		0.005	9
protein_40_YIL094C	2	LYS12:  Homo-isocitrate dehydrogenase, an NAD-linked mitochondrial enzyme required for the fourth step in the biosynthesis of lysine, in which homo-isocitrate is oxidatively decarboxylated to alpha-ketoadipate	[KYV][SIQ]KNK	47								Y	0.005	7
protein_40_YHR079C	2	IRE1:  Serine-threonine kinase and endoribonuclease; transmembrane protein that mediates the unfolded protein response (UPR) by regulating Hac1p synthesis through HAC1 mRNA splicing; Kar2p binds inactive Ire1p and releases from it upon ER stress	[IRD][PRQ].ATT	47									0.005	9
protein_40_YGR218W	2	CRM1:  Major karyopherin, involved in export of proteins, RNAs, and ribosomal subunits from the nucleus	SN.T[NQK][SGP]	47	N.[TS]	N-linked glycosylation site	Y				rRNA export from nucleus (1e-06)	Y	0.005	7
protein_40_YGR086C	2	PIL1:  Primary component of eisosomes, which are large immobile cell cortex structures associated with endocytosis; null mutants show activation of Pkc1p/Ypk1p stress resistance pathways; detected in phosphorylated state in mitochondria	[VIA]D[SMN]DD	47	D.D	Ribose moiety of UDP and manganese binding site in glucuronyl transferase							0.005	9
protein_40_YDR510W	2	SMT3:  Ubiquitin-like protein of the SUMO family, conjugated to lysine residues of target proteins; regulates chromatid cohesion, chromosome segregation, APC-mediated proteolysis, DNA replication and septin ring dynamics	DP[AKR]V[TAE]	47									0.005	9
protein_40_YDR510W	2	SMT3:  Ubiquitin-like protein of the SUMO family, conjugated to lysine residues of target proteins; regulates chromatid cohesion, chromosome segregation, APC-mediated proteolysis, DNA replication and septin ring dynamics	V.[DKG]A	47			Y				carboxylic acid metabolism (1e-04)		0.008	10
protein_40_YDR496C	2	PUF6:  Pumilio-homology domain protein that binds ASH1 mRNA at PUF consensus sequences in the 3' UTR and represses its translation, resulting in proper asymmetric localization of ASH1 mRNA	[DKE]D.[EKD]E	47	D.D	Ribose moiety of UDP and manganese binding site in glucuronyl transferase					cytoplasm organization and biogenesis (1e-27)		0.009	10
protein_40_YDR388W	2	RVS167:  Actin-associated protein, subunit of a complex (Rvs161p-Rvs167p) involved in regulation of actin cytoskeleton, endocytosis, and viability following starvation or osmotic stress; homolog of mammalian amphiphysin	P[PLR].[PAV]P	47	[RK]SP[RP][RKH]	Cdc2 kinase substrate motif					cell cortex (1e-06)	Y	0.009	10
protein_40_YDR356W	2	SPC110:  Inner plaque spindle pole body (SPB) component, ortholog of human kendrin; involved in connecting nuclear microtubules to SPB; interacts with Tub4p-complex and calmodulin; phosphorylated by Mps1p in cell cycle-dependent manner	L[KLE].N[IQT]S	47							microtubule nucleation (1e-06)		0.005	9
protein_40_YBR009C	2	HHF1:  One of two identical histone H4 proteins (see also HHF2); core histone required for chromatin assembly and chromosome function; contributes to telomeric silencing; N-terminal domain involved in maintaining genomic integrity	E..[DVP]E	47			Y				chromatin modification (1e-11)		0.009	10
protein_40_YBL026W	2	LSM2:  Lsm (Like Sm) protein; part of heteroheptameric complexes (Lsm2p-7p and either Lsm1p or 8p): cytoplasmic Lsm1p complex involved in mRNA decay; nuclear Lsm8p complex part of U6 snRNP and possibly involved in processing tRNA, snoRNA, and rRNA	A[KCH]..[KGM]VL	47							U4/U6 x U5 tri-snRNP complex (0.01)		0.006	9
protein_40_YAR007C	2	RFA1:  Subunit of heterotrimeric Replication Protein A (RPA), which is a highly conserved single-stranded DNA binding protein involved in DNA replication, repair, and recombination	[VRQ]LRG	47									0.005	8
oshea_vacuolar_membrane	2	oshea_vacuolar_membrane	IS[VRG]S[TIG]	47	S[ST]	MDC1 BRCT domain binding motif					vacuole (1e-07)	Y	0.006	10
protein_40_YPR103W	2	PRE2:  Beta 5 subunit of the 20S proteasome, responsible for the chymotryptic activity of the proteasome	VEYA	46	VIYAAPF	Abl kinase substrate motif	Y	Proteasome	1.E-09	-3.8	proteasome core complex, alpha-subunit complex (sensu Eukaryota) (1e-11)		0.005	9
protein_40_YDL188C	2	PPH22:  Catalytic subunit of protein phosphatase 2A, functionally redundant with Pph21p; methylated at C terminus; forms alternate complexes with several regulatory subunits; involved in signal transduction and regulation of mitosis	VE[YCR]A	46			Y	Proteasome	1.E-08	-3.1	proteasome core complex, alpha-subunit complex (sensu Eukaryota) (1e-10)		0.005	10
protein_40_YDR087C	2	RRP1:  Essential evolutionarily conserved nucleolar protein necessary for biogenesis of 60S ribosomal subunits and processing of pre-rRNAs to mature rRNAs, associated with several distinct 66S pre-ribosomal particles	K..K[KYG]	46	P.[ST]PKK.KK	Cdc2 like protein kinase substrate motif		Brix	1.E-04	-2.7	cytoplasm organization and biogenesis (1e-24)		0.008	10
yeast-410_GO-0007049	2	cell cycle	L..N[SKN]	46			Y	Pkinase	1.E-04	-1.8	cell cycle (1e-26)	Y	0.010	10
protein_40_YBR031W	2	RPL4A:  N-terminally acetylated protein component of the large (60S) ribosomal subunit, nearly identical to Rpl4Bp and has similarity to E. coli L4 and rat L4 ribosomal proteins	GR..[RGA][AYG]G	46	[AG]R	Protease matriptase protease site		DEAD	1.E-07	-1.8	RNA helicase activity (1e-06)		0.005	10
yeast-238_GO-0017111	2	nucleoside-triphosphatase activity	L[AYM]K	46	LLKIL	AP-2 binding motif in CXCR2 receptor		Helicase_C	1.E-11	-1.6	nucleoside-triphosphatase activity (1e-14)	Y	0.010	10
yeast-248_GO-0016072	2	rRNA metabolism	T[GCS].GK[TVN]	46	[SAG]GGTG[SA]G	TUBULIN PATTERN		Helicase_C	1.E-17	-1.2	ATP-dependent RNA helicase activity (1e-20)	Y	0.009	10
protein_40_YCL059C	2	KRR1:  Essential nucleolar protein required for the synthesis of 18S rRNA and for the assembly of 40S ribosomal subunit	TD..A[RSV][GEY]	46				DEAD	1.E-03	-1.2	rRNA processing (1e-05)		0.005	9
yeast-410_GO-0007049	2	cell cycle	KR...[SKM]	46	KR	CLV_PCSK_PC1ET2_1		Pkinase	1.E-05	-1.1	cell cycle (1e-19)	Y	0.009	10
protein_40_YNL061W	2	NOP2:  Probable RNA m(5)C methyltransferase, essential for processing and maturation of 27S pre-rRNA and large ribosomal subunit biogenesis; localized to the nucleolus; constituent of 66S pre-ribosomal particles	K..[EVK]E	46				Brix	1.E-03	-1	cytoplasm organization and biogenesis (1e-42)	Y	0.008	10
protein_40_YLL008W	2	DRS1:  Nucleolar DEAD-box protein required for ribosome assembly and function, including synthesis of 60S ribosomal subunits; constituent of 66S pre-ribosomal particles	[DTE]V[AF]AR	46	[AG]R	Protease matriptase protease site		DEAD	1.E-03	-1	ribosomal large subunit assembly and maintenance (1e-06)		0.005	10
yeast-437_GO-0044429	2	mitochondrial part	K[RNH]K	46	KRKQISVR	Phosphorylase kinase substrate motif		Helicase_C	1.E-03	-0.8	nuclear lumen (1e-14)		0.010	10
yeast-294_GO-0006366	2	transcription from RNA polymerase II promoter	[QN]Q.[LSN]L	46				Zn_clus	1.E-03	-0.6	transcription from RNA polymerase II promoter (1e-59)		0.010	10
protein_40_YPL240C	2	HSP82:  Hsp90 chaperone required for pheromone signaling and negative regulation of Hsf1p; docks with Tom70p for mitochondrial preprotein delivery; promotes telomerase DNA binding and nucleotide addition; interacts with Cns1p, Cpr6p, Cpr7p, Sti1p	V[DVA]L	46	DLL	Binding motif for clathrin heavy chain ear		AA_permease	1.E-02	-0.2		Y	0.008	10
protein_40_YBR159W	2	IFA38: Microsomal beta-keto-reductase; contains oleate response element (ORE) sequence in the promoter region; mutants exhibit reduced VLCFA synthesis, accumulate high levels of dihydrosphingosine, phytosphingosine and medium-chain ceramides	L[GLI]..[LIA]F	46				MFS_1	1.E-04	0	transporter activity (1e-07)	Y	0.009	10
protein_40_YPR119W	2	CLB2:  B-type cyclin involved in cell cycle progression; activates Cdc28p to promote the transition from G2 to M phase; accumulates during G2 and M, then targeted via a destruction box motif for ubiquitin-mediated degradation by the proteasome	[LQI]L[ESG]K	46				Pkinase	1.E-03	0.1	cell cycle (1e-07)	Y	0.008	10
protein_40_YBR106W	2	PHO88:  Probable membrane protein, involved in phosphate transport; pho88 pho86 double null mutant exhibits enhanced synthesis of repressible acid phosphatase at high inorganic phosphate concentrations	[AYI]F.G	46	FIGQY	Ankryn G binding motif in neurofascin	Y	MFS_1	1.E-06	0.1	transporter activity (1e-08)	Y	0.009	10
protein_40_YDR324C	2	UTP4:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	K..[KTD]L	46	K..[ST]	PKA kinase substrate motif		WD40	1.E-06	0.2	rRNA processing (1e-46)		0.008	10
yeast-238_GO-0017111	2	nucleoside-triphosphatase activity	E.[YDG]R	46	[AG]R	Protease matriptase protease site		Helicase_C	1.E-11	0.5	nucleoside-triphosphatase activity (1e-09)	Y	0.010	10
protein_40_YNL186W	2	UBP10:  Ubiquitin-specific protease that deubiquitinates ubiquitin-protein moieties; may regulate silencing by acting on Sir4p; involved in posttranscriptionally regulating Gap1p and possibly other transporters; primarily located in the nucleus	NT..[AT][ERM]	46	T..[SA]	FHA of KAPP binding motif, Thr must be phosphorylated		Pkinase	1.E-07	0.8	protein kinase activity (1e-06)	Y	0.006	10
protein_40_YDR224C	2	HTB1:  One of two nearly identical (see HTB2) histone H2B subtypes required for chromatin assembly and chromosome function; Rad6p-Bre1p-Lge1p mediated ubiquitination regulates transcriptional activation, meiotic DSB formation and H3 methylation	L[ARE].[NQK]AA	46				Histone	1.E-06	0.8	nuclear chromatin (1e-06)	Y	0.005	7
yeast-216_GO-0006325	2	establishment and/or maintenance of chromatin architecture	[ENK]EE	46	EED	Ankyrin B C-terminal motif that binds internal Ankyrin repeats		Myb_DNA-binding	1.E-05	1	establishment and/or maintenance of chromatin architecture (1e-19)	Y	0.010	10
yeast-216_GO-0006323	2	DNA packaging	[ENK]EE	46	EED	Ankyrin B C-terminal motif that binds internal Ankyrin repeats		Myb_DNA-binding	1.E-05	1	establishment and/or maintenance of chromatin architecture (1e-19)	Y	0.010	10
yeast-207_GO-0003677	2	DNA binding	T[GHT][EKA]K	46	GAKRH	HISTONE_H4 PATTERN		zf-C2H2	1.E-07	1.1	DNA binding (1e-59)		0.010	10
yeast-980_GO-0051179	2	localization	LS.[IAL][FGI]	46				Adaptin_N	1.E-02	1.4	establishment of cellular localization (1e-55)		0.009	10
yeast-601_GO-0005829	2	cytosol	[EL][EQV]..DDM	46				Ribosomal_60s	1.E-11	1.6	translational elongation (1e-10)		0.006	8
protein_40_YLR197W	2	SIK1:  Essential evolutionarily-conserved nucleolar protein component of the box C/D snoRNP complexes that direct 2'-O-methylation of pre-rRNA during its maturation; overexpression causes spindle orientation defects	[LYM]LSA[SRD]	46			Y	WD40	1.E-04	1.7	cytoplasm organization and biogenesis (1e-06)		0.005	8
oshea_microtubule	2	oshea_microtubule	SK.[TY][RY]L	46				Kinesin	1.E-09	2.1	microtubule (1e-07)		0.006	10
oshea_microtubule	2	oshea_microtubule	KL[TND][RYI]L	46				Kinesin	1.E-08	2.1	microtubule motor activity (1e-10)		0.006	8
yeast-261_GO-0016491	2	oxidoreductase activity	[LGF]G.[KMI]G	46				2-Hacid_dh_C	1.E-05	2.2	oxidoreductase activity (1e-54)		0.010	10
protein_40_YPL203W	2	TPK2:  cAMP-dependent protein kinase catalytic subunit; promotes vegetative growth in response to nutrients via the Ras-cAMP signaling pathway; inhibited by regulatory subunit Bcy1p in the absence of cAMP; partially redundant with Tpk1p and Tpk3p	GG[ED]LF	46				Pkinase	1.E-06	2.3	protein amino acid phosphorylation (1e-06)		0.005	8
protein_40_YKR048C	2	NAP1:  Protein that interacts with mitotic cyclin Clb2p; required for the regulation of microtubule dynamics during mitosis; controls bud morphogenesis; involved in the transport of H2A and H2B histones to the nucleus; phosphorylated by CK2	KP.[NEV][LID]L	46				Pkinase	1.E-12	2.4	protein kinase activity (1e-10)		0.006	10
protein_40_YDL013W	2	SLX5:  Subunit of the Slx5-Slx8 substrate-specific ubiquitin ligase complex; stimulated by prior attachment of SUMO to the substrate	H[RSW]..K[PKW]	46	R..K	SH3 binding motif for GADS SH3 recognizing slp-76 motif (nonconventional)		Pkinase	1.E-05	2.8	protein kinase activity (1e-04)	Y	0.006	10
yeast-256_GO-0016462	2	pyrophosphatase activity	[VIH]LD[ETG]	46				ABC_tran	1.E-09	2.9	pyrophosphatase activity (1e-67)	Y	0.010	10
protein_40_YNL175C	2	NOP13:  Protein of unknown function, localizes to the nucleolus and nucleoplasm; contains an RNA recognition motif (RRM) and has similarity to Nop12p, which is required for processing of pre-18S rRNA	[LNK]FSA[TFD]	46				DEAD	1.E-05	4	RNA helicase activity (1e-04)		0.005	8
yeast-335_GO-0016772	2	transferase activity, transferring phosphorus-containing groups	[LCD]G..[LHR]Y	46				Pkinase	1.E-19	4.8	transferase activity, transferring phosphorus-containing groups (1e-36)		0.010	10
yeast-335_GO-0016772	2	transferase activity, transferring phosphorus-containing groups	T...[MRC]AP	46				Pkinase	1.E-28	5.1	kinase activity (1e-23)	Y	0.010	10
yeast-335_GO-0016772	2	transferase activity, transferring phosphorus-containing groups	E[YFV]..G[GV]	46				Pkinase	1.E-28	5.5	transferase activity, transferring phosphorus-containing groups (1e-38)		0.010	10
yeast-661_GO-0050789	2	regulation of biological process	[AVY]C..C[RDE]	46	C..C	Motif on TIM mitochondrial translocation proteins		Zn_clus	1.E-19	17.2	regulation of cellular metabolism (1e-18)		0.010	10
yeast-942_GO-0043232	2	intracellular non-membrane-bound organelle	R[LRS]K[VET]	46							cytoskeleton (1e-19)		0.010	10
yeast-942_GO-0043228	2	non-membrane-bound organelle	R[LRS]K[VET]	46							cytoskeleton (1e-19)		0.010	10
yeast-596_GO-0044425	2	membrane part	[IFE]L.L[IGW]	46							intrinsic to membrane (1e-41)		0.010	10
yeast-301_GO-0044451	2	nucleoplasm part	[QIM]Q..Q[QHD]	46							nucleoplasm part (1e-62)		0.010	10
yeast-233_GO-0006629	2	lipid metabolism	[KQ]K.L[NP]P	46	DLPPP	EVH1 binding motif					cellular lipid metabolism (1e-08)		0.006	9
yeast-223_GO-0003735	2	structural constituent of ribosome	P...T	46									0.010	10
yeast-220_GO-0044255	2	cellular lipid metabolism	F.F[GLM]	46	F.F	WASP Homology 1 binding motif	Y				cellular lipid metabolism (1e-96)		0.010	10
yeast-205_GO-0005856	2	cytoskeleton	SP[TSR][KEP]	46	SP	ERK1, ERK2 Kinase substrate motif					cytoskeleton (1e-67)		0.010	10
protein_40_YPL211W	2	NIP7:  Nucleolar protein required for 60S ribosome subunit biogenesis, constituent of 66S pre-ribosomal particles; physically interacts with Nop8p and the exosome subunit Rrp43p	[DKG]D.[EKC]E	46	D.E	Sec24p					cytoplasm organization and biogenesis (1e-22)		0.009	10
protein_40_YPL076W	2	GPI2:  Protein involved in the synthesis of N-acetylglucosaminyl phosphatidylinositol (GlcNAc-PI), the first intermediate in the synthesis of glycosylphosphatidylinositol (GPI) anchors; homologous to the human PIG-C protein	S[LRF][LKF]VL	46							nuclear envelope-endoplasmic reticulum network (0.001)		0.005	8
protein_40_YOR133W	2	EFT1:  Elongation factor 2 (EF-2), also encoded by EFT2; catalyzes ribosomal translocation during protein synthesis; contains diphthamide, the unique posttranslationally modified histidine residue specifically ADP-ribosylated by diphtheria toxin	F[DQI]..[ATV]KE	46	KTKEGC	Repeating motif in alpha-synuclein that binds apolipoproteins							0.005	8
protein_40_YOL139C	2	CDC33:  Cytoplasmic mRNA cap binding protein; the eIF4E-cap complex is responsible for mediating cap-dependent mRNA translation via interactions with the translation initiation factor eIF4G (Tif4631p or Tif4632p)	[GVN]G.[RF]GR	46	[AG]R	Protease matriptase protease site							0.005	10
protein_40_YOL077C	2	BRX1:  Nucleolar protein, constituent of 66S pre-ribosomal particles; depletion leads to defects in rRNA processing and a block in the assembly of large ribosomal subunits; possesses a sigma(70)-like RNA-binding motif	E[ETI][ERH]E	46	EEEEYFELV	EGFR kinase substrate motif					cytoplasm organization and biogenesis (1e-25)	Y	0.009	10
protein_40_YNL118C	2	DCP2:  Catalytic subunit of the Dcp1p-Dcp2p decapping enzyme complex, which removes the 5' cap structure from mRNAs prior to their degradation; member of the Nudix hydrolase family	LK[KT][AGH]I	46								Y	0.005	9
protein_40_YMR290C	2	HAS1:  ATP-dependent RNA helicase; localizes to both the nuclear periphery and nucleolus; highly enriched in nuclear pore complex fractions; constituent of 66S pre-ribosomal particles	EE..[EKG][EKN]	46	EED	Ankyrin B C-terminal motif that binds internal Ankyrin repeats	Y				cytoplasm organization and biogenesis (1e-38)	Y	0.008	10
protein_40_YMR128W	2	ECM16:  Essential DEAH-box ATP-dependent RNA helicase specific to the U3 snoRNP, predominantly nucleolar in distribution, required for 18S rRNA synthesis	E[DLK].[SHM]AL	46			Y				small nucleolar ribonucleoprotein complex (1e-07)	Y	0.005	8
protein_40_YMR049C	2	ERB1:  Protein required for maturation of the 25S and 5.8S ribosomal RNAs; constituent of 66S pre-ribosomal particles; homologous to mammalian Bop1	[ATD]V..ET[LHV]	46									0.005	9
protein_40_YLL039C	2	UBI4:  Ubiquitin, becomes conjugated to proteins, marking them for selective degradation via the ubiquitin-26S proteasome system; essential for the cellular stress response; encoded as a polyubiquitin precursor comprised of 5 head-to-tail repeats	S[ILA]DK[LQT]	46								Y	0.005	10
protein_40_YLL008W	2	DRS1:  Nucleolar DEAD-box protein required for ribosome assembly and function, including synthesis of 60S ribosomal subunits; constituent of 66S pre-ribosomal particles	EE..[DGK][GEK]	46	EED	Ankyrin B C-terminal motif that binds internal Ankyrin repeats					cytoplasm organization and biogenesis (1e-27)		0.009	10
protein_40_YLL008W	2	DRS1:  Nucleolar DEAD-box protein required for ribosome assembly and function, including synthesis of 60S ribosomal subunits; constituent of 66S pre-ribosomal particles	K[RKP][SRA]K	46	KR	CLV_PCSK_PC1ET2_1					cytoplasm organization and biogenesis (1e-22)		0.009	10
protein_40_YKL014C	2	URB1:  Nucleolar protein required for the normal accumulation of 25S and 5.8S rRNAs, associated with the 27SA2 pre-ribosomal particle; proposed to be involved in the biogenesis of the 60S ribosomal subunit	E[ESD].[KIE]E	46							nucleolus (1e-32)		0.008	10
protein_40_YJR066W	2	TOR1:  PIK-related protein kinase and rapamycin target; subunit of TORC1, a complex that controls growth in response to nutrients by regulating translation, transcription, ribosome biogenesis, nutrient transport and autophagy; involved in meiosis	T[LHA]..AN[SDK]	46								Y	0.005	9
protein_40_YJL109C	2	UTP10:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	D[TKF][LHK]LT	46	LLTP	WD40 domain of Cdc4 binding motif, Thr must be phosphorylated, CPD motif	Y				rRNA processing (1e-06)		0.005	10
protein_40_YIL144W	2	TID3:  Component of the evolutionarily conserved kinetochore-associated Ndc80 complex (Ndc80p-Nuf2p-Spc24p-Spc25p); conserved coiled-coil protein involved in chromosome segregation, spindle checkpoint activity, kinetochore assembly and clustering	E[LKI]..L[EAF]T	46							microtubule nucleation (0.01)		0.005	9
protein_40_YIL061C	2	SNP1:  Component of U1 snRNP required for mRNA splicing via spliceosome; may interact with poly(A) polymerase to regulate polyadenylation; homolog of human U1 70K protein	[TFN]S[YLQ]KK	46	SQ	ATM kinase substrate motif					nuclear mRNA splicing, via spliceosome (0.001)		0.005	9
protein_40_YIL018W	2	RPL2B:  Protein component of the large (60S) ribosomal subunit, identical to Rpl2Ap and has similarity to E. coli L2 and rat L8 ribosomal proteins; expression is upregulated at low temperatures	NK.[KQR][KF]V	46			Y						0.005	8
protein_40_YGR274C	2	TAF1:  TFIID subunit (145 kDa), involved in RNA polymerase II transcription initiation, has histone acetyltransferase activity, involved in promoter binding and G1/S progression	P[LDE]LT[SEI]	46	P.L	Motif in C-Fos for protein instability	Y						0.005	9
protein_40_YGR086C	2	PIL1:  Primary component of eisosomes, which are large immobile cell cortex structures associated with endocytosis; null mutants show activation of Pkc1p/Ypk1p stress resistance pathways; detected in phosphorylated state in mitochondria	R[STR]..R[STK]S	46	R.S	PKA kinase substrate motif	Y						0.005	10
protein_40_YGR085C	2	RPL11B:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl11Ap; involved in ribosomal assembly; depletion causes degradation of proteins and RNA of the 60S subunit; has similarity to E. coli L5 and rat L11	K..[ARK]A	46	K[KR].[KR]	Nuclear localization motif					cytosolic ribosome (sensu Eukaryota) (1e-47)		0.009	10
protein_40_YGL147C	2	RPL9A:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl9Bp and has similarity to E. coli L6 and rat L9 ribosomal proteins	S.[LSG]S	46									0.008	10
protein_40_YGL106W	2	MLC1:  Essential light chain for Myo1p, light chain for Myo2p; stabilizes Myo2p by binding to the neck region; interacts with Myo1p, Iqg1p, and Myo2p to coordinate formation and contraction of the actomyosin ring with targeted membrane deposition	LS..S[AKT][IQR]	46	S..S	Casien kinase I phosphorylation site, 1st Ser must be phosphorylated						Y	0.005	10
protein_40_YGL105W	2	ARC1:  Protein that binds tRNA and methionyl- and glutamyl-tRNA synthetases (Mes1p and Gus1p), delivering tRNA to them, stimulating catalysis, and ensuring their localization to the cytoplasm; also binds quadruplex nucleic acids	FL..[KRD][NQP]L	46								Y	0.005	9
protein_40_YGL030W	2	RPL30:  Protein component of the large (60S) ribosomal subunit, has similarity to rat L30 ribosomal protein; involved in pre-rRNA processing in the nucleolus; autoregulates splicing of its transcript	[SVK][KHM]KA	46	RRRK[GK]SF[RK][RK]KA	PKC gamma kinase substrate motif					ribonucleoprotein complex (1e-07)		0.009	10
protein_40_YFL037W	2	TUB2:  Beta-tubulin; associates with alpha-tubulin (Tub1p and Tub3p) to form tubulin dimer, which polymerizes to form microtubules	[LDT]ALI[IGQ]	46								Y	0.005	9
protein_40_YFL002C	2	SPB4:  Putative ATP-dependent RNA helicase, nucleolar protein required for synthesis of 60S ribosomal subunits at a late step in the pathway; sediments with 66S pre-ribosomes in sucrose gradients	EE.E[EAG][EKW]	46	RE..E	Iron binding motif in ferritin L-chain and yeast Iron transport protein					cytoplasm organization and biogenesis (1e-12)	Y	0.007	10
protein_40_YER148W	2	SPT15:  TATA-binding protein, general transcription factor that interacts with other factors to form the preinitiation complex at promoters, essential for viability	ET.L[KTQ][IGQ]	46							G1-specific transcription in mitotic cell cycle (1e-05)		0.005	9
protein_40_YER112W	2	LSM4:  Lsm (Like Sm) protein; part of heteroheptameric complexes (Lsm2p-7p and either Lsm1p or 8p): cytoplasmic Lsm1p complex involved in mRNA decay; nuclear Lsm8p complex part of U6 snRNP and possibly involved in processing tRNA, snoRNA, and rRNA	[RHY]E..RL[RED]	46									0.005	7
protein_40_YER018C	2	SPC25:  Component of the evolutionarily conserved kinetochore-associated Ndc80 complex (Ndc80p-Nuf2p-Spc24p-Spc25p); involved in chromosome segregation, spindle checkpoint activity and kinetochore clustering	[QEI][QMA].LQ	46							microtubule cytoskeleton (0.001)		0.009	10
protein_40_YER006W	2	NUG1:  GTPase that associates with nuclear 60S pre-ribosomes, required for export of 60S ribosomal subunits from the nucleus	E[ENI]E[EMG]	46	S[DE][DE]E	BARD1 BRCT domain binding motif					cytoplasm organization and biogenesis (1e-24)		0.009	10
protein_40_YER006W	2	NUG1:  GTPase that associates with nuclear 60S pre-ribosomes, required for export of 60S ribosomal subunits from the nucleus	KQ.[LWK][DEF]A	46							nucleolus (1e-06)		0.005	9
protein_40_YDR356W	2	SPC110:  Inner plaque spindle pole body (SPB) component, ortholog of human kendrin; involved in connecting nuclear microtubules to SPB; interacts with Tub4p-complex and calmodulin; phosphorylated by Mps1p in cell cycle-dependent manner	KI.[KG][LMY]N	46							microtubule nucleation (1e-07)		0.005	9
protein_40_YDR303C	2	RSC3:  Component of the RSC chromatin remodeling complex; essential gene required for maintenance of proper ploidy and regulation of ribosomal protein genes and the cell wall/stress response; highly similar to Rsc30p	H[LPQ]Q[LGY]	46	HPQ	Biotin binding motif in streptavidin					RSC complex (0.01)		0.005	10
protein_40_YDL147W	2	RPN5:  Essential, non-ATPase regulatory subunit of the 26S proteasome lid, similar to mammalian p55 subunit and to another S. cerevisiae regulatory subunit, Rpn7p	[ILD]A.[LNV]DE	46	AEVD	Protease Caspase 10							0.005	10
protein_40_YDL055C	2	PSA1:  GDP-mannose pyrophosphorylase (mannose-1-phosphate guanyltransferase), synthesizes GDP-mannose from GTP and mannose-1-phosphate in cell wall biosynthesis; required for normal cell wall structure	D[FAG].SE[LVI]	46	[ST]E	G protein-coupled receptor kinase 1 substrate motif							0.005	7
protein_40_YDL055C	2	PSA1:  GDP-mannose pyrophosphorylase (mannose-1-phosphate guanyltransferase), synthesizes GDP-mannose from GTP and mannose-1-phosphate in cell wall biosynthesis; required for normal cell wall structure	V[LRD]..L[SPA]E	46	[ST]E	G protein-coupled receptor kinase 1 substrate motif							0.005	9
protein_40_YCL059C	2	KRR1:  Essential nucleolar protein required for the synthesis of 18S rRNA and for the assembly of 40S ribosomal subunit	E[ETF].DQ	46							rRNA processing (1e-11)		0.006	9
protein_40_YBR159W	2	IFA38: Microsomal beta-keto-reductase; contains oleate response element (ORE) sequence in the promoter region; mutants exhibit reduced VLCFA synthesis, accumulate high levels of dihydrosphingosine, phytosphingosine and medium-chain ceramides	[IVA]G.[ALC]I	46			Y				transporter activity (1e-07)		0.009	10
protein_40_YBL027W	2	RPL19B:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl19Ap and has similarity to rat L19 ribosomal protein; rpl19a and rpl19b single null mutations result in slow growth, while the double null mutation is lethal	[VYN]A[KNA]KR	46	KR	CLV_PCSK_PC1ET2_1					cytosolic ribosome (sensu Eukaryota) (1e-07)		0.005	9
oshea_ER	2	oshea_ER	L[VIY]F	46	ENLYFQ[GS]	Protease TEV - stringent	Y				endoplasmic reticulum (1e-75)	Y	0.009	10
oshea_bud	2	oshea_bud	N[KSN].L[KTD]T	46							bipolar bud site selection (0.001)	Y	0.005	9
genetic_YPL055C	2	LGE1: Protein of unknown function; null mutant forms abnormally large cells, and homozygous diploid null mutant displays delayed premeiotic DNA synthesis and reduced efficiency of meiotic nuclear division	[QID]IQQ[QAN]	46									0.005	10
genetic_YNL153C	2	GIM3: Subunit of the heterohexameric cochaperone prefoldin complex which binds specifically to cytosolic chaperonin and transfers target proteins to it	[NER]D..E	46							cell cycle (1e-10)		0.008	10
oshea_nucleolus	2	oshea_nucleolus	K[LEN]D	45	[NT]K.D	Motif for binding guanine nucleotides	Y	WD40	1.E-02	-1.9	nucleolus (1e-09)		0.009	10
protein_40_YMR242C	2	RPL20A:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl20Bp and has similarity to rat L18a ribosomal protein	[GQ][LI]DIP	45				DEAD	1.E-07	-1.5	RNA helicase activity (1e-07)		0.005	9
protein_40_YNL061W	2	NOP2:  Probable RNA m(5)C methyltransferase, essential for processing and maturation of 27S pre-rRNA and large ribosomal subunit biogenesis; localized to the nucleolus; constituent of 66S pre-ribosomal particles	[DNR]VA[AS]R	45	[AG]R	Protease matriptase protease site		DEAD	1.E-05	-1.1	ATP-dependent RNA helicase activity (1e-05)		0.005	8
protein_40_YLR222C	2	UTP13:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	[ARM]GG[DH]	45	GGRGG	Arginine methyl transferease substrate motif (PRMT1)		WD40	1.E-04	-1.1	snoRNA binding (0.001)	Y	0.005	9
protein_40_YPL153C	2	RAD53:  Protein kinase, required for cell-cycle arrest in response to DNA damage; activated by trans autophosphorylation when interacting with hyperphosphorylated Rad9p; also interacts with ARS1 and plays a role in initiation of DNA replication	[SPA]S.E	45				PH	1.E-02	-1	DNA damage response, signal transduction (1e-05)	Y	0.008	10
protein_40_YPL131W	2	RPL5:  Protein component of the large (60S) ribosomal subunit with similarity to E. coli L18 and rat L5 ribosomal proteins; binds 5S rRNA and is required for 60S subunit assembly	DVA[ACQ][RTP]	45	DVAD	Protease Caspase 2 -stringent	Y	DEAD	1.E-03	-1	ribosomal large subunit assembly and maintenance (1e-06)		0.005	10
yeast-1433_GO-0006139	2	nucleobase, nucleoside, nucleotide and nucleic acid metabolism	S.N	45	[LF][HQ]SENG[LIVF][LIVF][GA]	COA_TRANSF_2 PATTERN		Helicase_C	1.E-04	-0.9	transcription (1e-21)		0.009	10
protein_40_YGR090W	2	UTP22:  Possible U3 snoRNP protein involved in maturation of pre-18S rRNA, based on computational analysis of large-scale protein-protein interaction data	E..[EDW]D	45	P.E..[FYWHDE]	LIG_TRAF6		WD40	1.E-02	-0.8	ribosome biogenesis (1e-34)	Y	0.008	10
oshea_nucleus	2	oshea_nucleus	LF[LFY]	45	PL[YF][FY]..N	Trafficks functional nicotinic acetylcholine receptors from ER to cell surface		PI3_PI4_kinase	1.E-02	-0.7	endoplasmic reticulum (1e-18)		0.009	10
yeast-470_GO-0006259	2	DNA metabolism	QQ..[GLS][QKL]	45				Myb_DNA-binding	1.E-02	-0.6	DNA metabolism (1e-69)		0.010	10
oshea_bud_neck	2	oshea_bud_neck	EA.[KF][LMG]E	45				PH	1.E-03	-0.5	establishment of cell polarity (sensu Fungi) (1e-06)		0.006	8
protein_40_YMR047C	2	NUP116:  Subunit of the nuclear pore complex (NPC) that is localized to both sides of the pore; contains a repetitive GLFG motif that interacts with mRNA export factor Mex67p and with karyopherin Kap95p; homologous to Nup100p	LE.[DAR][EPD]	45	LEHD	Protease Caspase 9		IBN_N	1.E-02	-0.4	nucleocytoplasmic transport (1e-07)		0.008	10
protein_40_YLR276C	2	DBP9:  ATP-dependent RNA helicase of the DEAD-box family involved in biogenesis of the 60S ribosomal subunit	K[KLI]..[KRV]K	45				Brix	1.E-02	-0.3	cytoplasm organization and biogenesis (1e-17)		0.009	10
matsuyama_Golgi	2	matsuyama_Golgi	I[LFV]..V[AIY]	45			Y	MFS_1	1.E-02	0	Golgi apparatus (1e-49)		0.011	10
protein_40_YOL069W	2	NUF2:  Component of the evolutionarily conserved kinetochore-associated Ndc80 complex (Ndc80p-Nuf2p-Spc24p-Spc25p); involved in chromosome segregation, spindle checkpoint activity and kinetochore clustering	E[ESY][LN]K	45				SMC_N	1.E-03	0.1	condensed nuclear chromosome (1e-07)	Y	0.009	10
protein_40_YKR081C	2	RPF2:  Essential protein involved in the processing of pre-rRNA and the assembly of the 60S ribosomal subunit; interacts with ribosomal protein L11; localizes predominantly to the nucleolus; constituent of 66S pre-ribosomal particles	RK[RHT]	45	KAPRK[QH][LI]	HISTONE_H3_1 PATTERN		Helicase_C	1.E-03	0.1	cytoplasm organization and biogenesis (1e-22)		0.008	10
yeast-251_GO-0005886	2	plasma membrane	VL[GTI]	45	LTP	RAF1 kinase substrate motif		MFS_1	1.E-05	0.5	plasma membrane (1e-14)		0.009	10
yeast-240_GO-0006807	2	nitrogen compound metabolism	L..[ILMV]G	45				tRNA-synt_2b	1.E-05	0.5	nitrogen compound metabolism (1e-19)		0.009	10
protein_40_YNL186W	2	UBP10:  Ubiquitin-specific protease that deubiquitinates ubiquitin-protein moieties; may regulate silencing by acting on Sir4p; involved in posttranscriptionally regulating Gap1p and possibly other transporters; primarily located in the nucleus	VLG[TG][PHK]	45	LGG[HD]S[LI]	Thioester binding motif for non-ribosomal peptide synthesis of gramicidin		Pkinase	1.E-06	0.8	protein kinase activity (1e-04)		0.005	9
protein_40_YBR245C	2	ISW1:  Member of the imitation-switch (ISWI) class of ATP-dependent chromatin remodeling complexes; ATPase that forms a complex with Ioc2p and Ioc4p to regulate transcription elongation, and a complex with Ioc3p to repress transcription initiation	R[LNV].RR[GHL]	45	[KR]R	CLV_PCSK_KEX2_1		Histone	1.E-04	1.3	chromatin assembly or disassembly (0.001)		0.005	10
protein_40_YNL030W	2	HHF2:  One of two identical histone H4 proteins (see also HHF1); core histone required for chromatin assembly and chromosome function; contributes to telomeric silencing; N-terminal domain involved in maintaining genomic integrity	L[EQ]LA[GER]	45	DALDL	14-3-3 binding motif in ExoS	Y	Histone	1.E-04	1.5	nuclear chromatin (0.001)		0.005	9
yeast-312_GO-0006414	2	translational elongation	G[LM]FD	45	LFDLM	Binding motif in Clint for clathrin TD domain	Y	Ribosomal_60s	1.E-12	1.6	translational elongation (1e-12)	Y	0.006	10
protein_40_YOL012C	2	HTZ1:  Histone variant H2AZ, exchanged for histone H2A in nucleosomes by the SWR1 complex; involved in transcriptional regulation through prevention of the spread of silent heterochromatin	RL.[RI][RA]G	45				Histone	1.E-07	1.6	nuclear nucleosome (1e-06)		0.006	8
yeast-980_GO-0051179	2	localization	L..[GYM]L	45			Y	Mito_carr	1.E-11	1.8	cellular localization (1e-12)		0.009	10
yeast-256_GO-0016462	2	pyrophosphatase activity	L..A[KRM]	45	L.YA.L	SHP1 N-terminal SH2 domain binding motif	Y	ABC_tran	1.E-10	1.8	pyrophosphatase activity (1e-12)	Y	0.010	10
protein_40_YDL153C	2	SAS10:  Component of the small (ribosomal) subunit (SSU) processosome required for pre-18S rRNa processing; essential nucleolar protein that, when overproduced, disrupts silencing	[KQC]P.N[ILMV]	45	CP[ST]N[ILV]GT	GUANIDO_KINASE PATTERN	Y	Pkinase	1.E-20	2.7	protein kinase activity (1e-17)	Y	0.007	10
protein_40_YNL272C	2	SEC2:  Guanyl-nucleotide exchange factor for the small G-protein Sec4p, located on cytoplasmic vesicles; essential for post-Golgi vesicle transport	[KA]P.N[ILV]	45				Pkinase	1.E-22	2.9	protein kinase activity (1e-22)		0.008	10
protein_40_YLR002C	2	NOC3:  Protein that forms a nuclear complex with Noc2p that binds to 66S ribosomal precursors to mediate their intranuclear transport; also binds to chromatin to promote the association of DNA replication factors and replication initiation	[GRE]K.AA[FKS]	45				DEAD	1.E-03	3.2	cytoplasm organization and biogenesis (1e-06)	Y	0.005	7
protein_40_YLL034C	2	RIX7:  Putative ATPase of the AAA family, required for export of pre-ribosomal large subunits from the nucleus; distributed between the nucleolus, nucleoplasm, and nuclear periphery depending on growth conditions	G[KHL][TGI]AA	45				DEAD	1.E-03	3.2	ATP-dependent RNA helicase activity (0.01)		0.005	10
protein_40_YDL153C	2	SAS10:  Component of the small (ribosomal) subunit (SSU) processosome required for pre-18S rRNa processing; essential nucleolar protein that, when overproduced, disrupts silencing	K[PHS][DNEQ]N	45				Pkinase	1.E-24	3.4	protein kinase activity (1e-22)	Y	0.009	10
yeast-661_GO-0050789	2	regulation of biological process	E..[LSH]L	45				Pkinase	1.E-04	3.5	regulation of metabolism (1e-16)	Y	0.009	10
yeast-436_GO-0031323	2	regulation of cellular metabolism	K..R	45	R...K..R	Motif in Ebola virus that eliminates IFN-beta production	Y	zf-C2H2	1.E-07	3.6	regulation of cellular metabolism (10)		0.010	10
protein_40_YHR052W	2	CIC1:  Essential protein that interacts with proteasome components and has a potential role in proteasome substrate specificity; also copurifies with 66S pre-ribosomal particles	LFS[AEM][TPF]	45				DEAD	1.E-04	3.6	rRNA processing (1e-04)		0.005	8
protein_40_YMR229C	2	RRP5:  Protein required for the synthesis of both 18S and 5.8S rRNA; C-terminal region is crucial for the formation of 18S rRNA and N-terminal region is required for the 5.8S rRNA; component of small ribosomal subunit (SSU) processosome	[DK]V..R[GAM]L	45	R.L	Cyclin A motif that binds cdk2 complexes		Helicase_C	1.E-04	4	rRNA processing (1e-05)		0.005	9
yeast-1939_GO-0003824	2	catalytic activity	Y[RML].P[EQV]	45	[VIL].Y[MLF].P	SHP1, SHP2 SH2 domain binding motif		Pkinase	1.E-30	5.1	protein kinase activity (1e-31)		0.009	10
yeast-1340_GO-0044267	2	cellular protein metabolism	HRD[ILMV][KLS]	45	[LIVMF]PCHR[LIVMF][LIVMF]	MGMT PATTERN		Pkinase	1.E-55	6.7	protein amino acid phosphorylation (1e-62)		0.009	10
protein_40_YHR052W	2	CIC1:  Essential protein that interacts with proteasome components and has a potential role in proteasome substrate specificity; also copurifies with 66S pre-ribosomal particles	[HLG]R.G[RTK]	45	RGG	Alternative integrin binding site in FMDV virus		Helicase_C	1.E-08	6.9	cytoplasm organization and biogenesis (1e-11)	Y	0.009	10
yeast-1036_GO-0005739	2	mitochondrion	ML[RAS]	45	LRT	LKB1 Kinase substrate motif	Y				mitochondrial part (1e-34)		0.009	10
protein_40_YPR119W	2	CLB2:  B-type cyclin involved in cell cycle progression; activates Cdc28p to promote the transition from G2 to M phase; accumulates during G2 and M, then targeted via a destruction box motif for ubiquitin-mediated degradation by the proteasome	QY..[ETV][LA]P	45	Y..[LIV]	JAK2 autophosphorylation signal							0.005	9
protein_40_YPL153C	2	RAD53:  Protein kinase, required for cell-cycle arrest in response to DNA damage; activated by trans autophosphorylation when interacting with hyperphosphorylated Rad9p; also interacts with ARS1 and plays a role in initiation of DNA replication	S[ESN]..[DEL]N	45	S[ST]	MDC1 BRCT domain binding motif	Y					Y	0.008	10
protein_40_YPL153C	2	RAD53:  Protein kinase, required for cell-cycle arrest in response to DNA damage; activated by trans autophosphorylation when interacting with hyperphosphorylated Rad9p; also interacts with ARS1 and plays a role in initiation of DNA replication	SP..[NST]	45	SP	ERK1, ERK2 Kinase substrate motif					cell cortex part (0.01)	Y	0.008	10
protein_40_YPL012W	2	RRP12:  Protein required for export of the ribosomal subunits; associates with the RNA components of the pre-ribosomes; contains HEAT-repeats	[RWG]H..F[LCH]	45							nucleolus (1e-08)		0.005	10
protein_40_YOR326W	2	MYO2:  One of two type V myosin motors (along with MYO4) involved in actin-based transport of cargos; required for the polarized delivery of secretory vesicles, the vacuole, late Golgi elements, peroxisomes, and the mitotic spindle	[DPV]A.[KFG]KL	45			Y						0.005	9
protein_40_YOR181W	2	LAS17:  Actin assembly factor, activates the Arp2/3 protein complex that nucleates branched actin filaments; localizes with the Arp2/3 complex to actin patches; homolog of the human Wiskott-Aldrich syndrome protein (WASP)	[SAK][SMN]..QLQ	45							actin cytoskeleton (0.01)	Y	0.005	9
protein_40_YOR096W	2	RPS7A:  Protein component of the small (40S) ribosomal subunit, nearly identical to Rps7Bp; interacts with Kti11p; deletion causes hypersensitivity to zymocin; has similarity to rat S7 and Xenopus S8 ribosomal proteins	RA.[RKG]	45							ribonucleoprotein complex (1e-30)	Y	0.008	10
protein_40_YOL135C	2	MED7:  Subunit of the RNA polymerase II mediator complex; associates with core polymerase subunits to form the RNA polymerase II holoenzyme; essential for transcriptional regulation	V[APF]..[IY]Q	45	VP	Interleukin converting enzyme protease							0.005	9
protein_40_YNL308C	2	KRI1:  Essential nucleolar protein required for 40S ribosome biogenesis; physically and functionally interacts with Krr1p	[GKL]L[RAT]IG	45	FIGQY	Ankryn G binding motif in neurofascin					nucleolus (0.01)		0.005	7
protein_40_YNL308C	2	KRI1:  Essential nucleolar protein required for 40S ribosome biogenesis; physically and functionally interacts with Krr1p	K[DIN].[KNY]EK	45	YE	TPK-IIB/P38Syk kinase phosphorylation site (peptide screen)					rRNA processing (1e-06)		0.005	9
protein_40_YNL189W	2	SRP1:  Karyopherin alpha homolog, forms a dimer with karyopherin beta Kap95p to mediate import of nuclear proteins, binds the nuclear localization signal of the substrate during import; may also play a role in regulation of protein degradation	[LVS]DN[LSA]E	45	[ST]E	G protein-coupled receptor kinase 1 substrate motif							0.005	10
protein_40_YNL118C	2	DCP2:  Catalytic subunit of the Dcp1p-Dcp2p decapping enzyme complex, which removes the 5' cap structure from mRNAs prior to their degradation; member of the Nudix hydrolase family	[LNV]K..E[LER]D	45	EED	Ankyrin B C-terminal motif that binds internal Ankyrin repeats						Y	0.005	7
protein_40_YNL118C	2	DCP2:  Catalytic subunit of the Dcp1p-Dcp2p decapping enzyme complex, which removes the 5' cap structure from mRNAs prior to their degradation; member of the Nudix hydrolase family	GF.[ACP][GYQ]	45								Y	0.005	9
protein_40_YMR128W	2	ECM16:  Essential DEAH-box ATP-dependent RNA helicase specific to the U3 snoRNP, predominantly nucleolar in distribution, required for 18S rRNA synthesis	K[KRA]..SK[DPH]	45	KKR..S	Phosphorylation site for MLCK					ribosome biogenesis (1e-08)		0.005	10
protein_40_YMR047C	2	NUP116:  Subunit of the nuclear pore complex (NPC) that is localized to both sides of the pore; contains a repetitive GLFG motif that interacts with mRNA export factor Mex67p and with karyopherin Kap95p; homologous to Nup100p	S[KW].A[FGP]S	45							protein import into nucleus (1e-06)		0.006	10
protein_40_YMR047C	2	NUP116:  Subunit of the nuclear pore complex (NPC) that is localized to both sides of the pore; contains a repetitive GLFG motif that interacts with mRNA export factor Mex67p and with karyopherin Kap95p; homologous to Nup100p	T[TQ]..[GP]LF	45	F..LF	Androgen receptor motif that interacts with AF2					nuclear pore (1e-08)		0.005	10
protein_40_YML063W	2	RPS1B:  Ribosomal protein 10 (rp10) of the small (40S) subunit; nearly identical to Rps1Ap and has similarity to rat S3a ribosomal protein	[KGL]G.KV[TKV]	45							cytosolic ribosome (sensu Eukaryota) (1e-08)		0.005	9
protein_40_YML063W	2	RPS1B:  Ribosomal protein 10 (rp10) of the small (40S) subunit; nearly identical to Rps1Ap and has similarity to rat S3a ribosomal protein	KK.[APE]F[TIR]	45							translation (1e-05)		0.005	8
protein_40_YLR197W	2	SIK1:  Essential evolutionarily-conserved nucleolar protein component of the box C/D snoRNP complexes that direct 2'-O-methylation of pre-rRNA during its maturation; overexpression causes spindle orientation defects	DE..[PDS][KEQ]	45			Y				nucleolus (1e-21)		0.008	10
protein_40_YLR075W	2	RPL10:  Protein component of the large (60S) ribosomal subunit, responsible for joining the 40S and 60S subunits; regulates translation initiation; has similarity to rat L10 ribosomal protein and to members of the QM gene family	[AKL]A[REG]KA	45							cytosolic ribosome (sensu Eukaryota) (1e-07)		0.006	8
protein_40_YKL203C	2	TOR2:  PIK-related protein kinase and rapamycin target; subunit of TORC1, a complex that regulates growth in response to nutrients and TORC2, a complex that regulates cell-cycle dependent polarization of the actin cytoskeleton; involved in meiosis	L[IYV]F[KDG]K	45								Y	0.005	10
protein_40_YKL009W	2	MRT4:  Protein involved in mRNA turnover and ribosome assembly, localizes to the nucleolus	N[KNF].K[KF]V	45							nucleolus (0.01)		0.005	8
protein_40_YJL164C	2	TPK1:  cAMP-dependent protein kinase catalytic subunit; promotes vegetative growth in response to nutrients via the Ras-cAMP signaling pathway; inhibited by regulatory subunit Bcy1p in the absence of cAMP; partially redundant with Tpk2p and Tpk3p	T.T[TNK]	45	[KR].TQT	LIG_Dynein_DLC8_1	Y						0.008	10
protein_40_YJL092W	2	SRS2:  DNA helicase and DNA-dependent ATPase involved in DNA repair, needed for proper timing of commitment to meiotic recombination and transition from Meiosis I to II; affects genome stability by suppressing unscheduled homologous recombination	KP[EVS]	45	KP..[QK]	LIG_SH3_4							0.008	10
protein_40_YJL081C	2	ARP4:  Nuclear actin-related protein involved in chromatin remodeling, component of chromatin-remodeling enzyme complexes	A[AQI]EI[LKA]	45									0.005	9
protein_40_YJL074C	2	SMC3:  Subunit of the multiprotein cohesin complex required for sister chromatid cohesion in mitotic cells; also required, with Rec8p, for cohesion and recombination during meiosis; phylogenetically conserved SMC chromosomal ATPase family member	[VDM]T.[IDC]P	45									0.005	9
protein_40_YIL144W	2	TID3:  Component of the evolutionarily conserved kinetochore-associated Ndc80 complex (Ndc80p-Nuf2p-Spc24p-Spc25p); conserved coiled-coil protein involved in chromosome segregation, spindle checkpoint activity, kinetochore assembly and clustering	L[QKD].[EQM]N	45			Y				microtubule cytoskeleton (1e-06)		0.009	10
protein_40_YIL094C	2	LYS12:  Homo-isocitrate dehydrogenase, an NAD-linked mitochondrial enzyme required for the fourth step in the biosynthesis of lysine, in which homo-isocitrate is oxidatively decarboxylated to alpha-ketoadipate	[VLQ]LAA[RVF]	45			Y					Y	0.005	8
protein_40_YGR090W	2	UTP22:  Possible U3 snoRNP protein involved in maturation of pre-18S rRNA, based on computational analysis of large-scale protein-protein interaction data	K..[KRT]R	45	[KR]R	CLV_PCSK_KEX2_1					cytoplasm organization and biogenesis (1e-32)		0.008	10
protein_40_YGL207W	2	SPT16:  Subunit of the heterodimeric FACT complex (Spt16p-Pob3p), facilitates RNA Polymerase II transcription elongation through nucleosomes by destabilizing and then reassembling nucleosome structure	[KNA]L.Q[SQR]I	45									0.005	9
protein_40_YGL106W	2	MLC1:  Essential light chain for Myo1p, light chain for Myo2p; stabilizes Myo2p by binding to the neck region; interacts with Myo1p, Iqg1p, and Myo2p to coordinate formation and contraction of the actomyosin ring with targeted membrane deposition	N[EN]..PL[LFA]	45	RPL	VEGFR and neuropilin binding peptide	Y						0.005	7
protein_40_YGL076C	2	RPL7A:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl7Bp and has similarity to E. coli L30 and rat L7 ribosomal proteins; contains a conserved C-terminal Nucleic acid Binding Domain (NDB2)	EK..[AC]S[LSR]	45	S[ST]	MDC1 BRCT domain binding motif	Y						0.005	7
protein_40_YFR031C-A	2	RPL2A:  Protein component of the large (60S) ribosomal subunit, identical to Rpl2Bp and has similarity to E. coli L2 and rat L8 ribosomal proteins	V[VKG]V[VSD]G	45							cytosol (1e-04)		0.005	10
protein_40_YER133W	2	GLC7:  Catalytic subunit of type 1 serine/threonine protein phosphatase, involved in many processes including glycogen metabolism, sporulation, and mitosis; interacts with multiple regulatory subunits; predominantly isolated with Sds22p	[EQM]P..[KPR]EE	45	P..P	SH3 general ligand,	Y						0.005	10
protein_40_YER110C	2	KAP123:  Karyopherin beta, mediates nuclear import of ribosomal proteins prior to assembly into ribosomes and import of histones H3 and H4; localizes to the nuclear pore, nucleus, and cytoplasm; exhibits genetic interactions with RAI1	[GTN]L.GN[KY]	45	LFG	Protease Papain substrate, a prototype cysteine proteinase					snRNP protein import into nucleus (1e-04)		0.005	9
protein_40_YER110C	2	KAP123:  Karyopherin beta, mediates nuclear import of ribosomal proteins prior to assembly into ribosomes and import of histones H3 and H4; localizes to the nuclear pore, nucleus, and cytoplasm; exhibits genetic interactions with RAI1	GK.[TS]F[VGC]	45	[RK].[ST]	PKA kinase substrate motif	Y				nuclear organization and biogenesis (0.001)	Y	0.005	9
protein_40_YER018C	2	SPC25:  Component of the evolutionarily conserved kinetochore-associated Ndc80 complex (Ndc80p-Nuf2p-Spc24p-Spc25p); involved in chromosome segregation, spindle checkpoint activity and kinetochore clustering	TL.[PNG]N[DGM]	45			Y						0.005	10
protein_40_YDR496C	2	PUF6:  Pumilio-homology domain protein that binds ASH1 mRNA at PUF consensus sequences in the 3' UTR and represses its translation, resulting in proper asymmetric localization of ASH1 mRNA	SE.D[KL][KF]	45	E[ST]D	Ankyrin G binding motif in KNCQ2 and KNCQ3 potaqssium channels					nucleolus (1e-06)		0.005	9
protein_40_YDR225W	2	HTA1:  One of two nearly identical (see also HTA2) histone H2A subtypes; core histone required for chromatin assembly and chromosome function; DNA damage-dependent phosphorylation by Mec1p facilitates DNA repair; acetylated by Nat4p	KRI[SIK][GNE]	45	KR	CLV_PCSK_PC1ET2_1							0.005	7
protein_40_YDR167W	2	TAF10:  Subunit (145 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation and in chromatin modification	[SQE]LI[EAG]D	45							transcription factor complex (1e-05)	Y	0.005	7
protein_40_YDL055C	2	PSA1:  GDP-mannose pyrophosphorylase (mannose-1-phosphate guanyltransferase), synthesizes GDP-mannose from GTP and mannose-1-phosphate in cell wall biosynthesis; required for normal cell wall structure	V[VFE]..V[SLT]L	45	P.V.L	Shadow-Chromo domain binding motif						Y	0.005	7
protein_40_YDL031W	2	DBP10:  Putative ATP-dependent RNA helicase of the DEAD-box protein family, constituent of 66S pre-ribosomal particles; essential protein involved in ribosome biogenesis	[SKQ]K..K[RKS]	45	KR	CLV_PCSK_PC1ET2_1	Y				cytoplasm organization and biogenesis (1e-24)		0.009	10
protein_40_YDL031W	2	DBP10:  Putative ATP-dependent RNA helicase of the DEAD-box protein family, constituent of 66S pre-ribosomal particles; essential protein involved in ribosome biogenesis	EE..[DKG][GEK]	45	EED	Ankyrin B C-terminal motif that binds internal Ankyrin repeats					cytoplasm organization and biogenesis (1e-21)		0.009	10
protein_40_YDL029W	2	ARP2:  Essential component of the Arp2/3 complex, which is a highly conserved actin nucleation center required for the motility and integrity of actin patches; involved in endocytosis and membrane growth and polarity	E[AD].[KRM]KG	45									0.005	9
protein_40_YBR010W	2	HHT1:  One of two identical histone H3 proteins (see also HHT2); core histone required for chromatin assembly, involved in heterochromatin-mediated telomeric and HM silencing; regulated by acetylation, methylation, and mitotic phosphorylation	[EVD]S..S[EQG]D	45	S..S	Casien kinase I phosphorylation site, 1st Ser must be phosphorylated							0.005	10
protein_40_YBL003C	2	HTA2:  One of two nearly identical (see also HTA1) histone H2A subtypes; core histone required for chromatin assembly and chromosome function; DNA damage-dependent phosphorylation by Mec1p facilitates DNA repair; acetylated by Nat4p	EN..[TKV]N[DPV]	45								Y	0.005	9
oshea_vacuole	2	oshea_vacuole	S[TFM]..[SLQ]TL	45	PLTLP	RAF1 kinase substrate motif					storage vacuole (1e-04)		0.007	9
oshea_bud	2	oshea_bud	[DIK]L..[EVF]ID	45	VEID	Protease Caspase 6 -stringent					bud (1e-08)		0.005	10
oshea_bud	2	oshea_bud	I[ECP].[LQY]LV	45							exocyst (1e-06)	Y	0.005	9
matsuyama_ER	2	matsuyama_ER	G..F[YFL]	45			Y				endoplasmic reticulum part (1e-20)	Y	0.011	10
genetic_YPL055C	2	LGE1: Protein of unknown function; null mutant forms abnormally large cells, and homozygous diploid null mutant displays delayed premeiotic DNA synthesis and reduced efficiency of meiotic nuclear division	E..[DIG]E	45							chromosome organization and biogenesis (sensu Eukaryota) (1e-17)		0.008	10
genetic_YER083C	2	GET2: Subunit of the GET complex; required for meiotic nuclear division and for the retrieval of HDEL proteins from the Golgi to the ER in an ERD2 dependent fashion; may be involved in cell wall function	SK[RLP]	45	SKRKYRK	TP1 PATTERN					chromosome organization and biogenesis (sensu Eukaryota) (1e-13)	Y	0.008	10
ucsf_loc_k_means_G6	6	Sub-cellular localization, 6 clusters	LF[LTW]	45				MFS_1	1.E-05	1.1	endoplasmic reticulum (1e-49)		0.027	10
protein_40_YNL061W	2	NOP2:  Probable RNA m(5)C methyltransferase, essential for processing and maturation of 27S pre-rRNA and large ribosomal subunit biogenesis; localized to the nucleolus; constituent of 66S pre-ribosomal particles	EE..[EKG][EKV]	44	EED	Ankyrin B C-terminal motif that binds internal Ankyrin repeats		DEAD	1.E-02	-1.8	cytoplasm organization and biogenesis (1e-28)		0.008	10
protein_40_YHR052W	2	CIC1:  Essential protein that interacts with proteasome components and has a potential role in proteasome substrate specificity; also copurifies with 66S pre-ribosomal particles	AR..[ARD]	44	[AG]R	Protease matriptase protease site	Y	DEAD	1.E-04	-1.7	cytoplasm organization and biogenesis (1e-26)	Y	0.008	10
yeast-410_GO-0007049	2	cell cycle	T...N[SEG]	44				Pkinase	1.E-03	-1.6	cell cycle (1e-20)	Y	0.009	10
protein_40_YBR031W	2	RPL4A:  N-terminally acetylated protein component of the large (60S) ribosomal subunit, nearly identical to Rpl4Bp and has similarity to E. coli L4 and rat L4 ribosomal proteins	AR..[ARD]	44	[AG]R	Protease matriptase protease site	Y	DEAD	1.E-02	-1.6	cytosolic ribosome (sensu Eukaryota) (1e-20)	Y	0.008	10
yeast-544_GO-0016070	2	RNA metabolism	DE[EAD][EDH]	44	YDE[PDV]	SH2 ligand for Nck1 and Nck2 (Tyr must be phosphorylated)		Helicase_C	1.E-09	-1.5	RNA metabolism (1e-11)	Y	0.009	10
yeast-207_GO-0003677	2	DNA binding	P.S[SLA]	44	YMPMS	PI3 Kinase p85 SH2 domain binding motif		zf-C2H2	1.E-09	-1.5	DNA binding (1e-17)		0.009	10
yeast-256_GO-0016462	2	pyrophosphatase activity	[LIP]T[GKR]E	44	CP[LP]T.E[ST].C	GM_CSF PATTERN	Y	Helicase_C	1.E-12	-1.3	pyrophosphatase activity (1e-65)	Y	0.009	10
protein_40_YPL211W	2	NIP7:  Nucleolar protein required for 60S ribosome subunit biogenesis, constituent of 66S pre-ribosomal particles; physically interacts with Nop8p and the exosome subunit Rrp43p	H[RTF]..R[TKF]	44				DEAD	1.E-06	-1.3	ribosomal large subunit assembly and maintenance (1e-12)	Y	0.005	8
yeast-320_GO-0006355	2	regulation of transcription, DNA-dependent	LP[SKH]	44	[KR].LP..P	SH3 ligand motif for Sho1p	Y	Zn_clus	1.E-09	-1.2	regulation of transcription, DNA-dependent (1e-20)	Y	0.009	10
protein_40_YKL172W	2	EBP2:  Essential protein required for the maturation of 25S rRNA and 60S ribosomal subunit assembly, localizes to the nucleolus; constituent of 66S pre-ribosomal particles	K..[KIM]K	44	P.[ST]PKK.KK	Cdc2 like protein kinase substrate motif		Brix	1.E-04	-1.2	cytoplasm organization and biogenesis (1e-33)	Y	0.008	10
protein_40_YOR206W	2	NOC2:  Protein that forms a nucleolar complex with Mak21p that binds to 90S and 66S pre-ribosomes, as well as a nuclear complex with Noc3p that binds to 66S pre-ribosomes; both complexes mediate intranuclear transport of ribosomal precursors	E[EKD].E.E	44	SEDEE	CKII kinase phosphorylation site (peptide screen)		Brix	1.E-02	-1.1	nucleolus (1e-26)	Y	0.009	10
protein_40_YGL111W	2	NSA1:  Constituent of 66S pre-ribosomal particles, involved in 60S ribosomal subunit biogenesis	[GY][RH]TAR	44	[AG]R	Protease matriptase protease site		DEAD	1.E-05	-1.1	ATP-dependent RNA helicase activity (1e-05)	Y	0.005	9
protein_40_YDL153C	2	SAS10:  Component of the small (ribosomal) subunit (SSU) processosome required for pre-18S rRNa processing; essential nucleolar protein that, when overproduced, disrupts silencing	[RDK]RSS[LAE]	44	[KR]R	CLV_PCSK_KEX2_1		Pkinase	1.E-04	-1.1	protein serine/threonine kinase activity (0.001)	Y	0.005	10
protein_40_YAR019C	2	CDC15:  Protein kinase of the Mitotic Exit Network that is localized to the spindle pole bodies at late anaphase; promotes mitotic exit by directly switching on the kinase activity of Dbf2p	H[KHT]..S[SHN]	44	S[ST]	MDC1 BRCT domain binding motif		Pkinase	1.E-10	-1	protein kinase activity (1e-09)		0.007	10
protein_40_YPL153C	2	RAD53:  Protein kinase, required for cell-cycle arrest in response to DNA damage; activated by trans autophosphorylation when interacting with hyperphosphorylated Rad9p; also interacts with ARS1 and plays a role in initiation of DNA replication	N.K[ARY]	44	KR	CLV_PCSK_PC1ET2_1		Ank	1.E-02	-0.8		Y	0.008	10
protein_40_YNL186W	2	UBP10:  Ubiquitin-specific protease that deubiquitinates ubiquitin-protein moieties; may regulate silencing by acting on Sir4p; involved in posttranscriptionally regulating Gap1p and possibly other transporters; primarily located in the nucleus	QA..[QWR][SYF]	44				Pkinase	1.E-02	-0.7		Y	0.005	8
protein_40_YKR081C	2	RPF2:  Essential protein involved in the processing of pre-rRNA and the assembly of the 60S ribosomal subunit; interacts with ribosomal protein L11; localizes predominantly to the nucleolus; constituent of 66S pre-ribosomal particles	[TRM]G.[GMS]KT	44				Helicase_C	1.E-08	-0.7	ribosome biogenesis (1e-07)		0.005	10
yeast-251_GO-0005886	2	plasma membrane	S..[SHF]T	44	S..[ST]	Casein Kinase I consensus phosphorylation site (N-term Ser must first be phosphorylated)	Y	MFS_1	1.E-05	-0.6	plasma membrane (1e-15)		0.009	10
yeast-244_GO-0000279	2	M phase	N..I[NLP]	44			Y	MutS_III	1.E-03	-0.6	M phase (1e-16)		0.009	10
yeast-1433_GO-0006139	2	nucleobase, nucleoside, nucleotide and nucleic acid metabolism	I..[EKA]R	44	[KR]R	CLV_PCSK_KEX2_1		Helicase_C	1.E-04	-0.3	DNA metabolism (1e-62)		0.009	10
protein_40_YPR144C	2	NOC4:  Nucleolar protein, forms a complex with Nop14p that mediates maturation and nuclear export of 40S ribosomal subunits	LL[ACF][VIA]G	44	FIGQY	Ankryn G binding motif in neurofascin		WD40	1.E-02	-0.2	snoRNA binding (1e-07)	Y	0.005	8
protein_40_YLR129W	2	DIP2:  Nucleolar protein, specifically associated with the U3 snoRNA, part of the large ribonucleoprotein complex known as the small subunit (SSU) processome, required for 18S rRNA biogenesis, part of the active pre-rRNA processing complex	A[QM]..K[EIN]	44				WD40	1.E-03	-0.2	snoRNA binding (1e-15)	Y	0.006	10
yeast-255_GO-0042254	2	ribosome biogenesis and assembly	KR..[KVG]	44	KR	CLV_PCSK_PC1ET2_1		DEAD	1.E-02	0.2	cytoplasm organization and biogenesis (1e-15)		0.009	10
yeast-255_GO-0007028	2	cytoplasm organization and biogenesis	KR..[KVG]	44	KR	CLV_PCSK_PC1ET2_1		DEAD	1.E-02	0.2	cytoplasm organization and biogenesis (1e-15)		0.009	10
yeast-244_GO-0000279	2	M phase	[SQN]L..[KER]K	44				MutS_III	1.E-02	0.2	M phase (1e-90)		0.009	10
half_life_belle_q3	3	half_life_belle quantized 3	S..D[GNT]	44	S..D	Pyruvate dehydrogenase kinase substrate motif	Y	zf-C2H2	1.E-02	0.4	regulation of biological process (1e-04)		0.018	10
protein_40_YPR119W	2	CLB2:  B-type cyclin involved in cell cycle progression; activates Cdc28p to promote the transition from G2 to M phase; accumulates during G2 and M, then targeted via a destruction box motif for ubiquitin-mediated degradation by the proteasome	I.D	44	[IV].DS[GAS][GASC][GAST][GA]T	ALKALINE_PHOSPHATASE PATTERN		Pkinase	1.E-06	0.5	cell cycle (1e-16)	Y	0.008	10
yeast-251_GO-0005886	2	plasma membrane	F..[AVW]Y	44				MFS_1	1.E-02	0.6	plasma membrane (1e-74)		0.010	10
yeast-1115_GO-0006996	2	organelle organization and biogenesis	G..[GNL]K	44	G.G..G	Phosphate, FAD, NADH, binding motif		WD40	1.E-05	1	chromosome organization and biogenesis (sensu Eukaryota) (1e-57)		0.009	10
protein_40_YBL002W	2	HTB2:  One of two nearly identical (see HTB1) histone H2B subtypes required for chromatin assembly and chromosome function; Rad6p-Bre1p-Lge1p mediated ubiquitination regulates transcriptional activation, meiotic DSB formation and H3 methylation	V[LQW]E[YRQ]L	44				Histone	1.E-03	1.5	chromatin assembly or disassembly (0.001)		0.005	9
yeast-256_GO-0016462	2	pyrophosphatase activity	T[AGC]..[ETL]R	44			Y	Ras	1.E-12	2	pyrophosphatase activity (1e-42)	Y	0.010	10
protein_40_YGL105W	2	ARC1:  Protein that binds tRNA and methionyl- and glutamyl-tRNA synthetases (Mes1p and Gus1p), delivering tRNA to them, stimulating catalysis, and ensuring their localization to the cytoplasm; also binds quadruplex nucleic acids	E[YQF]..G[GQD]	44	[FYW]..G.GY[KR]F	ENT_VIR_OMP_2 PATTERN		Pkinase	1.E-09	2.7	protein kinase activity (1e-11)	Y	0.007	10
protein_40_YLL034C	2	RIX7:  Putative ATPase of the AAA family, required for export of pre-ribosomal large subunits from the nucleus; distributed between the nucleolus, nucleoplasm, and nuclear periphery depending on growth conditions	D[EIN]AD[RPL]	44	[LIVMF][LIVMF]DEAD[RKEN].[LIVMFYGSTN]	DEAD_ATP_HELICASE PATTERN		DEAD	1.E-03	3	rRNA processing (0.001)		0.005	7
yeast-299_GO-0005730	2	nucleolus	[GEI]K[TWK]LA	44				DEAD	1.E-08	3.1	nucleolus (1e-17)		0.009	10
yeast-238_GO-0017111	2	nucleoside-triphosphatase activity	[VIF]LD[EAG]	44				ABC_tran	1.E-13	3.4	nucleoside-triphosphatase activity (1e-68)	Y	0.010	10
protein_40_YLR002C	2	NOC3:  Protein that forms a nuclear complex with Noc2p that binds to 66S ribosomal precursors to mediate their intranuclear transport; also binds to chromatin to promote the association of DNA replication factors and replication initiation	[SK]GKT[AGN]	44				DEAD	1.E-05	3.5	RNA helicase activity (1e-04)		0.005	9
protein_40_YLL045C	2	RPL8B:  Ribosomal protein L4 of the large (60S) ribosomal subunit, nearly identical to Rpl8Ap and has similarity to rat L7a ribosomal protein; mutation results in decreased amounts of free 60S subunits	[RTE]A[ADG]R	44	[AG]R	Protease matriptase protease site		DEAD	1.E-04	3.6	cytoplasm organization and biogenesis (1e-06)		0.009	10
yeast-942_GO-0043232	2	intracellular non-membrane-bound organelle	[DAR]EA[DNR]	44	E[ST][EA]REA[RK].[LI]	RIBOSOMAL_S28E PATTERN		DEAD	1.E-08	3.8	nucleolus (1e-20)		0.009	10
yeast-942_GO-0043228	2	non-membrane-bound organelle	[DAR]EA[DNR]	44	E[ST][EA]REA[RK].[LI]	RIBOSOMAL_S28E PATTERN		DEAD	1.E-08	3.8	nucleolus (1e-20)		0.009	10
yeast-217_GO-0007046	2	ribosome biogenesis	[PTF]TRE[LKY]	44	RE..E	Iron binding motif in ferritin L-chain and yeast Iron transport protein		DEAD	1.E-10	3.8	ribosome biogenesis (1e-14)	Y	0.008	9
protein_40_YGL111W	2	NSA1:  Constituent of 66S pre-ribosomal particles, involved in 60S ribosomal subunit biogenesis	[TR]G.[GM]KT	44				DEAD	1.E-08	3.9	ATP-dependent RNA helicase activity (1e-08)		0.005	9
yeast-335_GO-0016772	2	transferase activity, transferring phosphorus-containing groups	Y[LMC]H	44	Y[VLTFIC]	LIG_SH2_STAT5		Pkinase	1.E-47	4.7	transferase activity, transferring phosphorus-containing groups (1e-58)	Y	0.009	10
yeast-335_GO-0016772	2	transferase activity, transferring phosphorus-containing groups	G[YKH].P[FWY]	44	[WFY][KR]P[WFY]	LIG_WRPW_2		Pkinase	1.E-24	5.5	transferase activity, transferring phosphorus-containing groups (1e-32)	Y	0.010	10
yeast-685_GO-0016740	2	transferase activity	[YVW]A[ILMV]K	44			Y	Pkinase	1.E-52	5.8	protein kinase activity (1e-53)	Y	0.009	10
yeast-460_GO-0006351	2	transcription, DNA-dependent	RK[RPD]	44	VRKRTLRRL	PAK1 kinase substrate motif		Zn_clus	1.E-05	7.7	transcription, DNA-dependent (1e-17)		0.009	10
yeast-341_GO-0045449	2	regulation of transcription	CR.[RKS][KCH]	44	R.[ST]	PKA consensus phosphorylation site	Y	Zn_clus	1.E-24	17.9	regulation of transcription (1e-23)		0.010	10
yeast-792_GO-0006412	2	protein biosynthesis	[KW]MS[KA]S	44	WM	Substrate binding motif of barley alpha-amylase 1 (AMY1) enzyme					ligase activity, forming aminoacyl-tRNA and related compounds (1e-16)		0.007	10
yeast-457_GO-0007001	2	chromosome organization and biogenesis (sensu Eukaryota)	EE[DNS][EKQ]	44	EED	Ankyrin B C-terminal motif that binds internal Ankyrin repeats					chromosome organization and biogenesis (sensu Eukaryota) (1e-09)		0.009	10
yeast-284_GO-0005740	2	mitochondrial envelope	S..[DNEQ]E	44	S..[ED]	Casein kinase II substrate motif							0.009	10
yeast-267_GO-0000003	2	reproduction	[SPT]S[SFG]S	44	S[ST]	MDC1 BRCT domain binding motif					reproduction (1e-12)		0.009	10
yeast-238_GO-0017111	2	nucleoside-triphosphatase activity	KT..A[KIY][AGS]	44	T..[SA]	FHA of KAPP binding motif, Thr must be phosphorylated					nucleoside-triphosphatase activity (1e-09)		0.006	7
yeast-235_GO-0000278	2	mitotic cell cycle	[NEV]D.D[EDV]	44	D.D	Ribose moiety of UDP and manganese binding site in glucuronyl transferase					mitotic cell cycle (1e-96)		0.009	10
yeast-233_GO-0006629	2	lipid metabolism	F.F[LGV]	44	F.F	WASP Homology 1 binding motif	Y				lipid metabolism (1e-09)		0.010	10
yeast-233_GO-0006629	2	lipid metabolism	P[LPR].L[LFH]I	44	P.L	Motif in C-Fos for protein instability					cellular lipid metabolism (1e-09)		0.006	8
yeast-1062_GO-0016020	2	membrane	[SLA]Y[ILMV]V	44	Y[VLTFIC]	LIG_SH2_STAT5					plasma membrane (1e-12)	Y	0.009	10
protein_40_YPR144C	2	NOC4:  Nucleolar protein, forms a complex with Nop14p that mediates maturation and nuclear export of 40S ribosomal subunits	AK..[KHM][KSI]V	44							35S primary transcript processing (0.01)		0.005	7
protein_40_YPL203W	2	TPK2:  cAMP-dependent protein kinase catalytic subunit; promotes vegetative growth in response to nutrients via the Ras-cAMP signaling pathway; inhibited by regulatory subunit Bcy1p in the absence of cAMP; partially redundant with Tpk1p and Tpk3p	[RHG]R.S[VFS]	44	R.S	PKA kinase substrate motif							0.009	10
protein_40_YPL153C	2	RAD53:  Protein kinase, required for cell-cycle arrest in response to DNA damage; activated by trans autophosphorylation when interacting with hyperphosphorylated Rad9p; also interacts with ARS1 and plays a role in initiation of DNA replication	SI[LEP]P[VRA]	44	PPR	LIG_WW_3	Y					Y	0.004	8
protein_40_YOR061W	2	CKA2:  Alpha' catalytic subunit of casein kinase 2, a Ser/Thr protein kinase with roles in cell growth and proliferation; the holoenzyme also contains CKA1, CKB1 and CKB2, the many substrates include transcription factors and all RNA polymerases	K[LHY]..K[STM]K	44									0.005	10
protein_40_YOL069W	2	NUF2:  Component of the evolutionarily conserved kinetochore-associated Ndc80 complex (Ndc80p-Nuf2p-Spc24p-Spc25p); involved in chromosome segregation, spindle checkpoint activity and kinetochore clustering	EI..[LMI][KEC]	44							microtubule cytoskeleton (1e-06)		0.009	10
protein_40_YOL001W	2	PHO80:  Cyclin, negatively regulates phosphate metabolism; Pho80p-Pho85p (cyclin-CDK complex) phosphorylates Pho4p and Swi5p; deletion of PHO80 leads to aminoglycoside supersensitivity; truncated form of PHO80 affects vacuole inheritance	[DWP]G..[LNS]VN	44	HLVNK	Motif for targeting CD44 to basolateral membranes							0.005	9
protein_40_YNL307C	2	MCK1:  Protein serine/threonine/tyrosine (dual-specificity) kinase involved in control of chromosome segregation and in regulating entry into meiosis; related to mammalian glycogen synthase kinases of the GSK-3 family	R..S[VIN]	44	KKR..S	Phosphorylation site for MLCK	Y						0.008	10
protein_40_YNL124W	2	NAF1:  Protein required for the assembly of box H/ACA snoRNPs and for pre-rRNA processing, forms a complex with Shq1p and interacts with H/ACA snoRNP components Nhp2p and Cbf5p; has similarity to Gar1p and other RNA-binding proteins	[RKA]A..[VKG]A	44							cytosolic ribosome (sensu Eukaryota) (1e-19)		0.009	10
protein_40_YNL110C	2	NOP15:  Constituent of 66S pre-ribosomal particles, involved in 60S ribosomal subunit biogenesis; localizes to both nucleolus and cytoplasm	[LA][EHW].INN	44									0.005	9
protein_40_YMR240C	2	CUS1:  Protein required for assembly of U2 snRNP into the spliceosome, forms a complex with Hsh49p and Hsh155p	T[VEG]FS[EKT]	44	S[ST]	MDC1 BRCT domain binding motif					RNA splicing factor activity, transesterification mechanism (0.001)		0.005	10
protein_40_YMR117C	2	SPC24:  Component of the evolutionarily conserved kinetochore-associated Ndc80 complex (Ndc80p-Nuf2p-Spc24p-Spc25p); involved in chromosome segregation, spindle checkpoint activity and kinetochore clustering	D[STH].[LDY]KI	44									0.005	8
protein_40_YLR432W	2	IMD3:  Inosine monophosphate dehydrogenase, catalyzes the first step of GMP biosynthesis, member of a four-gene family in S. cerevisiae, constitutively expressed	L[LG]R[RID]G	44	[AG]R	Protease matriptase protease site							0.005	7
protein_40_YLR423C	2	ATG17:  Scaffold potein responsible for pre-autophagosomal structure organization; interacts with and is required for activation of Apg1p protein kinase; involved in autophagy but not in the Cvt (cytoplasm to vacuole targeting) pathway	[VEK]T.LL[TYI]	44	DLL	Binding motif for clathrin heavy chain ear							0.005	9
protein_40_YLR423C	2	ATG17:  Scaffold potein responsible for pre-autophagosomal structure organization; interacts with and is required for activation of Apg1p protein kinase; involved in autophagy but not in the Cvt (cytoplasm to vacuole targeting) pathway	Q[QEM].[QPW]I	44									0.006	9
protein_40_YLR423C	2	ATG17:  Scaffold potein responsible for pre-autophagosomal structure organization; interacts with and is required for activation of Apg1p protein kinase; involved in autophagy but not in the Cvt (cytoplasm to vacuole targeting) pathway	QE.[EQD]E[LVD]	44									0.005	8
protein_40_YLR340W	2	RPP0:  Conserved ribosomal protein P0 similar to rat P0, human P0, and E. coli L10e; shown to be phosphorylated on serine 302	A[PAD]..[KYA]VV	44			Y				cytosolic large ribosomal subunit (sensu Eukaryota) (1e-04)		0.005	8
protein_40_YLR180W	2	SAM1:  S-adenosylmethionine synthetase, catalyzes transfer of the adenosyl group of ATP to the sulfur atom of methionine; one of two differentially regulated isozymes (Sam1p and Sam2p)	[LEA]T.E[TGE]	44	CP[LP]T.E[ST].C	GM_CSF PATTERN							0.009	10
protein_40_YLR180W	2	SAM1:  S-adenosylmethionine synthetase, catalyzes transfer of the adenosyl group of ATP to the sulfur atom of methionine; one of two differentially regulated isozymes (Sam1p and Sam2p)	FG[IE][NCE]	44									0.006	10
protein_40_YLL011W	2	SOF1:  Essential protein required for biogenesis of 40S (small) ribosomal subunit; has similarity to the beta subunit of trimeric G-proteins and the splicing factor Prp4p	E[DKL].[SHM]AL	44			Y				small nucleolar ribonucleoprotein complex (1e-07)		0.005	10
protein_40_YKL203C	2	TOR2:  PIK-related protein kinase and rapamycin target; subunit of TORC1, a complex that regulates growth in response to nutrients and TORC2, a complex that regulates cell-cycle dependent polarization of the actin cytoskeleton; involved in meiosis	[HCW]K..V[VCW]	44			Y				plasma membrane (1e-04)	Y	0.005	7
protein_40_YKL104C	2	GFA1:  Glutamine-fructose-6-phosphate amidotransferase, catalyzes the formation of glucosamine-6-P and glutamate from fructose-6-P and glutamine in the first step of chitin biosynthesis	A..A[FDN]	44	A.AA.VP....VP........P	PLU-1 transcription factor binding motif in BF-1 and PAX9					amino acid metabolism (1e-04)	Y	0.008	10
protein_40_YJR022W	2	LSM8:  Lsm (Like Sm) protein; forms heteroheptameric complex (with Lsm2p, Lsm3p, Lsm4p, Lsm5p, Lsm6p, and Lsm7p) that is part of spliceosomal U6 snRNP and is also implicated in processing of pre-tRNA, pre-snoRNA, and pre-rRNA	DI..[LCN][EPS]D	44									0.005	9
protein_40_YJL081C	2	ARP4:  Nuclear actin-related protein involved in chromatin remodeling, component of chromatin-remodeling enzyme complexes	SE.[KVD][EQG]N	44	[ST]E	G protein-coupled receptor kinase 1 substrate motif					nucleoplasm part (0.001)		0.005	9
protein_40_YIL095W	2	PRK1:  Protein serine/threonine kinase; regulates the organization and function of the actin cytoskeleton through the phosphorylation of the Pan1p-Sla1p-End3p protein complex	S[PD]SR[SG]	44	SP	ERK1, ERK2 Kinase substrate motif							0.005	8
protein_40_YHR196W	2	UTP9:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	M[SCT]..[SPG]SL	44	RSSLHL	Motif in beta-arrestin 2 for interaction with Jnk3					small nucleolar ribonucleoprotein complex (1e-07)		0.005	9
protein_40_YHR196W	2	UTP9:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	VS.L[SMT][DWF]	44							snoRNA binding (1e-09)		0.005	9
protein_40_YHR135C	2	YCK1:  Palmitoylated, plasma membrane-bound casein kinase I isoform; shares redundant functions with Yck2p in morphogenesis, proper septin assembly, endocytic trafficking; provides an essential function overlapping with that of Yck2p	SA[NDH]	44	[EDA][DE][ED][ED]S[EDA][DEA][ED][ED]	Casein Kinase II substrate motif							0.008	10
protein_40_YHR041C	2	SRB2:  Subunit of the RNA polymerase II mediator complex; associates with core polymerase subunits to form the RNA polymerase II holoenzyme; general transcription factor involved in telomere maintenance	[NFP]N..[QAL]QQ	44							general RNA polymerase II transcription factor activity (1e-05)		0.005	9
protein_40_YHR041C	2	SRB2:  Subunit of the RNA polymerase II mediator complex; associates with core polymerase subunits to form the RNA polymerase II holoenzyme; general transcription factor involved in telomere maintenance	E[EMR]..SL[LN]	44							general RNA polymerase II transcription factor activity (1e-09)		0.005	8
protein_40_YGR128C	2	UTP8:  Nucleolar protein required for export of tRNAs from the nucleus; also copurifies with the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	D[TAK]LL[TA]	44	LLTP	WD40 domain of Cdc4 binding motif, Thr must be phosphorylated, CPD motif					small nucleolar ribonucleoprotein complex (1e-07)		0.005	9
protein_40_YGR086C	2	PIL1:  Primary component of eisosomes, which are large immobile cell cortex structures associated with endocytosis; null mutants show activation of Pkc1p/Ypk1p stress resistance pathways; detected in phosphorylated state in mitochondria	[KNR]DDD[DVY]	44	DDDD..S	Casein kinase 1 phosphorylation motif							0.006	9
protein_40_YGL106W	2	MLC1:  Essential light chain for Myo1p, light chain for Myo2p; stabilizes Myo2p by binding to the neck region; interacts with Myo1p, Iqg1p, and Myo2p to coordinate formation and contraction of the actomyosin ring with targeted membrane deposition	L[LWF]..[AVH]EK	44									0.005	8
protein_40_YGL076C	2	RPL7A:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl7Bp and has similarity to E. coli L30 and rat L7 ribosomal proteins; contains a conserved C-terminal Nucleic acid Binding Domain (NDB2)	LR..[RTA][LYA]K	44	LRT	LKB1 Kinase substrate motif					cytosolic ribosome (sensu Eukaryota) (1e-04)		0.005	8
protein_40_YGL048C	2	RPT6:  One of six ATPases of the 19S regulatory particle of the 26S proteasome involved in the degradation of ubiquitinated substrates; bound by ubiquitin-protein ligases Ubr1p and Ufd4p; localized mainly to the nucleus throughout the cell cycle	[LK]R[DCH]F	44	KR	CLV_PCSK_PC1ET2_1					proteasome complex (sensu Eukaryota) (1e-04)		0.006	10
protein_40_YGL019W	2	CKB1:  Beta regulatory subunit of casein kinase 2, a Ser/Thr protein kinase with roles in cell growth and proliferation; the holoenzyme also contains CKA1, CKA2 and CKB2, the many substrates include transcription factors and all RNA polymerases	[SDY]D[SEM]D	44							RNA elongation from RNA polymerase II promoter (1e-11)		0.008	10
protein_40_YER177W	2	BMH1:  14-3-3 protein, major isoform; controls proteome at post-transcriptional level, binds proteins and DNA, involved in regulation of many processes including exocytosis, vesicle transport, Ras/MAPK signaling, and rapamycin-sensitive signaling	N[LVS]S[LSK]N	44	S[ST]	MDC1 BRCT domain binding motif							0.006	10
protein_40_YER133W	2	GLC7:  Catalytic subunit of type 1 serine/threonine protein phosphatase, involved in many processes including glycogen metabolism, sporulation, and mitosis; interacts with multiple regulatory subunits; predominantly isolated with Sds22p	[KSQ]K[SKE]K	44	KKKKKK[ST]	TGF beta receptor kinase substrate motif							0.008	10
protein_40_YER110C	2	KAP123:  Karyopherin beta, mediates nuclear import of ribosomal proteins prior to assembly into ribosomes and import of histones H3 and H4; localizes to the nuclear pore, nucleus, and cytoplasm; exhibits genetic interactions with RAI1	[EQK]E.GK[KAF]	44	G[KR][KR]	Amidation after cleavage after Gly (must be in secretory pathway)							0.005	8
protein_40_YER110C	2	KAP123:  Karyopherin beta, mediates nuclear import of ribosomal proteins prior to assembly into ribosomes and import of histones H3 and H4; localizes to the nuclear pore, nucleus, and cytoplasm; exhibits genetic interactions with RAI1	L[FSR].AK[PAQ]	44							snRNP protein import into nucleus (0.01)		0.005	10
protein_40_YER036C	2	ARB1:  ATPase of the ATP-binding cassette (ABC) family involved in 40S and 60S ribosome biogenesis, has similarity to Gcn20p; shuttles from nucleus to cytoplasm, physically interacts with Tif6p, Lsg1p	KK[LTW][RQA]A	44	KKKLPATGDYMNMSPVGD	Insulin receptor kinase substrate motif	Y						0.005	9
protein_40_YDR447C	2	RPS17B:  Ribosomal protein 51 (rp51) of the small (40s) subunit; nearly identical to Rps17Ap and has similarity to rat S17 ribosomal protein	AK[AVK][KAR]V	44			Y				ribonucleoprotein complex (1e-04)		0.005	8
protein_40_YDR145W	2	TAF12:  Subunit (61/68 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation and in chromatin modification, similar to histone H2A	[LQS][NSC]EC	44	[ST]E	G protein-coupled receptor kinase 1 substrate motif					SAGA complex (0.01)		0.005	8
protein_40_YDL213C	2	NOP6:  Putative RNA-binding protein implicated in ribosome biogenesis; contains an RNA recognition motif (RRM) and has similarity to hydrophilins; NOP6 may be a fungal-specific gene as no homologs have been yet identified in higher eukaryotes	D[DQI]E[EVL]	44	S[LW]LD[DE]EL[LM]	TRG_LysEnd_GGAAcLL_2					nucleolus (1e-18)	Y	0.008	10
protein_40_YDL147W	2	RPN5:  Essential, non-ATPase regulatory subunit of the 26S proteasome lid, similar to mammalian p55 subunit and to another S. cerevisiae regulatory subunit, Rpn7p	I[LS].K[VKY]V	44									0.005	7
protein_40_YDL055C	2	PSA1:  GDP-mannose pyrophosphorylase (mannose-1-phosphate guanyltransferase), synthesizes GDP-mannose from GTP and mannose-1-phosphate in cell wall biosynthesis; required for normal cell wall structure	[IKW]V[KDR]A	44							cytosol (0.001)	Y	0.009	10
protein_40_YDL055C	2	PSA1:  GDP-mannose pyrophosphorylase (mannose-1-phosphate guanyltransferase), synthesizes GDP-mannose from GTP and mannose-1-phosphate in cell wall biosynthesis; required for normal cell wall structure	V[AK].[EGD]AA	44									0.005	8
protein_40_YCR086W	2	CSM1:  Nucleolar protein that forms a complex with Lrs4p which binds Mam1p at kinetochores during meiosis I to mediate accurate chromosome segregation, may be involved in premeiotic DNA replication; possible role in telomere maintenance	[GSV]G..G[SDG]A	44									0.005	8
protein_40_YCL059C	2	KRR1:  Essential nucleolar protein required for the synthesis of 18S rRNA and for the assembly of 40S ribosomal subunit	S[GK]AK[GND]	44							35S primary transcript processing (0.01)		0.005	9
protein_40_YAR007C	2	RFA1:  Subunit of heterotrimeric Replication Protein A (RPA), which is a highly conserved single-stranded DNA binding protein involved in DNA replication, repair, and recombination	K[VNK]V[DTF]S	44			Y						0.005	8
oshea_cytoplasm	2	oshea_cytoplasm	F[FLR]F[FLV]	44	EE[DE]IYFFFF	CSK kinase substrate motif							0.008	10
matsuyama_Spindle_or_SPB	2	matsuyama_Spindle_or_SPB	[SPT]L[LNS]D	44	LLDLL	Clathrin binding motif in AP1					spindle (1e-82)		0.011	10
matsuyama_Spindle_or_SPB	2	matsuyama_Spindle_or_SPB	SK..[SEH]	44	K..[ST]	PKA kinase substrate motif					spindle (1e-16)		0.011	10
matsuyama_Cytosol	2	matsuyama_Cytosol	D..[GSV]N	44	DDDD..S	Casein kinase 1 phosphorylation motif					cell septum (0.001)	Y	0.011	10
matsuyama_Cytosol	2	matsuyama_Cytosol	L.K[VEH]	44	G[SA]LNK	GDP-mannose binding motif in transporter					ATP binding (1e-08)	Y	0.011	10
genetic_YLR262C	2	YPT6: GTPase, Ras-like GTP binding protein involved in the secretory pathway, required for fusion of endosome-derived vesicles with the late Golgi, maturation of the vacuolar carboxypeptidase Y; has similarity to the human GTPase, Rab6	Q.[SED]Q	44	[ST]Q	ATM kinase phosphorylation site					DNA metabolism (1e-08)	Y	0.008	10
yeast-299_GO-0005730	2	nucleolus	[HG]R.G[RFC]	43	[AG]R	Protease matriptase protease site		DEAD	1.E-19	-2.5	nucleolus (1e-30)		0.010	10
matsuyama_Cytosol	2	matsuyama_Cytosol	V[ANP]...S	43	VP	Interleukin converting enzyme protease		Pkinase	1.E-05	-2.3	ATP binding (1e-08)		0.010	10
protein_40_YHR066W	2	SSF1:  Constituent of 66S pre-ribosomal particles, required for ribosomal large subunit maturation; functionally redundant with Ssf2p; member of the Brix family	E[DEQ]..[EGK]E	43				Brix	1.E-03	-2.2	nucleolus (1e-25)		0.008	10
yeast-235_GO-0000278	2	mitotic cell cycle	S..E[DNEQ]	43	QPS..E	Phosphorylation motif in alpha 3A, alpha 6A, alpha 7A Integrin tails		HEAT	1.E-02	-1.8	mitotic cell cycle (1e-20)		0.009	10
protein_40_YPL126W	2	NAN1:  U3 snoRNP protein, component of the small (ribosomal) subunit (SSU) processosome containing U3 snoRNA; required for the biogenesis of18S rRNA	K..E[RDQ]	43				WD40	1.E-05	-1.8	small nucleolar ribonucleoprotein complex (1e-35)		0.008	10
protein_40_YGL111W	2	NSA1:  Constituent of 66S pre-ribosomal particles, involved in 60S ribosomal subunit biogenesis	[EIT]EE[EGY]	43	EEEYF	EGFR kinase phosphorylation site (peptide screen)		DEAD	1.E-02	-1.6	nucleolus (1e-24)	Y	0.008	10
protein_40_YNL272C	2	SEC2:  Guanyl-nucleotide exchange factor for the small G-protein Sec4p, located on cytoplasmic vesicles; essential for post-Golgi vesicle transport	[NWY]DH[LHA]	43				Pkinase	1.E-07	-1.5	protein kinase activity (1e-05)		0.005	9
yeast-217_GO-0007046	2	ribosome biogenesis	[TFD][GLS]SGK	43	SG.G	Glycosaminoglycan attachment site	Y	Helicase_C	1.E-18	-1.3	ribosome biogenesis (1e-24)	Y	0.010	10
protein_40_YDR356W	2	SPC110:  Inner plaque spindle pole body (SPB) component, ortholog of human kendrin; involved in connecting nuclear microtubules to SPB; interacts with Tub4p-complex and calmodulin; phosphorylated by Mps1p in cell cycle-dependent manner	L[ST]..SP[KNR]	43	SP	ERK1, ERK2 Kinase substrate motif		Kinesin	1.E-02	-1.2	spindle pole body (0.001)	Y	0.005	9
yeast-200_GO-0006519	2	amino acid and derivative metabolism	A.[IVE]L	43	[FHYM].A[AV].[VAC]L[MV].[MI]	LIG_Sin3_2		tRNA-synt_2b	1.E-02	-1.1	amino acid and derivative metabolism (1e-15)	Y	0.009	10
protein_40_YHR066W	2	SSF1:  Constituent of 66S pre-ribosomal particles, required for ribosomal large subunit maturation; functionally redundant with Ssf2p; member of the Brix family	G[RH]TA[RQ]	43				DEAD	1.E-05	-1.1	ATP-dependent RNA helicase activity (1e-06)		0.005	8
protein_40_YDR388W	2	RVS167:  Actin-associated protein, subunit of a complex (Rvs161p-Rvs167p) involved in regulation of actin cytoskeleton, endocytosis, and viability following starvation or osmotic stress; homolog of mammalian amphiphysin	K[AIS]E	43	[VILMAFP]K.E	MOD_SUMO		HEAT	1.E-02	-0.9	cell cortex (1e-06)		0.008	10
yeast-631_GO-0050794	2	regulation of cellular process	T..[DNQ]E	43	PT..[DI]	FHA binding motif		Zn_clus	1.E-04	-0.8	regulation of metabolism (1e-11)		0.009	10
yeast-630_GO-0051244	2	regulation of cellular physiological process	T..[DNQ]E	43	PT..[DI]	FHA binding motif		Zn_clus	1.E-04	-0.8	regulation of metabolism (1e-11)		0.009	10
yeast-235_GO-0009653	2	morphogenesis	[PES]A..[PHY]P	43				Pkinase	1.E-03	-0.8	cellular morphogenesis (1e-36)		0.009	10
yeast-235_GO-0000902	2	cellular morphogenesis	[PES]A..[PHY]P	43				Pkinase	1.E-03	-0.8	cellular morphogenesis (1e-36)		0.009	10
protein_40_YCL059C	2	KRR1:  Essential nucleolar protein required for the synthesis of 18S rRNA and for the assembly of 40S ribosomal subunit	T[GRH]S[GIF]K	43				Helicase_C	1.E-06	-0.8	cytoplasm organization and biogenesis (1e-06)		0.005	8
yeast-244_GO-0000279	2	M phase	E[KDI]L	43	DLL	Binding motif for clathrin heavy chain ear		MutS_III	1.E-05	-0.6	M phase (1e-22)		0.009	10
yeast-752_GO-0016787	2	hydrolase activity	R.V	43	[RK].V.F	PPI binding sites		UCH	1.E-09	-0.5	hydrolase activity, acting on acid anhydrides (1e-10)	Y	0.009	10
protein_40_YDL014W	2	NOP1:  Nucleolar protein, component of the small subunit processome complex, which is required for processing of pre-18S rRNA; has similarity to mammalian fibrillarin	K[AQT]...L	43				Helicase_C	1.E-03	-0.3	nucleolus (1e-43)		0.008	10
protein_40_YER082C	2	UTP7:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	A.[LGK]V	43	RALAHGVRVL	Mitochondrial targetting motif in hepititis C core protein		WD40	1.E-02	-0.2	small nucleolar ribonucleoprotein complex (1e-21)		0.008	10
protein_40_YOL069W	2	NUF2:  Component of the evolutionarily conserved kinetochore-associated Ndc80 complex (Ndc80p-Nuf2p-Spc24p-Spc25p); involved in chromosome segregation, spindle checkpoint activity and kinetochore clustering	SD..[NM]K[ELQ]	43	SD.E	Casein kinase II substrate motif		Kinesin	1.E-02	0.2	spindle (1e-05)		0.005	8
protein_40_YDL013W	2	SLX5:  Subunit of the Slx5-Slx8 substrate-specific ubiquitin ligase complex; stimulated by prior attachment of SUMO to the substrate	[SNT][SYQ]..KSR	43				Pkinase	1.E-03	0.5	protein kinase activity (0.01)	Y	0.005	8
oshea_bud_neck	2	oshea_bud_neck	S..[EQY]L	43	S..[ED]	Casein kinase II substrate motif		RhoGAP	1.E-06	0.7	site of polarized growth (1e-62)		0.008	10
protein_40_YPL153C	2	RAD53:  Protein kinase, required for cell-cycle arrest in response to DNA damage; activated by trans autophosphorylation when interacting with hyperphosphorylated Rad9p; also interacts with ARS1 and plays a role in initiation of DNA replication	E[LQN]..N	43				Septin	1.E-02	1	cell cortex part (1e-04)		0.008	10
yeast-1721_GO-0016043	2	cell organization and biogenesis	N.T[ANS]	43	N.[TS]	N-linked glycosylation site		HEAT	1.E-02	1.2	chromosome organization and biogenesis (1e-45)		0.009	10
protein_40_YBR159W	2	IFA38: Microsomal beta-keto-reductase; contains oleate response element (ORE) sequence in the promoter region; mutants exhibit reduced VLCFA synthesis, accumulate high levels of dihydrosphingosine, phytosphingosine and medium-chain ceramides	F..[ILMV]G	43				MFS_1	1.E-07	1.2	transporter activity (1e-11)	Y	0.008	10
yeast-980_GO-0051179	2	localization	LF[VGR][SIG]	43	LFG	Protease Papain substrate, a prototype cysteine proteinase		MFS_1	1.E-02	1.4	cellular localization (1e-21)	Y	0.009	10
protein_40_YPR137W	2	RRP9:  Protein involved in pre-rRNA processing, associated with U3 snRNP; component of small ribosomal subunit (SSU) processosome; ortholog of the human U3-55k protein	D[GDP]..K[VYW]	43			Y	WD40	1.E-04	1.4	rRNA processing (1e-12)		0.007	10
protein_40_YBR106W	2	PHO88:  Probable membrane protein, involved in phosphate transport; pho88 pho86 double null mutant exhibits enhanced synthesis of repressible acid phosphatase at high inorganic phosphate concentrations	G[LFI].[VFW]G	43				Sugar_tr	1.E-03	1.4	transporter activity (1e-10)		0.008	10
protein_40_YNL031C	2	HHT2:  One of two identical histone H3 proteins (see also HHT1); core histone required for chromatin assembly, involved in heterochromatin-mediated telomeric and HM silencing; regulated by acetylation, methylation, and mitotic phosphorylation	AI..D[DNE][EFI]	43				Histone	1.E-04	1.5	nuclear chromatin (0.001)		0.005	8
protein_40_YBR106W	2	PHO88:  Probable membrane protein, involved in phosphate transport; pho88 pho86 double null mutant exhibits enhanced synthesis of repressible acid phosphatase at high inorganic phosphate concentrations	I[FLG]..L[AGM]	43	L...I...[IL]	Corepressor nuclear box motif binds to nuclear receptors		MFS_1	1.E-06	1.6	transporter activity (1e-11)		0.008	10
protein_40_YHR030C	2	SLT2:  Serine/threonine MAP kinase involved in regulating the maintenance of cell wall integrity and progression through the cell cycle; regulated by the PKC1-mediated signaling pathway	H[RYE].I[KFA]	43				Pkinase	1.E-05	3	kinase activity (0.001)		0.006	9
yeast-685_GO-0016740	2	transferase activity	PE..[LIF][LGR]	43				Pkinase	1.E-27	3.3	kinase activity (1e-36)	Y	0.009	10
protein_40_YNL061W	2	NOP2:  Probable RNA m(5)C methyltransferase, essential for processing and maturation of 27S pre-rRNA and large ribosomal subunit biogenesis; localized to the nucleolus; constituent of 66S pre-ribosomal particles	[PNR][TH].IQ	43	GIQVD	dynein light chain LC8 interacting motif -alternative		DEAD	1.E-04	3.6	cytoplasm organization and biogenesis (1e-09)		0.006	9
yeast-685_GO-0016740	2	transferase activity	[GAH]L.Y[LMC]H	43	Y[VLTFIC]	LIG_SH2_STAT5		Pkinase	1.E-24	4.7	protein kinase activity (1e-23)	Y	0.010	10
yeast-462_GO-0019222	2	regulation of metabolism	KR[KRY]	43	KR	CLV_PCSK_PC1ET2_1		Zn_clus	1.E-07	4.8	regulation of metabolism (1e-22)		0.009	10
yeast-410_GO-0007049	2	cell cycle	H..[ILF]KP	43				Pkinase	1.E-27	4.8	cell cycle (1e-31)		0.009	10
yeast-462_GO-0019222	2	regulation of metabolism	[ASW][CDI]..CR	43	C..C	Motif on TIM mitochondrial translocation proteins		Zn_clus	1.E-26	19.1	regulation of metabolism (1e-26)		0.010	10
yeast-437_GO-0044429	2	mitochondrial part	T.[SFQ]S	43	T..[SA]	FHA of KAPP binding motif, Thr must be phosphorylated							0.009	10
yeast-341_GO-0045449	2	regulation of transcription	[RI]KFLL	43							regulation of transcription, DNA-dependent (1e-05)		0.006	8
yeast-324_GO-0030528	2	transcription regulator activity	S[ENT][EGM]E	43	S[DE][DE]E	BARD1 BRCT domain binding motif					transcription regulator activity (1e-84)	Y	0.009	10
yeast-251_GO-0005886	2	plasma membrane	[IGH]FG[LTQ]	43	FGRA	DNA binding motif in ssDNA binding proteins					plasma membrane (1e-40)		0.010	9
yeast-235_GO-0009653	2	morphogenesis	T[VRD]..A[AW]T	43							cellular morphogenesis (1e-05)		0.006	9
yeast-235_GO-0000902	2	cellular morphogenesis	T[VRD]..A[AW]T	43							cellular morphogenesis (1e-05)		0.006	9
yeast-217_GO-0007046	2	ribosome biogenesis	EK.N[AMH][LFP]	43	KEN	LIG_APCC_KENbox_2					ribosome biogenesis (1e-09)		0.006	7
yeast-216_GO-0006325	2	establishment and/or maintenance of chromatin architecture	[QMW]Q..[SLK]K	43							establishment and/or maintenance of chromatin architecture (1e-42)	Y	0.010	10
yeast-216_GO-0006323	2	DNA packaging	[QMW]Q..[SLK]K	43							establishment and/or maintenance of chromatin architecture (1e-42)	Y	0.010	10
protein_40_YPR144C	2	NOC4:  Nucleolar protein, forms a complex with Nop14p that mediates maturation and nuclear export of 40S ribosomal subunits	[LMR]ISI[LDF]	43	RR.SI	PKA kinase phosphorylation site (peptide screen)					snoRNA binding (1e-04)		0.005	8
protein_40_YPR144C	2	NOC4:  Nucleolar protein, forms a complex with Nop14p that mediates maturation and nuclear export of 40S ribosomal subunits	D[TAK]LL[TAI]	43	LLTP	WD40 domain of Cdc4 binding motif, Thr must be phosphorylated, CPD motif					small nucleolar ribonucleoprotein complex (1e-09)	Y	0.005	9
protein_40_YPL213W	2	LEA1:  Component of U2 snRNP; disruption causes reduced U2 snRNP levels; physically interacts with Msl1p; invovled in telomere maintenance; putative homolog of human U2A' snRNP protein	[DQF]P[SRV]LN	43	P[ST]	DNA dependent Protein kinase substrate motif					spliceosome (1e-09)		0.005	8
protein_40_YPL198W	2	RPL7B:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl7Ap and has similarity to E. coli L30 and rat L7 ribosomal proteins; contains a conserved C-terminal Nucleic acid Binding Domain (NDB2)	[AKM]R...K	43	R...K..R	Motif in Ebola virus that eliminates IFN-beta production	Y				cytosolic ribosome (sensu Eukaryota) (1e-14)		0.008	10
protein_40_YPL093W	2	NOG1:  Putative GTPase that associates with free 60S ribosomal subunits in the nucleolus and is required for 60S ribosomal subunit biogenesis; constituent of 66S pre-ribosomal particles; member of the ODN family of nucleolar G-proteins	K[KLV]..G[IK]	43							cytoplasm organization and biogenesis (1e-11)		0.008	10
protein_40_YNR054C	2	ESF2:  Essential nucleolar protein involved in pre-18S rRNA processing; component of the small subunit (SSU) processome; has sequence similarity to mABT1, a mouse transcription activator	[EAM]E.[EQY]K	43			Y				nucleolus (1e-14)	Y	0.008	10
protein_40_YNR054C	2	ESF2:  Essential nucleolar protein involved in pre-18S rRNA processing; component of the small subunit (SSU) processome; has sequence similarity to mABT1, a mouse transcription activator	A[FCM]..[KY]I	43							nucleolus (1e-07)		0.005	9
protein_40_YNL118C	2	DCP2:  Catalytic subunit of the Dcp1p-Dcp2p decapping enzyme complex, which removes the 5' cap structure from mRNAs prior to their degradation; member of the Nudix hydrolase family	D[HCF].[FPN]Q	43							cytoplasmic mRNA processing body (0.001)		0.005	8
protein_40_YMR047C	2	NUP116:  Subunit of the nuclear pore complex (NPC) that is localized to both sides of the pore; contains a repetitive GLFG motif that interacts with mRNA export factor Mex67p and with karyopherin Kap95p; homologous to Nup100p	R[SLP].S[KWR]K	43	KKR..S	Phosphorylation site for MLCK	Y				nuclear pore organization and biogenesis (1e-04)	Y	0.004	9
protein_40_YML085C	2	TUB1:  Alpha-tubulin; associates with beta-tubulin (Tub2p) to form tubulin dimer, which polymerizes to form microtubules	[KG]K.S[SYQ]D	43	RKK.[ST]	ZIP kinase phosphorylation motif						Y	0.005	9
protein_40_YML069W	2	POB3:  Subunit of the heterodimeric FACT complex (Spt16p-Pob3p), which facilitates RNA Pol II transcription elongation through nucleosomes by destabilizing and then reassembling nucleosome structure; interacts with DNA polymerase alpha (Pol1p)	[SWH]R[VC]E	43			Y						0.005	8
protein_40_YML048W	2	GSF2:  ER localized integral membrane protein that may promote secretion of certain hexose transporters, including Gal2p; involved in glucose-dependent repression	TL[GHI][TAN]G	43	PLTLP	RAF1 kinase substrate motif						Y	0.005	7
protein_40_YML007W	2	YAP1:  Basic leucine zipper (bZIP) transcription factor required for oxidative stress tolerance; activated by H2O2 through the multistep formation of disulfide bonds and transit from the cytoplasm to the nucleus; mediates resistance to cadmium	TT[SNT]V[NMQ]	43							RNA polymerase II transcription mediator activity (0.01)		0.005	9
protein_40_YLR180W	2	SAM1:  S-adenosylmethionine synthetase, catalyzes transfer of the adenosyl group of ATP to the sulfur atom of methionine; one of two differentially regulated isozymes (Sam1p and Sam2p)	K[ITH]SI[KGQ]	43	RKK.[ST]	ZIP kinase phosphorylation motif							0.005	8
protein_40_YLL008W	2	DRS1:  Nucleolar DEAD-box protein required for ribosome assembly and function, including synthesis of 60S ribosomal subunits; constituent of 66S pre-ribosomal particles	RTL[LNS][ITY]	43	R.L	Cyclin A motif that binds cdk2 complexes	Y				ribosome biogenesis (0.01)		0.005	9
protein_40_YKR026C	2	GCN3:  Alpha subunit of the translation initiation factor eIF2B, the guanine-nucleotide exchange factor for eIF2; activity subsequently regulated by phosphorylated eIF2; first identified as a positive regulator of GCN4 expression	AG[LCA][DYM]	43	G[GA]G[ASC][FY]S.K[DE]	ADOMET_SYNTHETASE_2 PATTERN					eukaryotic translation initiation factor 2B complex (0.001)		0.006	7
protein_40_YKL203C	2	TOR2:  PIK-related protein kinase and rapamycin target; subunit of TORC1, a complex that regulates growth in response to nutrients and TORC2, a complex that regulates cell-cycle dependent polarization of the actin cytoskeleton; involved in meiosis	I[YMI]S[ARD]L	43	IY	cFGR and Csk kinase phosphorylation site (peptide screen)						Y	0.005	10
protein_40_YJR066W	2	TOR1:  PIK-related protein kinase and rapamycin target; subunit of TORC1, a complex that controls growth in response to nutrients by regulating translation, transcription, ribosome biogenesis, nutrient transport and autophagy; involved in meiosis	AS..[SEG]	43	YASI	SHP2 phosphatase substrate motif					plasma membrane (1e-20)	Y	0.008	10
protein_40_YJR002W	2	MPP10:  Component of the SSU processome, which is required for pre-18S rRNA processing, interacts with and controls the stability of Imp3p and Imp4p, essential for viability; similar to human Mpp10p	[AYN]L[LKG]TI	43	GTALL	Receptor recycling motif					small nucleolar ribonucleoprotein complex (0.001)		0.005	9
protein_40_YJL138C	2	TIF2:  Translation initiation factor eIF4A, identical to Tif1p; DEA(D/H)-box RNA helicase that couples ATPase activity to RNA binding and unwinding; forms a dumbbell structure of two compact domains connected by a linker; interacts with eIF4G	K[EID][FLG]EG	43	IEGR	Protease Protease Factor X a						Y	0.005	7
protein_40_YJL092W	2	SRS2:  DNA helicase and DNA-dependent ATPase involved in DNA repair, needed for proper timing of commitment to meiotic recombination and transition from Meiosis I to II; affects genome stability by suppressing unscheduled homologous recombination	SS[SDG][PRM]F	43									0.005	9
protein_40_YJL081C	2	ARP4:  Nuclear actin-related protein involved in chromatin remodeling, component of chromatin-remodeling enzyme complexes	DQ.[VIR][TRF]	43							chromatin remodeling complex (1e-05)		0.005	8
protein_40_YJL074C	2	SMC3:  Subunit of the multiprotein cohesin complex required for sister chromatid cohesion in mitotic cells; also required, with Rec8p, for cohesion and recombination during meiosis; phylogenetically conserved SMC chromosomal ATPase family member	Q[QYS].[VR]N	43							cohesin complex (1e-06)		0.006	9
protein_40_YIL144W	2	TID3:  Component of the evolutionarily conserved kinetochore-associated Ndc80 complex (Ndc80p-Nuf2p-Spc24p-Spc25p); conserved coiled-coil protein involved in chromosome segregation, spindle checkpoint activity, kinetochore assembly and clustering	L[ETS].[EAQ]TE	43	[ST]E	G protein-coupled receptor kinase 1 substrate motif							0.004	9
protein_40_YIL095W	2	PRK1:  Protein serine/threonine kinase; regulates the organization and function of the actin cytoskeleton through the phosphorylation of the Pan1p-Sla1p-End3p protein complex	EK..L[EGY][DQY]	43									0.005	10
protein_40_YIL061C	2	SNP1:  Component of U1 snRNP required for mRNA splicing via spliceosome; may interact with poly(A) polymerase to regulate polyadenylation; homolog of human U1 70K protein	L[REF][LEN]PF	43	NPF	EH EF hand domain binding motif, Class I							0.005	8
protein_40_YHR197W	2	RIX1:  Essential component of the Rix1 complex (Rix1p, Ipi1p, Ipi3p) that is required for processing of ITS2 sequences from 35S pre-rRNA; Rix1 complex associates with Mdn1p in pre-60S ribosomal particles	[RSC]G..I[PY]	43	IY	cFGR and Csk kinase phosphorylation site (peptide screen)	Y				ribosome biogenesis (1e-04)		0.005	9
protein_40_YHR052W	2	CIC1:  Essential protein that interacts with proteasome components and has a potential role in proteasome substrate specificity; also copurifies with 66S pre-ribosomal particles	[GQV]K[IAV]LG	43							rRNA processing (0.001)		0.005	8
protein_40_YHR052W	2	CIC1:  Essential protein that interacts with proteasome components and has a potential role in proteasome substrate specificity; also copurifies with 66S pre-ribosomal particles	E[ETN]E[EWM]	43	[ST]E	G protein-coupled receptor kinase 1 substrate motif					cytoplasm organization and biogenesis (1e-30)		0.008	10
protein_40_YGR218W	2	CRM1:  Major karyopherin, involved in export of proteins, RNAs, and ribosomal subunits from the nucleus	[SN]GG[LT]F	43	GGQ	N-methylation motif in E. coli, Gln residue in methylated, mimics CCA motif at the end of tRNA molecule	Y				snRNP protein import into nucleus (1e-08)		0.005	7
protein_40_YGR086C	2	PIL1:  Primary component of eisosomes, which are large immobile cell cortex structures associated with endocytosis; null mutants show activation of Pkc1p/Ypk1p stress resistance pathways; detected in phosphorylated state in mitochondria	[ECL]KLS[TKP]	43	S[ST]	MDC1 BRCT domain binding motif							0.005	10
protein_40_YGL195W	2	GCN1:  Positive regulator of the Gcn2p kinase activity, forms a complex with Gcn20p; proposed to stimulate Gcn2p activation by an uncharged tRNA	[ICK]T.D[AHM]	43									0.006	8
protein_40_YGL112C	2	TAF6:  Subunit (60 kDa) of TFIID and SAGA complexes, involved in transcription initiation of RNA polymerase II and in chromatin modification, similar to histone H4	[VRP]LE[YFQ]L	43	L..[LM]E	Sec24p	Y				SLIK (SAGA-like) complex (0.01)		0.005	8
protein_40_YGL051W	2	MST27:  Putative integral membrane protein, involved in vesicle formation; forms complex with Mst28p; member of DUP240 gene family; binds COPI and COPII vesicles	[YCM][GAW]RR	43	[AG]R	Protease matriptase protease site							0.004	7
protein_40_YFR052W	2	RPN12:  Subunit of the 19S regulatory particle of the 26S proteasome lid; synthetically lethal with RPT1, which is an ATPase component of the 19S regulatory particle; physically interacts with Nob1p and Rpn3p	[ST][AK]VAS	43									0.005	9
protein_40_YFR010W	2	UBP6:  Ubiquitin-specific protease situated in the base subcomplex of the 26S proteasome, releases free ubiquitin from branched polyubiquitin chains; deletion causes hypersensitivity to cycloheximide and other toxic compounds	DE[AGN]K[EW]	43	YDE[PDV]	SH2 ligand for Nck1 and Nck2 (Tyr must be phosphorylated)						Y	0.005	9
protein_40_YFL037W	2	TUB2:  Beta-tubulin; associates with alpha-tubulin (Tub1p and Tub3p) to form tubulin dimer, which polymerizes to form microtubules	[KW]Y..[TVA]F	43	Y..[LIV]	JAK2 autophosphorylation signal	Y					Y	0.005	9
protein_40_YER177W	2	BMH1:  14-3-3 protein, major isoform; controls proteome at post-transcriptional level, binds proteins and DNA, involved in regulation of many processes including exocytosis, vesicle transport, Ras/MAPK signaling, and rapamycin-sensitive signaling	[QLP]F[KAF]SK	43									0.005	9
protein_40_YER146W	2	LSM5:  Lsm (Like Sm) protein; part of heteroheptameric complexes (Lsm2p-7p and either Lsm1p or 8p): cytoplasmic Lsm1p complex involved in mRNA decay; nuclear Lsm8p complex part of U6 snRNP and possibly involved in processing tRNA, snoRNA, and rRNA	[RIA][DQT].ILT	43							U4/U6 x U5 tri-snRNP complex (0.01)		0.005	8
protein_40_YER133W	2	GLC7:  Catalytic subunit of type 1 serine/threonine protein phosphatase, involved in many processes including glycogen metabolism, sporulation, and mitosis; interacts with multiple regulatory subunits; predominantly isolated with Sds22p	EK..[RAS]A[LM]	43	K..[ST]	PKA kinase substrate motif							0.005	7
protein_40_YER133W	2	GLC7:  Catalytic subunit of type 1 serine/threonine protein phosphatase, involved in many processes including glycogen metabolism, sporulation, and mitosis; interacts with multiple regulatory subunits; predominantly isolated with Sds22p	KK..G[EIF][IYK]	43	RKK.[ST]	ZIP kinase phosphorylation motif							0.005	9
protein_40_YER102W	2	RPS8B:  Protein component of the small (40S) ribosomal subunit; identical to Rps8Ap and has similarity to rat S8 ribosomal protein	K[LID].A[KFV]R	43	[KR]R	CLV_PCSK_KEX2_1					ribonucleoprotein complex (1e-04)		0.005	10
protein_40_YDR303C	2	RSC3:  Component of the RSC chromatin remodeling complex; essential gene required for maintenance of proper ploidy and regulation of ribosomal protein genes and the cell wall/stress response; highly similar to Rsc30p	[SHK]II[NSK]N	43	SYII	RAD9 BRCT domain binding motif	Y				RSC complex (0.001)		0.005	10
protein_40_YDR145W	2	TAF12:  Subunit (61/68 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation and in chromatin modification, similar to histone H2A	[DRN]I[STW]M	43	WM	Substrate binding motif of barley alpha-amylase 1 (AMY1) enzyme					transcription from RNA polymerase II promoter (1e-05)		0.006	10
protein_40_YDR145W	2	TAF12:  Subunit (61/68 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation and in chromatin modification, similar to histone H2A	Q[QKR]Q[LST]	43							transcription factor complex (1e-14)	Y	0.009	10
protein_40_YDR091C	2	RLI1:  Essential iron-sulfur protein required for ribosome biogenesis and translation initiation; facilitates binding of a multifactor complex (MFC) of translation initiation factors to the small ribosomal subunit; predicted ABC family ATPase	AE..[DAW][DHA]	43							cytosolic ribosome (sensu Eukaryota) (1e-07)		0.007	10
protein_40_YDR060W	2	MAK21:  Constituent of 66S pre-ribosomal particles, required for large (60S) ribosomal subunit biogenesis; involved in nuclear export of pre-ribosomes; required for maintenance of dsRNA virus; homolog of human CAATT-binding protein	AR..[ARY]	43	[AG]R	Protease matriptase protease site					cytoplasm organization and biogenesis (1e-14)		0.008	10
protein_40_YDL185W	2	TFP1:  Vacuolar ATPase V1 domain subunit A containing the catalytic nucleotide binding sites; protein precursor undergoes self-catalyzed splicing to yield the extein Tfp1p and the intein Vde (PI-SceI), which is a site-specific endonuclease	E[LKH]..L[QKG]T	43	[IV]DLGT[ST].[SC]	HSP70_1 PATTERN							0.005	7
protein_40_YDL015C	2	TSC13:  Enoyl reductase that catalyzes the last step in each cycle of very long chain fatty acid elongation, localizes to the ER, highly enriched in a structure marking nuclear-vacuolar junctions, coimmunoprecipitates with elongases Fen1p and Sur4p	M[LMP].[LT]I	43									0.005	7
protein_40_YBR200W	2	BEM1:  Protein containing SH3-domains, involved in establishing cell polarity and morphogenesis; functions as a scaffold protein for complexes that include Cdc24p, Ste5p, Ste20p, and Rsr1p	DK.[QSA]L[DQV]	43			Y				cytokinesis, site selection (0.001)		0.004	10
protein_40_YBR017C	2	KAP104:  Transportin, cytosolic karyopherin beta 2 involved in delivery of heterogeneous nuclear ribonucleoproteins to the nucleoplasm, binds rg-nuclear localization signals on Nab2p and Hrp1p, plays a role in cell-cycle progression	SGG[LFT]F	43	[ED]GSG[DE]	Glycosaminoglycan attachment site					snRNP protein import into nucleus (1e-08)		0.005	8
oshea_spindle_pole	2	oshea_spindle_pole	EI..[LHY][KGQ]	43							microtubule cytoskeleton (1e-22)		0.009	10
matsuyama_Spindle_or_SPB	2	matsuyama_Spindle_or_SPB	D[MF]..[SFT]SG	43			Y				spindle (1e-05)		0.006	7
matsuyama_Spindle_or_SPB	2	matsuyama_Spindle_or_SPB	ENG[SPD][PAM]	43	GP	Protease TTP cleavage site					spindle (1e-09)	Y	0.008	10
matsuyama_Microtubule	2	matsuyama_Microtubule	KT..[KHM][DGK]L	43							microtubule cytoskeleton (1e-06)		0.006	9
matsuyama_Golgi	2	matsuyama_Golgi	I[VIF].[ICA]I	43							Golgi apparatus (1e-41)	Y	0.011	10
genetic_YLR200W	2	YKE2: Subunit of the heterohexameric Gim/prefoldin protein complex involved in the folding of alpha-tubulin, beta-tubulin, and actin	YF[NW]D[SYC]	43			Y						0.005	8
genetic_YGL058W	2	RAD6: Ubiquitin-conjugating enzyme (E2), involved in postreplication repair (with Rad18p), sporulation, telomere silencing, and ubiquitin-mediated N-end rule protein degradation (with Ubr1p)	E..[KQF]K	43							DNA metabolism (1e-15)	Y	0.008	10
genetic_YGL058W	2	RAD6: Ubiquitin-conjugating enzyme (E2), involved in postreplication repair (with Rad18p), sporulation, telomere silencing, and ubiquitin-mediated N-end rule protein degradation (with Ubr1p)	N.N	43							DNA metabolism (1e-25)		0.008	10
genetic_YEL003W	2	GIM4: Subunit of the heterohexameric cochaperone prefoldin complex which binds specifically to cytosolic chaperonin and transfers target proteins to it	E[LNQ]E	43	KEN	LIG_APCC_KENbox_2					establishment of organelle localization (1e-07)	Y	0.008	10
genetic_YAL024C	2	LTE1: Putative GDP/GTP exchange factor required for mitotic exit at low temperatures; acts as a guanine nucleotide exchange factor (GEF) for Tem1p, which is a key regulator of mitotic exit; physically associates with Ras2p-GTP	S.[PQH]S	43	SGHSL	14-3-3-zeta binding motif in platelet adhesion receptor, glycoprotein (GP) Ib-IX					cell cycle (1e-20)		0.008	10
protein_40_YBR160W	2	CDC28:  Catalytic subunit of the main cell cycle cyclin-dependent kinase (CDK); alternately associates with G1 cyclins (CLNs) and G2/M cyclins (CLBs) which direct the CDK to specific substrates	V.[KNY]R	43				Pkinase	1.E-02	-0.2	cell cycle (1e-06)		0.008	10
protein_40_YDL153C	2	SAS10:  Component of the small (ribosomal) subunit (SSU) processosome required for pre-18S rRNa processing; essential nucleolar protein that, when overproduced, disrupts silencing	PR[TNG][TFH]	42	LVPRG	Protease Thrombin		Pkinase	1.E-09	-1.7	protein kinase activity (1e-09)	Y	0.005	8
protein_40_YLR029C	2	RPL15A:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl15Bp and has similarity to rat L15 ribosomal protein; binds to 5.8 S rRNA	[VLD][AQ]..GLD	42	[AC]GL.FPV	HISTONE_H2A PATTERN		DEAD	1.E-05	-1.4	RNA helicase activity (1e-04)		0.005	9
protein_40_YDR060W	2	MAK21:  Constituent of 66S pre-ribosomal particles, required for large (60S) ribosomal subunit biogenesis; involved in nuclear export of pre-ribosomes; required for maintenance of dsRNA virus; homolog of human CAATT-binding protein	G[RQY][TMK]A	42	G[KR][KR]	Amidation after cleavage after Gly (must be in secretory pathway)		DEAD	1.E-05	-1.4	ATP-dependent RNA helicase activity (1e-06)		0.007	10
yeast-376_GO-0019219	2	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism	S..[TQE]T	42	S..[ST]	Casein Kinase I consensus phosphorylation site (N-term Ser must first be phosphorylated)		Zn_clus	1.E-10	-1.2	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism (1e-20)	Y	0.009	10
protein_40_YPL043W	2	NOP4:  Nucleolar protein, essential for processing and maturation of 27S pre-rRNA and large ribosomal subunit biogenesis; constituent of 66S pre-ribosomal particles; contains four RNA recognition motifs (RRMs)	[HA]R..R[TI]A	42	R.[RK]R	CLV_PCSK_FUR_1		DEAD	1.E-05	-1.2	ATP-dependent RNA helicase activity (1e-06)	Y	0.005	8
protein_40_YHR052W	2	CIC1:  Essential protein that interacts with proteasome components and has a potential role in proteasome substrate specificity; also copurifies with 66S pre-ribosomal particles	VAA[RA][GWH]	42				DEAD	1.E-05	-1.2	ribosome assembly (1e-05)	Y	0.005	10
protein_40_YPR016C	2	TIF6:  Constituent of 66S pre-ribosomal particles, has similarity to human translation initiation factor 6 (eIF6); may be involved in the biogenesis and or stability of 60S ribosomal subunits	K.[KQE]R	42	[KR]R	CLV_PCSK_KEX2_1	Y	Brix	1.E-02	-1.1	cytoplasm organization and biogenesis (1e-22)	Y	0.007	10
protein_40_YLL008W	2	DRS1:  Nucleolar DEAD-box protein required for ribosome assembly and function, including synthesis of 60S ribosomal subunits; constituent of 66S pre-ribosomal particles	[ALI]R..DI[PW]	42	[AG]R	Protease matriptase protease site		DEAD	1.E-03	-1	rRNA processing (0.001)		0.005	8
protein_40_YMR229C	2	RRP5:  Protein required for the synthesis of both 18S and 5.8S rRNA; C-terminal region is crucial for the formation of 18S rRNA and N-terminal region is required for the 5.8S rRNA; component of small ribosomal subunit (SSU) processosome	TG[SPL][GIA]K	42	[SAG]GGTG[SA]G	TUBULIN PATTERN		Helicase_C	1.E-09	-0.9	helicase activity (1e-08)	Y	0.006	10
yeast-251_GO-0005886	2	plasma membrane	WG	42	[DE]AT..[DE]PWG[PA]	PI(4,5)P2 binding motif in epsin		MFS_1	1.E-07	-0.7	plasma membrane (1e-10)		0.009	10
oshea_bud_neck	2	oshea_bud_neck	[NRH]I.Q[NPV]	42				PH	1.E-04	-0.6	site of polarized growth (1e-22)	Y	0.009	10
protein_40_YBR106W	2	PHO88:  Probable membrane protein, involved in phosphate transport; pho88 pho86 double null mutant exhibits enhanced synthesis of repressible acid phosphatase at high inorganic phosphate concentrations	F..A[VTI]	42				MFS_1	1.E-10	-0.4	transporter activity (1e-08)	Y	0.008	10
yeast-1115_GO-0006996	2	organelle organization and biogenesis	VN[HDP]	42	Y[VI]N	SH2 ligand for Grb2 in IRS-1, EGFR, and Shc 		PI3_PI4_kinase	1.E-03	-0.3	chromosome organization and biogenesis (1e-58)	Y	0.009	10
yeast-312_GO-0006414	2	translational elongation	[TWN]V[KRW]A	42				Ribosomal_60s	1.E-02	-0.2	translational elongation (1e-15)		0.006	9
protein_40_YGR086C	2	PIL1:  Primary component of eisosomes, which are large immobile cell cortex structures associated with endocytosis; null mutants show activation of Pkc1p/Ypk1p stress resistance pathways; detected in phosphorylated state in mitochondria	[AHY][SFN]LSK	42				Cpn60_TCP1	1.E-02	-0.1			0.004	9
yeast-413_GO-0005215	2	transporter activity	I..G[LAI]	42			Y	MFS_1	1.E-09	0.1	transporter activity (1e-17)	Y	0.009	10
yeast-1974_GO-0005634	2	nucleus	I..[KNE]N	42			Y	SMC_N	1.E-03	0.1	nuclear lumen (1e-45)		0.009	10
yeast-295_GO-0016192	2	vesicle-mediated transport	Q..[LST]Q	42	[ST]Q	ATM kinase phosphorylation site		SNARE	1.E-05	0.3	vesicle-mediated transport (1e-13)		0.009	10
oshea_bud_neck	2	oshea_bud_neck	P.I[PNR]	42	PWI	Motif in SRM160 for binding DNA and RNA		RhoGAP	1.E-03	0.3	site of polarized growth (1e-47)	Y	0.008	10
yeast-410_GO-0007049	2	cell cycle	S.[KDT]R	42	RRK.S.KR	PKCgamma kinase phosphorylation site (peptide screen)		MutS_III	1.E-02	0.6	cell cycle (1e-18)		0.009	10
yeast-413_GO-0005215	2	transporter activity	A.[LFG]L	42	LMA[EQ]GLYN	ENGRAILED PATTERN		Mito_carr	1.E-16	1	transporter activity (1e-20)	Y	0.009	10
protein_40_YGR128C	2	UTP8:  Nucleolar protein required for export of tRNAs from the nucleus; also copurifies with the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	GS.[GDI]G[FNL]	42	[ED]GSG[DE]	Glycosaminoglycan attachment site		WD40	1.E-02	1.1	small nucleolar ribonucleoprotein complex (1e-05)		0.005	7
protein_40_YBR106W	2	PHO88:  Probable membrane protein, involved in phosphate transport; pho88 pho86 double null mutant exhibits enhanced synthesis of repressible acid phosphatase at high inorganic phosphate concentrations	I[AYG]..[GIA]F	42	IY	cFGR and Csk kinase phosphorylation site (peptide screen)		MFS_1	1.E-05	1.6	transporter activity (1e-06)	Y	0.009	10
yeast-256_GO-0016462	2	pyrophosphatase activity	SA..[GLP][EN]	42				ABC_tran	1.E-08	1.8	pyrophosphatase activity (1e-49)		0.009	10
yeast-244_GO-0000279	2	M phase	E[FES]L[NSK]	42				MutS_III	1.E-04	1.8	M phase (1e-09)	Y	0.009	10
protein_40_YDL140C	2	RPO21:  RNA polymerase II largest subunit B220, part of central core; phosphorylation of C-terminal heptapeptide repeat domain regulates association with transcription and splicing factors; similar to bacterial beta-prime	YR.P[ELK][LIT]	42	Y..P	SH2 ligand group 1B-Crk, SH2 binding motif for ITK, Nck and RasGAP to Doc-R (needs to be Tyr phosphorylated)		Pkinase	1.E-05	1.8	protein serine/threonine kinase activity (1e-06)		0.004	7
protein_40_YNR054C	2	ESF2:  Essential nucleolar protein involved in pre-18S rRNA processing; component of the small subunit (SSU) processome; has sequence similarity to mABT1, a mouse transcription activator	[IPA]K.WD	42	PWDLW	LIG_Clathr_ClatBox_2		WD40	1.E-02	1.9	processing of 20S pre-rRNA (1e-08)		0.005	8
yeast-205_GO-0005856	2	cytoskeleton	[LWD]A[GVH]SE	42	[ST]E	G protein-coupled receptor kinase 1 substrate motif		Kinesin	1.E-08	2.1	cytoskeleton (1e-09)		0.006	9
protein_40_YER125W	2	RSP5:  Ubiquitin-protein ligase involved in ubiquitin-mediated protein degradation; functions in multivesicular body sorting, heat shock response and ubiquitylation of arrested RNAPII; contains a hect (homologous to E6-AP carboxyl terminus) domain	K[IA]AD[FLG]	42				Pkinase	1.E-03	2.1	protein kinase activity (0.01)		0.005	9
protein_40_YPL031C	2	PHO85:  Cyclin-dependent kinase, with ten cyclin partners; involved in regulating the cellular response to nutrient levels and environmental conditions and progression through the cell cycle	AK..[NR]D[SH]	42				Cyclin_N	1.E-04	2.2	cyclin-dependent protein kinase regulator activity (0.01)		0.005	9
protein_40_YHR082C	2	KSP1:  Nonessential putative serine/threonine protein kinase of unknown cellular role; overproduction causes allele-specific suppression of the prp20-10 mutation	[LGF]K.[QED]N	42	[VILAFP]K.E	Motif recognized for modification by SUMO-1		Pkinase	1.E-04	2.3	protein kinase activity (1e-04)		0.008	10
yeast-267_GO-0044265	2	cellular macromolecule catabolism	G[NTY].[VS]IQ	42			Y	PUF	1.E-07	2.5	mRNA catabolism (1e-07)		0.005	9
yeast-256_GO-0016462	2	pyrophosphatase activity	I[PIV][VFL]I	42	RRRRSIIFI	PKA kinase substrate motif		DEAD	1.E-04	2.6	pyrophosphatase activity (1e-56)	Y	0.009	10
protein_40_YNL272C	2	SEC2:  Guanyl-nucleotide exchange factor for the small G-protein Sec4p, located on cytoplasmic vesicles; essential for post-Golgi vesicle transport	I[TWN].[FIC]G	42				Pkinase	1.E-10	2.7	protein kinase activity (1e-09)	Y	0.006	10
protein_40_YOR181W	2	LAS17:  Actin assembly factor, activates the Arp2/3 protein complex that nucleates branched actin filaments; localizes with the Arp2/3 complex to actin patches; homolog of the human Wiskott-Aldrich syndrome protein (WASP)	A[EPG]..D[EVD]L	42			Y	SH3_1	1.E-03	2.8		Y	0.005	8
matsuyama_Cytosol	2	matsuyama_Cytosol	D..[SAC]L	42	DDDD..S	Casein kinase 1 phosphorylation motif	Y	Pkinase	1.E-06	2.9	ATP binding (1e-09)	Y	0.010	10
protein_40_YKR048C	2	NAP1:  Protein that interacts with mitotic cyclin Clb2p; required for the regulation of microtubule dynamics during mitosis; controls bud morphogenesis; involved in the transport of H2A and H2B histones to the nucleus; phosphorylated by CK2	R[DMW].K[PQ]	42				Pkinase	1.E-10	3	protein kinase activity (1e-10)		0.006	8
protein_40_YGL207W	2	SPT16:  Subunit of the heterodimeric FACT complex (Spt16p-Pob3p), facilitates RNA Polymerase II transcription elongation through nucleosomes by destabilizing and then reassembling nucleosome structure	[ATD]D[FYD]G	42				Pkinase	1.E-07	3	protein kinase activity (1e-06)	Y	0.008	10
protein_40_YNL186W	2	UBP10:  Ubiquitin-specific protease that deubiquitinates ubiquitin-protein moieties; may regulate silencing by acting on Sir4p; involved in posttranscriptionally regulating Gap1p and possibly other transporters; primarily located in the nucleus	[YLD]..PE	42				Pkinase	1.E-29	3.1	protein kinase activity (1e-29)	Y	0.008	10
protein_40_YGR103W	2	NOP7:  Nucleolar protein involved in rRNA processing and 60S ribosomal subunit biogenesis; constituent of several different pre-ribosomal particles; required for exit from G<sub>0</sub> and the initiation of cell proliferation	P[NAV]..KS[SQE]	42	S[ST]	MDC1 BRCT domain binding motif		MMR_HSR1	1.E-03	3.1	ribosome biogenesis (0.001)		0.005	7
protein_40_YNL272C	2	SEC2:  Guanyl-nucleotide exchange factor for the small G-protein Sec4p, located on cytoplasmic vesicles; essential for post-Golgi vesicle transport	K[PSI][EDS]N	42				Pkinase	1.E-24	3.4	protein kinase activity (1e-24)		0.008	10
yeast-345_GO-0006396	2	RNA processing	I[VIM]..TP[GP]	42	[ST]P	LIG_WW_4		DEAD	1.E-11	3.5	RNA helicase activity (1e-10)		0.007	9
protein_40_YLR002C	2	NOC3:  Protein that forms a nuclear complex with Noc2p that binds to 66S ribosomal precursors to mediate their intranuclear transport; also binds to chromatin to promote the association of DNA replication factors and replication initiation	DEA[DAI][RL]	42				DEAD	1.E-05	3.5	RNA helicase activity (1e-04)		0.004	7
yeast-685_GO-0016740	2	transferase activity	IK..[NAM][LI]	42				Pkinase	1.E-27	3.7	transferase activity, transferring phosphorus-containing groups (1e-40)	Y	0.009	10
yeast-238_GO-0017111	2	nucleoside-triphosphatase activity	DE.[DCT][RAS]	42	LPDEL	Motif in CBP for interaction with PPARg-LBD (secondary site)	Y	AAA	1.E-13	3.7	ATPase activity (1e-59)	Y	0.010	10
protein_40_YNL272C	2	SEC2:  Guanyl-nucleotide exchange factor for the small G-protein Sec4p, located on cytoplasmic vesicles; essential for post-Golgi vesicle transport	[LIW]K.[EDQ]N	42	[VILAFP]K.E	Motif recognized for modification by SUMO-1		Pkinase	1.E-29	3.9	protein kinase activity (1e-30)	Y	0.008	10
protein_40_YMR229C	2	RRP5:  Protein required for the synthesis of both 18S and 5.8S rRNA; C-terminal region is crucial for the formation of 18S rRNA and N-terminal region is required for the 5.8S rRNA; component of small ribosomal subunit (SSU) processosome	K[PAF].N[LIF]L	42				Pkinase	1.E-16	4.2	protein kinase activity (1e-16)		0.007	10
protein_40_YGL105W	2	ARC1:  Protein that binds tRNA and methionyl- and glutamyl-tRNA synthetases (Mes1p and Gus1p), delivering tRNA to them, stimulating catalysis, and ensuring their localization to the cytoplasm; also binds quadruplex nucleic acids	D.W[SAR]	42	PWDLW	LIG_Clathr_ClatBox_2		Pkinase	1.E-19	4.6	protein kinase activity (1e-19)	Y	0.008	10
protein_40_YNL061W	2	NOP2:  Probable RNA m(5)C methyltransferase, essential for processing and maturation of 27S pre-rRNA and large ribosomal subunit biogenesis; localized to the nucleolus; constituent of 66S pre-ribosomal particles	R.[GKA]R	42	[AG]R	Protease matriptase protease site		Helicase_C	1.E-05	5.4	cytoplasm organization and biogenesis (1e-23)	Y	0.008	10
yeast-685_GO-0016740	2	transferase activity	G..P[FWY]	42	[ILVM]LG..P	LIG_RRM_PRI_1		Pkinase	1.E-44	7.2	transferase activity, transferring phosphorus-containing groups (1e-52)	Y	0.009	10
yeast-939_GO-0051234	2	establishment of localization	LF[VGR][SGI]	42	LFG	Protease Papain substrate, a prototype cysteine proteinase					transporter activity (1e-21)		0.009	10
yeast-792_GO-0006412	2	protein biosynthesis	D[DKS]N	42	Y.D.NHKPE	PMI_I_1 PATTERN							0.009	10
yeast-628_GO-0043037	2	translation	[AEK]AA[KR]K	42							translation (1e-18)		0.009	10
yeast-324_GO-0030528	2	transcription regulator activity	RHN[LRW][SIL]	42							transcription regulator activity (1e-08)		0.007	10
yeast-235_GO-0009653	2	morphogenesis	Q[SEN]..[VSQ]N	42							cellular morphogenesis (1e-56)		0.009	10
yeast-235_GO-0000902	2	cellular morphogenesis	Q[SEN]..[VSQ]N	42							cellular morphogenesis (1e-56)		0.009	10
yeast-205_GO-0005856	2	cytoskeleton	IR.E[KPR][IDK]	42	[DET]E[RK].PL[LI]	TRG_LysEnd_APsAcLL_3					cytoskeletal part (1e-08)		0.005	9
yeast-1721_GO-0016043	2	cell organization and biogenesis	LD.[SLI][IAQ]	42	DALDL	14-3-3 binding motif in ExoS					cellular localization (1e-19)	Y	0.009	10
protein_40_YPL204W	2	HRR25:  Protein kinase involved in regulating diverse events including vesicular trafficking, DNA repair, and chromosome segregation; binds the CTD of RNA pol II; homolog of mammalian casein kinase 1delta (CK1delta)	[LR]G[ETH]LE	42									0.004	8
protein_40_YPL141C	2	FRK1:  Putative protein kinase; similar to Kin4p; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm; YPL141C is not an essential gene	D[EDF]..[EFL]E	42									0.008	10
protein_40_YPL129W	2	TAF14:  Subunit of TFIID, TFIIF, INO80, SWI/SNF, and NuA3 complexes, involved in RNA polymerase II transcription initiation and in chromatin modification; contains a YEATS domain	N[IA].[NSD]NI	42							general RNA polymerase II transcription factor activity (1e-07)		0.004	8
protein_40_YPL043W	2	NOP4:  Nucleolar protein, essential for processing and maturation of 27S pre-rRNA and large ribosomal subunit biogenesis; constituent of 66S pre-ribosomal particles; contains four RNA recognition motifs (RRMs)	[LRY][RVQ]..KEL	42			Y				ribosome assembly (1e-04)	Y	0.004	7
protein_40_YOR326W	2	MYO2:  One of two type V myosin motors (along with MYO4) involved in actin-based transport of cargos; required for the polarized delivery of secretory vesicles, the vacuole, late Golgi elements, peroxisomes, and the mitotic spindle	[REK]LS[SAG]V	42							Rho protein signal transduction (0.01)	Y	0.005	8
protein_40_YOR133W	2	EFT1:  Elongation factor 2 (EF-2), also encoded by EFT2; catalyzes ribosomal translocation during protein synthesis; contains diphthamide, the unique posttranslationally modified histidine residue specifically ADP-ribosylated by diphtheria toxin	SE.[IFS]E[KAV]	42	[ST]E	G protein-coupled receptor kinase 1 substrate motif						Y	0.005	10
protein_40_YNL308C	2	KRI1:  Essential nucleolar protein required for 40S ribosome biogenesis; physically and functionally interacts with Krr1p	[FAT]G.A[RHC]	42	FGRA	DNA binding motif in ssDNA binding proteins					rRNA processing (1e-06)		0.005	10
protein_40_YNL209W	2	SSB2:  Cytoplasmic ATPase that is a ribosome-associated molecular chaperone, functions with J-protein partner Zuo1p; may be involved in the folding of newly-synthesized polypeptide chains; member of the HSP70 family; homolog of SSB1	NK.[TLA]D[ADL]	42									0.004	8
protein_40_YMR236W	2	TAF9:  Subunit (17 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation and in chromatin modification, similar to histone H3	[NYM][SC]TQ	42	S[QT]Q	ATM phosphorylation of this motif on Chk2					nucleoplasm part (1e-04)		0.005	9
protein_40_YMR236W	2	TAF9:  Subunit (17 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation and in chromatin modification, similar to histone H3	[RAY]D[GCH]T	42	Q[DEK]..[LIVMGTA][GA]DGT	TCP1_3 PATTERN					nucleoplasm part (1e-07)		0.005	8
protein_40_YMR116C	2	ASC1:  G-protein beta subunit and guanine nucleotide dissociation inhibitor for Gpa2p; ortholog of RACK1 that inhibits translation; core component of the small (40S) ribosomal subunit; represses Gcn4p in the absence of amino acid starvation	[EPF]E.[VPI]E	42									0.008	10
protein_40_YLR293C	2	GSP1:  GTP binding protein (mammalian Ranp homolog) involved in the maintenance of nuclear organization, RNA processing and transport; regulated by Prp20p, Rna1p, Yrb1p, Yrb2p, Yrp4p, Yrb30p, Cse1p and Kap95p; yeast Gsp2p homolog	IIT[SQK][LAI]	42							nuclear transport (0.01)		0.005	8
protein_40_YLR186W	2	EMG1:  Protein required for the maturation of the 18S rRNA and for 40S ribosome production; associated with spindle/microtubules; nuclear localization depends on physical interaction with Nop14p; may bind snoRNAs	[RWE]H..[FIE]L	42							snoRNA binding (1e-12)	Y	0.006	9
protein_40_YLR180W	2	SAM1:  S-adenosylmethionine synthetase, catalyzes transfer of the adenosyl group of ATP to the sulfur atom of methionine; one of two differentially regulated isozymes (Sam1p and Sam2p)	[TGA]G..[IDT]V	42							carboxylic acid metabolism (0.001)	Y	0.008	10
protein_40_YLR180W	2	SAM1:  S-adenosylmethionine synthetase, catalyzes transfer of the adenosyl group of ATP to the sulfur atom of methionine; one of two differentially regulated isozymes (Sam1p and Sam2p)	S[ECN].LE[AE]	42									0.005	7
protein_40_YLR166C	2	SEC10:  Essential 100kDa subunit of the exocyst complex (Sec3p, Sec5p, Sec6p, Sec8p, Sec10p, Sec15p, Exo70p, and Exo84p), which has the essential function of mediating polarized targeting of secretory vesicles to active sites of exocytosis	K[VH][LI]SA	42									0.005	10
protein_40_YLR029C	2	RPL15A:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl15Bp and has similarity to rat L15 ribosomal protein; binds to 5.8 S rRNA	K..[RAK]A	42	K[KR].[KR]	Nuclear localization motif					cytosolic ribosome (sensu Eukaryota) (1e-30)	Y	0.007	10
protein_40_YLL011W	2	SOF1:  Essential protein required for biogenesis of 40S (small) ribosomal subunit; has similarity to the beta subunit of trimeric G-proteins and the splicing factor Prp4p	A[EN][KRP]AL	42	DALDL	14-3-3 binding motif in ExoS	Y				35S primary transcript processing (1e-05)		0.005	8
protein_40_YKR026C	2	GCN3:  Alpha subunit of the translation initiation factor eIF2B, the guanine-nucleotide exchange factor for eIF2; activity subsequently regulated by phosphorylated eIF2; first identified as a positive regulator of GCN4 expression	A[KN].AA[SRM]	42			Y						0.005	10
protein_40_YKR001C	2	VPS1:  Dynamin-like GTPase required for vacuolar sorting; also involved in actin cytoskeleton organization, late Golgi-retention of some proteins, regulating peroxisome biogenesis	PA..[AKW][PTY]	42							establishment and/or maintenance of chromatin architecture (0.01)		0.006	9
protein_40_YKL180W	2	RPL17A:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl17Bp and has similarity to E. coli L22 and rat L17 ribosomal proteins; copurifies with the Dam1 complex (aka DASH complex)	[RGW]A[AYI]R	42	[AG]R	Protease matriptase protease site					cytosolic ribosome (sensu Eukaryota) (1e-11)		0.007	10
protein_40_YKL173W	2	SNU114:  GTPase component of U5 snRNP involved in mRNA splicing via spliceosome; binds directly to U5 snRNA; proposed to be involved in conformational changes of the spliceosome; similarity to ribosomal translocation factor EF-2	[TAV]G..[DRF]LK	42							mRNA metabolism (1e-06)		0.005	9
protein_40_YKL104C	2	GFA1:  Glutamine-fructose-6-phosphate amidotransferase, catalyzes the formation of glucosamine-6-P and glutamate from fructose-6-P and glutamine in the first step of chitin biosynthesis	[TYW]Q.[VHY]V	42	[ST]Q	ATM kinase phosphorylation site							0.005	7
protein_40_YJR123W	2	RPS5:  Protein component of the small (40S) ribosomal subunit, the least basic of the non-acidic ribosomal proteins; phosphorylated in vivo; essential for viability; has similarity to E. coli S7 and rat S5 ribosomal proteins	A[AKG]..[KAR]A	42							cytosolic ribosome (sensu Eukaryota) (1e-25)	Y	0.008	10
protein_40_YJL203W	2	PRP21:  Subunit of the SF3a splicing factor complex, required for spliceosome assembly	LRE[ENK][IG]	42									0.004	7
protein_40_YJL074C	2	SMC3:  Subunit of the multiprotein cohesin complex required for sister chromatid cohesion in mitotic cells; also required, with Rec8p, for cohesion and recombination during meiosis; phylogenetically conserved SMC chromosomal ATPase family member	[KMP]T..V[KNR]	42								Y	0.007	10
protein_40_YIL133C	2	RPL16A:  N-terminally acetylated protein component of the large (60S) ribosomal subunit, binds to 5.8 S rRNA; has similarity to Rpl16Bp, E. coli L13 and rat L13a ribosomal proteins; transcriptionally regulated by Rap1p	IA.S[RT][RYK]	42	S[ST]	MDC1 BRCT domain binding motif					ribosome (0.001)		0.004	8
protein_40_YIL075C	2	RPN2:  Subunit of the 26S proteasome, substrate of the N-acetyltransferase Nat1p	L[ADI].[GML]GE	42	EGGELGY	PHOSPHOKETOLASE_1 PATTERN					proteasome regulatory particle (sensu Eukaryota) (0.01)		0.005	8
protein_40_YHR152W	2	SPO12:  Nucleolar protein of unknown function, positive regulator of mitotic exit; involved in regulating release of Cdc14p from the nucleolus in early anaphase, may play similar role in meiosis	[QV]Y..[SE]V	42									0.005	9
protein_40_YHR140W	2	YHR140W:  Putative integral membrane protein of unknown function	V[LVD]..LV[LAH]	42									0.005	9
protein_40_YHR135C	2	YCK1:  Palmitoylated, plasma membrane-bound casein kinase I isoform; shares redundant functions with Yck2p in morphogenesis, proper septin assembly, endocytic trafficking; provides an essential function overlapping with that of Yck2p	PT	42	LPTSY	SMAD interacting motif- FM1 in motif for binding in XFoxH1							0.008	10
protein_40_YHR010W	2	RPL27A:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl27Bp and has similarity to rat L27 ribosomal protein	KK.[KAL][KAS]	42	K[KR].[KR]	Nuclear localization motif					cytoplasm organization and biogenesis (1e-11)	Y	0.008	10
protein_40_YGR218W	2	CRM1:  Major karyopherin, involved in export of proteins, RNAs, and ribosomal subunits from the nucleus	[KER]K.[EKF]E	42	KTKEGC	Repeating motif in alpha-synuclein that binds apolipoproteins						Y	0.008	10
protein_40_YGR086C	2	PIL1:  Primary component of eisosomes, which are large immobile cell cortex structures associated with endocytosis; null mutants show activation of Pkc1p/Ypk1p stress resistance pathways; detected in phosphorylated state in mitochondria	KQ[KVE][LSN]E	42	[ST]E	G protein-coupled receptor kinase 1 substrate motif					SWR1 complex (0.001)		0.005	9
protein_40_YFR031C-A	2	RPL2A:  Protein component of the large (60S) ribosomal subunit, identical to Rpl2Bp and has similarity to E. coli L2 and rat L8 ribosomal proteins	[IAQ]D..R[NLA]S	42	R.S	PKA kinase substrate motif							0.004	8
protein_40_YFL002C	2	SPB4:  Putative ATP-dependent RNA helicase, nucleolar protein required for synthesis of 60S ribosomal subunits at a late step in the pathway; sediments with 66S pre-ribosomes in sucrose gradients	R[KAV].A[KLV]E	42							nucleolus (1e-04)		0.005	7
protein_40_YER082C	2	UTP7:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	[SAI]S..LA[INE]	42							processing of 20S pre-rRNA (1e-07)		0.005	8
protein_40_YER082C	2	UTP7:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	VG.[SK]T[RI]	42									0.005	7
protein_40_YEL037C	2	RAD23:  Protein with ubiquitin-like N terminus, recognizes and binds damaged DNA (with Rad4p) during nucleotide excision repair; regulates Rad4p levels, subunit of Nuclear Excision Repair Factor 2 (NEF2); homolog of human HR23A and HR23B proteins	T[IPS].NV[KC]	42									0.005	10
protein_40_YDR471W	2	RPL27B:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl27Ap and has similarity to rat L27 ribosomal protein	[KLG]G.KV[TK]	42							cytosolic ribosome (sensu Eukaryota) (1e-07)		0.004	8
protein_40_YDR450W	2	RPS18A:  Protein component of the small (40S) ribosomal subunit; nearly identical to Rps18Bp and has similarity to E. coli S13 and rat S18 ribosomal proteins	E[SIG]..EE[GHK]	42							preribosome (0.001)		0.005	9
protein_40_YDR356W	2	SPC110:  Inner plaque spindle pole body (SPB) component, ortholog of human kendrin; involved in connecting nuclear microtubules to SPB; interacts with Tub4p-complex and calmodulin; phosphorylated by Mps1p in cell cycle-dependent manner	S[VHR]..DS[VLD]	42			Y				nuclear chromosome part (0.001)	Y	0.004	8
protein_40_YDR224C	2	HTB1:  One of two nearly identical (see HTB2) histone H2B subtypes required for chromatin assembly and chromosome function; Rad6p-Bre1p-Lge1p mediated ubiquitination regulates transcriptional activation, meiotic DSB formation and H3 methylation	N[EFH]T[PC]	42									0.005	8
protein_40_YDR172W	2	SUP35:  Translation termination factor eRF3; altered protein conformation creates the [PSI(+)] prion, a dominant cytoplasmically inherited protein aggregate that alters translational fidelity and creates a nonsense suppressor phenotype	A[SWY][LV]EK	42									0.005	8
protein_40_YDL185W	2	TFP1:  Vacuolar ATPase V1 domain subunit A containing the catalytic nucleotide binding sites; protein precursor undergoes self-catalyzed splicing to yield the extein Tfp1p and the intein Vde (PI-SceI), which is a site-specific endonuclease	[ID]N..PS[LP]	42	SPSP	Motif for hydroxylation of Proline residues, which can further be modified with arabinogalactan							0.005	9
protein_40_YDL148C	2	NOP14:  Nucleolar protein, forms a complex with Noc4p that mediates maturation and nuclear export of 40S ribosomal subunits; also present in the small subunit processome complex, which is required for processing of pre-18S rRNA	N[RVS]D[TQR]L	42	DLL	Binding motif for clathrin heavy chain ear					processing of 20S pre-rRNA (0.001)		0.005	7
protein_40_YDL140C	2	RPO21:  RNA polymerase II largest subunit B220, part of central core; phosphorylation of C-terminal heptapeptide repeat domain regulates association with transcription and splicing factors; similar to bacterial beta-prime	[ST]N..NL[IWP]	42			Y				RNA polymerase II transcription elongation factor activity (0.01)		0.005	9
protein_40_YDL083C	2	RPS16B:  Protein component of the small (40S) ribosomal subunit; identical to Rps16Ap and has similarity to E. coli S9 and rat S16 ribosomal proteins	[KNL][GY].KVT	42							cytosolic ribosome (sensu Eukaryota) (1e-07)	Y	0.005	10
protein_40_YDL055C	2	PSA1:  GDP-mannose pyrophosphorylase (mannose-1-phosphate guanyltransferase), synthesizes GDP-mannose from GTP and mannose-1-phosphate in cell wall biosynthesis; required for normal cell wall structure	DG.[TSA][SCR]A	42								Y	0.005	10
protein_40_YDL055C	2	PSA1:  GDP-mannose pyrophosphorylase (mannose-1-phosphate guanyltransferase), synthesizes GDP-mannose from GTP and mannose-1-phosphate in cell wall biosynthesis; required for normal cell wall structure	VA[YFC][GVA]	42	DVAD	Protease Caspase 2 -stringent						Y	0.007	10
protein_40_YBR159W	2	IFA38: Microsomal beta-keto-reductase; contains oleate response element (ORE) sequence in the promoter region; mutants exhibit reduced VLCFA synthesis, accumulate high levels of dihydrosphingosine, phytosphingosine and medium-chain ceramides	I.F[VMG]	42	[RK].[VI].F	PP1 protein phosphatase substrate recognition motif					endoplasmic reticulum (1e-07)		0.008	10
protein_40_YBR159W	2	IFA38: Microsomal beta-keto-reductase; contains oleate response element (ORE) sequence in the promoter region; mutants exhibit reduced VLCFA synthesis, accumulate high levels of dihydrosphingosine, phytosphingosine and medium-chain ceramides	LV.G[FMR][QSP]	42									0.004	8
protein_40_YBL026W	2	LSM2:  Lsm (Like Sm) protein; part of heteroheptameric complexes (Lsm2p-7p and either Lsm1p or 8p): cytoplasmic Lsm1p complex involved in mRNA decay; nuclear Lsm8p complex part of U6 snRNP and possibly involved in processing tRNA, snoRNA, and rRNA	N[PRW].[GC]W	42			Y						0.005	8
protein_40_YAL032C	2	PRP45:  Protein required for pre-mRNA splicing; associates with the spliceosome and interacts with splicing factors Prp22p and Prp46p; orthologous to human transcriptional coactivator SKIP and can activate transcription of a reporter gene	IQ..[NC][TEA]	42								Y	0.005	10
protein_40_YAL032C	2	PRP45:  Protein required for pre-mRNA splicing; associates with the spliceosome and interacts with splicing factors Prp22p and Prp46p; orthologous to human transcriptional coactivator SKIP and can activate transcription of a reporter gene	K[RLQ]K	42	KRKQISVR	Phosphorylase kinase substrate motif					nuclear mRNA splicing, via spliceosome (1e-17)	Y	0.008	10
protein_40_YAL032C	2	PRP45:  Protein required for pre-mRNA splicing; associates with the spliceosome and interacts with splicing factors Prp22p and Prp46p; orthologous to human transcriptional coactivator SKIP and can activate transcription of a reporter gene	KA..[QIM][FHN]	42								Y	0.007	10
matsuyama_nuclear_envelope_or_dots	2	matsuyama_nuclear_envelope_or_dots	PP[SAF][SHR]	42			Y				nuclear envelope (1e-09)	Y	0.011	10
genetic_YNL153C	2	GIM3: Subunit of the heterohexameric cochaperone prefoldin complex which binds specifically to cytosolic chaperonin and transfers target proteins to it	D.I[GNL]	42			Y				cell cycle (1e-11)		0.008	10
genetic_YLR200W	2	YKE2: Subunit of the heterohexameric Gim/prefoldin protein complex involved in the folding of alpha-tubulin, beta-tubulin, and actin	[LMV]G..[LK]DG	42	Q[MLVI]DG..[DE]	CLV_TASPASE1	Y						0.005	8
genetic_YLR200W	2	YKE2: Subunit of the heterohexameric Gim/prefoldin protein complex involved in the folding of alpha-tubulin, beta-tubulin, and actin	R.L[KSE]	42	R.L	Cyclin A motif that binds cdk2 complexes					cell cycle (1e-09)		0.008	10
genetic_YLR200W	2	YKE2: Subunit of the heterohexameric Gim/prefoldin protein complex involved in the folding of alpha-tubulin, beta-tubulin, and actin	S[TDQ]N	42	S[ST]	MDC1 BRCT domain binding motif					mitotic cell cycle (1e-06)		0.007	10
genetic_YLR039C	2	RIC1: Protein involved in retrograde transport to the cis-Golgi network; forms heterodimer with Rgp1p that acts as a GTP exchange factor for Ypt6p; involved in transcription of rRNA and ribosomal protein genes	E..D[ERT]	42							chromosome organization and biogenesis (1e-11)		0.008	10
genetic_YGL058W	2	RAD6: Ubiquitin-conjugating enzyme (E2), involved in postreplication repair (with Rad18p), sporulation, telomere silencing, and ubiquitin-mediated N-end rule protein degradation (with Ubr1p)	[SPW]K[DVK]D	42							DNA metabolism (0.001)	Y	0.008	10
protein_40_YPR103W	2	PRE2:  Beta 5 subunit of the 20S proteasome, responsible for the chymotryptic activity of the proteasome	E[YQL].LE[ASD]	41			Y	Proteasome	1.E-11	-3.1	proteasome core complex (sensu Eukaryota) (1e-11)	Y	0.004	8
protein_40_YGR103W	2	NOP7:  Nucleolar protein involved in rRNA processing and 60S ribosomal subunit biogenesis; constituent of several different pre-ribosomal particles; required for exit from G<sub>0</sub> and the initiation of cell proliferation	KR..[VEK][EKN]	41	KR	CLV_PCSK_PC1ET2_1		Brix	1.E-02	-2.3	cytoplasm organization and biogenesis (1e-24)		0.008	10
yeast-376_GO-0019219	2	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism	H[TS].E[KRN]P	41				zf-C2H2	1.E-20	-1.2	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism (1e-14)		0.009	10
yeast-345_GO-0006396	2	RNA processing	TG.[GMV]K[TV]	41	TGY	ERK6/SAPK3 activation sites for HOG/p38 activation	Y	Helicase_C	1.E-21	-1.2	RNA helicase activity (1e-25)		0.009	10
oshea_bud_neck	2	oshea_bud_neck	S..[PTF]Q	41	[ST]Q	ATM kinase phosphorylation site		RhoGAP	1.E-05	-1.2	site of polarized growth (1e-39)		0.008	10
yeast-504_GO-0006350	2	transcription	LP[PKT]	41	LPKY	WW motif (non-conventional ) in spt23 for binding to WW domain of RSP5p, also for NEDD4 WW domain	Y	Zn_clus	1.E-06	-1.1	transcription (1e-25)		0.009	10
yeast-200_GO-0006519	2	amino acid and derivative metabolism	[LIC][VGA].SG	41	KSGST	eIF4 motif phosphorylation motif	Y	GATase	1.E-02	-1.1	amino acid metabolism (1e-60)		0.009	10
protein_40_YOR272W	2	YTM1:  Constituent of 66S pre-ribosomal particles, required for maturation of the large ribosomal subunit	K[ESR]K[KVD]	41	KR	CLV_PCSK_PC1ET2_1	Y	DEAD	1.E-02	-1.1	nucleolus (1e-22)		0.008	10
protein_40_YMR290C	2	HAS1:  ATP-dependent RNA helicase; localizes to both the nuclear periphery and nucleolus; highly enriched in nuclear pore complex fractions; constituent of 66S pre-ribosomal particles	[HAR]R..R[TAD]A	41	R.[RK]R	CLV_PCSK_FUR_1		DEAD	1.E-05	-1.1	ribosomal large subunit assembly and maintenance (1e-05)		0.004	8
yeast-504_GO-0006350	2	transcription	TT[AND]	41	[DGH][IVSAC]T[ST]NP[STA][LIVMF][LIVMF]	TRANSALDOLASE_1 PATTERN		Zn_clus	1.E-05	-1	transcription (1e-20)	Y	0.009	10
protein_40_YPL043W	2	NOP4:  Nucleolar protein, essential for processing and maturation of 27S pre-rRNA and large ribosomal subunit biogenesis; constituent of 66S pre-ribosomal particles; contains four RNA recognition motifs (RRMs)	[AIL]R..D[IA]P	41	[AG]R	Protease matriptase protease site		DEAD	1.E-03	-1	rRNA processing (0.001)		0.005	8
protein_40_YKL009W	2	MRT4:  Protein involved in mRNA turnover and ribosome assembly, localizes to the nucleolus	[RML][GS].DIP	41	S.D	CAMKII phosphorylation site		DEAD	1.E-03	-0.9	ribosome biogenesis (1e-05)		0.005	7
yeast-312_GO-0006414	2	translational elongation	GK[STN][TP]	41	K[ST]P.K	GSK-3, ERK1, ERK2, CDK5 substrate motif	Y	GTP_EFTU_D2	1.E-05	-0.8	translational elongation (1e-21)		0.006	9
yeast-235_GO-0009653	2	morphogenesis	AP..[VPN][SFT]	41	P..P	SH3 general ligand,		SH3_1	1.E-02	-0.8	cellular morphogenesis (1e-47)		0.009	10
yeast-235_GO-0000902	2	cellular morphogenesis	AP..[VPN][SFT]	41	P..P	SH3 general ligand,		SH3_1	1.E-02	-0.8	cellular morphogenesis (1e-47)		0.009	10
yeast-1074_GO-0044428	2	nuclear part	D..[TDR]K	41				Helicase_C	1.E-03	-0.8	nuclear lumen (1e-09)	Y	0.009	10
yeast-388_GO-0007275	2	development	[ASN][QTK]..KS	41				RasGEF_N	1.E-02	-0.6	multicellular organismal development (1e-93)		0.009	10
protein_40_YOL133W	2	HRT1:  RING finger containing subunit of Skp1-Cullin-F-box ubiquitin protein ligases (SCF); required for Gic2p, Far1p, Sic1p and Cln2p degradation; may tether Cdc34p (a ubiquitin conjugating enzyme or E2) and Cdc53p (a cullin) subunits of SCF	AI[DEC]	41				F-box	1.E-05	-0.6	protein catabolism (1e-04)	Y	0.008	10
protein_40_YMR047C	2	NUP116:  Subunit of the nuclear pore complex (NPC) that is localized to both sides of the pore; contains a repetitive GLFG motif that interacts with mRNA export factor Mex67p and with karyopherin Kap95p; homologous to Nup100p	D..[GLD]D	41	D..G	motif that binds phosphate in GDP and GTP binding proteins		IBN_N	1.E-05	-0.6	nuclear transport (1e-24)	Y	0.007	10
protein_40_YER110C	2	KAP123:  Karyopherin beta, mediates nuclear import of ribosomal proteins prior to assembly into ribosomes and import of histones H3 and H4; localizes to the nuclear pore, nucleus, and cytoplasm; exhibits genetic interactions with RAI1	SE.[SVQ]E[NDT]	41	[ST]E	G protein-coupled receptor kinase 1 substrate motif		Sec7	1.E-02	-0.5	mRNA-binding (hnRNP) protein import into nucleus (0.01)		0.004	7
yeast-1062_GO-0016020	2	membrane	S..L[TIF]	41			Y	MFS_1	1.E-03	-0.3	endomembrane system (1e-67)		0.008	10
matsuyama_Cytosol	2	matsuyama_Cytosol	E.[LAK]T	41				Pkinase	1.E-03	-0.3	ATP binding (1e-07)	Y	0.010	10
protein_40_YLR276C	2	DBP9:  ATP-dependent RNA helicase of the DEAD-box family involved in biogenesis of the 60S ribosomal subunit	[ETG]EE[EDG]	41	EED	Ankyrin B C-terminal motif that binds internal Ankyrin repeats	Y	Brix	1.E-03	0	nucleolus (1e-18)		0.008	10
protein_40_YPR144C	2	NOC4:  Nucleolar protein, forms a complex with Nop14p that mediates maturation and nuclear export of 40S ribosomal subunits	K..K[LRK]	41	KR	CLV_PCSK_PC1ET2_1		WD40	1.E-05	0.1	nucleolus (1e-37)	Y	0.007	10
protein_40_YOL069W	2	NUF2:  Component of the evolutionarily conserved kinetochore-associated Ndc80 complex (Ndc80p-Nuf2p-Spc24p-Spc25p); involved in chromosome segregation, spindle checkpoint activity and kinetochore clustering	S[ERL].NS[SLK]	41	S[ST]	MDC1 BRCT domain binding motif		SMC_N	1.E-02	0.1			0.005	9
yeast-213_GO-0009719	2	response to endogenous stimulus	L[SER]T[QHI]	41	LRT	LKB1 Kinase substrate motif	Y	SMC_N	1.E-04	0.3	response to endogenous stimulus (1e-63)		0.008	10
protein_40_YJL081C	2	ARP4:  Nuclear actin-related protein involved in chromatin remodeling, component of chromatin-remodeling enzyme complexes	[LMN]A..[AE]AR	41	[AG]R	Protease matriptase protease site		Histone	1.E-04	0.4	establishment and/or maintenance of chromatin architecture (1e-05)		0.005	9
yeast-244_GO-0000279	2	M phase	L..N[KNS]	41			Y	MutS_III	1.E-03	0.5	M phase (1e-20)	Y	0.009	10
protein_40_YBR159W	2	IFA38: Microsomal beta-keto-reductase; contains oleate response element (ORE) sequence in the promoter region; mutants exhibit reduced VLCFA synthesis, accumulate high levels of dihydrosphingosine, phytosphingosine and medium-chain ceramides	I..[VFL]I	41				MFS_1	1.E-05	0.6	transporter activity (1e-09)		0.008	10
matsuyama_Nucleus	2	matsuyama_Nucleus	F[LFA]F	41	A[EA]EEY[FV]F[LFMIV]F	FGFR kinase substrate motif		MFS_1	1.E-06	0.6	endoplasmic reticulum (1e-37)		0.010	10
matsuyama_Spindle_or_SPB	2	matsuyama_Spindle_or_SPB	L.[RQS]S	41			Y	Pkinase	1.E-02	0.8	spindle (1e-19)	Y	0.010	10
yeast-238_GO-0017111	2	nucleoside-triphosphatase activity	[ATR]L..E[LIS]	41				AAA	1.E-08	0.9	nucleoside-triphosphatase activity (1e-73)	Y	0.009	10
protein_40_YLR340W	2	RPP0:  Conserved ribosomal protein P0 similar to rat P0, human P0, and E. coli L10e; shown to be phosphorylated on serine 302	E[EVQ].K[EGI]E	41				Ribosomal_60s	1.E-07	0.9	translational elongation (1e-04)		0.006	10
genetic_YLR262C	2	YPT6: GTPase, Ras-like GTP binding protein involved in the secretory pathway, required for fusion of endosome-derived vesicles with the late Golgi, maturation of the vacuolar carboxypeptidase Y; has similarity to the human GTPase, Rab6	GN[DSE]	41	[LIVMA]G[EQ]HG[DN][ST]	L_LDH PATTERN		Myb_DNA-binding	1.E-02	0.9	chromatin modification (1e-10)		0.007	10
protein_40_YGR103W	2	NOP7:  Nucleolar protein involved in rRNA processing and 60S ribosomal subunit biogenesis; constituent of several different pre-ribosomal particles; required for exit from G<sub>0</sub> and the initiation of cell proliferation	[DGN]L..L[LRG]P	41	L..LL	Motif for interaction with nuclear receptors, docking motif for p300 on p53 to promote acetylation		Brix	1.E-02	1.1	cytoplasm organization and biogenesis (0.001)	Y	0.005	8
protein_40_YGR275W	2	RTT102:  Component of both the SWI/SNF and RSC chromatin remodeling complexes, suggested role in chromosome maintenance; possible weak regulator of Ty1 transposition	VL..[LPN]A[AD]	41				Histone	1.E-02	1.2			0.005	7
protein_40_YCL059C	2	KRR1:  Essential nucleolar protein required for the synthesis of 18S rRNA and for the assembly of 40S ribosomal subunit	I[KHC].W[DCT]	41				WD40	1.E-07	1.3	snoRNA binding (1e-11)		0.005	8
protein_40_YBR010W	2	HHT1:  One of two identical histone H3 proteins (see also HHT2); core histone required for chromatin assembly, involved in heterochromatin-mediated telomeric and HM silencing; regulated by acetylation, methylation, and mitotic phosphorylation	RL.[RTD]R[GAL]	41	[KR]R	CLV_PCSK_KEX2_1	Y	Histone	1.E-04	1.4	nuclear nucleosome (0.001)	Y	0.004	8
yeast-610_GO-0031090	2	organelle membrane	G[LVA].[FAI]G	41				Mito_carr	1.E-09	1.5	envelope (1e-29)		0.008	10
protein_40_YER110C	2	KAP123:  Karyopherin beta, mediates nuclear import of ribosomal proteins prior to assembly into ribosomes and import of histones H3 and H4; localizes to the nuclear pore, nucleus, and cytoplasm; exhibits genetic interactions with RAI1	SS.I[ARK][ANG]	41	S[ST]	MDC1 BRCT domain binding motif		Sec7	1.E-02	1.6			0.004	10
protein_40_YLL008W	2	DRS1:  Nucleolar DEAD-box protein required for ribosome assembly and function, including synthesis of 60S ribosomal subunits; constituent of 66S pre-ribosomal particles	[LAP]LK[AHK]L	41	LLKIL	AP-2 binding motif in CXCR2 receptor		Pkinase	1.E-02	2.1	rRNA processing (0.001)		0.006	10
protein_40_YGR128C	2	UTP8:  Nucleolar protein required for export of tRNAs from the nucleus; also copurifies with the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	[DET]K.[VTD]K	41				WD40	1.E-05	2.1	small nucleolar ribonucleoprotein complex (1e-22)		0.008	10
yeast-1939_GO-0003824	2	catalytic activity	[DEQ]T[AID]GQ	41				Ras	1.E-36	2.7	GTPase activity (1e-27)		0.009	10
protein_40_YAR019C	2	CDC15:  Protein kinase of the Mitotic Exit Network that is localized to the spindle pole bodies at late anaphase; promotes mitotic exit by directly switching on the kinase activity of Dbf2p	FG[SLF][ACW]	41				Pkinase	1.E-16	3	protein kinase activity (1e-15)		0.006	8
protein_40_YPL211W	2	NIP7:  Nucleolar protein required for 60S ribosome subunit biogenesis, constituent of 66S pre-ribosomal particles; physically interacts with Nop8p and the exosome subunit Rrp43p	GK.A[AL][FKP]	41				DEAD	1.E-03	3.1	ribosomal large subunit assembly and maintenance (1e-04)		0.005	9
protein_40_YNL272C	2	SEC2:  Guanyl-nucleotide exchange factor for the small G-protein Sec4p, located on cytoplasmic vesicles; essential for post-Golgi vesicle transport	Y..[PMW]E	41	Y..[ILM]	SH2 ligand FOR Shc group 3 (phospho-peptide) Syk also		Pkinase	1.E-26	3.2	protein kinase activity (1e-26)	Y	0.008	10
protein_40_YOL127W	2	RPL25:  Primary rRNA-binding ribosomal protein component of the large (60S) ribosomal subunit, has similarity to E. coli L23 and rat L23a ribosomal proteins; binds to 26S rRNA via a conserved C-terminal motif	IA[TK][PMS]G	41	KSGST	eIF4 motif phosphorylation motif		DEAD	1.E-05	3.6	RNA helicase activity (1e-04)		0.004	8
protein_40_YNL061W	2	NOP2:  Probable RNA m(5)C methyltransferase, essential for processing and maturation of 27S pre-rRNA and large ribosomal subunit biogenesis; localized to the nucleolus; constituent of 66S pre-ribosomal particles	[TCF]PG[RW]	41	[ST]P	LIG_WW_4		DEAD	1.E-07	4	ribosomal large subunit assembly and maintenance (1e-08)		0.004	10
protein_40_YOL127W	2	RPL25:  Primary rRNA-binding ribosomal protein component of the large (60S) ribosomal subunit, has similarity to E. coli L23 and rat L23a ribosomal proteins; binds to 26S rRNA via a conserved C-terminal motif	[TRF][GNY].GKT	41				DEAD	1.E-09	4.2	RNA helicase activity (1e-08)		0.005	9
yeast-1389_GO-0044260	2	cellular macromolecule metabolism	HRD[ILMV][KLS]	41	[LIVMF]PCHR[LIVMF][LIVMF]	MGMT PATTERN		Pkinase	1.E-55	6.9	protein amino acid phosphorylation (1e-62)		0.009	10
yeast-544_GO-0016070	2	RNA metabolism	[HFG]R.G[RFW]	41	RGG	Alternative integrin binding site in FMDV virus	Y	Helicase_C	1.E-23	10.9	RNA metabolism (1e-31)		0.009	10
yeast-294_GO-0006366	2	transcription from RNA polymerase II promoter	[CFA]R.[RKD]K	41	R.RKGSF	PKC delta kinase substrate motif	Y	Zn_clus	1.E-11	13.3	transcription from RNA polymerase II promoter (1e-48)		0.009	10
yeast-460_GO-0006351	2	transcription, DNA-dependent	CR.[RKT][KWH]	41	R.[ST]	PKA consensus phosphorylation site		Zn_clus	1.E-21	17.9	transcription, DNA-dependent (1e-24)		0.009	10
yeast-589_GO-0050896	2	response to stimulus	[LPV]E.P[KMR]	41	[ST]P[KR]	Growth associated histone HI kinase substrate motif					response to stress (1e-24)	Y	0.009	10
yeast-388_GO-0007275	2	development	K[NIM]K[NMH]	41							multicellular organismal development (1e-53)		0.009	10
yeast-320_GO-0006355	2	regulation of transcription, DNA-dependent	Q[VMS]L[LTP]	41							regulation of transcription, DNA-dependent (1e-63)		0.009	10
yeast-295_GO-0016192	2	vesicle-mediated transport	SL..[LVE][PQH]	41			Y				vesicle-mediated transport (1e-81)		0.009	10
yeast-251_GO-0005886	2	plasma membrane	C..[SYF]G	41			Y				plasma membrane (1e-57)	Y	0.009	10
yeast-248_GO-0031966	2	mitochondrial membrane	S..S[DHN]	41	S..S	Casien kinase I phosphorylation site, 1st Ser must be phosphorylated							0.009	10
yeast-235_GO-0009653	2	morphogenesis	Q..[SQN]H	41							cellular morphogenesis (1e-71)	Y	0.009	10
yeast-235_GO-0000902	2	cellular morphogenesis	Q..[SQN]H	41							cellular morphogenesis (1e-71)	Y	0.009	10
yeast-223_GO-0003735	2	structural constituent of ribosome	T[ETV]T	41	YTV	14-3-3 domain binding motif							0.009	10
yeast-219_GO-0046903	2	secretion	D[FHV]L[LIW]K	41	LLKIL	AP-2 binding motif in CXCR2 receptor					secretion (1e-13)		0.007	10
yeast-1547_GO-0043283	2	biopolymer metabolism	KF[GKN]	41	KFG.GDG	NMT_2 PATTERN					RNA metabolism (1e-60)		0.009	10
yeast-1134_GO-0044249	2	cellular biosynthesis	A[AGQ].[KER]A	41			Y				macromolecule biosynthetic process (1e-33)		0.009	10
yeast-1134_GO-0044249	2	cellular biosynthesis	E..[NQC]E	41							nuclear lumen (1e-13)	Y	0.009	10
yeast-1036_GO-0005739	2	mitochondrion	D[EDS]D	41	D[SGDN]D[PE][LIVMF]D[LIVMGAC]	PPASE PATTERN	Y				cell cycle (1e-15)		0.009	10
protein_40_YPL146C	2	NOP53:  Nucleolar protein; involved in biogenesis of the 60S subunit of the ribosome; interacts with rRNA processing factors Cbf5p and Nop2p; null mutant is viable but growth is severely impaired	[EWF]IL[RIP]S	41	LLKIL	AP-2 binding motif in CXCR2 receptor						Y	0.004	8
protein_40_YPL129W	2	TAF14:  Subunit of TFIID, TFIIF, INO80, SWI/SNF, and NuA3 complexes, involved in RNA polymerase II transcription initiation and in chromatin modification; contains a YEATS domain	[LVK]A[ENH]LI	41							nucleoplasm part (0.001)		0.004	9
protein_40_YPL090C	2	RPS6A:  Protein component of the small (40S) ribosomal subunit; identical to Rps6Bp and has similarity to rat S6 ribosomal protein	R[RGA].A[RQM]	41							cytosolic ribosome (sensu Eukaryota) (1e-13)		0.007	10
protein_40_YOR310C	2	NOP58:  Protein involved in pre-rRNA processing, 18S rRNA synthesis, and snoRNA synthesis; component of the small subunit processome complex, which is required for processing of pre-18S rRNA	SE[SVT][EGM]S	41			Y				nucleolus (1e-08)		0.005	9
protein_40_YOR181W	2	LAS17:  Actin assembly factor, activates the Arp2/3 protein complex that nucleates branched actin filaments; localizes with the Arp2/3 complex to actin patches; homolog of the human Wiskott-Aldrich syndrome protein (WASP)	[PMN]E..[RAM]Y	41			Y				endocytosis (0.01)	Y	0.005	7
protein_40_YOR039W	2	CKB2:  Beta' regulatory subunit of casein kinase 2, a Ser/Thr protein kinase with roles in cell growth and proliferation; the holoenzyme also contains CKA1, CKA2 and CKB1, the many substrates include transcription factors and all RNA polymerases	SN.[GP]G[NHK]	41			Y						0.005	8
protein_40_YOL012C	2	HTZ1:  Histone variant H2AZ, exchanged for histone H2A in nucleosomes by the SWR1 complex; involved in transcriptional regulation through prevention of the spread of silent heterochromatin	[YMG][EPW]EV	41	[YW]EVD	Protease Caspase 1 /ICE					establishment and/or maintenance of chromatin architecture (1e-05)		0.005	9
protein_40_YNL209W	2	SSB2:  Cytoplasmic ATPase that is a ribosome-associated molecular chaperone, functions with J-protein partner Zuo1p; may be involved in the folding of newly-synthesized polypeptide chains; member of the HSP70 family; homolog of SSB1	[AFP]S.KA[IDV]	41									0.004	7
protein_40_YNL154C	2	YCK2:  Palmitoylated, plasma membrane-bound casein kinase I isoform; shares redundant functions with Yck1p in morphogenesis, proper septin assembly, endocytic trafficking; provides an essential function overlapping with that of Yck1p	PP[PHN]K[PN]	41	[DE]FPPP	EVH binding motif of Mena							0.004	8
protein_40_YMR290C	2	HAS1:  ATP-dependent RNA helicase; localizes to both the nuclear periphery and nucleolus; highly enriched in nuclear pore complex fractions; constituent of 66S pre-ribosomal particles	[DKQ]D.[EGK]E	41							cytoplasm organization and biogenesis (1e-28)		0.008	10
protein_40_YMR236W	2	TAF9:  Subunit (17 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation and in chromatin modification, similar to histone H3	[EMV]DE[DNV]E	41	S[DE][DE]E	BARD1 BRCT domain binding motif					transcription factor complex (1e-14)		0.006	9
protein_40_YMR139W	2	RIM11:  Protein kinase required for signal transduction during entry into meiosis; promotes the formation of the Ime1p-Ume6p complex by phosphorylating Ime1p and Ume6p; shares similarity with mammalian glycogen synthase kinase 3-beta	E[KT][LHN]IN	41			Y						0.005	7
protein_40_YMR012W	2	CLU1:  eIF3 component of unknown function; deletion causes defects in mitochondrial organization but not in growth or translation initiation, can rescue cytokinesis and mitochondrial organization defects of the Dictyostelium cluA- mutant	R[ETP]..[IQG]P	41	GP	Protease TTP cleavage site							0.006	8
protein_40_YML085C	2	TUB1:  Alpha-tubulin; associates with beta-tubulin (Tub2p) to form tubulin dimer, which polymerizes to form microtubules	SS..[LEN]N[KWQ]	41	S[ST]	MDC1 BRCT domain binding motif						Y	0.004	7
protein_40_YLR429W	2	CRN1:  Coronin, cortical actin cytoskeletal component that associates with the Arp2p/Arp3p complex to regulate its activity; plays a role in regulation of actin patch assembly	SS..[IK][LP]N	41	S[ST]	MDC1 BRCT domain binding motif							0.004	9
protein_40_YLR347C	2	KAP95:  Karyopherin beta, forms a dimeric complex with Srp1p (Kap60p) that mediates nuclear import of cargo proteins via a nuclear localization signal (NLS), interacts with nucleoporins to guide transport across the nuclear pore complex	[IVS]G.G[LA]F	41	SG.G	Glycosaminoglycan attachment site							0.005	8
protein_40_YLR347C	2	KAP95:  Karyopherin beta, forms a dimeric complex with Srp1p (Kap60p) that mediates nuclear import of cargo proteins via a nuclear localization signal (NLS), interacts with nucleoporins to guide transport across the nuclear pore complex	GG.[FAS][GHF]S	41	GGQ	N-methylation motif in E. coli, Gln residue in methylated, mimics CCA motif at the end of tRNA molecule					protein import into nucleus (1e-05)		0.004	7
protein_40_YKL203C	2	TOR2:  PIK-related protein kinase and rapamycin target; subunit of TORC1, a complex that regulates growth in response to nutrients and TORC2, a complex that regulates cell-cycle dependent polarization of the actin cytoskeleton; involved in meiosis	I[LTE]..IL[PEQ]	41							actin cytoskeleton organization and biogenesis (0.001)	Y	0.004	8
protein_40_YKL145W	2	RPT1:  One of six ATPases of the 19S regulatory particle of the 26S proteasome involved in the degradation of ubiquitinated substrates; required for optimal CDC20 transcription; interacts with Rpn12p and the E3 ubiquitin-protein ligase Ubr1p	[DYQ]MI[LQG]	41	YM	SH2 ligand for Vav1 (group II) (phospho-peptide)					proteasome complex (sensu Eukaryota) (0.001)	Y	0.005	10
protein_40_YJL130C	2	URA2:  Bifunctional carbamoylphosphate synthetase (CPSase)-aspartate transcarbamylase (ATCase), catalyzes the first two enzymatic steps in the de novo biosynthesis of pyrimidines; both activities are subject to feedback inhibition by UTP	[TV]V[AYM]AL	41	DALDL	14-3-3 binding motif in ExoS							0.005	10
protein_40_YJL130C	2	URA2:  Bifunctional carbamoylphosphate synthetase (CPSase)-aspartate transcarbamylase (ATCase), catalyzes the first two enzymatic steps in the de novo biosynthesis of pyrimidines; both activities are subject to feedback inhibition by UTP	ED[AR]D[DKA]	41	D.D	Ribose moiety of UDP and manganese binding site in glucuronyl transferase	Y						0.005	7
protein_40_YJL081C	2	ARP4:  Nuclear actin-related protein involved in chromatin remodeling, component of chromatin-remodeling enzyme complexes	K[LQ]..N[VFA]T	41							establishment and/or maintenance of chromatin architecture (0.001)		0.005	9
protein_40_YJL074C	2	SMC3:  Subunit of the multiprotein cohesin complex required for sister chromatid cohesion in mitotic cells; also required, with Rec8p, for cohesion and recombination during meiosis; phylogenetically conserved SMC chromosomal ATPase family member	[EDV]V.[EMI]I	41			Y					Y	0.007	10
protein_40_YJL010C	2	NOP9:  Essential component of pre-40S ribosomes that is required for early cleavages of 35S pre-rRNA and hence formation of 18S rRNA; binds RNA in vitro and contains multiple pumilio-like repeats	E[SDQ]..[EGP]E	41							nucleolus (1e-24)		0.008	10
protein_40_YIL094C	2	LYS12:  Homo-isocitrate dehydrogenase, an NAD-linked mitochondrial enzyme required for the fourth step in the biosynthesis of lysine, in which homo-isocitrate is oxidatively decarboxylated to alpha-ketoadipate	[EMP]K.[FH]V	41									0.005	10
protein_40_YIL094C	2	LYS12:  Homo-isocitrate dehydrogenase, an NAD-linked mitochondrial enzyme required for the fourth step in the biosynthesis of lysine, in which homo-isocitrate is oxidatively decarboxylated to alpha-ketoadipate	[SY]TYA[DA]	41	[LN][RI]TY	PDGFR kinase substrate motif	Y						0.005	9
protein_40_YIL094C	2	LYS12:  Homo-isocitrate dehydrogenase, an NAD-linked mitochondrial enzyme required for the fourth step in the biosynthesis of lysine, in which homo-isocitrate is oxidatively decarboxylated to alpha-ketoadipate	A[KAY]..E[REG]	41								Y	0.008	10
protein_40_YHR196W	2	UTP9:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	T[NL]..DD[NYK]	41	DDDK[ACDEFGHIKLMNQRSTVWY]	Protease Enterokinase					nucleolus (0.01)		0.005	7
protein_40_YHR148W	2	IMP3:  Component of the SSU processome, which is required for pre-18S rRNA processing, essential protein that interacts with Mpp10p and mediates interactions of Imp4p and Mpp10p with U3 snoRNA	[RWE]H..[FIE]L	41							nucleolus (1e-13)	Y	0.006	10
protein_40_YHR135C	2	YCK1:  Palmitoylated, plasma membrane-bound casein kinase I isoform; shares redundant functions with Yck2p in morphogenesis, proper septin assembly, endocytic trafficking; provides an essential function overlapping with that of Yck2p	KT[GKS]	41	[FY]PS[AGMS]CGKT[NS]	PEPCK_GTP PATTERN							0.008	10
protein_40_YHR088W	2	RPF1:  Nucleolar protein involved in the assembly of the large ribosomal subunit; constituent of 66S pre-ribosomal particles; contains a sigma(70)-like motif, which is thought to bind RNA	I[SGV]..LR[DTN]	41	LRT	LKB1 Kinase substrate motif					cytoplasm organization and biogenesis (0.01)		0.004	7
protein_40_YHR052W	2	CIC1:  Essential protein that interacts with proteasome components and has a potential role in proteasome substrate specificity; also copurifies with 66S pre-ribosomal particles	[KQC]KS[LV]E	41							ribosome biogenesis (0.001)		0.005	9
protein_40_YGR252W	2	GCN5:  Histone acetyltransferase, acetylates N-terminal lysines on histones H2B and H3; catalytic subunit of the ADA and SAGA histone acetyltransferase complexes; founding member of the Gcn5p-related N-acetyltransferase superfamily	[LSG]K.V[PLQ]T	41	VP	Interleukin converting enzyme protease							0.004	10
protein_40_YGR252W	2	GCN5:  Histone acetyltransferase, acetylates N-terminal lysines on histones H2B and H3; catalytic subunit of the ADA and SAGA histone acetyltransferase complexes; founding member of the Gcn5p-related N-acetyltransferase superfamily	L[IHW].[DC]AI	41	EDAIY	Abl kinase substrate motif					SAGA complex (0.01)		0.005	9
protein_40_YGR218W	2	CRM1:  Major karyopherin, involved in export of proteins, RNAs, and ribosomal subunits from the nucleus	EE.[KLA]S[SLK]	41	EED	Ankyrin B C-terminal motif that binds internal Ankyrin repeats							0.006	10
protein_40_YGR218W	2	CRM1:  Major karyopherin, involved in export of proteins, RNAs, and ribosomal subunits from the nucleus	G[NFT].N[TKN]	41							snRNP protein import into nucleus (1e-08)	Y	0.008	10
protein_40_YGR218W	2	CRM1:  Major karyopherin, involved in export of proteins, RNAs, and ribosomal subunits from the nucleus	L..Q[LPR]	41							rRNA export from nucleus (1e-05)	Y	0.007	10
protein_40_YGR103W	2	NOP7:  Nucleolar protein involved in rRNA processing and 60S ribosomal subunit biogenesis; constituent of several different pre-ribosomal particles; required for exit from G<sub>0</sub> and the initiation of cell proliferation	[DER][EGN]EE	41	EEEYF	EGFR kinase phosphorylation site (peptide screen)					cytoplasm organization and biogenesis (1e-26)	Y	0.008	10
protein_40_YGR103W	2	NOP7:  Nucleolar protein involved in rRNA processing and 60S ribosomal subunit biogenesis; constituent of several different pre-ribosomal particles; required for exit from G<sub>0</sub> and the initiation of cell proliferation	[KHR]K..K[ARQ]	41	KR	CLV_PCSK_PC1ET2_1					cytoplasm organization and biogenesis (1e-22)	Y	0.008	10
protein_40_YGR103W	2	NOP7:  Nucleolar protein involved in rRNA processing and 60S ribosomal subunit biogenesis; constituent of several different pre-ribosomal particles; required for exit from G<sub>0</sub> and the initiation of cell proliferation	E[DEP]..D[EGM]	41							cytoplasm organization and biogenesis (1e-20)	Y	0.008	10
protein_40_YGR090W	2	UTP22:  Possible U3 snoRNP protein involved in maturation of pre-18S rRNA, based on computational analysis of large-scale protein-protein interaction data	SD[DYE][EHQ]	41	S[DE][DE][DE]	Casein Kinase II substrate motif					rRNA processing (1e-19)		0.007	10
protein_40_YGR086C	2	PIL1:  Primary component of eisosomes, which are large immobile cell cortex structures associated with endocytosis; null mutants show activation of Pkc1p/Ypk1p stress resistance pathways; detected in phosphorylated state in mitochondria	[KPI]RRS[LEV]	41	[KR]R	CLV_PCSK_KEX2_1							0.005	9
protein_40_YGL158W	2	RCK1:  Protein kinase involved in the response to oxidative stress; identified as suppressor of S. pombe cell cycle checkpoint mutations	SS[DQY]D[EKQ]	41	S.D	CAMKII phosphorylation site							0.005	10
protein_40_YGL147C	2	RPL9A:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl9Bp and has similarity to E. coli L6 and rat L9 ribosomal proteins	[RIW]AA[RS]	41							cytosolic ribosome (sensu Eukaryota) (1e-15)		0.007	10
protein_40_YGL111W	2	NSA1:  Constituent of 66S pre-ribosomal particles, involved in 60S ribosomal subunit biogenesis	G[FP]..V[TMN]	41	GP	Protease TTP cleavage site					cytoplasm organization and biogenesis (1e-06)		0.005	10
protein_40_YGL105W	2	ARC1:  Protein that binds tRNA and methionyl- and glutamyl-tRNA synthetases (Mes1p and Gus1p), delivering tRNA to them, stimulating catalysis, and ensuring their localization to the cytoplasm; also binds quadruplex nucleic acids	[LGV]K..[TEM]LT	41	K..[ST]	PKA kinase substrate motif						Y	0.005	8
protein_40_YGL076C	2	RPL7A:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl7Bp and has similarity to E. coli L30 and rat L7 ribosomal proteins; contains a conserved C-terminal Nucleic acid Binding Domain (NDB2)	T[KDP][KSP]GL	41			Y				ribosomal large subunit biogenesis (1e-04)		0.005	7
protein_40_YFR034C	2	PHO4:  Basic helix-loop-helix (bHLH) transcription factor of the myc-family; binds cooperatively with Pho2p to the PHO5 promoter; function is regulated by phosphorylation at multiple sites and by phosphate availability	[IGD]G[APC]R	41	[AG]R	Protease matriptase protease site						Y	0.008	10
protein_40_YFL039C	2	ACT1:  Actin, structural protein involved in cell polarization, endocytosis, and other cytoskeletal functions	[EHT]LE[SEV]T	41	L..[LM]E	Sec24p					response to osmotic stress (0.001)		0.005	9
protein_40_YER172C	2	BRR2:  RNA-dependent ATPase RNA helicase (DEIH box); required for disruption of U4/U6 base-pairing in native snRNPs to activate the spliceosome for catalysis; homologous to human U5-200kD	[LKF]KL[ER]S	41									0.004	8
protein_40_YER133W	2	GLC7:  Catalytic subunit of type 1 serine/threonine protein phosphatase, involved in many processes including glycogen metabolism, sporulation, and mitosis; interacts with multiple regulatory subunits; predominantly isolated with Sds22p	E.[VDG]D	41	YE.[IV]	SH2 ligand for Fes (Tyr must be phosphorylated)					mRNA cleavage and polyadenylation specificity factor complex (1e-08)		0.008	10
protein_40_YER006W	2	NUG1:  GTPase that associates with nuclear 60S pre-ribosomes, required for export of 60S ribosomal subunits from the nucleus	L[EWL].I[NGH]N	41			Y				nucleolus (0.01)		0.004	9
protein_40_YDR449C	2	UTP6:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	T[DKL].SK[RK]	41	KR	CLV_PCSK_PC1ET2_1					cytoplasm organization and biogenesis (1e-06)		0.004	7
protein_40_YDR388W	2	RVS167:  Actin-associated protein, subunit of a complex (Rvs161p-Rvs167p) involved in regulation of actin cytoskeleton, endocytosis, and viability following starvation or osmotic stress; homolog of mammalian amphiphysin	P.[RQS]E	41	[ST]E	G protein-coupled receptor kinase 1 substrate motif					cell cortex (1e-04)		0.007	10
protein_40_YDR303C	2	RSC3:  Component of the RSC chromatin remodeling complex; essential gene required for maintenance of proper ploidy and regulation of ribosomal protein genes and the cell wall/stress response; highly similar to Rsc30p	Q[DWM].D[SDP]	41	P.Q..D	LIG_TRAF2_2							0.005	8
protein_40_YDR225W	2	HTA1:  One of two nearly identical (see also HTA2) histone H2A subtypes; core histone required for chromatin assembly and chromosome function; DNA damage-dependent phosphorylation by Mec1p facilitates DNA repair; acetylated by Nat4p	[SCI]I[LE]SP	41	SP	ERK1, ERK2 Kinase substrate motif							0.005	9
protein_40_YDR174W	2	HMO1:  Chromatin associated high mobility group (HMG) family member involved in genome maintenance; rDNA-binding component of the Pol I transcription system; associates with a 5'-3' DNA helicase and Fpr1p, a prolyl isomerase	[IKA]S..F[SQY]I	41	S..F	LIG_BRCT_BRCA1_1						Y	0.004	9
protein_40_YDR064W	2	RPS13:  Protein component of the small (40S) ribosomal subunit; has similarity to E. coli S15 and rat S13 ribosomal proteins	R..[VAK]R	41	[KR]R	CLV_PCSK_KEX2_1					ribonucleoprotein complex (1e-32)	Y	0.008	10
protein_40_YDR060W	2	MAK21:  Constituent of 66S pre-ribosomal particles, required for large (60S) ribosomal subunit biogenesis; involved in nuclear export of pre-ribosomes; required for maintenance of dsRNA virus; homolog of human CAATT-binding protein	[NVY]E..SD[SVA]	41	YE	TPK-IIB/P38Syk kinase phosphorylation site (peptide screen)					nucleolus (1e-06)		0.004	9
protein_40_YDR012W	2	RPL4B:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl4Ap and has similarity to E. coli L4 and rat L4 ribosomal proteins	[LAR]G.K[AKV]	41							cytosolic ribosome (sensu Eukaryota) (1e-15)	Y	0.008	10
protein_40_YDL213C	2	NOP6:  Putative RNA-binding protein implicated in ribosome biogenesis; contains an RNA recognition motif (RRM) and has similarity to hydrophilins; NOP6 may be a fungal-specific gene as no homologs have been yet identified in higher eukaryotes	[KNG]K.K[KVQ]	41	P.[ST]PKK.KK	Cdc2 like protein kinase substrate motif					nucleolus (1e-21)	Y	0.008	10
protein_40_YDL213C	2	NOP6:  Putative RNA-binding protein implicated in ribosome biogenesis; contains an RNA recognition motif (RRM) and has similarity to hydrophilins; NOP6 may be a fungal-specific gene as no homologs have been yet identified in higher eukaryotes	EE[SLV]S[GFK]	41	YEE[IV]	SH2 ligand group 1A, Src FGR SH2 domain (needs to be Tyr phosphorylated)	Y				RNA metabolism (1e-05)		0.005	8
protein_40_YDL055C	2	PSA1:  GDP-mannose pyrophosphorylase (mannose-1-phosphate guanyltransferase), synthesizes GDP-mannose from GTP and mannose-1-phosphate in cell wall biosynthesis; required for normal cell wall structure	A.D[VEI]	41	HAVDI	N-Cadherin ligand	Y				carboxylic acid metabolism (0.01)	Y	0.007	10
protein_40_YBR142W	2	MAK5:  Essential nucleolar protein, putative DEAD-box RNA helicase required for maintenance of M1 dsRNA virus; involved in biogenesis of large (60S) ribosomal subunits	[KGL]K..K[EVT]	41	P.[ST]PKK.KK	Cdc2 like protein kinase substrate motif					cytoplasm organization and biogenesis (1e-10)		0.008	10
protein_40_YBR048W	2	RPS11B:  Protein component of the small (40S) ribosomal subunit; identical to Rps11Ap and has similarity to E. coli S17 and rat S11 ribosomal proteins	[KAL]K.[AP]FT	41							ribosome (0.01)		0.005	7
protein_40_YBL016W	2	FUS3:  Mitogen-activated serine/threonine protein kinase involved in mating; phosphoactivated by Ste7p; substrates include Ste12p, Far1p, Bni1p, Sst2p; inhibits invasive growth during mating by phosphorylating Tec1p, promoting its degradation	[EGN]FA[SPW]L	41								Y	0.004	8
protein_40_YBL016W	2	FUS3:  Mitogen-activated serine/threonine protein kinase involved in mating; phosphoactivated by Ste7p; substrates include Ste12p, Far1p, Bni1p, Sst2p; inhibits invasive growth during mating by phosphorylating Tec1p, promoting its degradation	K..S[RPA]	41	K..[ST]	PKA kinase substrate motif					response to pheromone (1e-06)		0.008	10
protein_40_YBL003C	2	HTA2:  One of two nearly identical (see also HTA1) histone H2A subtypes; core histone required for chromatin assembly and chromosome function; DNA damage-dependent phosphorylation by Mec1p facilitates DNA repair; acetylated by Nat4p	D[ENY]E[EAG]	41	SEDEE	CKII kinase phosphorylation site (peptide screen)					chromosome (1e-04)	Y	0.008	10
protein_40_YAL032C	2	PRP45:  Protein required for pre-mRNA splicing; associates with the spliceosome and interacts with splicing factors Prp22p and Prp46p; orthologous to human transcriptional coactivator SKIP and can activate transcription of a reporter gene	[SEK]D..I[PHT]	41									0.008	10
protein_40_YAL032C	2	PRP45:  Protein required for pre-mRNA splicing; associates with the spliceosome and interacts with splicing factors Prp22p and Prp46p; orthologous to human transcriptional coactivator SKIP and can activate transcription of a reporter gene	K[MPW]..L[EMW]	41			Y					Y	0.006	10
oshea_nucleolus	2	oshea_nucleolus	[TEM]D.SK[RQP]	41	KR	CLV_PCSK_PC1ET2_1					nucleolus (1e-09)		0.005	9
oshea_cytoplasm	2	oshea_cytoplasm	S.[KDT]P	41	[ST]P	LIG_WW_4					regulation of cellular metabolism (1e-06)		0.008	10
oshea_ambiguous	2	oshea_ambiguous	E..N[SQW]	41							bud (1e-05)	Y	0.008	10
matsuyama_ER	2	matsuyama_ER	Y.[IFW]I	41	[IVL]Y.[PF]	ABL phosphorylation site					nuclear envelope-endoplasmic reticulum network (1e-09)		0.010	10
genetic_YPL055C	2	LGE1: Protein of unknown function; null mutant forms abnormally large cells, and homozygous diploid null mutant displays delayed premeiotic DNA synthesis and reduced efficiency of meiotic nuclear division	E[FEH].[EHN]S	41							DNA metabolism (1e-04)		0.008	10
genetic_YLR200W	2	YKE2: Subunit of the heterohexameric Gim/prefoldin protein complex involved in the folding of alpha-tubulin, beta-tubulin, and actin	N.E	41	[LIVMFY][DN]G[LIVMF][DN][LIVMF][DN].E	CHITINASE_18 PATTERN					cell cycle (1e-18)		0.008	10
genetic_YGL058W	2	RAD6: Ubiquitin-conjugating enzyme (E2), involved in postreplication repair (with Rad18p), sporulation, telomere silencing, and ubiquitin-mediated N-end rule protein degradation (with Ubr1p)	SI[IM]D[IYC]	41			Y					Y	0.005	9
protein_40_YBR160W	2	CDC28:  Catalytic subunit of the main cell cycle cyclin-dependent kinase (CDK); alternately associates with G1 cyclins (CLNs) and G2/M cyclins (CLBs) which direct the CDK to specific substrates	[EA]M.RL[EKF]	41							 		0.005	8
yeast-649_GO-0003676	2	nucleic acid binding	Q[QKM]Q	40				RRM_1	1.E-08	-3.5	nucleic acid binding (1e-12)		0.009	10
yeast-235_GO-0000278	2	mitotic cell cycle	S[SPN][SLV]K	40	S[ST]	MDC1 BRCT domain binding motif		Pkinase	1.E-03	-1.6	mitotic cell cycle (1e-09)		0.009	10
yeast-1721_GO-0016043	2	cell organization and biogenesis	T.[SNK]S	40				HEAT	1.E-03	-1.6	cellular localization (1e-62)		0.008	10
protein_40_YKL014C	2	URB1:  Nucleolar protein required for the normal accumulation of 25S and 5.8S rRNAs, associated with the 27SA2 pre-ribosomal particle; proposed to be involved in the biogenesis of the 60S ribosomal subunit	A[RPE][AGE]G	40				DEAD	1.E-05	-1.4	cytoplasm organization and biogenesis (1e-15)		0.008	10
yeast-513_GO-0005515	2	protein binding	E.[NLT]K	40				SH3_1	1.E-02	-1.3	protein binding (1e-26)	Y	0.008	10
protein_40_YKL014C	2	URB1:  Nucleolar protein required for the normal accumulation of 25S and 5.8S rRNAs, associated with the 27SA2 pre-ribosomal particle; proposed to be involved in the biogenesis of the 60S ribosomal subunit	[AEY]A..LD[IQ]	40				DEAD	1.E-03	-1.2	nucleolus (1e-05)		0.005	7
matsuyama_nuclear_envelope_or_dots	2	matsuyama_nuclear_envelope_or_dots	[QPD]AL	40	DALDL	14-3-3 binding motif in ExoS		IBN_N	1.E-06	-1.2	nuclear envelope (1e-29)		0.010	10
protein_40_YPL093W	2	NOG1:  Putative GTPase that associates with free 60S ribosomal subunits in the nucleolus and is required for 60S ribosomal subunit biogenesis; constituent of 66S pre-ribosomal particles; member of the ODN family of nucleolar G-proteins	[TRM]G..K[TGV]	40				Helicase_C	1.E-08	-1	cytoplasm organization and biogenesis (1e-15)		0.008	10
protein_40_YKR001C	2	VPS1:  Dynamin-like GTPase required for vacuolar sorting; also involved in actin cytoskeleton organization, late Golgi-retention of some proteins, regulating peroxisome biogenesis	AT..[THK]S[KPN]	40	SP	ERK1, ERK2 Kinase substrate motif		SNF2_N	1.E-02	-0.9		Y	0.005	8
protein_40_YHR196W	2	UTP9:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	K..[KFL]R	40	[KR]R	CLV_PCSK_KEX2_1		S4	1.E-02	-0.9	nucleolus (1e-29)		0.007	10
yeast-312_GO-0006414	2	translational elongation	[IV]D.PGH	40	D..G	motif that binds phosphate in GDP and GTP binding proteins		GTP_EFTU_D2	1.E-08	-0.8	translation elongation factor activity (1e-08)		0.005	7
yeast-294_GO-0006366	2	transcription from RNA polymerase II promoter	TT...[NPK]	40				Zn_clus	1.E-03	-0.8	transcription from RNA polymerase II promoter (1e-15)		0.008	10
yeast-215_GO-0005694	2	chromosome	L[LY].[LR]FD	40				SNF2_N	1.E-02	-0.8	chromosome (1e-09)		0.006	8
protein_40_YHR088W	2	RPF1:  Nucleolar protein involved in the assembly of the large ribosomal subunit; constituent of 66S pre-ribosomal particles; contains a sigma(70)-like motif, which is thought to bind RNA	A..A[EKF]	40	A.AA.VP....VP........P	PLU-1 transcription factor binding motif in BF-1 and PAX9		IBN_N	1.E-02	-0.8	cytoplasm organization and biogenesis (1e-24)		0.008	10
yeast-238_GO-0017111	2	nucleoside-triphosphatase activity	[TDG]I[GKD]V	40				Ras	1.E-05	-0.7	nucleoside-triphosphatase activity (1e-48)	Y	0.009	10
protein_40_YBR010W	2	HHT1:  One of two identical histone H3 proteins (see also HHT2); core histone required for chromatin assembly, involved in heterochromatin-mediated telomeric and HM silencing; regulated by acetylation, methylation, and mitotic phosphorylation	AL.[ERQ][LVT]A	40				HEAT	1.E-03	-0.7			0.004	8
protein_40_YLR293C	2	GSP1:  GTP binding protein (mammalian Ranp homolog) involved in the maintenance of nuclear organization, RNA processing and transport; regulated by Prp20p, Rna1p, Yrb1p, Yrb2p, Yrp4p, Yrb30p, Cse1p and Kap95p; yeast Gsp2p homolog	[EHQ]LL[ET]V	40	[DE]..LL	Di-Leu acidic motif for receptor endocytosis (recognized by VHS domain of GGA proteins)		IBN_N	1.E-02	-0.5	protein import into nucleus (0.001)	Y	0.005	7
protein_40_YJR066W	2	TOR1:  PIK-related protein kinase and rapamycin target; subunit of TORC1, a complex that controls growth in response to nutrients by regulating translation, transcription, ribosome biogenesis, nutrient transport and autophagy; involved in meiosis	[RKA]P..LK[TR]	40	KR	CLV_PCSK_PC1ET2_1		GATA	1.E-04	-0.5	nitrogen utilization (1e-06)	Y	0.005	8
protein_40_YMR093W	2	UTP15:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	[DHM]E[SEK]D	40	E[ST]D	Ankyrin G binding motif in KNCQ2 and KNCQ3 potaqssium channels		WD40	1.E-04	-0.3	nucleolus (1e-20)		0.008	10
yeast-610_GO-0031090	2	organelle membrane	L[LAM]G	40	LLG	Beta2-Integrin binding motif		Mito_carr	1.E-08	-0.1	envelope (1e-69)		0.008	10
yeast-1115_GO-0006996	2	organelle organization and biogenesis	Q.S[SGQ]	40	S[ST]	MDC1 BRCT domain binding motif		PI3_PI4_kinase	1.E-03	-0.1	chromosome organization and biogenesis (1e-63)		0.008	10
yeast-341_GO-0045449	2	regulation of transcription	L..[PNH]S	40				zf-C2H2	1.E-08	0	regulation of transcription (1e-21)		0.009	10
protein_40_YJL109C	2	UTP10:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	K..K[RL]	40	KR	CLV_PCSK_PC1ET2_1	Y	WD40	1.E-06	0.1	rRNA processing (1e-43)		0.007	10
protein_40_YJL074C	2	SMC3:  Subunit of the multiprotein cohesin complex required for sister chromatid cohesion in mitotic cells; also required, with Rec8p, for cohesion and recombination during meiosis; phylogenetically conserved SMC chromosomal ATPase family member	[VEN].TE	40	[ST]E	G protein-coupled receptor kinase 1 substrate motif		SMC_N	1.E-02	0.1	cohesin complex (1e-04)	Y	0.007	10
yeast-1433_GO-0006139	2	nucleobase, nucleoside, nucleotide and nucleic acid metabolism	G..K	40	G..G..K	Sulfonate donor binding site in sulfotransferases	Y	Helicase_C	1.E-05	0.2	RNA metabolism (1e-16)	Y	0.008	10
protein_40_YCL059C	2	KRR1:  Essential nucleolar protein required for the synthesis of 18S rRNA and for the assembly of 40S ribosomal subunit	K..K[RL]	40	KR	CLV_PCSK_PC1ET2_1	Y	WD40	1.E-05	0.2	cytoplasm organization and biogenesis (1e-39)		0.007	10
protein_40_YGL105W	2	ARC1:  Protein that binds tRNA and methionyl- and glutamyl-tRNA synthetases (Mes1p and Gus1p), delivering tRNA to them, stimulating catalysis, and ensuring their localization to the cytoplasm; also binds quadruplex nucleic acids	E.[IFD]L	40	YE.[IV]	SH2 ligand for Fes (Tyr must be phosphorylated)		Pkinase	1.E-13	0.3	protein kinase activity (1e-13)	Y	0.007	10
protein_40_YBR009C	2	HHF1:  One of two identical histone H4 proteins (see also HHF2); core histone required for chromatin assembly and chromosome function; contributes to telomeric silencing; N-terminal domain involved in maintaining genomic integrity	R..R[RYQ]	40	R.[RK]R	CLV_PCSK_FUR_1		Histone	1.E-07	0.4	nuclear chromatin (1e-08)		0.007	10
oshea_bud_neck	2	oshea_bud_neck	R..D	40				RhoGAP	1.E-05	0.6	site of polarized growth (1e-73)	Y	0.008	10
yeast-413_GO-0005215	2	transporter activity	L..[TGI]A	40				MFS_1	1.E-14	0.7	transporter activity (1e-19)	Y	0.008	10
yeast-335_GO-0016772	2	transferase activity, transferring phosphorus-containing groups	[KHA]Y..PS[NEK]	40	Y..P	SH2 ligand group 1B-Crk, SH2 binding motif for ITK, Nck and RasGAP to Doc-R (needs to be Tyr phosphorylated)		Pkinase	1.E-02	0.7	transferase activity, transferring phosphorus-containing groups (1e-09)		0.006	8
yeast-513_GO-0005515	2	protein binding	Q[QSE]L	40				HEAT	1.E-03	0.8	protein binding (1e-21)	Y	0.008	10
protein_40_YBR159W	2	IFA38: Microsomal beta-keto-reductase; contains oleate response element (ORE) sequence in the promoter region; mutants exhibit reduced VLCFA synthesis, accumulate high levels of dihydrosphingosine, phytosphingosine and medium-chain ceramides	V..[FAI]F	40			Y	MFS_1	1.E-05	1	transporter activity (1e-08)	Y	0.007	10
yeast-980_GO-0051179	2	localization	F..[VAL]F	40	F..LF	Androgen receptor motif that interacts with AF2		MFS_1	1.E-11	1.1	cellular localization (1e-64)	Y	0.008	10
yeast-235_GO-0009653	2	morphogenesis	D[GNW]..[GNL]KT	40				Ras	1.E-05	1.1	cellular morphogenesis (1e-07)		0.005	8
yeast-235_GO-0000902	2	cellular morphogenesis	D[GNW]..[GNL]KT	40				Ras	1.E-05	1.1	cellular morphogenesis (1e-07)		0.005	8
protein_40_YPL217Cs	2	BMS1:  Essential conserved nucleolar GTP-binding protein required for synthesis of 40S ribosomal subunits and for processing of the 35S pre-rRNA at sites A0, A1, and A2; interacts with Rcl1p, has similarity to Tsr1p	K..K[RKI]	40	KR	CLV_PCSK_PC1ET2_1		WD40	1.E-03	1.1	rRNA processing (1e-36)		0.007	10
protein_40_YDL126C	2	CDC48:  ATPase in ER, nuclear membrane and cytosol with homology to mammalian p97; in a complex with Npl4p and Ufd1p participates in retrotranslocation of ubiquitinated proteins from the ER into the cytosol for degradation by the proteasome	GI..[DG]Q[QP]	40				ubiquitin	1.E-02	1.1			0.005	7
yeast-255_GO-0042254	2	ribosome biogenesis and assembly	K.[LKA]A	40			Y	DEAD	1.E-05	1.2	cytoplasm organization and biogenesis (1e-17)	Y	0.009	10
yeast-238_GO-0017111	2	nucleoside-triphosphatase activity	E.[SNF]A	40				Ras	1.E-17	1.2	nucleoside-triphosphatase activity (1e-11)	Y	0.009	10
yeast-255_GO-0007028	2	cytoplasm organization and biogenesis	K.[LKA]A	40			Y	DEAD	1.E-05	1.3	cytoplasm organization and biogenesis (1e-17)	Y	0.009	10
yeast-274_GO-0005840	2	ribosome	A[ARE].GD[AFI]	40	RGD	LIG_RGD		Ribosomal_60s	1.E-08	1.5	ribosome (1e-08)		0.006	10
protein_40_YJL081C	2	ARP4:  Nuclear actin-related protein involved in chromatin remodeling, component of chromatin-remodeling enzyme complexes	A[IK]..DD[EH]	40	[VA]P[IL]A..E[SD]D	Ankryn G binding motif in voltage gated sodium channels		Histone	1.E-04	1.6	establishment and/or maintenance of chromatin architecture (0.001)		0.005	10
protein_40_YDR224C	2	HTB1:  One of two nearly identical (see HTB2) histone H2B subtypes required for chromatin assembly and chromosome function; Rad6p-Bre1p-Lge1p mediated ubiquitination regulates transcriptional activation, meiotic DSB formation and H3 methylation	IR.[DL]D[EA]	40	R.L	Cyclin A motif that binds cdk2 complexes	Y	Histone	1.E-04	1.6	establishment and/or maintenance of chromatin architecture (1e-05)	Y	0.005	9
protein_40_YER012W	2	PRE1:  Beta 4 subunit of the 20S proteasome; localizes to the nucleus throughout the cell cycle	[PA][FYR]GV	40	LVPRG	Protease Thrombin	Y	Proteasome	1.E-11	1.7	proteasome core complex (sensu Eukaryota) (1e-13)		0.007	10
yeast-238_GO-0017111	2	nucleoside-triphosphatase activity	I.I[LDV]	40			Y	AAA	1.E-11	2.3	nucleoside-triphosphatase activity (1e-13)	Y	0.009	10
protein_40_YGL105W	2	ARC1:  Protein that binds tRNA and methionyl- and glutamyl-tRNA synthetases (Mes1p and Gus1p), delivering tRNA to them, stimulating catalysis, and ensuring their localization to the cytoplasm; also binds quadruplex nucleic acids	[IGN][HMC]..IK	40				Pkinase	1.E-08	2.6	protein kinase activity (1e-08)		0.006	9
protein_40_YGR103W	2	NOP7:  Nucleolar protein involved in rRNA processing and 60S ribosomal subunit biogenesis; constituent of several different pre-ribosomal particles; required for exit from G<sub>0</sub> and the initiation of cell proliferation	R[EQK][LIE]A	40	MR[DE][IL]	TUBULIN_B_AUTOREG PATTERN	Y	DEAD	1.E-02	2.8	cytoplasm organization and biogenesis (1e-15)	Y	0.008	10
protein_40_YDL013W	2	SLX5:  Subunit of the Slx5-Slx8 substrate-specific ubiquitin ligase complex; stimulated by prior attachment of SUMO to the substrate	[KM][PIT]EN	40	[ST]E	G protein-coupled receptor kinase 1 substrate motif		Pkinase	1.E-07	3.1	protein kinase activity (1e-05)	Y	0.007	10
yeast-436_GO-0031323	2	regulation of cellular metabolism	L.Q[DHE]	40	LSQE	ATM kinase substrate motif	Y	zf-C2H2	1.E-05	3.3	regulation of cellular metabolism (1e-17)	Y	0.009	10
protein_40_YDL153C	2	SAS10:  Component of the small (ribosomal) subunit (SSU) processosome required for pre-18S rRNa processing; essential nucleolar protein that, when overproduced, disrupts silencing	AP[EAN][VL]	40			Y	Pkinase	1.E-16	3.4	protein kinase activity (1e-16)	Y	0.007	9
protein_40_YDR496C	2	PUF6:  Pumilio-homology domain protein that binds ASH1 mRNA at PUF consensus sequences in the 3' UTR and represses its translation, resulting in proper asymmetric localization of ASH1 mRNA	[TRQ]G.GK[TIE]	40	[SAG]GGTG[SA]G	TUBULIN PATTERN		DEAD	1.E-07	3.9	ATP-dependent RNA helicase activity (1e-07)		0.005	10
protein_40_YMR229C	2	RRP5:  Protein required for the synthesis of both 18S and 5.8S rRNA; C-terminal region is crucial for the formation of 18S rRNA and N-terminal region is required for the 5.8S rRNA; component of small ribosomal subunit (SSU) processosome	D[FGD]G	40	D.G.T..K.I	Pyrophosphate binding motif, active site for S-Adenosylmethionine (AdoMet) synthetase		Pkinase	1.E-13	4.6	rRNA metabolism (1e-14)	Y	0.007	9
protein_40_YDL014W	2	NOP1:  Nucleolar protein, component of the small subunit processome complex, which is required for processing of pre-18S rRNA; has similarity to mammalian fibrillarin	[RSG]R.[AKQ]R	40	R.[RK]R	CLV_PCSK_FUR_1		Helicase_C	1.E-03	4.6	nucleolus (1e-10)		0.007	10
protein_40_YGL120C	2	PRP43:  RNA helicase in the DEAH-box family, functions in both RNA polymerase I and polymerase II transcript metabolism, involved in release of the lariat-intron from the spliceosome	R..R[TER]	40	R.[RK]R	CLV_PCSK_FUR_1		Helicase_C	1.E-02	5.5	nucleolus (1e-25)		0.007	10
yeast-256_GO-0016462	2	pyrophosphatase activity	[RLF]G[LID]D	40	RGD	LIG_RGD		Helicase_C	1.E-11	6.4	pyrophosphatase activity (1e-54)		0.008	10
yeast-1939_GO-0003824	2	catalytic activity	[ILMV]K..NI[LFA]	40			Y	Pkinase	1.E-49	6.4	protein kinase activity (1e-49)		0.008	10
yeast-1389_GO-0044260	2	cellular macromolecule metabolism	K[LIE].[DEP]FG	40				Pkinase	1.E-45	6.4	protein amino acid phosphorylation (1e-53)		0.009	10
protein_40_YKL014C	2	URB1:  Nucleolar protein required for the normal accumulation of 25S and 5.8S rRNAs, associated with the 27SA2 pre-ribosomal particle; proposed to be involved in the biogenesis of the 60S ribosomal subunit	[HGA]R..R[TEY]	40	[AG]R	Protease matriptase protease site	Y	Helicase_C	1.E-08	6.6	nucleolus (1e-11)		0.007	10
yeast-341_GO-0045449	2	regulation of transcription	[ASL]C..C[RGE]	40	C..C	Motif on TIM mitochondrial translocation proteins	Y	Zn_clus	1.E-21	17.8	regulation of transcription (1e-34)	Y	0.009	10
yeast-376_GO-0019219	2	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism	[ASL]C..C[RGE]	40	C..C	Motif on TIM mitochondrial translocation proteins	Y	Zn_clus	1.E-21	18.9	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism (1e-34)	Y	0.008	10
yeast-523_GO-0030529	2	ribonucleoprotein complex	[KGR]K.R[GAT]	40							ribonucleoprotein complex (1e-54)		0.008	10
yeast-462_GO-0019222	2	regulation of metabolism	[EA][ENV]DEV	40	DEVD	Protease Caspase 2, 3, 7 					regulation of metabolism (1e-14)		0.009	10
yeast-388_GO-0007275	2	development	I[DPT]N[SPH]	40							multicellular organismal development (1e-55)		0.009	10
yeast-267_GO-0000003	2	reproduction	[STH]PA[SAG]	40	[ST]P	LIG_WW_4	Y				reproduction (1e-50)	Y	0.009	10
yeast-235_GO-0009653	2	morphogenesis	[PSQ]QQ[SIT]	40	S[QT]Q	ATM phosphorylation of this motif on Chk2	Y				cellular morphogenesis (1e-47)		0.009	10
yeast-235_GO-0000902	2	cellular morphogenesis	[PSQ]QQ[SIT]	40	S[QT]Q	ATM phosphorylation of this motif on Chk2	Y				cellular morphogenesis (1e-47)		0.009	10
yeast-205_GO-0005856	2	cytoskeleton	E[LEC][LDM]K	40	EED	Ankyrin B C-terminal motif that binds internal Ankyrin repeats					cytoskeleton (1e-76)	Y	0.009	10
yeast-1721_GO-0016043	2	cell organization and biogenesis	Q[KQD]I[LGA]	40							intracellular transport (1e-14)	Y	0.008	10
yeast-1062_GO-0016020	2	membrane	T.[TGA]F	40							integral to membrane (1e-31)	Y	0.008	10
protein_40_YPR144C	2	NOC4:  Nucleolar protein, forms a complex with Nop14p that mediates maturation and nuclear export of 40S ribosomal subunits	[ENH][ETR].DQ	40							snoRNA binding (1e-07)	Y	0.006	10
protein_40_YPL198W	2	RPL7B:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl7Ap and has similarity to E. coli L30 and rat L7 ribosomal proteins; contains a conserved C-terminal Nucleic acid Binding Domain (NDB2)	[NQG][KCY].VVV	40							cytosolic ribosome (sensu Eukaryota) (0.001)		0.004	7
protein_40_YPL153C	2	RAD53:  Protein kinase, required for cell-cycle arrest in response to DNA damage; activated by trans autophosphorylation when interacting with hyperphosphorylated Rad9p; also interacts with ARS1 and plays a role in initiation of DNA replication	[VQE]K..K[KSQ]	40									0.008	10
protein_40_YPL012W	2	RRP12:  Protein required for export of the ribosomal subunits; associates with the RNA components of the pre-ribosomes; contains HEAT-repeats	[KTV]K..K[KRV]	40	KR	CLV_PCSK_PC1ET2_1					nucleolus (1e-19)	Y	0.008	10
protein_40_YOR272W	2	YTM1:  Constituent of 66S pre-ribosomal particles, required for maturation of the large ribosomal subunit	E[ETV][EHR]E	40	EEEEYFELV	EGFR kinase substrate motif					cytoplasm organization and biogenesis (1e-20)	Y	0.008	10
protein_40_YOL133W	2	HRT1:  RING finger containing subunit of Skp1-Cullin-F-box ubiquitin protein ligases (SCF); required for Gic2p, Far1p, Sic1p and Cln2p degradation; may tether Cdc34p (a ubiquitin conjugating enzyme or E2) and Cdc53p (a cullin) subunits of SCF	[VKF]E.Y[IRP]	40	[DE].Y	SHP1 phosphatase substrate motif						Y	0.007	10
protein_40_YNL244C	2	SUI1:  Translation initiation factor eIF1; component of a complex involved in recognition of the initiator codon; modulates translation accuracy at the initiation phase	K[VEW].[EFG]V	40							translation initiation factor activity (1e-04)		0.007	10
protein_40_YNL178W	2	RPS3:  Protein component of the small (40S) ribosomal subunit, has apurinic/apyrimidinic (AP) endonuclease activity; essential for viability; has similarity to E. coli S3 and rat S3 ribosomal proteins	R[RAV].A[RKL]	40			Y				cytosolic ribosome (sensu Eukaryota) (1e-19)		0.008	10
protein_40_YNL118C	2	DCP2:  Catalytic subunit of the Dcp1p-Dcp2p decapping enzyme complex, which removes the 5' cap structure from mRNAs prior to their degradation; member of the Nudix hydrolase family	M[ALH].L[TEY]	40			Y					Y	0.006	7
protein_40_YML063W	2	RPS1B:  Ribosomal protein 10 (rp10) of the small (40S) subunit; nearly identical to Rps1Ap and has similarity to rat S3a ribosomal protein	R[VAT].[GIR]G	40							cytosolic ribosome (sensu Eukaryota) (1e-14)		0.008	10
protein_40_YLR180W	2	SAM1:  S-adenosylmethionine synthetase, catalyzes transfer of the adenosyl group of ATP to the sulfur atom of methionine; one of two differentially regulated isozymes (Sam1p and Sam2p)	E..K[EQV]	40			Y				carboxylic acid metabolism (0.001)	Y	0.007	10
protein_40_YLR096W	2	KIN2:  Serine/threonine protein kinase involved in regulation of exocytosis; localizes to the cytoplasmic face of the plasma membrane; closely related to Kin1p	Y[GAM]..[EYD]D	40	YM	SH2 ligand for Vav1 (group II) (phospho-peptide)							0.005	10
protein_40_YLR029C	2	RPL15A:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl15Bp and has similarity to rat L15 ribosomal protein; binds to 5.8 S rRNA	AR[AYP][GKY]	40	[AG]R	Protease matriptase protease site					cytosolic ribosome (sensu Eukaryota) (1e-08)		0.007	9
protein_40_YLL034C	2	RIX7:  Putative ATPase of the AAA family, required for export of pre-ribosomal large subunits from the nucleus; distributed between the nucleolus, nucleoplasm, and nuclear periphery depending on growth conditions	[TK]AFT[KDC]	40									0.005	9
protein_40_YLL011W	2	SOF1:  Essential protein required for biogenesis of 40S (small) ribosomal subunit; has similarity to the beta subunit of trimeric G-proteins and the splicing factor Prp4p	RKR[SGL][KD]	40	KR	CLV_PCSK_PC1ET2_1					rRNA processing (0.001)		0.005	8
protein_40_YLL011W	2	SOF1:  Essential protein required for biogenesis of 40S (small) ribosomal subunit; has similarity to the beta subunit of trimeric G-proteins and the splicing factor Prp4p	VS.L[SYT][DFL]	40							snoRNA binding (1e-07)		0.004	9
protein_40_YKL203C	2	TOR2:  PIK-related protein kinase and rapamycin target; subunit of TORC1, a complex that regulates growth in response to nutrients and TORC2, a complex that regulates cell-cycle dependent polarization of the actin cytoskeleton; involved in meiosis	AS..[STG][SFM]	40	S..[ST]	Casein Kinase I consensus phosphorylation site (N-term Ser must first be phosphorylated)					plasma membrane (1e-12)		0.008	10
protein_40_YKL166C	2	TPK3:  cAMP-dependent protein kinase catalytic subunit; promotes vegetative growth in response to nutrients via the Ras-cAMP signaling pathway; inhibited by regulatory subunit Bcy1p in the absence of cAMP; partially redundant with Tpk1p and Tpk2p	DS.V[VAG][KLI]	40	R.DSPVR	14-3-3 binding motif on N-terminal domain of Nitrate Reductase necessary for 14-3-3 binding for inactivation in the dark							0.005	9
protein_40_YKL145W	2	RPT1:  One of six ATPases of the 19S regulatory particle of the 26S proteasome involved in the degradation of ubiquitinated substrates; required for optimal CDC20 transcription; interacts with Rpn12p and the E3 ubiquitin-protein ligase Ubr1p	YD.[AWM][LYT]	40							proteasome complex (sensu Eukaryota) (1e-05)		0.005	8
protein_40_YKL101W	2	HSL1:  Nim1p-related protein kinase that regulates the morphogenesis and septin checkpoints; associates with the assembled septin filament; required along with Hsl7p for bud neck recruitment, phosphorylation, and degradation of Swe1p	SV[EDK][EDI]	40	YRSVDE	Branched chain alpha-ketoacid dehydrogenase kinase substrate motif							0.008	10
protein_40_YJR145C	2	RPS4A:  Protein component of the small (40S) ribosomal subunit; mutation affects 20S pre-rRNA processing; identical to Rps4Bp and has similarity to rat S4 ribosomal protein	[ADG]E.[EAN]A	40							ribonucleoprotein complex (1e-05)		0.008	10
protein_40_YJR010C-A	2	SPC1:  Subunit of the signal peptidase complex (SPC), which cleaves the signal sequence from proteins targeted to the endoplasmic reticulum (ER), homolog of the SPC12 subunit of mammalian signal peptidase complex	I[GID]..[LYM]LV	40	D..LL	Di-Leu motif for receptor endocytosis (recognized by VHS domain of GGA proteins)							0.004	7
protein_40_YJR002W	2	MPP10:  Component of the SSU processome, which is required for pre-18S rRNA processing, interacts with and controls the stability of Imp3p and Imp4p, essential for viability; similar to human Mpp10p	[DGP][TAL]LLT	40	LLTP	WD40 domain of Cdc4 binding motif, Thr must be phosphorylated, CPD motif					small nucleolar ribonucleoprotein complex (1e-05)		0.004	8
protein_40_YJR002W	2	MPP10:  Component of the SSU processome, which is required for pre-18S rRNA processing, interacts with and controls the stability of Imp3p and Imp4p, essential for viability; similar to human Mpp10p	[LE]K..G[LN]T	40							processing of 20S pre-rRNA (1e-06)		0.005	8
protein_40_YJL164C	2	TPK1:  cAMP-dependent protein kinase catalytic subunit; promotes vegetative growth in response to nutrients via the Ras-cAMP signaling pathway; inhibited by regulatory subunit Bcy1p in the absence of cAMP; partially redundant with Tpk2p and Tpk3p	K...A[SKN]	40									0.007	10
protein_40_YJL138C	2	TIF2:  Translation initiation factor eIF4A, identical to Tif1p; DEA(D/H)-box RNA helicase that couples ATPase activity to RNA binding and unwinding; forms a dumbbell structure of two compact domains connected by a linker; interacts with eIF4G	L[DE][EIK]PT	40	P[ST]	DNA dependent Protein kinase substrate motif	Y				ATPase activity (0.01)		0.005	10
protein_40_YJL095W	2	BCK1:  Mitogen-activated protein (MAP) kinase kinase kinase acting in the protein kinase C signaling pathway, which controls cell integrity; upon activation by Pkc1p phosphorylates downstream kinases Mkk1p and Mkk2p	PE..[SVH][YH]	40									0.006	10
protein_40_YJL092W	2	SRS2:  DNA helicase and DNA-dependent ATPase involved in DNA repair, needed for proper timing of commitment to meiotic recombination and transition from Meiosis I to II; affects genome stability by suppressing unscheduled homologous recombination	[PIY]S..E	40	QPS..E	Phosphorylation motif in alpha 3A, alpha 6A, alpha 7A Integrin tails	Y				DNA metabolism (0.01)	Y	0.007	10
protein_40_YIL094C	2	LYS12:  Homo-isocitrate dehydrogenase, an NAD-linked mitochondrial enzyme required for the fourth step in the biosynthesis of lysine, in which homo-isocitrate is oxidatively decarboxylated to alpha-ketoadipate	I[TDF].E[LTE]	40	F.E	DNA binding motif in MutS					protein carrier activity (0.01)		0.008	10
protein_40_YIL061C	2	SNP1:  Component of U1 snRNP required for mRNA splicing via spliceosome; may interact with poly(A) polymerase to regulate polyadenylation; homolog of human U1 70K protein	L[LAV]..AD[NKS]	40									0.004	8
protein_40_YHR135C	2	YCK1:  Palmitoylated, plasma membrane-bound casein kinase I isoform; shares redundant functions with Yck2p in morphogenesis, proper septin assembly, endocytic trafficking; provides an essential function overlapping with that of Yck2p	T.[NSR]D	40	T..D	FHA1 binding motif, Thr must be phosphorylated, binding motif of proteins binding to Chk2							0.007	10
protein_40_YHR114W	2	BZZ1:  SH3 domain protein implicated in the regulation of actin polymerization, able to recruit actin polymerization machinery through its SH3 domains, colocalizes with cortical actin patches and Las17p, interacts with type I myosins	[ETI][TC]YE	40	YE	TPK-IIB/P38Syk kinase phosphorylation site (peptide screen)							0.004	8
protein_40_YHR088W	2	RPF1:  Nucleolar protein involved in the assembly of the large ribosomal subunit; constituent of 66S pre-ribosomal particles; contains a sigma(70)-like motif, which is thought to bind RNA	[DKG]D.[EDN]E	40	D.D	Ribose moiety of UDP and manganese binding site in glucuronyl transferase					cytoplasm organization and biogenesis (1e-19)		0.008	10
protein_40_YHR088W	2	RPF1:  Nucleolar protein involved in the assembly of the large ribosomal subunit; constituent of 66S pre-ribosomal particles; contains a sigma(70)-like motif, which is thought to bind RNA	EA..[DS][SHF]D	40									0.005	9
protein_40_YHL030W	2	ECM29:  Major component of the proteasome; tethers the proteasome core particle to the regulatory particle, and enhances the stability of the proteasome	LV.Q[LY][NK]	40									0.005	9
protein_40_YHL001W	2	RPL14B:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl14Ap and has similarity to rat L14 ribosomal protein	K[AT]..AE[ICQ]	40							cytosolic ribosome (sensu Eukaryota) (0.001)		0.005	8
protein_40_YGR245C	2	SDA1:  Highly conserved nuclear protein required for actin cytoskeleton organization and passage through Start, plays a critical role in G1 events, binds Nap1p, also involved in 60S ribosome biogenesis	[THG][KWT]..KQ	40							ribosome biogenesis (1e-04)	Y	0.005	9
protein_40_YGR218W	2	CRM1:  Major karyopherin, involved in export of proteins, RNAs, and ribosomal subunits from the nucleus	[NEG]P..[FPC]A	40	P..P	SH3 general ligand,							0.006	10
protein_40_YGL179C	2	TOS3:  Protein kinase, related to and functionally redundant with Elm1p and Sak1p for the phosphorylation and activation of Snf1p; functionally orthologous to LKB1, a mammalian kinase associated with Peutz-Jeghers cancer-susceptibility syndrome	S[AEQ].S[SLG]	40	S[ST]	MDC1 BRCT domain binding motif							0.008	10
protein_40_YFR034C	2	PHO4:  Basic helix-loop-helix (bHLH) transcription factor of the myc-family; binds cooperatively with Pho2p to the PHO5 promoter; function is regulated by phosphorylation at multiple sites and by phosphate availability	A[RAE]K[AVF]	40			Y				cytosolic part (1e-07)	Y	0.007	10
protein_40_YEL037C	2	RAD23:  Protein with ubiquitin-like N terminus, recognizes and binds damaged DNA (with Rad4p) during nucleotide excision repair; regulates Rad4p levels, subunit of Nuclear Excision Repair Factor 2 (NEF2); homolog of human HR23A and HR23B proteins	IV..[GT][GWY]S	40			Y				Arp2/3 protein complex (1e-04)		0.005	7
protein_40_YDR477W	2	SNF1:  AMP-activated serine/threonine protein kinase found in a complex containing Snf4p and members of the Sip1p/Sip2p/Gal83p family; required for transcription of glucose-repressed genes, thermotolerance, sporulation, and peroxisome biogenesis	D.[FLE]N	40	SD.E	Casein kinase II substrate motif					response to external stimulus (0.01)		0.007	10
protein_40_YDR450W	2	RPS18A:  Protein component of the small (40S) ribosomal subunit; nearly identical to Rps18Bp and has similarity to E. coli S13 and rat S18 ribosomal proteins	[AVG]RV[TGR]	40	[AG]R	Protease matriptase protease site					eukaryotic 43S preinitiation complex (0.001)		0.006	10
protein_40_YDR388W	2	RVS167:  Actin-associated protein, subunit of a complex (Rvs161p-Rvs167p) involved in regulation of actin cytoskeleton, endocytosis, and viability following starvation or osmotic stress; homolog of mammalian amphiphysin	ED[LVP]	40	EED	Ankyrin B C-terminal motif that binds internal Ankyrin repeats					cell cortex (1e-07)	Y	0.007	10
protein_40_YDR381W	2	YRA1:  Nuclear protein that binds to RNA and to Mex67p, required for export of poly(A)+ mRNA from the nucleus; member of the REF (RNA and export factor binding proteins) family; another family member, Yra2p, can substitute for Yra1p function	R.[ISQ]K	40	R.[ST]	PKA consensus phosphorylation site					nuclear lumen (1e-05)		0.007	10
protein_40_YDR324C	2	UTP4:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	[EM][ETF].DQ	40							small nucleolar ribonucleoprotein complex (1e-13)		0.005	9
protein_40_YDR224C	2	HTB1:  One of two nearly identical (see HTB2) histone H2B subtypes required for chromatin assembly and chromosome function; Rad6p-Bre1p-Lge1p mediated ubiquitination regulates transcriptional activation, meiotic DSB formation and H3 methylation	S[EQ].DK[KRM]	40	SQ	ATM kinase substrate motif							0.004	8
protein_40_YDL147W	2	RPN5:  Essential, non-ATPase regulatory subunit of the 26S proteasome lid, similar to mammalian p55 subunit and to another S. cerevisiae regulatory subunit, Rpn7p	[SHF]L.[EIK]AS	40							proteasome complex (sensu Eukaryota) (0.001)		0.004	7
protein_40_YDL083C	2	RPS16B:  Protein component of the small (40S) ribosomal subunit; identical to Rps16Ap and has similarity to E. coli S9 and rat S16 ribosomal proteins	RA.[KRG][VGA]	40							cytosolic ribosome (sensu Eukaryota) (1e-22)		0.008	10
protein_40_YDL055C	2	PSA1:  GDP-mannose pyrophosphorylase (mannose-1-phosphate guanyltransferase), synthesizes GDP-mannose from GTP and mannose-1-phosphate in cell wall biosynthesis; required for normal cell wall structure	KI[SPD][IPY]K	40									0.004	9
protein_40_YBR059C	2	AKL1:  Ser-Thr protein kinase, member (with Ark1p and Prk1p) of the Ark kinase family; involved in endocytosis and actin cytoskeleton organization	SNN[PAS][FEQ]	40	NPF	EH EF hand domain binding motif, Class I	Y				endocytosis (1e-05)		0.004	9
protein_40_YBR009C	2	HHF1:  One of two identical histone H4 proteins (see also HHF2); core histone required for chromatin assembly and chromosome function; contributes to telomeric silencing; N-terminal domain involved in maintaining genomic integrity	[RLD]AA[RPE]	40							cytosolic part (1e-05)		0.007	10
protein_40_YBL026W	2	LSM2:  Lsm (Like Sm) protein; part of heteroheptameric complexes (Lsm2p-7p and either Lsm1p or 8p): cytoplasmic Lsm1p complex involved in mRNA decay; nuclear Lsm8p complex part of U6 snRNP and possibly involved in processing tRNA, snoRNA, and rRNA	ET..[KEY][LK]R	40	KR	CLV_PCSK_PC1ET2_1						Y	0.004	10
protein_40_YAR007C	2	RFA1:  Subunit of heterotrimeric Replication Protein A (RPA), which is a highly conserved single-stranded DNA binding protein involved in DNA replication, repair, and recombination	K[EN][VW]Y	40									0.004	7
oshea_vacuolar_membrane	2	oshea_vacuolar_membrane	Q[VD]F[EW]G	40							vacuolar membrane (1e-05)		0.006	8
oshea_Total__	8	oshea_Total__	F[FLW]F[LFV]	40	F.F	WASP Homology 1 binding motif							0.017	10
oshea_bud	2	oshea_bud	[VES][PVL]..QQQ	40							bud neck (0.001)		0.005	9
oshea_bud	2	oshea_bud	E[VHY]..K[LG]E	40							establishment of cell polarity (sensu Fungi) (1e-04)	Y	0.005	9
matsuyama_Cytosol	2	matsuyama_Cytosol	[RQG]S..[VGW]S	40	S...S	WD40 binding motif, Ser residues must be phosphorylated							0.009	10
genetic_YPL055C	2	LGE1: Protein of unknown function; null mutant forms abnormally large cells, and homozygous diploid null mutant displays delayed premeiotic DNA synthesis and reduced efficiency of meiotic nuclear division	T[NQD]..[EYL]E	40	YE	TPK-IIB/P38Syk kinase phosphorylation site (peptide screen)					DNA metabolism (1e-04)		0.007	10
genetic_YNL153C	2	GIM3: Subunit of the heterohexameric cochaperone prefoldin complex which binds specifically to cytosolic chaperonin and transfers target proteins to it	KE..[QHE]S[IQP]	40	KEN	LIG_APCC_KENbox_2							0.006	10
genetic_YLR200W	2	YKE2: Subunit of the heterohexameric Gim/prefoldin protein complex involved in the folding of alpha-tubulin, beta-tubulin, and actin	K.[PLG]S	40	KSGST	eIF4 motif phosphorylation motif					cell cycle (1e-08)	Y	0.007	10
genetic_YLR200W	2	YKE2: Subunit of the heterohexameric Gim/prefoldin protein complex involved in the folding of alpha-tubulin, beta-tubulin, and actin	S[DHP]D	40	S.D	CAMKII phosphorylation site					cell cycle (1e-08)		0.007	10
genetic_YAL024C	2	LTE1: Putative GDP/GTP exchange factor required for mitotic exit at low temperatures; acts as a guanine nucleotide exchange factor (GEF) for Tem1p, which is a key regulator of mitotic exit; physically associates with Ras2p-GTP	Q.Q[REK]	40							mitotic cell cycle (1e-06)		0.007	10
yeast-1433_GO-0006139	2	nucleobase, nucleoside, nucleotide and nucleic acid metabolism	I[NRA]K	39	RRT[IV][ATN]KYR	SIGMA54_2 PATTERN		Helicase_C	1.E-05	-1.6	transcription (1e-77)		0.008	10
protein_40_YNL002C	2	RLP7:  Nucleolar protein with similarity to large ribosomal subunit L7 proteins; constituent of 66S pre-ribosomal particles; plays an essential role in processing of precursors to the large ribosomal subunit RNAs	E[EDQ]..[MDK]E	39				Brix	1.E-03	-1.5	cytoplasm organization and biogenesis (1e-33)		0.007	10
protein_40_YPR161C	2	SGV1:  Cyclin (Bur2p)-dependent protein kinase that functions in transcriptional regulation; phosphorylates the carboxy-terminal domain of Rpo21p, which is the largest subunit of RNA polymerase II; regulated by Cak1p	[LQR][EDK].KK	39	RKK.[ST]	ZIP kinase phosphorylation motif	Y	HMG_box	1.E-02	-1.4	nucleic acid binding (1e-04)		0.007	10
protein_40_YOL077C	2	BRX1:  Nucleolar protein, constituent of 66S pre-ribosomal particles; depletion leads to defects in rRNA processing and a block in the assembly of large ribosomal subunits; possesses a sigma(70)-like RNA-binding motif	KR..[VEA][EKD]	39	KR	CLV_PCSK_PC1ET2_1		Brix	1.E-03	-1.4	cytoplasm organization and biogenesis (1e-16)		0.008	10
protein_40_YHR066W	2	SSF1:  Constituent of 66S pre-ribosomal particles, required for ribosomal large subunit maturation; functionally redundant with Ssf2p; member of the Brix family	[KVH]K..K[KRQ]	39	KR	CLV_PCSK_PC1ET2_1		DEAD	1.E-03	-1.4	cytoplasm organization and biogenesis (1e-18)		0.008	10
yeast-341_GO-0045449	2	regulation of transcription	S[ETN]E[ELR]	39	[ST]E	G protein-coupled receptor kinase 1 substrate motif		bZIP_1	1.E-06	-1.2	regulation of transcription (1e-09)		0.008	10
protein_40_YGL111W	2	NSA1:  Constituent of 66S pre-ribosomal particles, involved in 60S ribosomal subunit biogenesis	G[RTY]..R[AIW]	39				DEAD	1.E-04	-1.1	ATP-dependent RNA helicase activity (1e-04)	Y	0.005	8
protein_40_YOR181W	2	LAS17:  Actin assembly factor, activates the Arp2/3 protein complex that nucleates branched actin filaments; localizes with the Arp2/3 complex to actin patches; homolog of the human Wiskott-Aldrich syndrome protein (WASP)	Q[QAH]..[QFG]A	39				SH3_1	1.E-06	-1	endocytosis (1e-07)		0.006	10
yeast-341_GO-0045449	2	regulation of transcription	E.E[NVM]	39	Y.E.E	Src phosphorylation site		Zn_clus	1.E-05	-0.8	regulation of transcription (1e-16)		0.008	10
oshea_bud_neck	2	oshea_bud_neck	L[NQS]..[ANS]T	39				SH3_1	1.E-02	-0.8	bud (1e-30)		0.008	10
yeast-388_GO-0007275	2	development	[ASD]N.[SQR]L	39	N.[TS]	N-linked glycosylation site		RasGEF_N	1.E-02	-0.6	multicellular organismal development (1e-79)		0.008	10
yeast-1115_GO-0006996	2	organelle organization and biogenesis	S.[IQH]E	39				Helicase_C	1.E-03	-0.5	chromosome organization and biogenesis (1e-69)		0.008	10
protein_40_YLL008W	2	DRS1:  Nucleolar DEAD-box protein required for ribosome assembly and function, including synthesis of 60S ribosomal subunits; constituent of 66S pre-ribosomal particles	K.[EVY]E	39	YE	TPK-IIB/P38Syk kinase phosphorylation site (peptide screen)		Pkinase	1.E-07	-0.5	cytoplasm organization and biogenesis (1e-27)		0.007	10
protein_40_YLR293C	2	GSP1:  GTP binding protein (mammalian Ranp homolog) involved in the maintenance of nuclear organization, RNA processing and transport; regulated by Prp20p, Rna1p, Yrb1p, Yrb2p, Yrp4p, Yrb30p, Cse1p and Kap95p; yeast Gsp2p homolog	[NMT]E[TSC]SK	39				IBN_N	1.E-02	-0.4	nuclear pore (1e-05)		0.004	8
protein_40_YDL213C	2	NOP6:  Putative RNA-binding protein implicated in ribosome biogenesis; contains an RNA recognition motif (RRM) and has similarity to hydrophilins; NOP6 may be a fungal-specific gene as no homologs have been yet identified in higher eukaryotes	EL[AM]K[HTI]	39				HEAT	1.E-02	-0.4		Y	0.004	9
yeast-233_GO-0006629	2	lipid metabolism	L[LFM]G	39				PAP2	1.E-03	-0.2	lipid metabolism (1e-14)		0.008	10
protein_40_YNL186W	2	UBP10:  Ubiquitin-specific protease that deubiquitinates ubiquitin-protein moieties; may regulate silencing by acting on Sir4p; involved in posttranscriptionally regulating Gap1p and possibly other transporters; primarily located in the nucleus	[EDR]E.L[YW]	39	ENLYFQ[GS]	Protease TEV - stringent		Pkinase	1.E-03	-0.1	protein kinase activity (1e-04)		0.005	10
matsuyama_ER	2	matsuyama_ER	Y.L[GFW]	39				MFS_1	1.E-03	-0.1	endoplasmic reticulum part (1e-05)	Y	0.010	10
protein_40_YNL132W	2	KRE33:  Essential protein of unknown function; heterozygous mutant shows haploinsufficiency in K1 killer toxin resistance	K..K[RLA]	39	KR	CLV_PCSK_PC1ET2_1	Y	WD40	1.E-05	0	cytoplasm organization and biogenesis (1e-35)		0.007	10
yeast-256_GO-0016462	2	pyrophosphatase activity	V.E[LAY]	39				Helicase_C	1.E-14	0.1	pyrophosphatase activity (1e-13)	Y	0.008	10
yeast-238_GO-0017111	2	nucleoside-triphosphatase activity	V..[DAP]E	39				Helicase_C	1.E-11	0.1	nucleoside-triphosphatase activity (1e-11)		0.008	10
protein_40_YOL069W	2	NUF2:  Component of the evolutionarily conserved kinetochore-associated Ndc80 complex (Ndc80p-Nuf2p-Spc24p-Spc25p); involved in chromosome segregation, spindle checkpoint activity and kinetochore clustering	LK[DLI][SEL]	39	LLKIL	AP-2 binding motif in CXCR2 receptor		SMC_N	1.E-03	0.1	microtubule cytoskeleton (1e-07)	Y	0.008	9
matsuyama_Mitochondria	2	matsuyama_Mitochondria	D.[VPN]L	39	D.D.[TV]	Motif in PRS1 and PRS-2 required for phosphatase activity and salt stress response		HEAT	1.E-04	0.3	GTPase regulator activity (0.01)		0.010	10
matsuyama_Cytosol	2	matsuyama_Cytosol	QR[ARC]	39	RRR	ER retention signal in NR1 glutamate receptor		RhoGEF	1.E-02	0.3	cell septum (0.01)	Y	0.010	10
yeast-238_GO-0017111	2	nucleoside-triphosphatase activity	V.E[LAY]	39				Helicase_C	1.E-11	0.4	nucleoside-triphosphatase activity (1e-12)	Y	0.008	10
yeast-240_GO-0006807	2	nitrogen compound metabolism	G..[IAV]A	39				GATase	1.E-02	0.6	nitrogen compound metabolism (1e-13)	Y	0.008	10
yeast-1493_GO-0043234	2	protein complex	[DIL]E..[DLS]E	39	[ST]E	G protein-coupled receptor kinase 1 substrate motif		HEAT	1.E-02	0.6	nucleoplasm part (1e-24)		0.008	10
protein_40_YDR427W	2	RPN9:  Non-ATPase regulatory subunit of the 26S proteasome, has similarity to putative proteasomal subunits in other species; null mutant is temperature sensitive and exhibits cell cycle and proteasome assembly defects	[NRQ]N.[SEI]LL	39	N.[TS]	N-linked glycosylation site		PCI	1.E-02	0.9	proteasome regulatory particle (sensu Eukaryota) (0.01)		0.004	8
yeast-1974_GO-0005634	2	nucleus	S..[PKG]S	39	S...S	WD40 binding motif, Ser residues must be phosphorylated		WD40	1.E-10	1.1	transcription (1e-85)		0.008	10
protein_40_YOL018C	2	TLG2:  Syntaxin-like t-SNARE that forms a complex with Tlg1p and Vti1p and mediates fusion of endosome-derived vesicles with the late Golgi; binds Vps45p, which prevents Tlg2p degradation and also facilitates t-SNARE complex formation	[GP]Q[EDN]R	39			Y	Ras	1.E-05	1.1	GTPase activity (1e-05)		0.004	7
yeast-661_GO-0050789	2	regulation of biological process	H..[ITN]I	39				Pkinase	1.E-03	1.3	regulation of metabolism (1e-57)		0.008	10
yeast-1062_GO-0016020	2	membrane	L..V[AFP]	39	VP	Interleukin converting enzyme protease		MFS_1	1.E-05	1.3	intrinsic to membrane (1e-59)	Y	0.008	10
protein_40_YDR449C	2	UTP6:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	[FT][SRM].DG	39	S.D	CAMKII phosphorylation site		WD40	1.E-06	1.3	small nucleolar ribonucleoprotein complex (1e-14)		0.006	10
yeast-1721_GO-0016043	2	cell organization and biogenesis	L..[LAS]N	39			Y	IBN_N	1.E-04	1.5	cellular localization (1e-89)		0.008	10
protein_40_YDL013W	2	SLX5:  Subunit of the Slx5-Slx8 substrate-specific ubiquitin ligase complex; stimulated by prior attachment of SUMO to the substrate	[LVI]N[HR]P	39	Y[ILV]N[VP]	SH2 ligand for SEM5 (C.elegans Grb2) (Tyr must be phosphorylated)		Pkinase	1.E-04	1.5	protein kinase activity (0.001)		0.005	8
protein_40_YBR009C	2	HHF1:  One of two identical histone H4 proteins (see also HHF2); core histone required for chromatin assembly and chromosome function; contributes to telomeric silencing; N-terminal domain involved in maintaining genomic integrity	LE..[GMA][NKE]A	39				Histone	1.E-03	1.5			0.005	10
yeast-648_GO-0050791	2	regulation of physiological process	H..[INT]I	39				Pkinase	1.E-04	2	regulation of metabolism (1e-57)		0.008	10
yeast-335_GO-0016772	2	transferase activity, transferring phosphorus-containing groups	GS..[VKT][YDV]	39	S..[ST]	Casein Kinase I consensus phosphorylation site (N-term Ser must first be phosphorylated)		Pkinase	1.E-18	2	transferase activity, transferring phosphorus-containing groups (1e-59)		0.009	10
protein_40_YLL008W	2	DRS1:  Nucleolar DEAD-box protein required for ribosome assembly and function, including synthesis of 60S ribosomal subunits; constituent of 66S pre-ribosomal particles	LLDK[NMT]	39				Pkinase	1.E-03	2.2	protein kinase activity (0.01)	Y	0.004	8
protein_40_YER036C	2	ARB1:  ATPase of the ATP-binding cassette (ABC) family involved in 40S and 60S ribosome biogenesis, has similarity to Gcn20p; shuttles from nucleus to cytoplasm, physically interacts with Tif6p, Lsg1p	[TE][RIS]ELA	39	[ST]E	G protein-coupled receptor kinase 1 substrate motif	Y	DEAD	1.E-03	2.3	RNA helicase activity (0.01)		0.004	7
protein_40_YLR186W	2	EMG1:  Protein required for the maturation of the 18S rRNA and for 40S ribosome production; associated with spindle/microtubules; nuclear localization depends on physical interaction with Nop14p; may bind snoRNAs	[DGT]G.[IVN]K	39				WD40	1.E-07	2.4	rRNA processing (1e-19)	Y	0.007	10
protein_40_YAR019C	2	CDC15:  Protein kinase of the Mitotic Exit Network that is localized to the spindle pole bodies at late anaphase; promotes mitotic exit by directly switching on the kinase activity of Dbf2p	PE..[LTV][LSI]	39				Pkinase	1.E-18	2.4	protein kinase activity (1e-13)	Y	0.008	10
protein_40_YNL298W	2	CLA4:  Cdc42p activated signal transducing kinase of the PAK (p21-activated kinase) family, involved in septin ring assembly and cytokinesis; directly phosphorylates septins Cdc3p and Cdc10p; other yeast PAK family members are Ste20p and Skm1p	V[KQ]..D[FY]G	39				Pkinase	1.E-03	2.7	protein kinase activity (0.01)		0.005	9
yeast-238_GO-0017111	2	nucleoside-triphosphatase activity	A..[AGR]L	39	[FHYM].A[AV].[VAC]L[MV].[MI]	LIG_Sin3_2		ABC_tran	1.E-13	2.8	nucleoside-triphosphatase activity (1e-12)		0.008	10
protein_40_YDR324C	2	UTP4:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	D[KG][TRH]VK	39			Y	WD40	1.E-04	2.9	processing of 20S pre-rRNA (1e-09)		0.005	7
genetic_YNL153C	2	GIM3: Subunit of the heterohexameric cochaperone prefoldin complex which binds specifically to cytosolic chaperonin and transfers target proteins to it	[THD]R.[KIL]K	39	R..K	SH3 binding motif for GADS SH3 recognizing slp-76 motif (nonconventional)		Pkinase	1.E-04	2.9	phosphotransferase activity, alcohol group as acceptor (1e-04)	Y	0.007	10
protein_40_YER006W	2	NUG1:  GTPase that associates with nuclear 60S pre-ribosomes, required for export of 60S ribosomal subunits from the nucleus	GK.[AS]A[FMK]	39				DEAD	1.E-03	3.1	ribosome assembly (0.001)		0.005	8
protein_40_YPL203W	2	TPK2:  cAMP-dependent protein kinase catalytic subunit; promotes vegetative growth in response to nutrients via the Ras-cAMP signaling pathway; inhibited by regulatory subunit Bcy1p in the absence of cAMP; partially redundant with Tpk1p and Tpk3p	[AIC][DAH]FG	39	LFG	Protease Papain substrate, a prototype cysteine proteinase		Pkinase	1.E-07	3.2	protein kinase activity (1e-06)		0.005	9
yeast-1974_GO-0005634	2	nucleus	R[DKE]I	39	MR[DE][IL]	TUBULIN_B_AUTOREG PATTERN		Zn_clus	1.E-05	3.3	nuclear lumen (1e-46)		0.008	10
protein_40_YKL021C	2	MAK11:  Protein involved in an early, nucleolar step of 60S ribosomal subunit biogenesis; essential for cell growth and replication of killer M1 dsRNA virus; contains four beta-transducin repeats	[PR][THS].IQ	39	GIQVD	dynein light chain LC8 interacting motif -alternative		DEAD	1.E-06	3.7	ribosome biogenesis (1e-10)	Y	0.005	8
yeast-1115_GO-0006996	2	organelle organization and biogenesis	D..I[RKQ]	39				WD40	1.E-14	5.1	chromosome organization and biogenesis (1e-57)		0.008	10
yeast-335_GO-0016772	2	transferase activity, transferring phosphorus-containing groups	M[EDH]Y	39	[DE]YY	Tyr phosphorylated in activation loop of Jak	Y	Pkinase	1.E-32	5.2	transferase activity, transferring phosphorus-containing groups (1e-49)	Y	0.008	10
yeast-565_GO-0006464	2	protein modification	[ILMV]K..N[ILR]L	39				Pkinase	1.E-42	6.3	protein amino acid phosphorylation (1e-53)		0.008	9
yeast-706_GO-0043412	2	biopolymer modification	[ILMV]K..N[ILF]L	39				Pkinase	1.E-49	6.5	protein amino acid phosphorylation (1e-62)		0.008	10
yeast-294_GO-0006366	2	transcription from RNA polymerase II promoter	R[KYF]R	39	HHH[RK]SPR[RK]R	Cdc2 kinase substrate motif		Zn_clus	1.E-02	8.4	transcription from RNA polymerase II promoter (1e-11)	Y	0.008	10
yeast-256_GO-0016462	2	pyrophosphatase activity	[GW]R..R[AGK]	39	R.[RK]R	CLV_PCSK_FUR_1	Y	Helicase_C	1.E-22	9.2	nucleoside-triphosphatase activity (1e-29)		0.009	10
yeast-320_GO-0006355	2	regulation of transcription, DNA-dependent	[ASY]C..C[RDE]	39	C..C	Motif on TIM mitochondrial translocation proteins	Y	Zn_clus	1.E-21	17.2	regulation of transcription, DNA-dependent (1e-27)		0.009	10
yeast-436_GO-0031323	2	regulation of cellular metabolism	[ALS]C..C[REG]	39	C..C	Motif on TIM mitochondrial translocation proteins	Y	Zn_clus	1.E-20	17.7	regulation of cellular metabolism (1e-34)		0.008	10
yeast-376_GO-0019219	2	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism	CR.[RKT][KHY]	39	R.[ST]	PKA consensus phosphorylation site		Zn_clus	1.E-22	18.2	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism (1e-24)		0.009	10
yeast-628_GO-0043037	2	translation	E..F	39									0.008	10
yeast-468_GO-0051276	2	chromosome organization and biogenesis	[DNC]R..S[TFK]T	39	R..S	Calmodulin-dependent protein kinase II substrate motif					chromosome organization and biogenesis (1e-11)	Y	0.008	10
yeast-468_GO-0051276	2	chromosome organization and biogenesis	ND.EL[SP]	39	D.E	Sec24p					chromosome organization and biogenesis (1e-06)		0.006	8
yeast-343_GO-0005198	2	structural molecule activity	L[SFI]L	39									0.008	10
yeast-295_GO-0016192	2	vesicle-mediated transport	DD[LNF][LFY]	39							vesicle-mediated transport (1e-63)	Y	0.008	10
yeast-244_GO-0000279	2	M phase	N..[VDH]D	39			Y				M phase (1e-13)		0.008	10
yeast-235_GO-0009653	2	morphogenesis	[PVT]T[TPD]T	39	TPTP	Motif for hydroxylation of Pro residues, which can further be modified with arabinogalactan					cellular morphogenesis (1e-62)		0.008	10
yeast-235_GO-0000902	2	cellular morphogenesis	[PVT]T[TPD]T	39	TPTP	Motif for hydroxylation of Pro residues, which can further be modified with arabinogalactan					cellular morphogenesis (1e-62)		0.008	10
yeast-1721_GO-0016043	2	cell organization and biogenesis	A[TEM]N	39							cellular localization (1e-25)		0.008	10
protein_40_YPL146C	2	NOP53:  Nucleolar protein; involved in biogenesis of the 60S subunit of the ribosome; interacts with rRNA processing factors Cbf5p and Nop2p; null mutant is viable but growth is severely impaired	K[EH][AGY]LE	39									0.004	7
protein_40_YPL093W	2	NOG1:  Putative GTPase that associates with free 60S ribosomal subunits in the nucleolus and is required for 60S ribosomal subunit biogenesis; constituent of 66S pre-ribosomal particles; member of the ODN family of nucleolar G-proteins	[DGV]D.[EK]E	39	D.E	Sec24p					cytoplasm organization and biogenesis (1e-26)	Y	0.008	10
protein_40_YOR310C	2	NOP58:  Protein involved in pre-rRNA processing, 18S rRNA synthesis, and snoRNA synthesis; component of the small subunit processome complex, which is required for processing of pre-18S rRNA	[GMS]K..VQ[LN]	39							snoRNA binding (0.01)		0.005	7
protein_40_YOR290C	2	SNF2:  Catalytic subunit of the SWI/SNF chromatin remodeling complex involved in transcriptional regulation; contains DNA-stimulated ATPase activity; functions interdependently in transcriptional activation with Snf5p and Snf6p	[AD][KVE]VEE	39									0.004	7
protein_40_YOL133W	2	HRT1:  RING finger containing subunit of Skp1-Cullin-F-box ubiquitin protein ligases (SCF); required for Gic2p, Far1p, Sic1p and Cln2p degradation; may tether Cdc34p (a ubiquitin conjugating enzyme or E2) and Cdc53p (a cullin) subunits of SCF	[YI][KR].PE	39								Y	0.005	9
protein_40_YOL133W	2	HRT1:  RING finger containing subunit of Skp1-Cullin-F-box ubiquitin protein ligases (SCF); required for Gic2p, Far1p, Sic1p and Cln2p degradation; may tether Cdc34p (a ubiquitin conjugating enzyme or E2) and Cdc53p (a cullin) subunits of SCF	VQ..I[PQ][LQK]	39								Y	0.004	8
protein_40_YOL120C	2	RPL18A:  Protein component of the large (60S) ribosomal subunit, identical to Rpl18Bp and has similarity to rat L18 ribosomal protein; intron of RPL18A pre-mRNA forms stem-loop structures that are a target for Rnt1p cleavage leading to degradation	[ITF]A.G[KTI]S	39								Y	0.004	8
protein_40_YOL069W	2	NUF2:  Component of the evolutionarily conserved kinetochore-associated Ndc80 complex (Ndc80p-Nuf2p-Spc24p-Spc25p); involved in chromosome segregation, spindle checkpoint activity and kinetochore clustering	[IQG]K.L[KEQ]	39			Y				microtubule cytoskeleton (1e-07)		0.008	10
protein_40_YOL041C	2	NOP12:  Nucleolar protein, required for pre-25S rRNA processing; contains an RNA recognition motif (RRM) and has similarity to Nop13p, Nsr1p, and putative orthologs in Drosophila and S. pombe	[GAM][SPK]RP	39	[KR]R	CLV_PCSK_KEX2_1						Y	0.006	9
protein_40_YOL018C	2	TLG2:  Syntaxin-like t-SNARE that forms a complex with Tlg1p and Vti1p and mediates fusion of endosome-derived vesicles with the late Golgi; binds Vps45p, which prevents Tlg2p degradation and also facilitates t-SNARE complex formation	LNK[IFT][KVQ]	39	G[SA]LNK	GDP-mannose binding motif in transporter							0.004	9
protein_40_YOL001W	2	PHO80:  Cyclin, negatively regulates phosphate metabolism; Pho80p-Pho85p (cyclin-CDK complex) phosphorylates Pho4p and Swi5p; deletion of PHO80 leads to aminoglycoside supersensitivity; truncated form of PHO80 affects vacuole inheritance	PE[EHG]	39	EED	Ankyrin B C-terminal motif that binds internal Ankyrin repeats							0.007	10
protein_40_YNL154C	2	YCK2:  Palmitoylated, plasma membrane-bound casein kinase I isoform; shares redundant functions with Yck1p in morphogenesis, proper septin assembly, endocytic trafficking; provides an essential function overlapping with that of Yck1p	NA[TDS]	39								Y	0.007	10
protein_40_YNL132W	2	KRE33:  Essential protein of unknown function; heterozygous mutant shows haploinsufficiency in K1 killer toxin resistance	R..A[RKN]	39							ribonucleoprotein complex (1e-26)		0.007	10
protein_40_YNL118C	2	DCP2:  Catalytic subunit of the Dcp1p-Dcp2p decapping enzyme complex, which removes the 5' cap structure from mRNAs prior to their degradation; member of the Nudix hydrolase family	V[DAP].[VA]N	39	VP	Interleukin converting enzyme protease							0.006	9
protein_40_YNL002C	2	RLP7:  Nucleolar protein with similarity to large ribosomal subunit L7 proteins; constituent of 66S pre-ribosomal particles; plays an essential role in processing of precursors to the large ribosomal subunit RNAs	DD.[EKP][EYT]	39	D.E	Sec24p					cytoplasm organization and biogenesis (1e-25)		0.008	10
protein_40_YMR242C	2	RPL20A:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl20Bp and has similarity to rat L18a ribosomal protein	RA[AGP][RSK]	39							cytosolic ribosome (sensu Eukaryota) (1e-17)		0.008	10
protein_40_YMR236W	2	TAF9:  Subunit (17 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation and in chromatin modification, similar to histone H3	[IMV][LI]GKL	39							transcription from RNA polymerase II promoter (0.01)	Y	0.005	7
protein_40_YMR236W	2	TAF9:  Subunit (17 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation and in chromatin modification, similar to histone H3	I[LVS]..L[QYE]N	39	L...I...[IL]	Corepressor nuclear box motif binds to nuclear receptors					transcription factor complex (1e-05)		0.004	8
protein_40_YMR116C	2	ASC1:  G-protein beta subunit and guanine nucleotide dissociation inhibitor for Gpa2p; ortholog of RACK1 that inhibits translation; core component of the small (40S) ribosomal subunit; represses Gcn4p in the absence of amino acid starvation	A[SEC].[KVR]I	39							RNA metabolism (0.01)		0.007	9
protein_40_YMR012W	2	CLU1:  eIF3 component of unknown function; deletion causes defects in mitochondrial organization but not in growth or translation initiation, can rescue cytokinesis and mitochondrial organization defects of the Dictyostelium cluA- mutant	[EMH]Q.[VCE]D	39									0.005	10
protein_40_YLR180W	2	SAM1:  S-adenosylmethionine synthetase, catalyzes transfer of the adenosyl group of ATP to the sulfur atom of methionine; one of two differentially regulated isozymes (Sam1p and Sam2p)	K[EGM].V[SGH]	39								Y	0.007	9
protein_40_YLR180W	2	SAM1:  S-adenosylmethionine synthetase, catalyzes transfer of the adenosyl group of ATP to the sulfur atom of methionine; one of two differentially regulated isozymes (Sam1p and Sam2p)	R[IFG][LQM]A	39									0.007	10
protein_40_YLR009W	2	RLP24:  Essential protein with similarity to Rpl24Ap and Rpl24Bp, associated with pre-60S ribosomal subunits and required for ribosomal large subunit biogenesis	[KDM]R...E	39	RE..E	Iron binding motif in ferritin L-chain and yeast Iron transport protein					cytoplasm organization and biogenesis (1e-26)	Y	0.007	9
protein_40_YLL039C	2	UBI4:  Ubiquitin, becomes conjugated to proteins, marking them for selective degradation via the ubiquitin-26S proteasome system; essential for the cellular stress response; encoded as a polyubiquitin precursor comprised of 5 head-to-tail repeats	[DPK]D[ED]LQ	39	LPDEL	Motif in CBP for interaction with PPARg-LBD (secondary site)					actin cortical patch (0.01)		0.005	9
protein_40_YLL008W	2	DRS1:  Nucleolar DEAD-box protein required for ribosome assembly and function, including synthesis of 60S ribosomal subunits; constituent of 66S pre-ribosomal particles	NT..[AL][EWA]T	39	T..[IL]	FHA2 binding motif, Thr must be phosphorylated							0.004	8
protein_40_YKL014C	2	URB1:  Nucleolar protein required for the normal accumulation of 25S and 5.8S rRNAs, associated with the 27SA2 pre-ribosomal particle; proposed to be involved in the biogenesis of the 60S ribosomal subunit	S[NR].[KVE]KD	39							ribosome biogenesis (1e-05)		0.004	9
protein_40_YJR145C	2	RPS4A:  Protein component of the small (40S) ribosomal subunit; mutation affects 20S pre-rRNA processing; identical to Rps4Bp and has similarity to rat S4 ribosomal protein	A[FM]..K[IQ]	39			Y				snoRNA binding (0.001)		0.005	10
protein_40_YJR022W	2	LSM8:  Lsm (Like Sm) protein; forms heteroheptameric complex (with Lsm2p, Lsm3p, Lsm4p, Lsm5p, Lsm6p, and Lsm7p) that is part of spliceosomal U6 snRNP and is also implicated in processing of pre-tRNA, pre-snoRNA, and pre-rRNA	[DV][ALS]..KIS	39									0.004	9
protein_40_YJL138C	2	TIF2:  Translation initiation factor eIF4A, identical to Tif1p; DEA(D/H)-box RNA helicase that couples ATPase activity to RNA binding and unwinding; forms a dumbbell structure of two compact domains connected by a linker; interacts with eIF4G	G[RQV]F[GCR]	39								Y	0.005	9
protein_40_YJL106W	2	IME2:  Serine/threonine protein kinase involved in activation of meiosis, associates with Ime1p and mediates its stability, activates Ndt80p; IME2 expression is positively regulated by Ime1p	[KIV]D..AL[ANG]	39									0.004	10
protein_40_YJL010C	2	NOP9:  Essential component of pre-40S ribosomes that is required for early cleavages of 35S pre-rRNA and hence formation of 18S rRNA; binds RNA in vitro and contains multiple pumilio-like repeats	[SKG]K..K[KLS]	39	P.[ST]PKK.KK	Cdc2 like protein kinase substrate motif					cytoplasm organization and biogenesis (1e-31)	Y	0.007	10
protein_40_YIL095W	2	PRK1:  Protein serine/threonine kinase; regulates the organization and function of the actin cytoskeleton through the phosphorylation of the Pan1p-Sla1p-End3p protein complex	S[RNT]..[SWE]NA	39	S[ST]	MDC1 BRCT domain binding motif							0.004	7
protein_40_YHR135C	2	YCK1:  Palmitoylated, plasma membrane-bound casein kinase I isoform; shares redundant functions with Yck2p in morphogenesis, proper septin assembly, endocytic trafficking; provides an essential function overlapping with that of Yck2p	N..[RNG]R	39	[KR]R	CLV_PCSK_KEX2_1					nucleic acid binding (0.001)		0.007	10
protein_40_YHR088W	2	RPF1:  Nucleolar protein involved in the assembly of the large ribosomal subunit; constituent of 66S pre-ribosomal particles; contains a sigma(70)-like motif, which is thought to bind RNA	EN..[KPL][KTQ]K	39							nucleolus (1e-05)		0.004	7
protein_40_YGR086C	2	PIL1:  Primary component of eisosomes, which are large immobile cell cortex structures associated with endocytosis; null mutants show activation of Pkc1p/Ypk1p stress resistance pathways; detected in phosphorylated state in mitochondria	EA[KQF]L[LVN]	39	IEAD	Protease Caspase 10							0.005	7
protein_40_YGL173C	2	KEM1:  Evolutionarily-conserved 5'-3' exonuclease component of cytoplasmic processing (P) bodies involved in mRNA decay; plays a role in microtubule-mediated processes, filamentous growth, ribosomal RNA maturation, and telomere maintenance	[RM]EV[KQM]	39							RNA metabolism (1e-04)		0.005	8
protein_40_YGL137W	2	SEC27:  Essential beta'-coat protein of the COPI coatomer, involved in ER-to-Golgi and Golgi-to-ER transport; contains WD40 domains that mediate cargo selective interactions; 45% sequence identity to mammalian beta'-COP	[IHS]K[EYV]VI	39							COPI vesicle coat (0.001)		0.004	8
protein_40_YGL105W	2	ARC1:  Protein that binds tRNA and methionyl- and glutamyl-tRNA synthetases (Mes1p and Gus1p), delivering tRNA to them, stimulating catalysis, and ensuring their localization to the cytoplasm; also binds quadruplex nucleic acids	[EQL]DGD[VE]	39	D.D	Ribose moiety of UDP and manganese binding site in glucuronyl transferase	Y					Y	0.004	7
protein_40_YGL031C	2	RPL24A:  Ribosomal protein L30 of the large (60S) ribosomal subunit, nearly identical to Rpl24Bp and has similarity to rat L24 ribosomal protein; not essential for translation but may be required for normal translation rate	K[ATQ]..AE[IQ]	39							cytosolic ribosome (sensu Eukaryota) (0.001)		0.005	10
protein_40_YFR034C	2	PHO4:  Basic helix-loop-helix (bHLH) transcription factor of the myc-family; binds cooperatively with Pho2p to the PHO5 promoter; function is regulated by phosphorylation at multiple sites and by phosphate availability	Q[TQ]K[LDS]T	39	[KR].TQT	LIG_Dynein_DLC8_1							0.004	7
protein_40_YFL039C	2	ACT1:  Actin, structural protein involved in cell polarization, endocytosis, and other cytoskeletal functions	K[SD]Q[LPR]D	39	SQ	ATM kinase substrate motif							0.004	7
protein_40_YFL037W	2	TUB2:  Beta-tubulin; associates with alpha-tubulin (Tub1p and Tub3p) to form tubulin dimer, which polymerizes to form microtubules	[DPY]R..[DCR]E	39			Y						0.005	10
protein_40_YER177W	2	BMH1:  14-3-3 protein, major isoform; controls proteome at post-transcriptional level, binds proteins and DNA, involved in regulation of many processes including exocytosis, vesicle transport, Ras/MAPK signaling, and rapamycin-sensitive signaling	R[KGT].S[FPN]	39	KKR..S	Phosphorylation site for MLCK						Y	0.007	10
protein_40_YER148W	2	SPT15:  TATA-binding protein, general transcription factor that interacts with other factors to form the preinitiation complex at promoters, essential for viability	N[IGE].[QDE]SL	39							RSC complex (0.01)		0.004	8
protein_40_YER110C	2	KAP123:  Karyopherin beta, mediates nuclear import of ribosomal proteins prior to assembly into ribosomes and import of histones H3 and H4; localizes to the nuclear pore, nucleus, and cytoplasm; exhibits genetic interactions with RAI1	[PQG][SDK]TG	39	STG	EH(3) EF hand domain binding motif of EPS15, Class II					snRNP protein import into nucleus (1e-06)	Y	0.007	10
protein_40_YDR471W	2	RPL27B:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl27Ap and has similarity to rat L27 ribosomal protein	S.[ILMV]S	39									0.007	10
protein_40_YDR388W	2	RVS167:  Actin-associated protein, subunit of a complex (Rvs161p-Rvs167p) involved in regulation of actin cytoskeleton, endocytosis, and viability following starvation or osmotic stress; homolog of mammalian amphiphysin	E..[LIQ]K	39							cell cortex (1e-05)	Y	0.007	10
protein_40_YDR172W	2	SUP35:  Translation termination factor eRF3; altered protein conformation creates the [PSI(+)] prion, a dominant cytoplasmically inherited protein aggregate that alters translational fidelity and creates a nonsense suppressor phenotype	LA[LIS]N[NF]	39									0.005	7
protein_40_YDR099W	2	BMH2:  14-3-3 protein, minor isoform; controls proteome at post-transcriptional level, binds proteins and DNA, involved in regulation of many processes including exocytosis, vesicle transport, Ras/MAPK signaling, and rapamycin-sensitive signaling	A[TQD]..[SEW]S	39									0.008	9
protein_40_YDR099W	2	BMH2:  14-3-3 protein, minor isoform; controls proteome at post-transcriptional level, binds proteins and DNA, involved in regulation of many processes including exocytosis, vesicle transport, Ras/MAPK signaling, and rapamycin-sensitive signaling	D[NT].N[EGW]	39									0.007	10
protein_40_YDR087C	2	RRP1:  Essential evolutionarily conserved nucleolar protein necessary for biogenesis of 60S ribosomal subunits and processing of pre-rRNAs to mature rRNAs, associated with several distinct 66S pre-ribosomal particles	[SEI]E.E[EAM]	39							nucleolus (1e-18)		0.008	10
protein_40_YDL213C	2	NOP6:  Putative RNA-binding protein implicated in ribosome biogenesis; contains an RNA recognition motif (RRM) and has similarity to hydrophilins; NOP6 may be a fungal-specific gene as no homologs have been yet identified in higher eukaryotes	LI..[LMP]D[PAL]	39									0.005	8
protein_40_YDL212W	2	SHR3:  Endoplasmic reticulum packaging chaperone, required for incorporation of amino acid permeases into COPII coated vesicles for transport to the cell surface	F[IQC]..G[LIF]	39							amine transporter activity (0.001)		0.006	10
protein_40_YDL055C	2	PSA1:  GDP-mannose pyrophosphorylase (mannose-1-phosphate guanyltransferase), synthesizes GDP-mannose from GTP and mannose-1-phosphate in cell wall biosynthesis; required for normal cell wall structure	[GDL]VE[TFA]	39	VEHD	Protease Caspase 6-stringent						Y	0.008	10
protein_40_YDL055C	2	PSA1:  GDP-mannose pyrophosphorylase (mannose-1-phosphate guanyltransferase), synthesizes GDP-mannose from GTP and mannose-1-phosphate in cell wall biosynthesis; required for normal cell wall structure	SN.[TEY][KSD]F	39	N.[TS]	N-linked glycosylation site							0.004	7
protein_40_YDL043C	2	PRP11:  Subunit of the SF3a splicing factor complex, required for spliceosome assembly	I[PMF]..DL[SEA]	39	WDL	Binding motif for AP-2 and clathrin heavy chain ear					RNA binding (1e-04)	Y	0.004	8
protein_40_YDL030W	2	PRP9:  Subunit of the SF3a splicing factor complex, required for spliceosome assembly; acts after the formation of the U1 snRNP-pre-mRNA complex	TG..[DF]L[KF]	39	TGY	ERK6/SAPK3 activation sites for HOG/p38 activation	Y				nuclear mRNA splicing, via spliceosome (0.01)		0.005	7
protein_40_YDL013W	2	SLX5:  Subunit of the Slx5-Slx8 substrate-specific ubiquitin ligase complex; stimulated by prior attachment of SUMO to the substrate	K[KQT]SK[IML]	39	RKK.[ST]	ZIP kinase phosphorylation motif						Y	0.004	7
protein_40_YDL013W	2	SLX5:  Subunit of the Slx5-Slx8 substrate-specific ubiquitin ligase complex; stimulated by prior attachment of SUMO to the substrate	Y[NWI]NN[NL]	39	Y.N	LIG_SH2_GRB2							0.005	7
protein_40_YBR245C	2	ISW1:  Member of the imitation-switch (ISWI) class of ATP-dependent chromatin remodeling complexes; ATPase that forms a complex with Ioc2p and Ioc4p to regulate transcription elongation, and a complex with Ioc3p to repress transcription initiation	E[IR].[KFQ]EI	39	EEEIYEEIE	cFPS/FES kinase phosphorylation site							0.005	10
protein_40_YBR059C	2	AKL1:  Ser-Thr protein kinase, member (with Ark1p and Prk1p) of the Ark kinase family; involved in endocytosis and actin cytoskeleton organization	S[SEN]TP[AE]	39	[ST]P	LIG_WW_4							0.005	7
protein_40_YBR048W	2	RPS11B:  Protein component of the small (40S) ribosomal subunit; identical to Rps11Ap and has similarity to E. coli S17 and rat S11 ribosomal proteins	R[ARG][AQH]R	39	[AG]R	Protease matriptase protease site					cytosolic ribosome (sensu Eukaryota) (1e-08)		0.007	10
protein_40_YBR036C	2	CSG2:  Endoplasmic reticulum membrane protein, required for mannosylation of inositolphosphorylceramide and for growth at high calcium concentrations	YY.[YCV][VL]	39	[DE]YY[RK]	PTP1B phosphatase substrate motif							0.004	8
protein_40_YBR031W	2	RPL4A:  N-terminally acetylated protein component of the large (60S) ribosomal subunit, nearly identical to Rpl4Bp and has similarity to E. coli L4 and rat L4 ribosomal proteins	ID..[RDQ][NI]S	39									0.004	8
protein_40_YAL032C	2	PRP45:  Protein required for pre-mRNA splicing; associates with the spliceosome and interacts with splicing factors Prp22p and Prp46p; orthologous to human transcriptional coactivator SKIP and can activate transcription of a reporter gene	AN..[LDP][KSF]	39									0.008	10
protein_40_YAL032C	2	PRP45:  Protein required for pre-mRNA splicing; associates with the spliceosome and interacts with splicing factors Prp22p and Prp46p; orthologous to human transcriptional coactivator SKIP and can activate transcription of a reporter gene	N..I[IRY]	39	IY	cFGR and Csk kinase phosphorylation site (peptide screen)					spliceosome (1e-08)	Y	0.007	10
oshea_vacuole	2	oshea_vacuole	F.[LYV]V	39	YF.[FPLY]	SH2 ligand for PTPN6-N (Tyr must be phosphorylated)					vacuole (1e-13)		0.008	10
oshea_vacuolar_membrane	2	oshea_vacuolar_membrane	[SYE]L[QGI]SS	39	S[ST]	MDC1 BRCT domain binding motif					vacuolar membrane (1e-13)		0.006	9
oshea_nuclear_periphery	2	oshea_nuclear_periphery	S[NDI]..S[LPF]	39	SP	ERK1, ERK2 Kinase substrate motif					nuclear envelope (1e-29)		0.008	10
oshea_mitochondrion	2	oshea_mitochondrion	[KEQ]K[KRY]K	39	KKKKKK[ST]	TGF beta receptor kinase substrate motif	Y						0.008	10
oshea_cell_periphery	2	oshea_cell_periphery	L[SNY][PYA]V	39			Y				plasma membrane (1e-10)		0.008	10
oshea_ambiguous	2	oshea_ambiguous	[NSK]T..L	39	T..[IL]	FHA2 binding motif, Thr must be phosphorylated					site of polarized growth (1e-07)		0.008	10
matsuyama_Spindle_or_SPB	2	matsuyama_Spindle_or_SPB	D..[LEP]E	39							spindle (1e-13)		0.010	10
matsuyama_Cytosol	2	matsuyama_Cytosol	A..[FAD]R	39	[AG]R	Protease matriptase protease site					cytosolic ribosome (sensu Eukaryota) (1e-05)	Y	0.010	9
genetic_YNL153C	2	GIM3: Subunit of the heterohexameric cochaperone prefoldin complex which binds specifically to cytosolic chaperonin and transfers target proteins to it	NL[RKQ]	39							cell cycle (1e-08)		0.007	10
genetic_YLR200W	2	YKE2: Subunit of the heterohexameric Gim/prefoldin protein complex involved in the folding of alpha-tubulin, beta-tubulin, and actin	DI[TSI]	39							microtubule-based process (1e-08)		0.007	10
genetic_YGL058W	2	RAD6: Ubiquitin-conjugating enzyme (E2), involved in postreplication repair (with Rad18p), sporulation, telomere silencing, and ubiquitin-mediated N-end rule protein degradation (with Ubr1p)	D.K[KIL]	39	[LI][IVCAP]D.K[LIFY]E[FI]G	SAICAR_SYNTHETASE_2 PATTERN					DNA metabolism (1e-25)	Y	0.007	10
genetic_YGL058W	2	RAD6: Ubiquitin-conjugating enzyme (E2), involved in postreplication repair (with Rad18p), sporulation, telomere silencing, and ubiquitin-mediated N-end rule protein degradation (with Ubr1p)	LR[ELP]	39	RPL	VEGFR and neuropilin binding peptide					DNA metabolism (1e-17)		0.007	10
protein_40_YBL003C	2	HTA2:  One of two nearly identical (see also HTA1) histone H2A subtypes; core histone required for chromatin assembly and chromosome function; DNA damage-dependent phosphorylation by Mec1p facilitates DNA repair; acetylated by Nat4p	K[APV].[RSL]K	38	KAPRK[QH][LI]	HISTONE_H3_1 PATTERN		Histone	1.E-02	-2.3	DNA metabolism (1e-08)		0.007	10
protein_40_YGR128C	2	UTP8:  Nucleolar protein required for export of tRNAs from the nucleus; also copurifies with the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	E[ELD].E[KED]	38	SEDEE	CKII kinase phosphorylation site (peptide screen)		WD40	1.E-05	-2.2	processing of 20S pre-rRNA (1e-27)	Y	0.007	10
oshea_bud_neck	2	oshea_bud_neck	N.[QDS]Q	38	[ST]Q	ATM kinase phosphorylation site		Pkinase	1.E-04	-1.7	site of polarized growth (1e-42)	Y	0.007	10
yeast-388_GO-0007275	2	development	P.[SLM]P	38	P.[ST]P	Erk p44 MAP kinase phosphorylation site		Pkinase	1.E-02	-1.6	multicellular organismal development (1e-14)		0.008	10
yeast-1547_GO-0043283	2	biopolymer metabolism	R..F[DNEQ]	38				PI3_PI4_kinase	1.E-03	-1.6	DNA metabolism (1e-39)		0.008	10
yeast-649_GO-0003676	2	nucleic acid binding	N[NHA]..[NVH]N	38				zf-C2H2	1.E-05	-1.4	nucleic acid binding (1e-76)		0.008	10
yeast-649_GO-0003676	2	nucleic acid binding	E[NES]E[DSF]	38	[ST]E	G protein-coupled receptor kinase 1 substrate motif		RRM_1	1.E-04	-1.2	nucleic acid binding (1e-10)	Y	0.008	10
protein_40_YNL002C	2	RLP7:  Nucleolar protein with similarity to large ribosomal subunit L7 proteins; constituent of 66S pre-ribosomal particles; plays an essential role in processing of precursors to the large ribosomal subunit RNAs	H[RFG]..R[TGK]	38			Y	DEAD	1.E-04	-1.2	ribosomal large subunit assembly and maintenance (1e-05)		0.005	8
yeast-322_GO-0005654	2	nucleoplasm	KR.[KRQ]	38	KR	CLV_PCSK_PC1ET2_1		PHD	1.E-03	-1	nucleoplasm (1e-17)	Y	0.008	10
yeast-320_GO-0006355	2	regulation of transcription, DNA-dependent	[HYP]TG[END]K	38	LP.TG	C-terminal sorting signal which targets surface proteins of Staphylococcus aureus to the cell wall peptidoglycan; Sortase cleaves between Thr and Gly and C-termini is used for crosslinking in cell wall		zf-C2H2	1.E-09	-1	regulation of transcription, DNA-dependent (1e-10)		0.007	10
yeast-320_GO-0006355	2	regulation of transcription, DNA-dependent	E.E[VEK]	38	Y.E.E	Src phosphorylation site		Zn_clus	1.E-07	-0.9	regulation of transcription, DNA-dependent (1e-22)	Y	0.008	10
yeast-504_GO-0006350	2	transcription	T.[ATY]P	38	[ST]P	LIG_WW_4		Zn_clus	1.E-04	-0.8	transcription (1e-14)		0.008	10
yeast-513_GO-0005515	2	protein binding	SS[EDA][LKW]	38	S[ST]	MDC1 BRCT domain binding motif		HEAT	1.E-02	-0.6	protein binding (1e-90)		0.008	10
yeast-436_GO-0031323	2	regulation of cellular metabolism	[DNI]AT[NIL]	38				Zn_clus	1.E-02	-0.5	regulation of cellular metabolism (1e-70)		0.008	10
protein_40_YGR085C	2	RPL11B:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl11Ap; involved in ribosomal assembly; depletion causes degradation of proteins and RNA of the 60S subunit; has similarity to E. coli L5 and rat L11	[KLF]G.K[VS]T	38				Ribosomal_L7Ae	1.E-02	-0.5	cytosolic ribosome (sensu Eukaryota) (1e-07)		0.004	9
protein_40_YAL032C	2	PRP45:  Protein required for pre-mRNA splicing; associates with the spliceosome and interacts with splicing factors Prp22p and Prp46p; orthologous to human transcriptional coactivator SKIP and can activate transcription of a reporter gene	D[SFC].[DIH]D	38				Helicase_C	1.E-02	-0.5	spliceosome (0.001)		0.007	10
yeast-256_GO-0016462	2	pyrophosphatase activity	L[IWG]D	38	WDL	Binding motif for AP-2 and clathrin heavy chain ear		ABC_tran	1.E-12	-0.2	pyrophosphatase activity (1e-12)		0.008	10
yeast-752_GO-0016787	2	hydrolase activity	L..D[AVY]	38			Y	AAA	1.E-04	-0.1	hydrolase activity, acting on ester bonds (1e-54)	Y	0.008	10
matsuyama_periphery	2	matsuyama_periphery	K[LPT]S	38	RK.SF	PKCepsilon kinase phosphorylation site (peptide screen)		PH	1.E-06	-0.1	barrier septum (1e-89)		0.009	10
protein_40_YOL069W	2	NUF2:  Component of the evolutionarily conserved kinetochore-associated Ndc80 complex (Ndc80p-Nuf2p-Spc24p-Spc25p); involved in chromosome segregation, spindle checkpoint activity and kinetochore clustering	[DKQ]L..K[LVI]	38				SMC_N	1.E-03	0.2	microtubule cytoskeleton (1e-06)		0.008	10
yeast-630_GO-0051244	2	regulation of cellular physiological process	K..[KSA]P	38	K..[ST]	PKA kinase substrate motif		Zn_clus	1.E-03	0.4	regulation of cellular metabolism (1e-12)	Y	0.008	10
yeast-215_GO-0005694	2	chromosome	D..Q[GQI]	38				SMC_N	1.E-06	0.4	chromosome (1e-89)		0.008	10
protein_40_YBR009C	2	HHF1:  One of two identical histone H4 proteins (see also HHF2); core histone required for chromatin assembly and chromosome function; contributes to telomeric silencing; N-terminal domain involved in maintaining genomic integrity	R[EKT]I	38	LRT	LKB1 Kinase substrate motif		Histone	1.E-02	0.4	DNA metabolism (1e-07)	Y	0.007	10
yeast-921_GO-0006810	2	transport	F..[VAL]F	38	F..LF	Androgen receptor motif that interacts with AF2		MFS_1	1.E-10	0.6	intracellular transport (1e-61)	Y	0.008	10
yeast-661_GO-0050789	2	regulation of biological process	K..[KSA]P	38	K..[ST]	PKA kinase substrate motif		Zn_clus	1.E-02	0.6	regulation of metabolism (1e-12)	Y	0.008	10
yeast-752_GO-0016787	2	hydrolase activity	P..[LRG]I	38			Y	UCH	1.E-05	1.1	hydrolase activity, acting on ester bonds (1e-38)	Y	0.008	10
protein_40_YNL298W	2	CLA4:  Cdc42p activated signal transducing kinase of the PAK (p21-activated kinase) family, involved in septin ring assembly and cytokinesis; directly phosphorylates septins Cdc3p and Cdc10p; other yeast PAK family members are Ste20p and Skm1p	N[VGQ]I[DI]T	38	[IL][ILP]TP[RK]	CDC4 WD40 domain binding motif	Y	Septin	1.E-05	1.1	phospholipid binding (1e-05)		0.004	8
yeast-939_GO-0051234	2	establishment of localization	S..[TFI]G	38	S..[ST]	Casein Kinase I consensus phosphorylation site (N-term Ser must first be phosphorylated)	Y	MFS_1	1.E-09	1.3	establishment of cellular localization (1e-89)	Y	0.008	10
protein_40_YMR047C	2	NUP116:  Subunit of the nuclear pore complex (NPC) that is localized to both sides of the pore; contains a repetitive GLFG motif that interacts with mRNA export factor Mex67p and with karyopherin Kap95p; homologous to Nup100p	L..[KEP]D	38				IBN_N	1.E-07	1.3	nucleocytoplasmic transport (1e-33)	Y	0.007	10
yeast-312_GO-0006414	2	translational elongation	[EPD]SV[GC]	38	R..[ST]V	CamKII consensus phosphorylation site more stringent		Ribosomal_60s	1.E-05	1.5	translational elongation (1e-12)	Y	0.005	8
protein_40_YNL031C	2	HHT2:  One of two identical histone H3 proteins (see also HHT1); core histone required for chromatin assembly, involved in heterochromatin-mediated telomeric and HM silencing; regulated by acetylation, methylation, and mitotic phosphorylation	[RFH]H[LPV]Q	38	HPQ	Biotin binding motif in streptavidin	Y	Histone	1.E-03	1.5	establishment and/or maintenance of chromatin architecture (0.01)		0.005	8
protein_40_YLR197W	2	SIK1:  Essential evolutionarily-conserved nucleolar protein component of the box C/D snoRNP complexes that direct 2'-O-methylation of pre-rRNA during its maturation; overexpression causes spindle orientation defects	K.L[ADM]	38	LLKIL	AP-2 binding motif in CXCR2 receptor	Y	WD40	1.E-04	1.8	nucleolus (1e-34)		0.007	10
yeast-939_GO-0051234	2	establishment of localization	F.G[ILG]	38	FRGGT	Phosphoinositide binding motif in ATG18 and ATG21		Mito_carr	1.E-11	1.9	establishment of cellular localization (1e-67)	Y	0.008	10
yeast-939_GO-0051234	2	establishment of localization	[LFS]D..K[TVS]R	38				Mito_carr	1.E-27	2	transporter activity (1e-12)		0.008	9
yeast-235_GO-0000278	2	mitotic cell cycle	K[LSF][QRT]R	38	[KR]R	CLV_PCSK_KEX2_1		Kinesin	1.E-02	2	mitotic cell cycle (1e-53)	Y	0.008	10
protein_40_YOL133W	2	HRT1:  RING finger containing subunit of Skp1-Cullin-F-box ubiquitin protein ligases (SCF); required for Gic2p, Far1p, Sic1p and Cln2p degradation; may tether Cdc34p (a ubiquitin conjugating enzyme or E2) and Cdc53p (a cullin) subunits of SCF	L..[ILR]D	38				F-box	1.E-13	2	ubiquitin ligase complex (1e-13)	Y	0.007	10
yeast-238_GO-0017111	2	nucleoside-triphosphatase activity	A..[GEQ]R	38	[AG]R	Protease matriptase protease site	Y	Ras	1.E-12	2.1	nucleoside-triphosphatase activity (1e-97)	Y	0.008	10
oshea_microtubule	2	oshea_microtubule	SSRSH	38	S[ST]	MDC1 BRCT domain binding motif		Kinesin	1.E-09	2.1	microtubule motor activity (1e-08)		0.005	8
protein_40_YAR019C	2	CDC15:  Protein kinase of the Mitotic Exit Network that is localized to the spindle pole bodies at late anaphase; promotes mitotic exit by directly switching on the kinase activity of Dbf2p	PE.[INY][LTI]	38			Y	Pkinase	1.E-19	2.6	protein kinase activity (1e-14)	Y	0.007	10
protein_40_YGL245W	2	GUS1:  Glutamyl-tRNA synthetase (GluRS), forms a complex with methionyl-tRNA synthetase (Mes1p) and Arc1p; complex formation increases the catalytic efficiency of both tRNA synthetases and ensures their correct localization to the cytoplasm	[HWN]P.[ISH]V	38				Pkinase	1.E-04	2.8	protein kinase activity (1e-06)		0.006	9
protein_40_YOL139C	2	CDC33:  Cytoplasmic mRNA cap binding protein; the eIF4E-cap complex is responsible for mediating cap-dependent mRNA translation via interactions with the translation initiation factor eIF4G (Tif4631p or Tif4632p)	EN.[LEN]L[DTN]	38				Pkinase	1.E-04	3.2	protein kinase activity (0.001)		0.004	10
protein_40_YPR016C	2	TIF6:  Constituent of 66S pre-ribosomal particles, has similarity to human translation initiation factor 6 (eIF6); may be involved in the biogenesis and or stability of 60S ribosomal subunits	PN..KS[SLK]	38	KSP...K	GSK-3, ERK1, ERK2, CDK5 substrate motif	Y	MMR_HSR1	1.E-04	3.3	ribosome biogenesis (0.001)		0.004	9
protein_40_YGL207W	2	SPT16:  Subunit of the heterodimeric FACT complex (Spt16p-Pob3p), facilitates RNA Polymerase II transcription elongation through nucleosomes by destabilizing and then reassembling nucleosome structure	RD.[KRV]	38				Pkinase	1.E-10	3.5	protein kinase activity (1e-10)		0.007	10
protein_40_YDR324C	2	UTP4:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	[DAW]G.I[RKE]	38			Y	WD40	1.E-04	3.7	snoRNA binding (1e-19)	Y	0.007	10
yeast-460_GO-0006351	2	transcription, DNA-dependent	K..R	38	R...K..R	Motif in Ebola virus that eliminates IFN-beta production		zf-C2H2	1.E-07	3.8	transcription, DNA-dependent (10)		0.008	10
yeast-335_GO-0016772	2	transferase activity, transferring phosphorus-containing groups	M.YC	38				Pkinase	1.E-13	3.8	transferase activity, transferring phosphorus-containing groups (1e-14)	Y	0.007	9
yeast-335_GO-0016772	2	transferase activity, transferring phosphorus-containing groups	[GHA]V.[LTI]Y	38	IY	cFGR and Csk kinase phosphorylation site (peptide screen)		Pkinase	1.E-13	4.2	transferase activity, transferring phosphorus-containing groups (1e-35)	Y	0.009	10
yeast-1340_GO-0044267	2	cellular protein metabolism	K[LIA].[DGS]FG	38				Pkinase	1.E-43	6.2	protein amino acid phosphorylation (1e-50)		0.008	9
yeast-1464_GO-0019538	2	protein metabolism	K[ILY].D[FLT]G	38				Pkinase	1.E-46	6.7	protein amino acid phosphorylation (1e-50)		0.008	10
yeast-589_GO-0050896	2	response to stimulus	NS.[LMY][NEG]	38							response to stress (1e-37)		0.008	10
yeast-523_GO-0030529	2	ribonucleoprotein complex	I..[ILMV]L	38	[LIV]..[LM]L.AA.[FY][LI]	LIG_Sin3_1							0.008	10
yeast-513_GO-0005515	2	protein binding	G[TC].DV[SLY]	38							protein binding (1e-04)		0.005	9
yeast-470_GO-0006259	2	DNA metabolism	KS[TGQ][TIR]	38	S[ST]	MDC1 BRCT domain binding motif					DNA metabolism (1e-75)	Y	0.008	10
yeast-410_GO-0007049	2	cell cycle	L[IER].[EMH]D	38							cell cycle (1e-58)		0.008	10
yeast-410_GO-0007049	2	cell cycle	T[LSF].K[MAP]	38							cell cycle (1e-54)		0.008	10
yeast-388_GO-0007275	2	development	L[SNP]..K[NTC]	38							multicellular organismal development (1e-76)		0.008	10
yeast-320_GO-0006355	2	regulation of transcription, DNA-dependent	DD.[IQY]E[DGR]	38	DD.Y	Shb PTB domain binding motif					regulation of transcription, DNA-dependent (1e-15)		0.008	10
yeast-284_GO-0005740	2	mitochondrial envelope	E.[DSH]S	38	[LIVMA].EG[DN]SA.[STAG]	TOPOISOMERASE_II PATTERN							0.008	10
yeast-284_GO-0005740	2	mitochondrial envelope	KR[KHV]	38	KR	CLV_PCSK_PC1ET2_1							0.008	10
yeast-256_GO-0016021	2	integral to membrane	[AGP]S..[ILF]IL	38	S..F	LIG_BRCT_BRCA1_1					integral to membrane (1e-12)		0.007	9
yeast-255_GO-0042254	2	ribosome biogenesis and assembly	[LSE]TR[NTQ]I	38							rRNA processing (1e-07)		0.005	8
yeast-255_GO-0007028	2	cytoplasm organization and biogenesis	[LSE]TR[NTQ]I	38							rRNA processing (1e-07)		0.005	8
yeast-248_GO-0043285	2	biopolymer catabolism	TLN[SM][IHP]	38							biopolymer catabolism (1e-07)		0.005	7
yeast-244_GO-0000279	2	M phase	P.[IQN]R	38	P..R..KP	SH3 binding motif for GRB2 C-term					M phase (1e-90)		0.008	10
yeast-235_GO-0009653	2	morphogenesis	T[KAS]..[NQK]N	38			Y				cellular morphogenesis (1e-65)		0.008	10
yeast-235_GO-0000902	2	cellular morphogenesis	T[KAS]..[NQK]N	38			Y				cellular morphogenesis (1e-65)		0.008	10
yeast-215_GO-0007010	2	cytoskeleton organization and biogenesis	[ILG]Q[EAI]E	38							cytoskeleton organization and biogenesis (1e-46)	Y	0.008	10
yeast-207_GO-0006974	2	response to DNA damage stimulus	L[SEC]T[QIR]	38	IRRLSTRRR	Nek 2 kinase substrate motif					response to DNA damage stimulus (1e-60)		0.008	10
yeast-1547_GO-0043283	2	biopolymer metabolism	IY..[DQG][IVF]	38	IY	cFGR and Csk kinase phosphorylation site (peptide screen)					protein modification (1e-09)		0.008	10
protein_40_YPR120C	2	CLB5:  B-type cyclin involved in DNA replication during S phase; activates Cdc28p to promote initiation of DNA synthesis; functions in formation of mitotic spindles along with Clb3p and Clb4p; most abundant during late G1 phase	[VK]H..[LNK]K	38								Y	0.006	10
protein_40_YPR080W	2	TEF1:  Translational elongation factor EF-1 alpha; also encoded by TEF2; functions in the binding reaction of aminoacyl-tRNA (AA-tRNA) to ribosomes	Q[RWQ][GFP]G	38	RGG	Alternative integrin binding site in FMDV virus							0.005	10
protein_40_YPL209C	2	IPL1:  Aurora kinase involved in regulating kinetochore-microtubule attachments; helps maintain condensed chromosomes during anaphase and early telophase; associates with Sli15p, which promotes Ipl1p association with mitotic spindle	PK..[KQG][ECW]	38									0.006	10
protein_40_YPL141C	2	FRK1:  Putative protein kinase; similar to Kin4p; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm; YPL141C is not an essential gene	DIR[SPD][LQ]	38									0.004	7
protein_40_YPL093W	2	NOG1:  Putative GTPase that associates with free 60S ribosomal subunits in the nucleolus and is required for 60S ribosomal subunit biogenesis; constituent of 66S pre-ribosomal particles; member of the ODN family of nucleolar G-proteins	A.[GVR]K	38	KAPRK[QH][LI]	HISTONE_H3_1 PATTERN					cytoplasm organization and biogenesis (1e-29)		0.007	10
protein_40_YOR294W	2	RRS1:  Essential protein that binds ribosomal protein L11 and is required for nuclear export of the 60S pre-ribosomal subunit during ribosome biogenesis; mouse homolog shows altered expression in Huntington's disease model mice	[ENT]R..A[FRM]	38							cytoplasm organization and biogenesis (1e-07)	Y	0.006	10
protein_40_YOR133W	2	EFT1:  Elongation factor 2 (EF-2), also encoded by EFT2; catalyzes ribosomal translocation during protein synthesis; contains diphthamide, the unique posttranslationally modified histidine residue specifically ADP-ribosylated by diphtheria toxin	D[KPT]R[EV]	38	[KR]R	CLV_PCSK_KEX2_1							0.005	9
protein_40_YOL133W	2	HRT1:  RING finger containing subunit of Skp1-Cullin-F-box ubiquitin protein ligases (SCF); required for Gic2p, Far1p, Sic1p and Cln2p degradation; may tether Cdc34p (a ubiquitin conjugating enzyme or E2) and Cdc53p (a cullin) subunits of SCF	NF[VLW][SRH]	38			Y				macromolecule catabolism (1e-04)	Y	0.007	10
protein_40_YOL086C	2	ADH1:  Alcohol dehydrogenase, fermentative isozyme active as homo- or heterotetramers; required for the reduction of acetaldehyde to ethanol, the last step in the glycolytic pathway	KLN[NM][GKS]	38								Y	0.005	7
protein_40_YOL004W	2	SIN3:  Component of the Sin3p-Rpd3p histone deacetylase complex, involved in transcriptional repression and activation of diverse processes, including mating-type switching and meiosis; involved in the maintenance of chromosomal integrity	N[NKA].[NDL]S	38	NK.D	Motif for specificity of guanine in purine binding proteins					histone deacetylase complex (1e-08)	Y	0.008	10
protein_40_YNR054C	2	ESF2:  Essential nucleolar protein involved in pre-18S rRNA processing; component of the small subunit (SSU) processome; has sequence similarity to mABT1, a mouse transcription activator	DV..[RIP][GDK]	38							nucleolus (1e-14)		0.007	9
protein_40_YNL298W	2	CLA4:  Cdc42p activated signal transducing kinase of the PAK (p21-activated kinase) family, involved in septin ring assembly and cytokinesis; directly phosphorylates septins Cdc3p and Cdc10p; other yeast PAK family members are Ste20p and Skm1p	[LD]A.NK[GMK]	38									0.004	9
protein_40_YNL289W	2	PCL1:  Pho85 cyclin of the Pcl1,2-like subfamily, involved in entry into the mitotic cell cycle and regulation of morphogenesis, localizes to sites of polarized cell growth	D..S[VDG]	38	DDDD..S	Casein kinase 1 phosphorylation motif							0.007	10
protein_40_YNL118C	2	DCP2:  Catalytic subunit of the Dcp1p-Dcp2p decapping enzyme complex, which removes the 5' cap structure from mRNAs prior to their degradation; member of the Nudix hydrolase family	D[LHQ].N[FAY]	38			Y					Y	0.006	8
protein_40_YMR194W	2	RPL36A:  N-terminally acetylated protein component of the large (60S) ribosomal subunit, nearly identical to Rpl36Bp and has similarity to rat L36 ribosomal protein; binds to 5.8 S rRNA	A[RAG].[KRV]A	38			Y				cytosolic ribosome (sensu Eukaryota) (1e-30)	Y	0.008	10
protein_40_YMR139W	2	RIM11:  Protein kinase required for signal transduction during entry into meiosis; promotes the formation of the Ime1p-Ume6p complex by phosphorylating Ime1p and Ume6p; shares similarity with mammalian glycogen synthase kinase 3-beta	[TAI]NT[SNV]	38									0.007	10
protein_40_YMR116C	2	ASC1:  G-protein beta subunit and guanine nucleotide dissociation inhibitor for Gpa2p; ortholog of RACK1 that inhibits translation; core component of the small (40S) ribosomal subunit; represses Gcn4p in the absence of amino acid starvation	[IKD]S..SD[EC]	38	S..S	Casien kinase I phosphorylation site, 1st Ser must be phosphorylated							0.004	9
protein_40_YMR001C	2	CDC5:  Polo-like kinase with similarity to Xenopus Plx1 and S. pombe Plo1p; found at bud neck, nucleus and SPBs; has multiple functions in mitosis and cytokinesis through phosphorylation of substrates; may be a Cdc28p substrate	YQ.T[LCQ]	38									0.004	9
protein_40_YML063W	2	RPS1B:  Ribosomal protein 10 (rp10) of the small (40S) subunit; nearly identical to Rps1Ap and has similarity to rat S3a ribosomal protein	R[RAE].A[RLV]	38							cytosolic ribosome (sensu Eukaryota) (1e-18)	Y	0.007	10
protein_40_YLR448W	2	RPL6B:  Protein component of the large (60S) ribosomal subunit, has similarity to Rpl6Ap and to rat L6 ribosomal protein; binds to 5.8S rRNA	RA..[VKM][KAF]	38			Y				cytosolic ribosome (sensu Eukaryota) (1e-16)	Y	0.007	10
protein_40_YLR429W	2	CRN1:  Coronin, cortical actin cytoskeletal component that associates with the Arp2p/Arp3p complex to regulate its activity; plays a role in regulation of actin patch assembly	IE.[ESR][AYR]E	38	IEGR	Protease Protease Factor X a							0.004	7
protein_40_YLR180W	2	SAM1:  S-adenosylmethionine synthetase, catalyzes transfer of the adenosyl group of ATP to the sulfur atom of methionine; one of two differentially regulated isozymes (Sam1p and Sam2p)	A[IGR].[VWP]L	38								Y	0.007	10
protein_40_YLR029C	2	RPL15A:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl15Bp and has similarity to rat L15 ribosomal protein; binds to 5.8 S rRNA	RA.[RAP][AFK]	38			Y				cytosolic ribosome (sensu Eukaryota) (1e-04)		0.007	10
protein_40_YLR002C	2	NOC3:  Protein that forms a nuclear complex with Noc2p that binds to 66S ribosomal precursors to mediate their intranuclear transport; also binds to chromatin to promote the association of DNA replication factors and replication initiation	EE.E[EAG][EKW]	38	RE..E	Iron binding motif in ferritin L-chain and yeast Iron transport protein					nucleolus (1e-09)	Y	0.006	10
protein_40_YKL021C	2	MAK11:  Protein involved in an early, nucleolar step of 60S ribosomal subunit biogenesis; essential for cell growth and replication of killer M1 dsRNA virus; contains four beta-transducin repeats	R[VMR]..IV	38	RR.SI	PKA kinase phosphorylation site (peptide screen)	Y				nucleolus (1e-06)		0.004	9
protein_40_YJR002W	2	MPP10:  Component of the SSU processome, which is required for pre-18S rRNA processing, interacts with and controls the stability of Imp3p and Imp4p, essential for viability; similar to human Mpp10p	R[HEQ]..F[LVD]	38	RQ.SFD	CAM Kinase II kinase phosphorylation site (peptide screen)					snoRNA binding (1e-07)		0.006	10
protein_40_YJL164C	2	TPK1:  cAMP-dependent protein kinase catalytic subunit; promotes vegetative growth in response to nutrients via the Ras-cAMP signaling pathway; inhibited by regulatory subunit Bcy1p in the absence of cAMP; partially redundant with Tpk2p and Tpk3p	G[KFG].[KPQ]Q	38								Y	0.007	10
protein_40_YJL130C	2	URA2:  Bifunctional carbamoylphosphate synthetase (CPSase)-aspartate transcarbamylase (ATCase), catalyzes the first two enzymatic steps in the de novo biosynthesis of pyrimidines; both activities are subject to feedback inhibition by UTP	V[EPA].Y[IH]	38	Y[LI]	SH2 ligand for PLCgamma1 N-term.)group 3(phospho-peptide)							0.004	9
protein_40_YJL109C	2	UTP10:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	LL.[KAE][LDT]S	38	LLG	Beta2-Integrin binding motif	Y				small nucleolar ribonucleoprotein complex (1e-06)		0.005	10
protein_40_YIL094C	2	LYS12:  Homo-isocitrate dehydrogenase, an NAD-linked mitochondrial enzyme required for the fourth step in the biosynthesis of lysine, in which homo-isocitrate is oxidatively decarboxylated to alpha-ketoadipate	[AV]N..[KVW]T	38									0.006	9
protein_40_YIL094C	2	LYS12:  Homo-isocitrate dehydrogenase, an NAD-linked mitochondrial enzyme required for the fourth step in the biosynthesis of lysine, in which homo-isocitrate is oxidatively decarboxylated to alpha-ketoadipate	[SCE][VCM].QD	38									0.004	8
protein_40_YHR196W	2	UTP9:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	V..[TIL]K	38							nucleolus (1e-31)		0.007	10
protein_40_YHR088W	2	RPF1:  Nucleolar protein involved in the assembly of the large ribosomal subunit; constituent of 66S pre-ribosomal particles; contains a sigma(70)-like motif, which is thought to bind RNA	KK[SDA][KVR]	38	KKSRGDYMTMQIG	Insulin receptor kinase substrate motif					cytoplasm organization and biogenesis (1e-18)		0.008	10
protein_40_YHR079C	2	IRE1:  Serine-threonine kinase and endoribonuclease; transmembrane protein that mediates the unfolded protein response (UPR) by regulating Hac1p synthesis through HAC1 mRNA splicing; Kar2p binds inactive Ire1p and releases from it upon ER stress	D..N[DPG]	38									0.007	10
protein_40_YHR010W	2	RPL27A:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl27Bp and has similarity to rat L27 ribosomal protein	A..[KAP]K	38							cytoplasm organization and biogenesis (1e-12)		0.007	10
protein_40_YHL030W	2	ECM29:  Major component of the proteasome; tethers the proteasome core particle to the regulatory particle, and enhances the stability of the proteasome	LA.[GL][GRL]E	38							proteasome complex (sensu Eukaryota) (1e-06)		0.004	8
protein_40_YGR218W	2	CRM1:  Major karyopherin, involved in export of proteins, RNAs, and ribosomal subunits from the nucleus	FG..[NGQ]	38	G..G..K	Sulfonate donor binding site in sulfotransferases					rRNA export from nucleus (1e-10)	Y	0.007	10
protein_40_YGR218W	2	CRM1:  Major karyopherin, involved in export of proteins, RNAs, and ribosomal subunits from the nucleus	S..[SVW]G	38	S..[ST]	Casein Kinase I consensus phosphorylation site (N-term Ser must first be phosphorylated)	Y				rRNA export from nucleus (1e-09)		0.007	10
protein_40_YGR060W	2	ERG25:  C-4 methyl sterol oxidase, catalyzes the first of three steps required to remove two C-4 methyl groups from an intermediate in ergosterol biosynthesis; mutants accumulate the sterol intermediate 4,4-dimethylzymosterol	IS[GTW][FPI]I	38	S[ST]	MDC1 BRCT domain binding motif							0.004	7
protein_40_YGL105W	2	ARC1:  Protein that binds tRNA and methionyl- and glutamyl-tRNA synthetases (Mes1p and Gus1p), delivering tRNA to them, stimulating catalysis, and ensuring their localization to the cytoplasm; also binds quadruplex nucleic acids	[FM]SSVS	38	S[ST]	MDC1 BRCT domain binding motif							0.005	10
protein_40_YGL076C	2	RPL7A:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl7Bp and has similarity to E. coli L30 and rat L7 ribosomal proteins; contains a conserved C-terminal Nucleic acid Binding Domain (NDB2)	[EL]SD[DQ]D	38	DDDK[ACDEFGHIKLMNQRSTVWY]	Protease Enterokinase					ribosome assembly (0.01)		0.004	7
protein_40_YGL076C	2	RPL7A:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl7Bp and has similarity to E. coli L30 and rat L7 ribosomal proteins; contains a conserved C-terminal Nucleic acid Binding Domain (NDB2)	[GK]K[TA]LA	38							nucleolus (0.01)		0.004	7
protein_40_YFR052W	2	RPN12:  Subunit of the 19S regulatory particle of the 26S proteasome lid; synthetically lethal with RPT1, which is an ATPase component of the 19S regulatory particle; physically interacts with Nob1p and Rpn3p	TNR[PF]D	38	RGD	LIG_RGD					proteasome complex (sensu Eukaryota) (0.01)	Y	0.004	7
protein_40_YFR034C	2	PHO4:  Basic helix-loop-helix (bHLH) transcription factor of the myc-family; binds cooperatively with Pho2p to the PHO5 promoter; function is regulated by phosphorylation at multiple sites and by phosphate availability	K..[ARK]A	38	K[KR].[KR]	Nuclear localization motif					cytosolic part (1e-19)		0.007	9
protein_40_YFR031C-A	2	RPL2A:  Protein component of the large (60S) ribosomal subunit, identical to Rpl2Bp and has similarity to E. coli L2 and rat L8 ribosomal proteins	G[YWR]..[VQ]GK	38								Y	0.005	8
protein_40_YER177W	2	BMH1:  14-3-3 protein, major isoform; controls proteome at post-transcriptional level, binds proteins and DNA, involved in regulation of many processes including exocytosis, vesicle transport, Ras/MAPK signaling, and rapamycin-sensitive signaling	KV[ED][DFS]I	38									0.004	7
protein_40_YER148W	2	SPT15:  TATA-binding protein, general transcription factor that interacts with other factors to form the preinitiation complex at promoters, essential for viability	[SNL]A.N[TAG]P	38	[ST]P	LIG_WW_4							0.004	8
protein_40_YER125W	2	RSP5:  Ubiquitin-protein ligase involved in ubiquitin-mediated protein degradation; functions in multivesicular body sorting, heat shock response and ubiquitylation of arrested RNAPII; contains a hect (homologous to E6-AP carboxyl terminus) domain	[YFG][VGT]DDT	38	DD.Y	Shb PTB domain binding motif							0.004	8
protein_40_YDR388W	2	RVS167:  Actin-associated protein, subunit of a complex (Rvs161p-Rvs167p) involved in regulation of actin cytoskeleton, endocytosis, and viability following starvation or osmotic stress; homolog of mammalian amphiphysin	A[TAP]N	38							protein amino acid phosphorylation (0.01)	Y	0.007	10
protein_40_YDR145W	2	TAF12:  Subunit (61/68 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation and in chromatin modification, similar to histone H2A	I[ESG].[PS]QL	38	SQ	ATM kinase substrate motif					transcription from RNA polymerase II promoter (0.01)	Y	0.004	7
protein_40_YDL213C	2	NOP6:  Putative RNA-binding protein implicated in ribosome biogenesis; contains an RNA recognition motif (RRM) and has similarity to hydrophilins; NOP6 may be a fungal-specific gene as no homologs have been yet identified in higher eukaryotes	K.[LEH]A	38	[VILMAFP]K.E	MOD_SUMO					nucleolus (1e-21)	Y	0.007	10
protein_40_YDL140C	2	RPO21:  RNA polymerase II largest subunit B220, part of central core; phosphorylation of C-terminal heptapeptide repeat domain regulates association with transcription and splicing factors; similar to bacterial beta-prime	K[EPG]..SL[IFN]	38									0.004	10
protein_40_YDL055C	2	PSA1:  GDP-mannose pyrophosphorylase (mannose-1-phosphate guanyltransferase), synthesizes GDP-mannose from GTP and mannose-1-phosphate in cell wall biosynthesis; required for normal cell wall structure	[LMR]SK[DIS]L	38			Y				ligase activity (0.01)		0.005	9
protein_40_YDL055C	2	PSA1:  GDP-mannose pyrophosphorylase (mannose-1-phosphate guanyltransferase), synthesizes GDP-mannose from GTP and mannose-1-phosphate in cell wall biosynthesis; required for normal cell wall structure	[SWH]F.[DAS]FL	38									0.004	7
protein_40_YDL055C	2	PSA1:  GDP-mannose pyrophosphorylase (mannose-1-phosphate guanyltransferase), synthesizes GDP-mannose from GTP and mannose-1-phosphate in cell wall biosynthesis; required for normal cell wall structure	GG[GDY]	38	RGG	Alternative integrin binding site in FMDV virus						Y	0.007	10
protein_40_YDL055C	2	PSA1:  GDP-mannose pyrophosphorylase (mannose-1-phosphate guanyltransferase), synthesizes GDP-mannose from GTP and mannose-1-phosphate in cell wall biosynthesis; required for normal cell wall structure	R..[EVY]E	38	YE	TPK-IIB/P38Syk kinase phosphorylation site (peptide screen)					proteasome regulatory particle, base subcomplex (sensu Eukaryota) (1e-04)	Y	0.007	10
protein_40_YDL047W	2	SIT4:  Type 2A-related serine-threonine phosphatase that functions in the G1/S transition of the mitotic cycle; cytoplasmic and nuclear protein that modulates functions mediated by Pkc1p including cell wall and actin cytoskeleton organization	D[PRW]..L[RFD]	38	R..L	LIG_APCC_Dbox_1							0.007	10
protein_40_YBR181C	2	RPS6B:  Protein component of the small (40S) ribosomal subunit; identical to Rps6Ap and has similarity to rat S6 ribosomal protein	S.L[STP]	38									0.007	10
protein_40_YBL027W	2	RPL19B:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl19Ap and has similarity to rat L19 ribosomal protein; rpl19a and rpl19b single null mutations result in slow growth, while the double null mutation is lethal	S.[LSA]S	38	S..S	Casien kinase I phosphorylation site, 1st Ser must be phosphorylated							0.007	10
protein_40_YAL032C	2	PRP45:  Protein required for pre-mRNA splicing; associates with the spliceosome and interacts with splicing factors Prp22p and Prp46p; orthologous to human transcriptional coactivator SKIP and can activate transcription of a reporter gene	[RSM]I...L	38							nuclear mRNA splicing, via spliceosome (1e-12)	Y	0.007	10
protein_40_YAL032C	2	PRP45:  Protein required for pre-mRNA splicing; associates with the spliceosome and interacts with splicing factors Prp22p and Prp46p; orthologous to human transcriptional coactivator SKIP and can activate transcription of a reporter gene	ED.[ERY][ERI]	38	YEDP	Fyn SH2 domain binding motif					nuclear mRNA splicing, via spliceosome (1e-06)		0.007	10
matsuyama_Nucleus	2	matsuyama_Nucleus	KR[KRM]	38	KR	CLV_PCSK_PC1ET2_1					DNA metabolism (1e-24)		0.009	10
matsuyama_Nucleus	2	matsuyama_Nucleus	LG[LHA]	38	LLG	Beta2-Integrin binding motif					carboxylic acid metabolism (1e-12)		0.009	10
matsuyama_nuclear_envelope_or_dots	2	matsuyama_nuclear_envelope_or_dots	SN.[RTQ]	38	N.[TS]	N-linked glycosylation site					nuclear envelope (1e-29)	Y	0.009	10
matsuyama_Cytosol	2	matsuyama_Cytosol	[RPC]RL[NR]	38	[KR]R	CLV_PCSK_KEX2_1					purine nucleotide binding (0.01)		0.009	10
genetic_YLR262C	2	YPT6: GTPase, Ras-like GTP binding protein involved in the secretory pathway, required for fusion of endosome-derived vesicles with the late Golgi, maturation of the vacuolar carboxypeptidase Y; has similarity to the human GTPase, Rab6	S[QDK].L[KED]	38	SQ	ATM kinase substrate motif					regulation of metabolism (1e-08)	Y	0.007	10
genetic_YLR200W	2	YKE2: Subunit of the heterohexameric Gim/prefoldin protein complex involved in the folding of alpha-tubulin, beta-tubulin, and actin	KI	38	LLKIL	AP-2 binding motif in CXCR2 receptor					cell cycle (1e-19)		0.007	10
protein_40_YBR160W	2	CDC28:  Catalytic subunit of the main cell cycle cyclin-dependent kinase (CDK); alternately associates with G1 cyclins (CLNs) and G2/M cyclins (CLBs) which direct the CDK to specific substrates	SK[LDP]N[NQE]	37							 		0.007	10
protein_40_YER012W	2	PRE1:  Beta 4 subunit of the 20S proteasome; localizes to the nucleus throughout the cell cycle	VE[YWN][AHM]	37			Y	Proteasome	1.E-09	-4.1	proteasome complex (sensu Eukaryota) (1e-10)	Y	0.006	8
protein_40_YJR059W	2	PTK2:  Putative serine/threonine protein kinase involved in regulation of ion transport across plasma membrane; enhances spermine uptake	ST[SAP]	37	HSTSDD	Branched chain alpha-ketoacid dehydrogenase kinase substrate motif		Pkinase	1.E-02	-2.6	phosphotransferase activity, alcohol group as acceptor (0.01)		0.007	10
matsuyama_nucleolus	2	matsuyama_nucleolus	[HG]R..R[TH]A	37	R.[RK]R	CLV_PCSK_FUR_1	Y	DEAD	1.E-10	-1.6	ATP-dependent RNA helicase activity (1e-09)		0.006	9
yeast-220_GO-0044255	2	cellular lipid metabolism	V.[ILW]L	37	P.V.L	Shadow-Chromo domain binding motif	Y	PI3_PI4_kinase	1.E-02	-1.5	cellular lipid metabolism (1e-14)		0.008	10
yeast-256_GO-0016462	2	pyrophosphatase activity	VV..[EPC]	37			Y	Helicase_C	1.E-06	-1.3	nucleoside-triphosphatase activity (1e-09)		0.008	10
protein_40_YAR019C	2	CDC15:  Protein kinase of the Mitotic Exit Network that is localized to the spindle pole bodies at late anaphase; promotes mitotic exit by directly switching on the kinase activity of Dbf2p	[AR]PK[PQ]P	37	K[ST]P.K	GSK-3, ERK1, ERK2, CDK5 substrate motif		Pkinase	1.E-03	-1.3	protein kinase activity (0.001)		0.005	7
yeast-1166_GO-0005488	2	binding	R..[QKN]K	37	L..RR..KK	ERK docking motif in RSK stringent	Y	HEAT	1.E-02	-1.1	nucleic acid binding (1e-09)		0.008	10
yeast-294_GO-0006366	2	transcription from RNA polymerase II promoter	[SNY]S.S[PKQ]	37	SPSP	Motif for hydroxylation of Proline residues, which can further be modified with arabinogalactan		zf-C2H2	1.E-04	-1	transcription from RNA polymerase II promoter (1e-09)		0.008	10
protein_40_YOL133W	2	HRT1:  RING finger containing subunit of Skp1-Cullin-F-box ubiquitin protein ligases (SCF); required for Gic2p, Far1p, Sic1p and Cln2p degradation; may tether Cdc34p (a ubiquitin conjugating enzyme or E2) and Cdc53p (a cullin) subunits of SCF	L[SVC]..E[PFY]	37	[ST]..E	Casien kinase II consensus phosphorylation site		F-box	1.E-06	-0.7	ubiquitin ligase complex (0.001)	Y	0.007	10
yeast-648_GO-0050791	2	regulation of physiological process	[RSV]P..[LKE]K	37	[ST]P	LIG_WW_4	Y	GATA	1.E-02	-0.6	regulation of metabolism (1e-45)		0.008	10
yeast-521_GO-0051649	2	establishment of cellular localization	N[ENK]..E[DAM]	37				IBN_N	1.E-03	-0.6	establishment of cellular localization (1e-68)		0.008	10
yeast-324_GO-0030528	2	transcription regulator activity	[IQT]P.N[SPM]	37	[ST]P	LIG_WW_4	Y	Zn_clus	1.E-07	-0.6	transcription regulator activity (1e-44)		0.008	10
protein_40_YOR294W	2	RRS1:  Essential protein that binds ribosomal protein L11 and is required for nuclear export of the 60S pre-ribosomal subunit during ribosome biogenesis; mouse homolog shows altered expression in Huntington's disease model mice	S[IW]..Q[AKM]	37				Helicase_C	1.E-02	-0.6	cytoplasm organization and biogenesis (0.01)		0.004	7
protein_40_YMR047C	2	NUP116:  Subunit of the nuclear pore complex (NPC) that is localized to both sides of the pore; contains a repetitive GLFG motif that interacts with mRNA export factor Mex67p and with karyopherin Kap95p; homologous to Nup100p	SA.[GQV][TPM]	37				IBN_N	1.E-02	-0.5	nuclear pore (1e-13)	Y	0.007	10
protein_40_YFR052W	2	RPN12:  Subunit of the 19S regulatory particle of the 26S proteasome lid; synthetically lethal with RPT1, which is an ATPase component of the 19S regulatory particle; physically interacts with Nob1p and Rpn3p	S[VY]..[TY]LL	37	[DE]..LL	Di-Leu acidic motif for receptor endocytosis (recognized by VHS domain of GGA proteins)		HEAT	1.E-03	-0.5			0.004	7
yeast-1115_GO-0006996	2	organelle organization and biogenesis	S..[SGI]N	37	S..[ST]	Casein Kinase I consensus phosphorylation site (N-term Ser must first be phosphorylated)		WD40	1.E-07	-0.1	chromosome organization and biogenesis (1e-09)		0.008	10
yeast-410_GO-0007049	2	cell cycle	[LRD]FE[KTR]	37				SMC_N	1.E-02	0.2	cell cycle (1e-61)		0.008	10
yeast-222_GO-0009308	2	amine metabolism	E.A[KSG]	37				PALP	1.E-03	0.4	amine metabolism (1e-13)	Y	0.008	10
yeast-631_GO-0050794	2	regulation of cellular process	K..[KSA]P	37	K..[ST]	PKA kinase substrate motif		Zn_clus	1.E-03	0.5	regulation of cellular metabolism (1e-12)	Y	0.008	10
protein_40_YHR010W	2	RPL27A:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl27Bp and has similarity to rat L27 ribosomal protein	[APK]R..[AKV]K	37	[KR]R	CLV_PCSK_KEX2_1	Y	MMR_HSR1	1.E-02	0.5	nucleolus (1e-08)		0.007	10
yeast-1216_GO-0009058	2	biosynthesis	AG[AGF][RAC]	37				Ribosomal_60s	1.E-04	0.9	amine metabolism (1e-14)		0.008	10
protein_40_YLR340W	2	RPP0:  Conserved ribosomal protein P0 similar to rat P0, human P0, and E. coli L10e; shown to be phosphorylated on serine 302	[AE]A..[EMF]KE	37				Ribosomal_60s	1.E-08	0.9	translational elongation (1e-06)	Y	0.004	8
yeast-304_GO-0019752	2	carboxylic acid metabolism	G[NVE]P	37	G[FL]PGER..G	LIG_IBS_1		Zn_clus	1.E-02	1.1	carboxylic acid metabolism (1e-10)		0.008	10
yeast-215_GO-0005694	2	chromosome	AG[NS]A[AWT]	37			Y	Histone	1.E-03	1.1	chromosome (1e-07)		0.005	10
yeast-921_GO-0006810	2	transport	S..[TFI]G	37	S..[ST]	Casein Kinase I consensus phosphorylation site (N-term Ser must first be phosphorylated)	Y	MFS_1	1.E-09	1.2	intracellular transport (1e-84)	Y	0.008	10
yeast-304_GO-0006082	2	organic acid metabolism	G[NVE]P	37	G[FL]PGER..G	LIG_IBS_1		Zn_clus	1.E-02	1.2	carboxylic acid metabolism (1e-10)		0.008	10
protein_40_YBR159W	2	IFA38: Microsomal beta-keto-reductase; contains oleate response element (ORE) sequence in the promoter region; mutants exhibit reduced VLCFA synthesis, accumulate high levels of dihydrosphingosine, phytosphingosine and medium-chain ceramides	A..[TLS]F	37				MFS_1	1.E-02	1.2	transporter activity (1e-07)		0.007	9
yeast-295_GO-0016192	2	vesicle-mediated transport	[DVH]T..[QKF]E	37			Y	Ras	1.E-11	1.4	vesicle-mediated transport (1e-45)		0.008	10
yeast-610_GO-0031090	2	organelle membrane	L[DQW]..[KSM]TR	37				Mito_carr	1.E-18	1.5	mitochondrial inner membrane (1e-11)		0.008	10
genetic_YLR200W	2	YKE2: Subunit of the heterohexameric Gim/prefoldin protein complex involved in the folding of alpha-tubulin, beta-tubulin, and actin	[WRQ]YR[AV]P	37	VP	Interleukin converting enzyme protease		Pkinase	1.E-03	1.5	cyclin-dependent protein kinase activity (1e-04)		0.004	10
yeast-238_GO-0017111	2	nucleoside-triphosphatase activity	E..S[AVG]	37	[LIVMA].EG[DN]SA.[STAG]	TOPOISOMERASE_II PATTERN		Helicase_C	1.E-12	1.6	nucleoside-triphosphatase activity (1e-12)	Y	0.008	10
yeast-565_GO-0006464	2	protein modification	HP[NPF][IV]	37	HPQ	Biotin binding motif in streptavidin	Y	UQ_con	1.E-16	1.7	protein modification (1e-27)		0.008	10
yeast-1721_GO-0016043	2	cell organization and biogenesis	A[AES]S	37	RPVSSAASVY	14-3-3 domain binding motif		PI3_PI4_kinase	1.E-04	1.7	cellular localization (1e-52)		0.008	10
protein_40_YLR197W	2	SIK1:  Essential evolutionarily-conserved nucleolar protein component of the box C/D snoRNP complexes that direct 2'-O-methylation of pre-rRNA during its maturation; overexpression causes spindle orientation defects	D[QKM].[VTR]K	37				WD40	1.E-02	1.7	rRNA processing (1e-14)		0.007	10
protein_40_YKL014C	2	URB1:  Nucleolar protein required for the normal accumulation of 25S and 5.8S rRNAs, associated with the 27SA2 pre-ribosomal particle; proposed to be involved in the biogenesis of the 60S ribosomal subunit	K[TEQ][LAV]A	37				DEAD	1.E-06	1.8	nucleolus (1e-14)		0.007	10
yeast-376_GO-0019219	2	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism	DE[ELD][DKR]	37	YDE[PDV]	SH2 ligand for Nck1 and Nck2 (Tyr must be phosphorylated)		zf-C2H2	1.E-02	1.9	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism (1e-10)		0.008	10
yeast-921_GO-0006810	2	transport	D[VLA].[KRI]TR	37				Mito_carr	1.E-23	2.1	transporter activity (1e-11)	Y	0.008	10
yeast-1134_GO-0044249	2	cellular biosynthesis	N.[DSG]D	37	N.[TS]	N-linked glycosylation site		SRP1_TIP1	1.E-05	2.6	DNA metabolism (1e-10)		0.008	10
protein_40_YDR449C	2	UTP6:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	DG.[IVY][KRL]	37				WD40	1.E-09	2.7	small nucleolar ribonucleoprotein complex (1e-20)		0.007	10
protein_40_YPL203W	2	TPK2:  cAMP-dependent protein kinase catalytic subunit; promotes vegetative growth in response to nutrients via the Ras-cAMP signaling pathway; inhibited by regulatory subunit Bcy1p in the absence of cAMP; partially redundant with Tpk1p and Tpk3p	[KSH]PE[NPM]	37	[ST]P	LIG_WW_4		Pkinase	1.E-07	2.9	phosphotransferase activity, alcohol group as acceptor (1e-08)		0.006	10
yeast-1115_GO-0006996	2	organelle organization and biogenesis	S.D[ARS]	37	S.D	CAMKII phosphorylation site		WD40	1.E-15	3.1	chromosome organization and biogenesis (1e-75)		0.008	10
yeast-255_GO-0007028	2	cytoplasm organization and biogenesis	[PTF]TRE[LKY]	37	RE..E	Iron binding motif in ferritin L-chain and yeast Iron transport protein		DEAD	1.E-06	3.2	ribosome biogenesis (1e-12)	Y	0.006	10
yeast-255_GO-0042254	2	ribosome biogenesis and assembly	[PTF]TRE[LKY]	37	RE..E	Iron binding motif in ferritin L-chain and yeast Iron transport protein		DEAD	1.E-06	3.3	ribosome biogenesis (1e-12)	Y	0.006	10
protein_40_YNL186W	2	UBP10:  Ubiquitin-specific protease that deubiquitinates ubiquitin-protein moieties; may regulate silencing by acting on Sir4p; involved in posttranscriptionally regulating Gap1p and possibly other transporters; primarily located in the nucleus	DF..[ATN][KRM]	37			Y	Pkinase	1.E-14	3.6	protein kinase activity (1e-16)	Y	0.006	10
protein_40_YNL186W	2	UBP10:  Ubiquitin-specific protease that deubiquitinates ubiquitin-protein moieties; may regulate silencing by acting on Sir4p; involved in posttranscriptionally regulating Gap1p and possibly other transporters; primarily located in the nucleus	IG[ERK][GHF]	37				Pkinase	1.E-12	3.8	protein kinase activity (1e-11)	Y	0.006	9
protein_40_YNL186W	2	UBP10:  Ubiquitin-specific protease that deubiquitinates ubiquitin-protein moieties; may regulate silencing by acting on Sir4p; involved in posttranscriptionally regulating Gap1p and possibly other transporters; primarily located in the nucleus	A[PQ]E	37	A[EA]EEY[FV]F[LFMIV]F	FGFR kinase substrate motif	Y	Pkinase	1.E-17	4	protein kinase activity (1e-17)	Y	0.007	10
yeast-565_GO-0006464	2	protein modification	W[SQV][LFE]G	37			Y	Pkinase	1.E-19	4.3	protein modification (1e-27)		0.008	10
yeast-1939_GO-0003824	2	catalytic activity	KP.N[ILV][LMK]	37				Pkinase	1.E-59	6.5	protein kinase activity (1e-56)		0.008	10
yeast-601_GO-0005829	2	cytosol	[RPG]AA[RKG]	37							cytosol (1e-47)		0.008	10
yeast-470_GO-0006259	2	DNA metabolism	[TLD]S[EQG]E	37	[PLIM].[LIDE]SQ	ATM kinase substrate motif					DNA metabolism (1e-86)		0.008	10
yeast-470_GO-0006259	2	DNA metabolism	T[TPG]..K[KDR]	37	KR	CLV_PCSK_PC1ET2_1	Y				DNA metabolism (1e-64)		0.008	10
yeast-410_GO-0007049	2	cell cycle	ET..[KSN][INR]	37	T..[SA]	FHA of KAPP binding motif, Thr must be phosphorylated					cell cycle (1e-76)		0.008	10
yeast-388_GO-0007275	2	development	[TRQ]S.TT[EWC]	37							multicellular organismal development (1e-09)	Y	0.007	7
yeast-343_GO-0005198	2	structural molecule activity	[GPQ]G.[FM]GN	37							snRNP protein import into nucleus (1e-07)		0.005	8
yeast-301_GO-0044451	2	nucleoplasm part	[LVA]ENN[DMG]	37	KEN	LIG_APCC_KENbox_2					nucleoplasm part (1e-11)		0.007	10
yeast-301_GO-0044451	2	nucleoplasm part	D..D[DGI]	37							nucleoplasm part (1e-17)	Y	0.008	10
yeast-262_GO-0031224	2	intrinsic to membrane	A[SFR]..I[IL]L	37							integral to membrane (1e-11)		0.006	10
yeast-244_GO-0000279	2	M phase	NS[FRD][KMH]	37							M phase (1e-46)		0.008	10
yeast-238_GO-0017111	2	nucleoside-triphosphatase activity	[HDE]V.[HTC]GK	37			Y				nucleoside-triphosphatase activity (1e-09)	Y	0.005	7
yeast-238_GO-0017111	2	nucleoside-triphosphatase activity	I[SVL].E[ELI]G	37							nucleoside-triphosphatase activity (1e-15)		0.006	9
yeast-235_GO-0009653	2	morphogenesis	TG.[TPM][TPH]	37	TGY	ERK6/SAPK3 activation sites for HOG/p38 activation					cellular morphogenesis (1e-37)		0.008	10
yeast-235_GO-0000902	2	cellular morphogenesis	TG.[TPM][TPH]	37	TGY	ERK6/SAPK3 activation sites for HOG/p38 activation					cellular morphogenesis (1e-37)		0.008	10
yeast-223_GO-0003735	2	structural constituent of ribosome	E..G[VNF]	37									0.008	10
yeast-220_GO-0044255	2	cellular lipid metabolism	L.[LVR]T	37	PLARTLSVAGLP	Calmodulin-dependent protein kinase IV substrate motif	Y				cellular lipid metabolism (1e-15)		0.008	10
yeast-205_GO-0005856	2	cytoskeleton	L[QEN]E	37							cytoskeleton (1e-18)		0.008	10
yeast-205_GO-0005856	2	cytoskeleton	TL[DNM]D[LQ]	37	LFDLM	Binding motif in Clint for clathrin TD domain					cytoskeletal part (1e-10)	Y	0.005	9
yeast-1493_GO-0043234	2	protein complex	F[LSW]F	37	F.FP	LIG_MAPK_2					endoplasmic reticulum (1e-07)		0.008	10
yeast-1433_GO-0006139	2	nucleobase, nucleoside, nucleotide and nucleic acid metabolism	S[DFK]..[SYN]D	37							transcription, DNA-dependent (1e-28)		0.008	10
protein_40_YPR144C	2	NOC4:  Nucleolar protein, forms a complex with Nop14p that mediates maturation and nuclear export of 40S ribosomal subunits	[SL]T[LIT]EP	37	IEPD	Protease Granzyme B					processing of 20S pre-rRNA (0.001)		0.004	9
protein_40_YPR110C	2	RPC40:  RNA polymerase subunit, common to RNA polymerase I and III	D..[TRL]I	37							RNA polymerase complex (1e-09)		0.007	9
protein_40_YPL240C	2	HSP82:  Hsp90 chaperone required for pheromone signaling and negative regulation of Hsf1p; docks with Tom70p for mitochondrial preprotein delivery; promotes telomerase DNA binding and nucleotide addition; interacts with Cns1p, Cpr6p, Cpr7p, Sti1p	A[LKE].D[EDM]	37	AEVD	Protease Caspase 10							0.007	10
protein_40_YPL240C	2	HSP82:  Hsp90 chaperone required for pheromone signaling and negative regulation of Hsf1p; docks with Tom70p for mitochondrial preprotein delivery; promotes telomerase DNA binding and nucleotide addition; interacts with Cns1p, Cpr6p, Cpr7p, Sti1p	Q..V[EPN]	37	VP	Interleukin converting enzyme protease							0.007	10
protein_40_YPL240C	2	HSP82:  Hsp90 chaperone required for pheromone signaling and negative regulation of Hsf1p; docks with Tom70p for mitochondrial preprotein delivery; promotes telomerase DNA binding and nucleotide addition; interacts with Cns1p, Cpr6p, Cpr7p, Sti1p	TL.[DNEQ][LVA]	37	PLTLP	RAF1 kinase substrate motif							0.006	10
protein_40_YPL153C	2	RAD53:  Protein kinase, required for cell-cycle arrest in response to DNA damage; activated by trans autophosphorylation when interacting with hyperphosphorylated Rad9p; also interacts with ARS1 and plays a role in initiation of DNA replication	AN[LIA][EQM]	37			Y					Y	0.007	9
protein_40_YPL153C	2	RAD53:  Protein kinase, required for cell-cycle arrest in response to DNA damage; activated by trans autophosphorylation when interacting with hyperphosphorylated Rad9p; also interacts with ARS1 and plays a role in initiation of DNA replication	Q[QKS].L[LPM]	37								Y	0.007	9
protein_40_YPL043W	2	NOP4:  Nucleolar protein, essential for processing and maturation of 27S pre-rRNA and large ribosomal subunit biogenesis; constituent of 66S pre-ribosomal particles; contains four RNA recognition motifs (RRMs)	EE..V[EGD][EMK]	37	EED	Ankyrin B C-terminal motif that binds internal Ankyrin repeats	Y				cytoplasm organization and biogenesis (0.001)	Y	0.004	7
protein_40_YPL043W	2	NOP4:  Nucleolar protein, essential for processing and maturation of 27S pre-rRNA and large ribosomal subunit biogenesis; constituent of 66S pre-ribosomal particles; contains four RNA recognition motifs (RRMs)	NE..[SDM][DKE]S	37							rRNA metabolism (1e-04)		0.004	8
protein_40_YPL012W	2	RRP12:  Protein required for export of the ribosomal subunits; associates with the RNA components of the pre-ribosomes; contains HEAT-repeats	E.E[EK]	37	Y.E.E	Src phosphorylation site					nucleolus (1e-34)	Y	0.007	10
protein_40_YOR310C	2	NOP58:  Protein involved in pre-rRNA processing, 18S rRNA synthesis, and snoRNA synthesis; component of the small subunit processome complex, which is required for processing of pre-18S rRNA	E..[EC]D	37	RE..E	Iron binding motif in ferritin L-chain and yeast Iron transport protein					nucleolus (1e-21)		0.007	9
protein_40_YOR151C	2	RPB2:  RNA polymerase II second largest subunit B150, part of central core; similar to bacterial beta subunit	[SHL]TGRK	37	[AG]R	Protease matriptase protease site							0.004	9
protein_40_YOR133W	2	EFT1:  Elongation factor 2 (EF-2), also encoded by EFT2; catalyzes ribosomal translocation during protein synthesis; contains diphthamide, the unique posttranslationally modified histidine residue specifically ADP-ribosylated by diphtheria toxin	T[RQG]..V[EGA]	37							carboxylic acid metabolism (0.01)	Y	0.007	10
protein_40_YOR117W	2	RPT5:  One of six ATPases of the 19S regulatory particle of the 26S proteasome involved in the degradation of ubiquitinated substrates; recruited to the GAL1-10 promoter region upon induction of transcription	[LKA][FIY]ESL	37							proteasome complex (sensu Eukaryota) (0.001)		0.004	8
protein_40_YOL120C	2	RPL18A:  Protein component of the large (60S) ribosomal subunit, identical to Rpl18Bp and has similarity to rat L18 ribosomal protein; intron of RPL18A pre-mRNA forms stem-loop structures that are a target for Rnt1p cleavage leading to degradation	SV.[EPR]V	37	YRSVDE	Branched chain alpha-ketoacid dehydrogenase kinase substrate motif	Y					Y	0.006	9
protein_40_YOL069W	2	NUF2:  Component of the evolutionarily conserved kinetochore-associated Ndc80 complex (Ndc80p-Nuf2p-Spc24p-Spc25p); involved in chromosome segregation, spindle checkpoint activity and kinetochore clustering	SK.[LEH][SNM]	37			Y				condensed nuclear chromosome (0.001)		0.007	10
protein_40_YOL012C	2	HTZ1:  Histone variant H2AZ, exchanged for histone H2A in nucleosomes by the SWR1 complex; involved in transcriptional regulation through prevention of the spread of silent heterochromatin	SE.[KD][EQG]N	37	[ST]E	G protein-coupled receptor kinase 1 substrate motif					SWR1 complex (1e-06)		0.004	10
protein_40_YNR054C	2	ESF2:  Essential nucleolar protein involved in pre-18S rRNA processing; component of the small subunit (SSU) processome; has sequence similarity to mABT1, a mouse transcription activator	E[ETY].D[QAV]	37							small nucleolar ribonucleoprotein complex (1e-10)		0.007	10
protein_40_YNL308C	2	KRI1:  Essential nucleolar protein required for 40S ribosome biogenesis; physically and functionally interacts with Krr1p	[GT][LNT]DIP	37									0.004	8
protein_40_YNL298W	2	CLA4:  Cdc42p activated signal transducing kinase of the PAK (p21-activated kinase) family, involved in septin ring assembly and cytokinesis; directly phosphorylates septins Cdc3p and Cdc10p; other yeast PAK family members are Ste20p and Skm1p	S[KDT]..[SW]NV	37	S[ST]	MDC1 BRCT domain binding motif							0.004	7
protein_40_YNL289W	2	PCL1:  Pho85 cyclin of the Pcl1,2-like subfamily, involved in entry into the mitotic cell cycle and regulation of morphogenesis, localizes to sites of polarized cell growth	P[PDN]P	37	QHR.P[PL]PP[GS]H[RH]	Motif recognized by GYF domains							0.007	10
protein_40_YNL154C	2	YCK2:  Palmitoylated, plasma membrane-bound casein kinase I isoform; shares redundant functions with Yck1p in morphogenesis, proper septin assembly, endocytic trafficking; provides an essential function overlapping with that of Yck1p	[VKA]K..[TDM]L	37	K..[ST]	PKA kinase substrate motif	Y						0.007	10
protein_40_YNL154C	2	YCK2:  Palmitoylated, plasma membrane-bound casein kinase I isoform; shares redundant functions with Yck1p in morphogenesis, proper septin assembly, endocytic trafficking; provides an essential function overlapping with that of Yck1p	Q..[STD]P	37	[ST]P	LIG_WW_4							0.007	10
protein_40_YNL118C	2	DCP2:  Catalytic subunit of the Dcp1p-Dcp2p decapping enzyme complex, which removes the 5' cap structure from mRNAs prior to their degradation; member of the Nudix hydrolase family	D[ERF].[VSE]Y	37	[EDY]Y	TC-PTP phosphatase substrate motif	Y						0.006	9
protein_40_YMR308C	2	PSE1:  Karyopherin/importin that interacts with the nuclear pore complex; acts as the nuclear import receptor for specific proteins, including Pdr1p, Yap1p, Ste12p, and Aft1p	FG[QN]N[NG]	37							snRNP protein import into nucleus (1e-08)		0.005	8
protein_40_YMR304W	2	UBP15:  Ubiquitin-specific protease that may play a role in ubiquitin precursor processing	[GPM]SG[VRF]	37									0.007	10
protein_40_YMR128W	2	ECM16:  Essential DEAH-box ATP-dependent RNA helicase specific to the U3 snoRNP, predominantly nucleolar in distribution, required for 18S rRNA synthesis	T[DKR].[SRK]KR	37	KR	CLV_PCSK_PC1ET2_1					RNA processing (0.001)		0.004	10
protein_40_YMR047C	2	NUP116:  Subunit of the nuclear pore complex (NPC) that is localized to both sides of the pore; contains a repetitive GLFG motif that interacts with mRNA export factor Mex67p and with karyopherin Kap95p; homologous to Nup100p	N.A[SKQ]	37							nuclear pore (1e-36)		0.007	10
protein_40_YML049C	2	RSE1:  Protein involved in pre-mRNA splicing; component of the pre-spliceosome; associates with U2 snRNA; involved in ER to Golgi transport	[EY]K.KK[VMP]	37	P.[ST]PKK.KK	Cdc2 like protein kinase substrate motif					nuclear mRNA splicing, via spliceosome (1e-07)		0.004	7
protein_40_YLR429W	2	CRN1:  Coronin, cortical actin cytoskeletal component that associates with the Arp2p/Arp3p complex to regulate its activity; plays a role in regulation of actin patch assembly	Q[IKP].[PIA]LS	37									0.004	9
protein_40_YLR372W	2	SUR4:  Elongase, involved in fatty acid and sphingolipid biosynthesis; synthesizes very long chain 20-26-carbon fatty acids from C18-CoA primers; involved in regulation of sphingolipid biosynthesis	W[LTF]F	37	LFG	Protease Papain substrate, a prototype cysteine proteinase					endoplasmic reticulum (0.001)	Y	0.007	10
protein_40_YLR340W	2	RPP0:  Conserved ribosomal protein P0 similar to rat P0, human P0, and E. coli L10e; shown to be phosphorylated on serine 302	EK..K[KRH][ELY]	37	KR	CLV_PCSK_PC1ET2_1					nucleolus (0.01)	Y	0.005	9
protein_40_YLR287C-A	2	RPS30A:  Protein component of the small (40S) ribosomal subunit; nearly identical to Rps30Bp and has similarity to rat S30 ribosomal protein	R[RA].[AFQ]R	37	[AG]R	Protease matriptase protease site					cytosolic ribosome (sensu Eukaryota) (1e-15)		0.005	10
protein_40_YLR180W	2	SAM1:  S-adenosylmethionine synthetase, catalyzes transfer of the adenosyl group of ATP to the sulfur atom of methionine; one of two differentially regulated isozymes (Sam1p and Sam2p)	I[SMY].K[NFI]L	37	IY	cFGR and Csk kinase phosphorylation site (peptide screen)						Y	0.004	7
protein_40_YLR106C	2	MDN1:  Huge dynein-related AAA-type ATPase (midasin), forms extended pre-60S particle with the Rix1 complex (Rix1p-Ipi1p-Ipi3p), may mediate ATP-dependent remodeling of 60S subunits and subsequent export from nucleoplasm to cytoplasm	K[VQY]E[KH]E	37	[VILMAFP]K.E	MOD_SUMO						Y	0.004	7
protein_40_YLR002C	2	NOC3:  Protein that forms a nuclear complex with Noc2p that binds to 66S ribosomal precursors to mediate their intranuclear transport; also binds to chromatin to promote the association of DNA replication factors and replication initiation	[DVG]D.[EKQ]E	37	D.E	Sec24p					cytoplasm organization and biogenesis (1e-16)		0.007	10
protein_40_YKR001C	2	VPS1:  Dynamin-like GTPase required for vacuolar sorting; also involved in actin cytoskeleton organization, late Golgi-retention of some proteins, regulating peroxisome biogenesis	LK..[KVD]L[ISD]	37									0.004	8
protein_40_YJR066W	2	TOR1:  PIK-related protein kinase and rapamycin target; subunit of TORC1, a complex that controls growth in response to nutrients by regulating translation, transcription, ribosome biogenesis, nutrient transport and autophagy; involved in meiosis	E[VY]..V[EFS]N	37									0.004	9
protein_40_YJR022W	2	LSM8:  Lsm (Like Sm) protein; forms heteroheptameric complex (with Lsm2p, Lsm3p, Lsm4p, Lsm5p, Lsm6p, and Lsm7p) that is part of spliceosomal U6 snRNP and is also implicated in processing of pre-tRNA, pre-snoRNA, and pre-rRNA	F[LDN]..D[SR]V	37								Y	0.004	7
protein_40_YJL095W	2	BCK1:  Mitogen-activated protein (MAP) kinase kinase kinase acting in the protein kinase C signaling pathway, which controls cell integrity; upon activation by Pkc1p phosphorylates downstream kinases Mkk1p and Mkk2p	[GMY]HP[SV]	37	P[ST]	DNA dependent Protein kinase substrate motif							0.005	9
protein_40_YIL133C	2	RPL16A:  N-terminally acetylated protein component of the large (60S) ribosomal subunit, binds to 5.8 S rRNA; has similarity to Rpl16Bp, E. coli L13 and rat L13a ribosomal proteins; transcriptionally regulated by Rap1p	R[AGW][AIP]R	37	[AG]R	Protease matriptase protease site					cytosolic ribosome (sensu Eukaryota) (1e-16)	Y	0.007	10
protein_40_YIL133C	2	RPL16A:  N-terminally acetylated protein component of the large (60S) ribosomal subunit, binds to 5.8 S rRNA; has similarity to Rpl16Bp, E. coli L13 and rat L13a ribosomal proteins; transcriptionally regulated by Rap1p	V[KVA][KRY]A	37	AEV[IVLF]YAA[PF]F	Abl kinase substrate motif					cytosolic ribosome (sensu Eukaryota) (1e-09)		0.007	10
protein_40_YIL094C	2	LYS12:  Homo-isocitrate dehydrogenase, an NAD-linked mitochondrial enzyme required for the fourth step in the biosynthesis of lysine, in which homo-isocitrate is oxidatively decarboxylated to alpha-ketoadipate	S[KQW].V[PG]	37	VP	Interleukin converting enzyme protease							0.005	10
protein_40_YIL061C	2	SNP1:  Component of U1 snRNP required for mRNA splicing via spliceosome; may interact with poly(A) polymerase to regulate polyadenylation; homolog of human U1 70K protein	[LDK]L..[QKS]NY	37									0.004	7
protein_40_YIL018W	2	RPL2B:  Protein component of the large (60S) ribosomal subunit, identical to Rpl2Ap and has similarity to E. coli L2 and rat L8 ribosomal proteins; expression is upregulated at low temperatures	[ATG]R.[KGQ]A	37	[AG]R	Protease matriptase protease site					cytosolic ribosome (sensu Eukaryota) (1e-12)		0.007	10
protein_40_YHR197W	2	RIX1:  Essential component of the Rix1 complex (Rix1p, Ipi1p, Ipi3p) that is required for processing of ITS2 sequences from 35S pre-rRNA; Rix1 complex associates with Mdn1p in pre-60S ribosomal particles	[EMY][EKD]..EE	37	[EDTY].YEE	Syk kinase substrate motif					cytoplasm organization and biogenesis (1e-17)		0.007	10
protein_40_YHR196W	2	UTP9:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	Q[IGA]..[KLV]L	37							rRNA processing (1e-14)		0.007	10
protein_40_YHR135C	2	YCK1:  Palmitoylated, plasma membrane-bound casein kinase I isoform; shares redundant functions with Yck2p in morphogenesis, proper septin assembly, endocytic trafficking; provides an essential function overlapping with that of Yck2p	A.[TSD]G	37									0.007	10
protein_40_YHL007C	2	STE20:  Signal transducing kinase of the PAK (p21-activated kinase) family, involved in pheromone response and pseudohyphal/invasive growth pathways, activated by Cdc42p; binds Ste4p at a GBB motif present in noncatalytic domains of PAK kinases	N.S[SVY]	37	N.[TS]	N-linked glycosylation site					bud (0.01)		0.007	10
protein_40_YGR274C	2	TAF1:  TFIID subunit (145 kDa), involved in RNA polymerase II transcription initiation, has histone acetyltransferase activity, involved in promoter binding and G1/S progression	KQ.[ALE][LED]	37							transcription factor complex (1e-12)		0.007	10
protein_40_YGR274C	2	TAF1:  TFIID subunit (145 kDa), involved in RNA polymerase II transcription initiation, has histone acetyltransferase activity, involved in promoter binding and G1/S progression	QK[ADT][LI]E	37	W[KDN]..K[KRE][LI]E[RKN]	CECROPIN PATTERN							0.004	7
protein_40_YGR218W	2	CRM1:  Major karyopherin, involved in export of proteins, RNAs, and ribosomal subunits from the nucleus	[AGD][FSY].FG	37	LFG	Protease Papain substrate, a prototype cysteine proteinase					rRNA export from nucleus (1e-10)	Y	0.007	10
protein_40_YGR218W	2	CRM1:  Major karyopherin, involved in export of proteins, RNAs, and ribosomal subunits from the nucleus	N[NPV].[FIR]G	37			Y				rRNA export from nucleus (1e-08)	Y	0.007	10
protein_40_YGR086C	2	PIL1:  Primary component of eisosomes, which are large immobile cell cortex structures associated with endocytosis; null mutants show activation of Pkc1p/Ypk1p stress resistance pathways; detected in phosphorylated state in mitochondria	[IT]VKD[LP]	37									0.005	7
protein_40_YGL106W	2	MLC1:  Essential light chain for Myo1p, light chain for Myo2p; stabilizes Myo2p by binding to the neck region; interacts with Myo1p, Iqg1p, and Myo2p to coordinate formation and contraction of the actomyosin ring with targeted membrane deposition	[FRC]DD[EPQ]	37	DD.Y	Shb PTB domain binding motif						Y	0.006	9
protein_40_YGL103W	2	RPL28:  Ribosomal protein of the large (60S) ribosomal subunit, has similarity to E. coli L15 and rat L27a ribosomal proteins; may have peptidyl transferase activity; can mutate to cycloheximide resistance	K..[AKR]A	37	K[KR].[KR]	Nuclear localization motif					cytosolic ribosome (sensu Eukaryota) (1e-40)	Y	0.007	9
protein_40_YGL051W	2	MST27:  Putative integral membrane protein, involved in vesicle formation; forms complex with Mst28p; member of DUP240 gene family; binds COPI and COPII vesicles	[IE]L.V[GQ]S	37									0.004	8
protein_40_YGL031C	2	RPL24A:  Ribosomal protein L30 of the large (60S) ribosomal subunit, nearly identical to Rpl24Bp and has similarity to rat L24 ribosomal protein; not essential for translation but may be required for normal translation rate	[EHW]K[RMH]A	37	KR	CLV_PCSK_PC1ET2_1					cytosolic large ribosomal subunit (sensu Eukaryota) (1e-10)		0.005	9
protein_40_YGL019W	2	CKB1:  Beta regulatory subunit of casein kinase 2, a Ser/Thr protein kinase with roles in cell growth and proliferation; the holoenzyme also contains CKA1, CKA2 and CKB2, the many substrates include transcription factors and all RNA polymerases	[AQK]L.YL[EV]	37	Y[LI]	SH2 ligand for PLCgamma1 N-term.)group 3(phospho-peptide)							0.004	7
protein_40_YFR024C-A	2	LSB3:  Protein containing a C-terminal SH3 domain; binds Las17p, which is a homolog of human Wiskott-Aldrich Syndrome protein involved in actin patch assembly and actin polymerization	[QYA][LGD]QQ	37									0.006	10
protein_40_YFL037W	2	TUB2:  Beta-tubulin; associates with alpha-tubulin (Tub1p and Tub3p) to form tubulin dimer, which polymerizes to form microtubules	[TVY]Q.[VQA]V	37	[ST]Q	ATM kinase phosphorylation site						Y	0.006	10
protein_40_YFL037W	2	TUB2:  Beta-tubulin; associates with alpha-tubulin (Tub1p and Tub3p) to form tubulin dimer, which polymerizes to form microtubules	T[IR].A[GQV]	37									0.005	10
protein_40_YER177W	2	BMH1:  14-3-3 protein, major isoform; controls proteome at post-transcriptional level, binds proteins and DNA, involved in regulation of many processes including exocytosis, vesicle transport, Ras/MAPK signaling, and rapamycin-sensitive signaling	[PST][PS]KSP	37	SP	ERK1, ERK2 Kinase substrate motif						Y	0.004	8
protein_40_YER148W	2	SPT15:  TATA-binding protein, general transcription factor that interacts with other factors to form the preinitiation complex at promoters, essential for viability	[SHF]L.DY[VR]	37	DYR	cCbl and Cbl-b TKB domain binding motif for Met receptor, Tyr must be PO4					histone acetyltransferase complex (1e-06)		0.004	7
protein_40_YER112W	2	LSM4:  Lsm (Like Sm) protein; part of heteroheptameric complexes (Lsm2p-7p and either Lsm1p or 8p): cytoplasmic Lsm1p complex involved in mRNA decay; nuclear Lsm8p complex part of U6 snRNP and possibly involved in processing tRNA, snoRNA, and rRNA	S[LGQ]..[DHE]SL	37									0.005	9
protein_40_YER074W	2	RPS24A:  Protein component of the small (40S) ribosomal subunit; identical to Rps24Bp and has similarity to rat S24 ribosomal protein	S.[LSR]S	37	S..S	Casien kinase I phosphorylation site, 1st Ser must be phosphorylated							0.007	10
protein_40_YDR388W	2	RVS167:  Actin-associated protein, subunit of a complex (Rvs161p-Rvs167p) involved in regulation of actin cytoskeleton, endocytosis, and viability following starvation or osmotic stress; homolog of mammalian amphiphysin	L..[GYP]D	37	LG.GD	Aspartyl protease active site in Presenilin also a YD motif					actin cytoskeleton (0.001)	Y	0.006	10
protein_40_YDR388W	2	RVS167:  Actin-associated protein, subunit of a complex (Rvs161p-Rvs167p) involved in regulation of actin cytoskeleton, endocytosis, and viability following starvation or osmotic stress; homolog of mammalian amphiphysin	P[SAQ]..[SVT]AA	37	P[ST]	DNA dependent Protein kinase substrate motif					actin cortical patch (1e-04)		0.005	8
protein_40_YDR365C	2	ESF1:  Nucleolar protein involved in pre-rRNA processing; depletion causes severely decreased 18S rRNA levels	RG[GPR][RIM]	37	GGRGG	Arginine methyl transferease substrate motif (PRMT1)					nucleolus (1e-04)		0.006	10
protein_40_YDR356W	2	SPC110:  Inner plaque spindle pole body (SPB) component, ortholog of human kendrin; involved in connecting nuclear microtubules to SPB; interacts with Tub4p-complex and calmodulin; phosphorylated by Mps1p in cell cycle-dependent manner	E[LIH][ELK]E	37							spindle pole body (1e-25)		0.007	10
protein_40_YDR145W	2	TAF12:  Subunit (61/68 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation and in chromatin modification, similar to histone H2A	[SKH]..EN	37	KEN	LIG_APCC_KENbox_2					transcription factor complex (1e-22)		0.007	10
protein_40_YDL140C	2	RPO21:  RNA polymerase II largest subunit B220, part of central core; phosphorylation of C-terminal heptapeptide repeat domain regulates association with transcription and splicing factors; similar to bacterial beta-prime	[DSN]E[DMG]D	37	E[ST]D	Ankyrin G binding motif in KNCQ2 and KNCQ3 potaqssium channels					nucleoplasm (1e-19)		0.007	10
protein_40_YDL075W	2	RPL31A:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl31Bp and has similarity to rat L31 ribosomal protein; associates with the karyopherin Sxm1p	G[KIY]K[VAY]	37	G[KR][KR]	Amidation after cleavage after Gly (must be in secretory pathway)	Y				cytosolic large ribosomal subunit (sensu Eukaryota) (1e-20)		0.007	10
protein_40_YDL060W	2	TSR1:  Protein required for processing of 20S pre-rRNA in the cytoplasm, associates with pre-40S ribosomal particles	[GRT]R[GFD]G	37	RGG	Alternative integrin binding site in FMDV virus					rRNA processing (1e-05)		0.006	8
protein_40_YDL055C	2	PSA1:  GDP-mannose pyrophosphorylase (mannose-1-phosphate guanyltransferase), synthesizes GDP-mannose from GTP and mannose-1-phosphate in cell wall biosynthesis; required for normal cell wall structure	[IRG]AL[DTQ]	37								Y	0.007	10
protein_40_YDL055C	2	PSA1:  GDP-mannose pyrophosphorylase (mannose-1-phosphate guanyltransferase), synthesizes GDP-mannose from GTP and mannose-1-phosphate in cell wall biosynthesis; required for normal cell wall structure	L.[QEP]G	37	P.L.P	motif for interaction with MYND domain of BS69					proteasome regulatory particle, base subcomplex (sensu Eukaryota) (1e-04)	Y	0.007	10
protein_40_YDL029W	2	ARP2:  Essential component of the Arp2/3 complex, which is a highly conserved actin nucleation center required for the motility and integrity of actin patches; involved in endocytosis and membrane growth and polarity	[VP]P.[DPM]L	37	P.DLS	Binding motif on TGIF for CtBP						Y	0.005	7
protein_40_YCR086W	2	CSM1:  Nucleolar protein that forms a complex with Lrs4p which binds Mam1p at kinetochores during meiosis I to mediate accurate chromosome segregation, may be involved in premeiotic DNA replication; possible role in telomere maintenance	[LQ]P.I[TH]	37	PWI	Motif in SRM160 for binding DNA and RNA	Y						0.005	8
protein_40_YCR086W	2	CSM1:  Nucleolar protein that forms a complex with Lrs4p which binds Mam1p at kinetochores during meiosis I to mediate accurate chromosome segregation, may be involved in premeiotic DNA replication; possible role in telomere maintenance	Y[SFA].Q[SAP]	37	Y..Q	LIG_SH2_STAT3	Y						0.004	9
protein_40_YBR247C	2	ENP1:  Protein associated with U3 and U14 snoRNAs, required for pre-rRNA processing and 40S ribosomal subunit synthesis; localized in the nucleus and concentrated in the nucleolus	K[LIY][RW]A	37							ribonucleoprotein complex (1e-05)		0.006	10
protein_40_YBL026W	2	LSM2:  Lsm (Like Sm) protein; part of heteroheptameric complexes (Lsm2p-7p and either Lsm1p or 8p): cytoplasmic Lsm1p complex involved in mRNA decay; nuclear Lsm8p complex part of U6 snRNP and possibly involved in processing tRNA, snoRNA, and rRNA	[RHG]E..R[LQ]R	37									0.004	8
protein_40_YAL032C	2	PRP45:  Protein required for pre-mRNA splicing; associates with the spliceosome and interacts with splicing factors Prp22p and Prp46p; orthologous to human transcriptional coactivator SKIP and can activate transcription of a reporter gene	[ESQ][EPV]..NSS	37	S[ST]	MDC1 BRCT domain binding motif						Y	0.004	7
protein_40_YAL032C	2	PRP45:  Protein required for pre-mRNA splicing; associates with the spliceosome and interacts with splicing factors Prp22p and Prp46p; orthologous to human transcriptional coactivator SKIP and can activate transcription of a reporter gene	NT[QSE]	37	TEY	MEK phosphorylation of MAPK activation sites - stringent					spliceosome (1e-08)	Y	0.007	10
oshea_ER	2	oshea_ER	F..[AIV]V	37							endoplasmic reticulum (1e-53)	Y	0.007	10
oshea_cytoplasm	2	oshea_cytoplasm	Y..G	37	Y..GL	Tyr-based receptor endocytosis motif, noncanonical					amino acid and derivative metabolism (1e-09)		0.007	10
oshea_cell_periphery	2	oshea_cell_periphery	[TPF]T.[LKA]N	37							plasma membrane (1e-12)		0.007	10
oshea_ambiguous	2	oshea_ambiguous	[KFG]LY[GMR]L	37	NKLY	LIM3 domain in enigma binds to this site in Ret							0.005	7
matsuyama_nuclear_envelope_or_dots	2	matsuyama_nuclear_envelope_or_dots	N.Q[AQS]	37			Y				nuclear envelope (1e-14)	Y	0.009	10
matsuyama_ER	2	matsuyama_ER	[AGI]Y[GYF]L	37							endoplasmic reticulum part (1e-04)		0.009	10
matsuyama_Cytosol	2	matsuyama_Cytosol	A.L[SED]	37	GTALL	Receptor recycling motif	Y				ATP binding (1e-09)	Y	0.009	10
genetic_YLR262C	2	YPT6: GTPase, Ras-like GTP binding protein involved in the secretory pathway, required for fusion of endosome-derived vesicles with the late Golgi, maturation of the vacuolar carboxypeptidase Y; has similarity to the human GTPase, Rab6	K..[NKD]L	37							chromatin modification (1e-15)		0.007	10
genetic_YLR262C	2	YPT6: GTPase, Ras-like GTP binding protein involved in the secretory pathway, required for fusion of endosome-derived vesicles with the late Golgi, maturation of the vacuolar carboxypeptidase Y; has similarity to the human GTPase, Rab6	L.S[LKI]	37	WLNS	Lipid binding motif in C-terminus of Apolipoprotein AII					chromatin modification (1e-18)		0.007	10
genetic_YLR200W	2	YKE2: Subunit of the heterohexameric Gim/prefoldin protein complex involved in the folding of alpha-tubulin, beta-tubulin, and actin	D..[FNE]L	37	[DE]...L[LI]	AP complex deleucine sorting motif					mitotic cell cycle (1e-08)		0.006	10
genetic_YLR200W	2	YKE2: Subunit of the heterohexameric Gim/prefoldin protein complex involved in the folding of alpha-tubulin, beta-tubulin, and actin	KK[LTH]	37	KKKKKK[ST]	TGF beta receptor kinase substrate motif					nucleoplasm part (1e-09)	Y	0.007	10
genetic_YLR200W	2	YKE2: Subunit of the heterohexameric Gim/prefoldin protein complex involved in the folding of alpha-tubulin, beta-tubulin, and actin	T[LQV]Q	37	PTL	Motif in Fos for proteosome degredation					mitotic cell cycle (1e-08)		0.007	10
genetic_YLR039C	2	RIC1: Protein involved in retrograde transport to the cis-Golgi network; forms heterodimer with Rgp1p that acts as a GTP exchange factor for Ypt6p; involved in transcription of rRNA and ribosomal protein genes	GN[NEY]	37	[GD][FYWA]G[LIVM][LIVMFYD]G[KN][NHW]	CAP_GLY_1 PATTERN					vesicle-mediated transport (1e-06)		0.007	10
genetic_YLR039C	2	RIC1: Protein involved in retrograde transport to the cis-Golgi network; forms heterodimer with Rgp1p that acts as a GTP exchange factor for Ypt6p; involved in transcription of rRNA and ribosomal protein genes	SQ..[YKE][ILK]	37	SQ	ATM kinase substrate motif	Y						0.007	10
genetic_YGL058W	2	RAD6: Ubiquitin-conjugating enzyme (E2), involved in postreplication repair (with Rad18p), sporulation, telomere silencing, and ubiquitin-mediated N-end rule protein degradation (with Ubr1p)	E..E[TNF]	37	RE..E	Iron binding motif in ferritin L-chain and yeast Iron transport protein					DNA metabolism (1e-20)	Y	0.007	10
genetic_YGL058W	2	RAD6: Ubiquitin-conjugating enzyme (E2), involved in postreplication repair (with Rad18p), sporulation, telomere silencing, and ubiquitin-mediated N-end rule protein degradation (with Ubr1p)	L.D[IET]	37	LPDEL	Motif in CBP for interaction with PPARg-LBD (secondary site)					DNA metabolism (1e-14)		0.006	10
genetic_YER083C	2	GET2: Subunit of the GET complex; required for meiotic nuclear division and for the retrieval of HDEL proteins from the Golgi to the ER in an ERD2 dependent fashion; may be involved in cell wall function	S..L[EQT]	37							chromosome organization and biogenesis (sensu Eukaryota) (1e-12)		0.007	10
genetic_YAL024C	2	LTE1: Putative GDP/GTP exchange factor required for mitotic exit at low temperatures; acts as a guanine nucleotide exchange factor (GEF) for Tem1p, which is a key regulator of mitotic exit; physically associates with Ras2p-GTP	N[IGS]N	37							cell cycle (1e-19)		0.007	10
protein_40_YBR160W	2	CDC28:  Catalytic subunit of the main cell cycle cyclin-dependent kinase (CDK); alternately associates with G1 cyclins (CLNs) and G2/M cyclins (CLBs) which direct the CDK to specific substrates	S[DPQ].[DNK]DS	37							bud (0.001)		0.006	10
protein_40_YDL188C	2	PPH22:  Catalytic subunit of protein phosphatase 2A, functionally redundant with Pph21p; methylated at C terminus; forms alternate complexes with several regulatory subunits; involved in signal transduction and regulation of mitosis	[TIV][FH]SP	36	SP	ERK1, ERK2 Kinase substrate motif	Y	Proteasome	1.E-12	-4.5	proteasome core complex, alpha-subunit complex (sensu Eukaryota) (1e-16)	Y	0.005	8
protein_40_YDL188C	2	PPH22:  Catalytic subunit of protein phosphatase 2A, functionally redundant with Pph21p; methylated at C terminus; forms alternate complexes with several regulatory subunits; involved in signal transduction and regulation of mitosis	EY.[LS]E[AS]	36	[DE]Y	EGFR kinase substrate motif	Y	Proteasome	1.E-10	-4.1	proteasome core complex (sensu Eukaryota) (1e-09)	Y	0.004	9
protein_40_YPL031C	2	PHO85:  Cyclin-dependent kinase, with ten cyclin partners; involved in regulating the cellular response to nutrient levels and environmental conditions and progression through the cell cycle	SS[PTG]	36	S[ST]	MDC1 BRCT domain binding motif		Cyclin	1.E-09	-2.1	cyclin-dependent protein kinase regulator activity (1e-18)		0.007	10
protein_40_YDR099W	2	BMH2:  14-3-3 protein, minor isoform; controls proteome at post-transcriptional level, binds proteins and DNA, involved in regulation of many processes including exocytosis, vesicle transport, Ras/MAPK signaling, and rapamycin-sensitive signaling	N[NYM]..S[SED]	36	S[ST]	MDC1 BRCT domain binding motif		Pkinase	1.E-02	-1.7	phosphotransferase activity, alcohol group as acceptor (0.01)		0.007	10
protein_40_YPL093W	2	NOG1:  Putative GTPase that associates with free 60S ribosomal subunits in the nucleolus and is required for 60S ribosomal subunit biogenesis; constituent of 66S pre-ribosomal particles; member of the ODN family of nucleolar G-proteins	H[RGF]..R[TGK]	36				DEAD	1.E-10	-1.6	ribosomal large subunit assembly and maintenance (1e-11)		0.006	10
oshea_nucleus	2	oshea_nucleus	Q[QEK]Q	36				zf-C2H2	1.E-03	-1.6	transcription (1e-31)	Y	0.007	10
yeast-468_GO-0051276	2	chromosome organization and biogenesis	E.D[ELG]	36	AEVD	Protease Caspase 10		Bromodomain	1.E-03	-1.4	chromosome organization and biogenesis (1e-23)	Y	0.008	10
yeast-345_GO-0006396	2	RNA processing	AR..D[IFS][PLR]	36	[AG]R	Protease matriptase protease site		DEAD	1.E-06	-1.4	RNA processing (1e-08)		0.006	9
yeast-220_GO-0044255	2	cellular lipid metabolism	V[ITA]..L[IAF]	36				PAP2	1.E-02	-1.4	cellular lipid metabolism (1e-59)		0.008	10
protein_40_YIL035C	2	CKA1:  Alpha catalytic subunit of casein kinase 2, a Ser/Thr protein kinase with roles in cell growth and proliferation; the holoenzyme also contains CKA2, CKB1 and CKB2, the many substrates include transcription factors and all RNA polymerases	K..R[KIG]	36				Histone	1.E-04	-1.2	nuclear lumen (1e-12)	Y	0.007	10
oshea_bud_neck	2	oshea_bud_neck	T.D[TDL]	36	HSTSDD	Branched chain alpha-ketoacid dehydrogenase kinase substrate motif		RhoGAP	1.E-03	-1.2	site of polarized growth (1e-48)	Y	0.007	10
protein_40_YPL131W	2	RPL5:  Protein component of the large (60S) ribosomal subunit with similarity to E. coli L18 and rat L5 ribosomal proteins; binds 5S rRNA and is required for 60S subunit assembly	E..E[DAG]	36	RE..E	Iron binding motif in ferritin L-chain and yeast Iron transport protein		Brix	1.E-02	-1	cytoplasm organization and biogenesis (1e-27)		0.007	10
protein_40_YOL012C	2	HTZ1:  Histone variant H2AZ, exchanged for histone H2A in nucleosomes by the SWR1 complex; involved in transcriptional regulation through prevention of the spread of silent heterochromatin	G[GW]V[KL]	36				Histone	1.E-10	-1	nuclear nucleosome (1e-08)		0.004	8
protein_40_YPL153C	2	RAD53:  Protein kinase, required for cell-cycle arrest in response to DNA damage; activated by trans autophosphorylation when interacting with hyperphosphorylated Rad9p; also interacts with ARS1 and plays a role in initiation of DNA replication	QQ..[PDQ]	36				Ank	1.E-02	-0.9	cell cortex part (0.001)		0.007	10
protein_40_YDL148C	2	NOP14:  Nucleolar protein, forms a complex with Noc4p that mediates maturation and nuclear export of 40S ribosomal subunits; also present in the small subunit processome complex, which is required for processing of pre-18S rRNA	K..K[RLQ]	36	KR	CLV_PCSK_PC1ET2_1		WD40	1.E-05	-0.9	cytoplasm organization and biogenesis (1e-35)		0.007	10
yeast-513_GO-0005515	2	protein binding	S[TKL][IAY]E	36	[KRHEQSTAG]G[FYLIVM][ST][LT][LIVP]E[LIVMFWSTAG]	N-terminal methylation site in prokaryotes. Residue after G is methylated		HEAT	1.E-02	-0.8	protein binding (1e-80)		0.008	10
yeast-460_GO-0006351	2	transcription, DNA-dependent	TT[ANR]	36	[DGH][IVSAC]T[ST]NP[STA][LIVMF][LIVMF]	TRANSALDOLASE_1 PATTERN		zf-C2H2	1.E-04	-0.8	transcription, DNA-dependent (1e-18)	Y	0.008	10
protein_40_YMR047C	2	NUP116:  Subunit of the nuclear pore complex (NPC) that is localized to both sides of the pore; contains a repetitive GLFG motif that interacts with mRNA export factor Mex67p and with karyopherin Kap95p; homologous to Nup100p	IA[NFQ]	36	FED[LV]IA[DE][PA]	CAVEOLIN PATTERN		IBN_N	1.E-05	-0.7	nuclear pore (1e-26)	Y	0.007	10
protein_40_YGR128C	2	UTP8:  Nucleolar protein required for export of tRNAs from the nucleus; also copurifies with the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	[LSQ]T[GLI]Q	36	STG	EH(3) EF hand domain binding motif of EPS15, Class II		WD40	1.E-02	-0.6	rRNA processing (1e-12)		0.007	10
yeast-593_GO-0031981	2	nuclear lumen	I[NRL]K	36	RRT[IV][ATN]KYR	SIGMA54_2 PATTERN		Helicase_C	1.E-03	-0.4	nuclear lumen (1e-26)		0.008	10
protein_40_YKL203C	2	TOR2:  PIK-related protein kinase and rapamycin target; subunit of TORC1, a complex that regulates growth in response to nutrients and TORC2, a complex that regulates cell-cycle dependent polarization of the actin cytoskeleton; involved in meiosis	SD..[GPL]T[LM]	36	SD.E	Casein kinase II substrate motif		Cation_ATPase_N	1.E-02	-0.4	ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism (0.001)		0.004	9
yeast-235_GO-0000278	2	mitotic cell cycle	KR[KLR]	36	KR	CLV_PCSK_PC1ET2_1		HEAT	1.E-03	-0.2	mitotic cell cycle (1e-18)		0.008	10
yeast-752_GO-0016787	2	hydrolase activity	SK[IYW]	36	ES[RK][FY][YST]FH[PS][IV][ES]D	LIG_WH1		ABC_tran	1.E-06	0.1	hydrolase activity, acting on ester bonds (1e-66)	Y	0.008	10
yeast-1134_GO-0044249	2	cellular biosynthesis	[HRA].AG	36	GR.A	Protease tPA proteolytic site		Ribosomal_60s	1.E-04	0.1	macromolecule biosynthetic process (1e-65)		0.008	10
yeast-251_GO-0005886	2	plasma membrane	P..W[VLP]	36			Y	MFS_1	1.E-06	0.2	plasma membrane (1e-41)		0.008	10
protein_40_YML085C	2	TUB1:  Alpha-tubulin; associates with beta-tubulin (Tub2p) to form tubulin dimer, which polymerizes to form microtubules	[DPL]EL[NTL]	36	LPDEL	Motif in CBP for interaction with PPARg-LBD (secondary site)	Y	HEAT	1.E-04	0.3	microtubule (0.01)	Y	0.007	10
protein_40_YOL133W	2	HRT1:  RING finger containing subunit of Skp1-Cullin-F-box ubiquitin protein ligases (SCF); required for Gic2p, Far1p, Sic1p and Cln2p degradation; may tether Cdc34p (a ubiquitin conjugating enzyme or E2) and Cdc53p (a cullin) subunits of SCF	T.T[TSI]	36	[KR].TQT	LIG_Dynein_DLC8_1		F-box	1.E-13	0.4	ubiquitin ligase complex (1e-12)		0.007	10
oshea_bud_neck	2	oshea_bud_neck	E..K[RFT]	36	KR	CLV_PCSK_PC1ET2_1		RhoGAP	1.E-04	0.5	bud (1e-51)	Y	0.007	10
yeast-341_GO-0045449	2	regulation of transcription	E.[KQT]P	36	[DET]E[RK].PL[LI]	TRG_LysEnd_APsAcLL_3		Zn_clus	1.E-06	0.6	regulation of transcription (1e-12)	Y	0.008	10
yeast-939_GO-0051234	2	establishment of localization	F..[VAL]F	36	F..LF	Androgen receptor motif that interacts with AF2		MFS_1	1.E-10	0.7	establishment of cellular localization (1e-59)	Y	0.008	10
protein_40_YOR181W	2	LAS17:  Actin assembly factor, activates the Arp2/3 protein complex that nucleates branched actin filaments; localizes with the Arp2/3 complex to actin patches; homolog of the human Wiskott-Aldrich syndrome protein (WASP)	DG.[YTM][DRH]	36				Pkinase	1.E-02	0.7	endocytosis (1e-04)		0.005	10
yeast-251_GO-0005886	2	plasma membrane	F.G[YLT]	36	[ST]FCGT.[ED]Y	PDK1 phosphorylation motif		Sugar_tr	1.E-05	0.8	plasma membrane (1e-09)		0.008	10
protein_40_YGR128C	2	UTP8:  Nucleolar protein required for export of tRNAs from the nucleus; also copurifies with the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	[NQP]G.L[KEN]	36	G[SA]LNK	GDP-mannose binding motif in transporter		WD40	1.E-04	0.8	snoRNA binding (1e-21)		0.007	10
yeast-244_GO-0000279	2	M phase	I.D[LVD]	36				MutS_III	1.E-03	0.9	M phase (1e-17)		0.008	10
protein_40_YER082C	2	UTP7:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	KV[LIW][TKD]	36				WD40	1.E-04	0.9	snoRNA binding (1e-16)		0.007	10
protein_40_YBR159W	2	IFA38: Microsomal beta-keto-reductase; contains oleate response element (ORE) sequence in the promoter region; mutants exhibit reduced VLCFA synthesis, accumulate high levels of dihydrosphingosine, phytosphingosine and medium-chain ceramides	FT[MFL]	36	F..F[ST][FY]	Rsks are phosphorylated at this bulky ring site, Ser/Thr must be phosphorylated. This motif recruits PDK1 kinase	Y	Sugar_tr	1.E-02	0.9	endoplasmic reticulum (1e-05)		0.007	10
protein_40_YMR001C	2	CDC5:  Polo-like kinase with similarity to Xenopus Plx1 and S. pombe Plo1p; found at bud neck, nucleus and SPBs; has multiple functions in mitosis and cytokinesis through phosphorylation of substrates; may be a Cdc28p substrate	DF.[LDM][DA]	36				Pkinase	1.E-02	1	M phase (1e-04)	Y	0.006	10
yeast-685_GO-0016740	2	transferase activity	F..E	36				Pkinase	1.E-47	1.2	transferase activity, transferring phosphorus-containing groups (1e-14)	Y	0.007	10
yeast-235_GO-0009653	2	morphogenesis	D[SVG].[VSH]L	36				Pkinase	1.E-02	1.4	cellular morphogenesis (1e-63)	Y	0.007	10
yeast-235_GO-0000902	2	cellular morphogenesis	D[SVG].[VSH]L	36				Pkinase	1.E-02	1.4	cellular morphogenesis (1e-63)	Y	0.007	10
yeast-238_GO-0017111	2	nucleoside-triphosphatase activity	[SDC]A.T[GQI]	36				Ras	1.E-08	1.5	nucleoside-triphosphatase activity (1e-42)	Y	0.008	10
protein_40_YLR180W	2	SAM1:  S-adenosylmethionine synthetase, catalyzes transfer of the adenosyl group of ATP to the sulfur atom of methionine; one of two differentially regulated isozymes (Sam1p and Sam2p)	[GLT]I..G[RHV]	36				GATase	1.E-02	1.5		Y	0.007	10
yeast-706_GO-0043412	2	biopolymer modification	[GLK]P..TP[YLG]	36	[ST]P	LIG_WW_4		UQ_con	1.E-12	1.6	protein modification (1e-11)		0.008	10
yeast-649_GO-0003676	2	nucleic acid binding	R[LGC].[RFN]RG	36	[KR]R	CLV_PCSK_KEX2_1	Y	Histone	1.E-05	1.6	nucleic acid binding (1e-10)	Y	0.008	9
protein_40_YER110C	2	KAP123:  Karyopherin beta, mediates nuclear import of ribosomal proteins prior to assembly into ribosomes and import of histones H3 and H4; localizes to the nuclear pore, nucleus, and cytoplasm; exhibits genetic interactions with RAI1	[LNF]A[RAW]R	36	[KR]R	CLV_PCSK_KEX2_1		Histone	1.E-05	1.6	nuclear nucleosome (1e-04)		0.007	9
yeast-942_GO-0043232	2	intracellular non-membrane-bound organelle	LF[HYG]	36	LFG	Protease Papain substrate, a prototype cysteine proteinase	Y	UCH	1.E-02	1.8	lipid metabolism (1e-10)		0.007	10
yeast-942_GO-0043228	2	non-membrane-bound organelle	LF[HYG]	36	LFG	Protease Papain substrate, a prototype cysteine proteinase	Y	UCH	1.E-02	1.8	lipid metabolism (1e-10)		0.007	10
protein_40_YJR059W	2	PTK2:  Putative serine/threonine protein kinase involved in regulation of ion transport across plasma membrane; enhances spermine uptake	G.[THP]P	36	[ILVM]LG..P	LIG_RRM_PRI_1		Pkinase	1.E-04	1.8	protein kinase activity (0.001)	Y	0.007	10
protein_40_YIL094C	2	LYS12:  Homo-isocitrate dehydrogenase, an NAD-linked mitochondrial enzyme required for the fourth step in the biosynthesis of lysine, in which homo-isocitrate is oxidatively decarboxylated to alpha-ketoadipate	[LGE][SKE]..LA	36				IBN_N	1.E-02	1.9	protein carrier activity (0.01)		0.007	10
yeast-235_GO-0000278	2	mitotic cell cycle	[SEC]L..L[GKM]	36				Kinesin	1.E-04	2	mitotic cell cycle (1e-82)		0.008	10
yeast-235_GO-0009653	2	morphogenesis	K[PQ][DSH]N	36				Pkinase	1.E-03	2.1	cellular morphogenesis (1e-33)	Y	0.008	9
yeast-685_GO-0016740	2	transferase activity	L..[KPW]Y	36				Pkinase	1.E-08	2.2	transferase activity, transferring phosphorus-containing groups (1e-47)	Y	0.008	10
yeast-235_GO-0000902	2	cellular morphogenesis	K[PQ][DSH]N	36				Pkinase	1.E-03	2.2	cellular morphogenesis (1e-33)	Y	0.008	9
yeast-335_GO-0016772	2	transferase activity, transferring phosphorus-containing groups	H.N[NIL]	36	DHKNLD.D	PTPS_2 PATTERN		Pkinase	1.E-48	2.3	transferase activity, transferring phosphorus-containing groups (1e-91)	Y	0.008	10
protein_40_YPL240C	2	HSP82:  Hsp90 chaperone required for pheromone signaling and negative regulation of Hsf1p; docks with Tom70p for mitochondrial preprotein delivery; promotes telomerase DNA binding and nucleotide addition; interacts with Cns1p, Cpr6p, Cpr7p, Sti1p	EN[LIQ]	36	KEN	LIG_APCC_KENbox_2		Pkinase	1.E-02	2.5	kinase activity (0.001)		0.006	10
protein_40_YNL272C	2	SEC2:  Guanyl-nucleotide exchange factor for the small G-protein Sec4p, located on cytoplasmic vesicles; essential for post-Golgi vesicle transport	GV[IF][LT]Y	36	FTYP	Docking motif on c-Fos for Erk		Pkinase	1.E-06	2.5	protein kinase activity (1e-05)		0.004	9
protein_40_YLR186W	2	EMG1:  Protein required for the maturation of the 18S rRNA and for 40S ribosome production; associated with spindle/microtubules; nuclear localization depends on physical interaction with Nop14p; may bind snoRNAs	A[TV]..[YAH]D	36			Y	WD40	1.E-03	2.6	snoRNA binding (1e-13)	Y	0.005	10
protein_40_YMR229C	2	RRP5:  Protein required for the synthesis of both 18S and 5.8S rRNA; C-terminal region is crucial for the formation of 18S rRNA and N-terminal region is required for the 5.8S rRNA; component of small ribosomal subunit (SSU) processosome	K[PAM]..LL[LTN]	36	[DE]..LL	Di-Leu acidic motif for receptor endocytosis (recognized by VHS domain of GGA proteins)		Pkinase	1.E-04	3.1	protein kinase activity (0.001)		0.005	8
yeast-462_GO-0019222	2	regulation of metabolism	L.Q[DHE]	36	LSQE	ATM kinase substrate motif	Y	zf-C2H2	1.E-05	3.2	regulation of metabolism (1e-17)	Y	0.008	10
protein_40_YGR128C	2	UTP8:  Nucleolar protein required for export of tRNAs from the nucleus; also copurifies with the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	A[TVS]..[YAH]D	36			Y	WD40	1.E-05	3.2	snoRNA binding (1e-15)	Y	0.005	8
yeast-648_GO-0050791	2	regulation of physiological process	[IYQ]..DIK	36	P.Q..D	LIG_TRAF2_2		Pkinase	1.E-08	3.4	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism (1e-12)		0.008	9
yeast-335_GO-0016772	2	transferase activity, transferring phosphorus-containing groups	L.H[PKF]	36			Y	Pkinase	1.E-36	3.7	transferase activity, transferring phosphorus-containing groups (1e-97)	Y	0.008	10
yeast-256_GO-0016462	2	pyrophosphatase activity	[RFQ]EL[APR]	36	[KRHQSA][DENQ]EL	ER_TARGET PATTERN		DEAD	1.E-12	4.2	pyrophosphatase activity (1e-51)	Y	0.008	10
protein_40_YAR019C	2	CDC15:  Protein kinase of the Mitotic Exit Network that is localized to the spindle pole bodies at late anaphase; promotes mitotic exit by directly switching on the kinase activity of Dbf2p	[GKN]..HR	36				Pkinase	1.E-21	4.2	protein kinase activity (1e-17)	Y	0.007	10
yeast-752_GO-0016787	2	hydrolase activity	[LRF][YF].PPG	36				AAA	1.E-15	4.3	ATPase activity (1e-12)		0.007	9
protein_40_YDL153C	2	SAS10:  Component of the small (ribosomal) subunit (SSU) processosome required for pre-18S rRNa processing; essential nucleolar protein that, when overproduced, disrupts silencing	W.[ILMV]G	36				Pkinase	1.E-18	4.4	protein kinase activity (1e-16)		0.007	10
yeast-1340_GO-0044267	2	cellular protein metabolism	[VAY]K..D[FLA]G	36				Pkinase	1.E-24	4.9	protein amino acid phosphorylation (1e-29)		0.008	10
matsuyama_Cytosol	2	matsuyama_Cytosol	Y..P[EKV]	36	Y..P	SH2 ligand group 1B-Crk, SH2 binding motif for ITK, Nck and RasGAP to Doc-R (needs to be Tyr phosphorylated)		Pkinase	1.E-13	5	purine nucleotide binding (1e-13)	Y	0.009	10
yeast-649_GO-0003676	2	nucleic acid binding	[CIV]NA[CQI]G	36				GATA	1.E-11	6.2	nucleic acid binding (1e-08)		0.007	9
protein_40_YGL120C	2	PRP43:  RNA helicase in the DEAH-box family, functions in both RNA polymerase I and polymerase II transcript metabolism, involved in release of the lariat-intron from the spliceosome	GR.[AGN][RKA]	36	[AG]R	Protease matriptase protease site		Helicase_C	1.E-06	6.8	nucleolus (1e-09)		0.007	10
yeast-649_GO-0003676	2	nucleic acid binding	R..K[QKC]	36	R..K	SH3 binding motif for GADS SH3 recognizing slp-76 motif (nonconventional)		Zn_clus	1.E-07	9.5	nucleic acid binding (1e-15)		0.008	10
yeast-436_GO-0031323	2	regulation of cellular metabolism	CR..K[ITE][KGA]	36	R..K	SH3 binding motif for GADS SH3 recognizing slp-76 motif (nonconventional)	Y	Zn_clus	1.E-11	13.2	regulation of cellular metabolism (1e-09)	Y	0.007	9
yeast-792_GO-0006412	2	protein biosynthesis	K[AWF].[KAQ]A	36							translation (1e-52)		0.008	10
yeast-648_GO-0050791	2	regulation of physiological process	Q..E[KTD]	36							regulation of metabolism (1e-10)		0.008	10
yeast-470_GO-0006259	2	DNA metabolism	K[EFP].Q[QIS]	36							DNA metabolism (1e-53)		0.008	9
yeast-457_GO-0007001	2	chromosome organization and biogenesis (sensu Eukaryota)	E[EKH].D[ESW]	36							chromosome organization and biogenesis (sensu Eukaryota) (1e-78)		0.008	10
yeast-376_GO-0019219	2	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism	E[ENT][DLG]EV	36	[YL]EVD	Protease Caspase 1 and 4	Y				regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism (1e-18)		0.008	10
yeast-343_GO-0005198	2	structural molecule activity	L.[GQP]I	36	PL[ST]PIP[KRH]	CDK4 kinase substrate motif							0.008	10
yeast-336_GO-0005783	2	endoplasmic reticulum	F.I	36	F.[IV][WFY][WFY][IL][ILM]	EH1 motif binds to groucho/TLE corepressors					endoplasmic reticulum (10)	Y	0.008	10
yeast-267_GO-0000003	2	reproduction	[PFD]Y[QET]L	36	[EDY]Y	TC-PTP phosphatase substrate motif					reproduction (1e-45)		0.008	10
yeast-267_GO-0000003	2	reproduction	P[AYQ]..[PGV]P	36	GP	Protease TTP cleavage site					reproduction (1e-35)	Y	0.008	10
yeast-267_GO-0000003	2	reproduction	TT[KGT][IHW]	36	YTT[ILM]	Syk N-terminal SH2 domain binding motif					reproduction (1e-41)		0.008	10
yeast-240_GO-0006807	2	nitrogen compound metabolism	AD[IHT][QVF]	36							nitrogen compound metabolism (1e-39)		0.008	10
yeast-223_GO-0003735	2	structural constituent of ribosome	A[KVN]..KK[VWR]	36	KR	CLV_PCSK_PC1ET2_1					structural constituent of ribosome (1e-11)		0.006	9
yeast-207_GO-0006974	2	response to DNA damage stimulus	[EIC]NE[DVR]	36							response to DNA damage stimulus (1e-54)		0.007	10
ubiquitin_peng2003	2	ubiquitin_peng2003	LL.[FGN][TVS]I	36	LLG	Beta2-Integrin binding motif							0.007	10
protein_40_YPR182W	2	SMX3:  Core Sm protein Sm F; part of heteroheptameric complex (with Smb1p, Smd1p, Smd2p, Smd3p, Sme1p, and Smx2p) that is part of the spliceosomal U1, U2, U4, and U5 snRNPs; homolog of human Sm F	LL.L[SCA][KNH]	36	LLG	Beta2-Integrin binding motif					nuclear mRNA splicing, via spliceosome (1e-08)		0.004	8
protein_40_YPR120C	2	CLB5:  B-type cyclin involved in DNA replication during S phase; activates Cdc28p to promote initiation of DNA synthesis; functions in formation of mitotic spindles along with Clb3p and Clb4p; most abundant during late G1 phase	[EMT]E.E[EIY]	36	EEEYF	EGFR kinase phosphorylation site (peptide screen)							0.007	10
protein_40_YPR034W	2	ARP7:  Component of both the SWI/SNF and RSC chromatin remodeling complexes; actin-related protein involved in transcriptional regulation	[QG]L.K[LQ]N	36	KEN	LIG_APCC_KENbox_2					chromatin remodeling complex (0.001)		0.004	9
protein_40_YPL240C	2	HSP82:  Hsp90 chaperone required for pheromone signaling and negative regulation of Hsf1p; docks with Tom70p for mitochondrial preprotein delivery; promotes telomerase DNA binding and nucleotide addition; interacts with Cns1p, Cpr6p, Cpr7p, Sti1p	L.E[TVI]	36							protein folding (0.01)		0.006	10
protein_40_YPL217Cs	2	BMS1:  Essential conserved nucleolar GTP-binding protein required for synthesis of 40S ribosomal subunits and for processing of the 35S pre-rRNA at sites A0, A1, and A2; interacts with Rcl1p, has similarity to Tsr1p	[ETD]E.[INF]A	36	[ST]E	G protein-coupled receptor kinase 1 substrate motif					rRNA processing (1e-17)		0.007	10
protein_40_YPL204W	2	HRR25:  Protein kinase involved in regulating diverse events including vesicular trafficking, DNA repair, and chromosome segregation; binds the CTD of RNA pol II; homolog of mammalian casein kinase 1delta (CK1delta)	[TVP]KTS[IKF]	36			Y						0.004	7
protein_40_YPL204W	2	HRR25:  Protein kinase involved in regulating diverse events including vesicular trafficking, DNA repair, and chromosome segregation; binds the CTD of RNA pol II; homolog of mammalian casein kinase 1delta (CK1delta)	DE[NV][SHI]K	36	YDE[PDV]	SH2 ligand for Nck1 and Nck2 (Tyr must be phosphorylated)							0.004	7
protein_40_YPL131W	2	RPL5:  Protein component of the large (60S) ribosomal subunit with similarity to E. coli L18 and rat L5 ribosomal proteins; binds 5S rRNA and is required for 60S subunit assembly	R[EKT][LVI]A	36	MR[DE][IL]	TUBULIN_B_AUTOREG PATTERN					cytoplasm organization and biogenesis (1e-11)		0.007	10
protein_40_YPL126W	2	NAN1:  U3 snoRNP protein, component of the small (ribosomal) subunit (SSU) processosome containing U3 snoRNA; required for the biogenesis of18S rRNA	R[HRW]..F[LND]	36	W..F	VPR binding motif in uracil DNA glycosylase					nucleolus (1e-08)		0.005	10
protein_40_YPL090C	2	RPS6A:  Protein component of the small (40S) ribosomal subunit; identical to Rps6Bp and has similarity to rat S6 ribosomal protein	DV..I[EIK][LNV]	36									0.004	8
protein_40_YPL042C	2	SSN3:  Cyclin-dependent protein kinase, component of RNA polymerase II holoenzyme; involved in phosphorylation of the RNA polymerase II C-terminal domain; involved in glucose repression	P[QPT]Y[IVF]	36	NP.Y	LIG_PTB_1					transcription from RNA polymerase II promoter (1e-06)		0.005	9
protein_40_YPL004C	2	LSP1:  Primary component of eisosomes, which are large immobile patch structures at the cell cortex associated with endocytosis, along with Pil1p and Sur7p; null mutants show activation of Pkc1p/Ypk1p stress resistance pathways	IE.[GK][DC]	36									0.004	8
protein_40_YOR181W	2	LAS17:  Actin assembly factor, activates the Arp2/3 protein complex that nucleates branched actin filaments; localizes with the Arp2/3 complex to actin patches; homolog of the human Wiskott-Aldrich syndrome protein (WASP)	N[FPV]AS[TG]	36	S[ST]	MDC1 BRCT domain binding motif						Y	0.004	7
protein_40_YOR096W	2	RPS7A:  Protein component of the small (40S) ribosomal subunit, nearly identical to Rps7Bp; interacts with Kti11p; deletion causes hypersensitivity to zymocin; has similarity to rat S7 and Xenopus S8 ribosomal proteins	K[LIK][RAV]A	36							ribonucleoprotein complex (1e-17)	Y	0.007	10
protein_40_YOR061W	2	CKA2:  Alpha' catalytic subunit of casein kinase 2, a Ser/Thr protein kinase with roles in cell growth and proliferation; the holoenzyme also contains CKA1, CKB1 and CKB2, the many substrates include transcription factors and all RNA polymerases	[KVQ][RVF]..KP	36							RNA elongation from RNA polymerase II promoter (1e-04)		0.007	9
protein_40_YOR061W	2	CKA2:  Alpha' catalytic subunit of casein kinase 2, a Ser/Thr protein kinase with roles in cell growth and proliferation; the holoenzyme also contains CKA1, CKB1 and CKB2, the many substrates include transcription factors and all RNA polymerases	[LHD]V..E[DSY]	36							RNA polymerase II transcription elongation factor activity (1e-05)		0.007	10
protein_40_YOL139C	2	CDC33:  Cytoplasmic mRNA cap binding protein; the eIF4E-cap complex is responsible for mediating cap-dependent mRNA translation via interactions with the translation initiation factor eIF4G (Tif4631p or Tif4632p)	I[TR].Q[DA]L	36									0.004	10
protein_40_YOL133W	2	HRT1:  RING finger containing subunit of Skp1-Cullin-F-box ubiquitin protein ligases (SCF); required for Gic2p, Far1p, Sic1p and Cln2p degradation; may tether Cdc34p (a ubiquitin conjugating enzyme or E2) and Cdc53p (a cullin) subunits of SCF	V[IPN]E[IPW]	36	VP	Interleukin converting enzyme protease						Y	0.007	10
protein_40_YOL086C	2	ADH1:  Alcohol dehydrogenase, fermentative isozyme active as homo- or heterotetramers; required for the reduction of acetaldehyde to ethanol, the last step in the glycolytic pathway	M[SLE]D[SLR]	36	DMQD	Protease Caspase 3 -stringent						Y	0.006	10
protein_40_YOL041C	2	NOP12:  Nucleolar protein, required for pre-25S rRNA processing; contains an RNA recognition motif (RRM) and has similarity to Nop13p, Nsr1p, and putative orthologs in Drosophila and S. pombe	K[KEL]K[KRA]	36	KKKKKK[ST]	TGF beta receptor kinase substrate motif					cytoplasm organization and biogenesis (1e-15)	Y	0.007	10
protein_40_YOL018C	2	TLG2:  Syntaxin-like t-SNARE that forms a complex with Tlg1p and Vti1p and mediates fusion of endosome-derived vesicles with the late Golgi; binds Vps45p, which prevents Tlg2p degradation and also facilitates t-SNARE complex formation	F[IMY][VTM]F	36			Y						0.004	8
protein_40_YOL013C	2	HRD1:  Ubiquitin-protein ligase required for endoplasmic reticulum-associated degradation (ERAD) of misfolded proteins; genetically linked to the unfolded protein response (UPR); regulated through association with Hrd3p; contains an H2 ring finger	D[QVA]V	36	[IVT][LIVMC][IVT][HS]D[SGAV][AV]R	ISPD PATTERN					carboxylic acid metabolism (0.01)		0.007	9
protein_40_YNL308C	2	KRI1:  Essential nucleolar protein required for 40S ribosome biogenesis; physically and functionally interacts with Krr1p	K[YS]L[SDE]E	36	[ST]E	G protein-coupled receptor kinase 1 substrate motif							0.004	8
protein_40_YNL154C	2	YCK2:  Palmitoylated, plasma membrane-bound casein kinase I isoform; shares redundant functions with Yck1p in morphogenesis, proper septin assembly, endocytic trafficking; provides an essential function overlapping with that of Yck1p	N[NDF]S	36	N.[TS]	N-linked glycosylation site						Y	0.006	10
protein_40_YNL069C	2	RPL16B:  N-terminally acetylated protein component of the large (60S) ribosomal subunit, binds to 5.8 S rRNA; has similarity to Rpl16Ap, E. coli L13 and rat L13a ribosomal proteins; transcriptionally regulated by Rap1p	RA.[KRQ][VGA]	36							cytosolic ribosome (sensu Eukaryota) (1e-17)	Y	0.007	10
protein_40_YMR308C	2	PSE1:  Karyopherin/importin that interacts with the nuclear pore complex; acts as the nuclear import receptor for specific proteins, including Pdr1p, Yap1p, Ste12p, and Aft1p	S[NAF]SF[TE]	36			Y						0.004	8
protein_40_YMR304W	2	UBP15:  Ubiquitin-specific protease that may play a role in ubiquitin precursor processing	D[FYQ][DPY]G	36								Y	0.005	10
protein_40_YMR288W	2	HSH155:  U2-snRNP associated splicing factor that forms extensive associations with the branch site-3' splice site-3' exon region upon prespliceosome formation; similarity to the mammalian U2 snRNP-associated splicing factor SAP155	EI.[VR]S[FL]	36							nuclear mRNA splicing, via spliceosome (1e-04)		0.004	8
protein_40_YMR216C	2	SKY1:  SR protein kinase (SRPK) involved in regulating proteins involved in mRNA metabolism and cation homeostasis; similar to human SRPK1	G[ILMV]AV	36									0.005	8
protein_40_YMR215W	2	GAS3:  Putative 1,3-beta-glucanosyltransferase, has similarity to Gas1p; localizes to the cell wall	I[LYS]Y[LTC]	36	Y[VLTFIC]	LIG_SH2_STAT5					integral to membrane (0.001)		0.006	10
protein_40_YMR047C	2	NUP116:  Subunit of the nuclear pore complex (NPC) that is localized to both sides of the pore; contains a repetitive GLFG motif that interacts with mRNA export factor Mex67p and with karyopherin Kap95p; homologous to Nup100p	[KPT]K.K[SLR]R	36	[KR]R	CLV_PCSK_KEX2_1						Y	0.004	9
protein_40_YML073C	2	RPL6A:  N-terminally acetylated protein component of the large (60S) ribosomal subunit, has similarity to Rpl6Bp and to rat L6 ribosomal protein; binds to 5.8S rRNA	K..[RAK]A	36	K[KR].[KR]	Nuclear localization motif					cytosolic ribosome (sensu Eukaryota) (1e-41)	Y	0.007	10
protein_40_YML069W	2	POB3:  Subunit of the heterodimeric FACT complex (Spt16p-Pob3p), which facilitates RNA Pol II transcription elongation through nucleosomes by destabilizing and then reassembling nucleosome structure; interacts with DNA polymerase alpha (Pol1p)	GE[LYQ][ARD]	36	[WFY]G[PDE][WFYLM]	gamma-adaptin ear binding motif	Y				RNA elongation from RNA polymerase II promoter (0.001)		0.006	10
protein_40_YML010W	2	SPT5:  Protein that forms a complex with Spt4p and mediates both activation and inhibition of transcription elongation; Spt4p-Spt5p complex also plays a role in pre-mRNA processing	S.[AEQ]D	36							nuclear lumen (1e-17)		0.007	10
protein_40_YML007W	2	YAP1:  Basic leucine zipper (bZIP) transcription factor required for oxidative stress tolerance; activated by H2O2 through the multistep formation of disulfide bonds and transit from the cytoplasm to the nucleus; mediates resistance to cadmium	Y[IN].R[LQ]	36							nucleoplasm part (1e-06)		0.004	8
protein_40_YLR429W	2	CRN1:  Coronin, cortical actin cytoskeletal component that associates with the Arp2p/Arp3p complex to regulate its activity; plays a role in regulation of actin patch assembly	E..E[ATG]	36	RE..E	Iron binding motif in ferritin L-chain and yeast Iron transport protein					endocytosis (0.001)		0.007	10
protein_40_YLR287C-A	2	RPS30A:  Protein component of the small (40S) ribosomal subunit; nearly identical to Rps30Bp and has similarity to rat S30 ribosomal protein	S..[SND]S	36	S..[ST]	Casein Kinase I consensus phosphorylation site (N-term Ser must first be phosphorylated)							0.007	10
protein_40_YLR222C	2	UTP13:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	K[ERW]D[DT]	36	KR	CLV_PCSK_PC1ET2_1					nucleolus (1e-05)		0.005	10
protein_40_YLR222C	2	UTP13:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	T[DHC][LQ]D	36							processing of 20S pre-rRNA (1e-04)		0.005	10
protein_40_YLR180W	2	SAM1:  S-adenosylmethionine synthetase, catalyzes transfer of the adenosyl group of ATP to the sulfur atom of methionine; one of two differentially regulated isozymes (Sam1p and Sam2p)	I[KEC].V[GIV]	36									0.007	9
protein_40_YLR180W	2	SAM1:  S-adenosylmethionine synthetase, catalyzes transfer of the adenosyl group of ATP to the sulfur atom of methionine; one of two differentially regulated isozymes (Sam1p and Sam2p)	LA.[NKA][DPT]	36			Y				carboxylic acid metabolism (0.001)	Y	0.007	10
protein_40_YLR180W	2	SAM1:  S-adenosylmethionine synthetase, catalyzes transfer of the adenosyl group of ATP to the sulfur atom of methionine; one of two differentially regulated isozymes (Sam1p and Sam2p)	P..[GKF]V	36	KP..[QK]	LIG_SH3_4					carboxylic acid metabolism (0.01)		0.007	10
protein_40_YLR180W	2	SAM1:  S-adenosylmethionine synthetase, catalyzes transfer of the adenosyl group of ATP to the sulfur atom of methionine; one of two differentially regulated isozymes (Sam1p and Sam2p)	V[VTN]..[MVK]G	36								Y	0.006	10
protein_40_YLR009W	2	RLP24:  Essential protein with similarity to Rpl24Ap and Rpl24Bp, associated with pre-60S ribosomal subunits and required for ribosomal large subunit biogenesis	[ES]DD[DEG]	36	DDDK[ACDEFGHIKLMNQRSTVWY]	Protease Enterokinase					cytoplasm organization and biogenesis (1e-16)		0.007	10
protein_40_YKL203C	2	TOR2:  PIK-related protein kinase and rapamycin target; subunit of TORC1, a complex that regulates growth in response to nutrients and TORC2, a complex that regulates cell-cycle dependent polarization of the actin cytoskeleton; involved in meiosis	[GVD][QYG]..DS	36	R.DSPVR	14-3-3 binding motif on N-terminal domain of Nitrate Reductase necessary for 14-3-3 binding for inactivation in the dark					plasma membrane (1e-07)		0.007	9
protein_40_YKL180W	2	RPL17A:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl17Bp and has similarity to E. coli L22 and rat L17 ribosomal proteins; copurifies with the Dam1 complex (aka DASH complex)	S.S[SNI]	36	R.S.S.P	14-3-3 binding motifs, Ser must be phosphorylated							0.007	10
protein_40_YKL145W	2	RPT1:  One of six ATPases of the 19S regulatory particle of the 26S proteasome involved in the degradation of ubiquitinated substrates; required for optimal CDC20 transcription; interacts with Rpn12p and the E3 ubiquitin-protein ligase Ubr1p	TI[IMA][RQ]	36							proteasome complex (sensu Eukaryota) (1e-04)	Y	0.005	10
protein_40_YJR145C	2	RPS4A:  Protein component of the small (40S) ribosomal subunit; mutation affects 20S pre-rRNA processing; identical to Rps4Bp and has similarity to rat S4 ribosomal protein	S[KAE].A[AEQ]	36			Y				rRNA processing (1e-08)		0.007	10
protein_40_YJL164C	2	TPK1:  cAMP-dependent protein kinase catalytic subunit; promotes vegetative growth in response to nutrients via the Ras-cAMP signaling pathway; inhibited by regulatory subunit Bcy1p in the absence of cAMP; partially redundant with Tpk2p and Tpk3p	T.[SEQ]P	36	[ST]P	LIG_WW_4	Y					Y	0.007	10
protein_40_YJL138C	2	TIF2:  Translation initiation factor eIF4A, identical to Tif1p; DEA(D/H)-box RNA helicase that couples ATPase activity to RNA binding and unwinding; forms a dumbbell structure of two compact domains connected by a linker; interacts with eIF4G	HL..[AWC][IMG]	36									0.004	10
protein_40_YJL092W	2	SRS2:  DNA helicase and DNA-dependent ATPase involved in DNA repair, needed for proper timing of commitment to meiotic recombination and transition from Meiosis I to II; affects genome stability by suppressing unscheduled homologous recombination	E.[SRA]S	36							response to DNA damage stimulus (1e-04)		0.007	10
protein_40_YJL074C	2	SMC3:  Subunit of the multiprotein cohesin complex required for sister chromatid cohesion in mitotic cells; also required, with Rec8p, for cohesion and recombination during meiosis; phylogenetically conserved SMC chromosomal ATPase family member	[RAM]EK[ASW]	36								Y	0.006	9
protein_40_YJL033W	2	HCA4:  Putative nucleolar DEAD box RNA helicase; high-copy number suppression of a U14 snoRNA processing mutant suggests an involvement in 18S rRNA synthesis	A..K[KIC]	36							mRNA cleavage and polyadenylation specificity factor complex (1e-10)	Y	0.007	10
protein_40_YJL010C	2	NOP9:  Essential component of pre-40S ribosomes that is required for early cleavages of 35S pre-rRNA and hence formation of 18S rRNA; binds RNA in vitro and contains multiple pumilio-like repeats	[MWQ]S..[SG]SL	36	RSSLHL	Motif in beta-arrestin 2 for interaction with Jnk3					small nucleolar ribonucleoprotein complex (1e-08)	Y	0.004	10
protein_40_YIL069C	2	RPS24B:  Protein component of the small (40S) ribosomal subunit; identical to Rps24Ap and has similarity to rat S24 ribosomal protein	K[RYG]A	36	KR	CLV_PCSK_PC1ET2_1	Y				cytosolic ribosome (sensu Eukaryota) (1e-10)		0.006	10
protein_40_YIL035C	2	CKA1:  Alpha catalytic subunit of casein kinase 2, a Ser/Thr protein kinase with roles in cell growth and proliferation; the holoenzyme also contains CKA2, CKB1 and CKB2, the many substrates include transcription factors and all RNA polymerases	K[KER]..K[KIT]	36	K[KR].[KR]	Nuclear localization motif					nucleolus (1e-09)		0.007	10
protein_40_YIL016W	2	SNL1:  Protein of unknown function proposed to be involved in nuclear pore complex biogenesis and maintenance as well as protein folding; has similarity to the mammalian BAG-1 protein	[NGA][ELH].FF	36									0.005	9
protein_40_YHR203C	2	RPS4B:  Protein component of the small (40S) ribosomal subunit; identical to Rps4Ap and has similarity to rat S4 ribosomal protein	R[VAG].[GKI]G	36							cytosolic ribosome (sensu Eukaryota) (1e-13)		0.007	9
protein_40_YHR041C	2	SRB2:  Subunit of the RNA polymerase II mediator complex; associates with core polymerase subunits to form the RNA polymerase II holoenzyme; general transcription factor involved in telomere maintenance	[NV]I.[NPK]NI	36							general RNA polymerase II transcription factor activity (1e-05)		0.004	8
protein_40_YHL007C	2	STE20:  Signal transducing kinase of the PAK (p21-activated kinase) family, involved in pheromone response and pseudohyphal/invasive growth pathways, activated by Cdc42p; binds Ste4p at a GBB motif present in noncatalytic domains of PAK kinases	Y[APM].G[SN]	36									0.005	8
protein_40_YGR085C	2	RPL11B:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl11Ap; involved in ribosomal assembly; depletion causes degradation of proteins and RNA of the 60S subunit; has similarity to E. coli L5 and rat L11	S.[SLI]S	36	S..S	Casien kinase I phosphorylation site, 1st Ser must be phosphorylated							0.006	10
protein_40_YGR060W	2	ERG25:  C-4 methyl sterol oxidase, catalyzes the first of three steps required to remove two C-4 methyl groups from an intermediate in ergosterol biosynthesis; mutants accumulate the sterol intermediate 4,4-dimethylzymosterol	IL[YVI][LVF]	36	L[IVLMF][IVLMF][DE]	Clathrin box motif on cargo adapter proteins					endoplasmic reticulum (1e-06)		0.007	10
protein_40_YGL147C	2	RPL9A:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl9Bp and has similarity to E. coli L6 and rat L9 ribosomal proteins	G[KIY]K[VAY]	36	G[KR][KR]	Amidation after cleavage after Gly (must be in secretory pathway)	Y				cytosolic ribosome (sensu Eukaryota) (1e-21)		0.007	10
protein_40_YGL120C	2	PRP43:  RNA helicase in the DEAH-box family, functions in both RNA polymerase I and polymerase II transcript metabolism, involved in release of the lariat-intron from the spliceosome	K[LER]SD[SVA]	36	KR	CLV_PCSK_PC1ET2_1							0.004	7
protein_40_YGL120C	2	PRP43:  RNA helicase in the DEAH-box family, functions in both RNA polymerase I and polymerase II transcript metabolism, involved in release of the lariat-intron from the spliceosome	R[ACN][LEI]KT	36							RNA processing (1e-05)		0.004	8
protein_40_YGL106W	2	MLC1:  Essential light chain for Myo1p, light chain for Myo2p; stabilizes Myo2p by binding to the neck region; interacts with Myo1p, Iqg1p, and Myo2p to coordinate formation and contraction of the actomyosin ring with targeted membrane deposition	[RAS][LGN]..DLE	36	D.E	Sec24p						Y	0.004	7
protein_40_YGL105W	2	ARC1:  Protein that binds tRNA and methionyl- and glutamyl-tRNA synthetases (Mes1p and Gus1p), delivering tRNA to them, stimulating catalysis, and ensuring their localization to the cytoplasm; also binds quadruplex nucleic acids	GG[EA][LV]F	36	FRGGT	Phosphoinositide binding motif in ATG18 and ATG21						Y	0.004	8
protein_40_YGL076C	2	RPL7A:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl7Bp and has similarity to E. coli L30 and rat L7 ribosomal proteins; contains a conserved C-terminal Nucleic acid Binding Domain (NDB2)	D[KQ]..[EH]DL	36			Y						0.004	8
protein_40_YER148W	2	SPT15:  TATA-binding protein, general transcription factor that interacts with other factors to form the preinitiation complex at promoters, essential for viability	[KPL]S.Q[SQ]S	36	S[QT]Q	ATM phosphorylation of this motif on Chk2					transcription factor complex (0.001)		0.004	9
protein_40_YER133W	2	GLC7:  Catalytic subunit of type 1 serine/threonine protein phosphatase, involved in many processes including glycogen metabolism, sporulation, and mitosis; interacts with multiple regulatory subunits; predominantly isolated with Sds22p	[DET]D..[SKP]S	36							phosphatase regulator activity (1e-07)	Y	0.007	10
protein_40_YER112W	2	LSM4:  Lsm (Like Sm) protein; part of heteroheptameric complexes (Lsm2p-7p and either Lsm1p or 8p): cytoplasmic Lsm1p complex involved in mRNA decay; nuclear Lsm8p complex part of U6 snRNP and possibly involved in processing tRNA, snoRNA, and rRNA	[VFI]R.E[IFP]	36									0.006	10
protein_40_YER110C	2	KAP123:  Karyopherin beta, mediates nuclear import of ribosomal proteins prior to assembly into ribosomes and import of histones H3 and H4; localizes to the nuclear pore, nucleus, and cytoplasm; exhibits genetic interactions with RAI1	AV..[AQF][IKG]	36								Y	0.007	10
protein_40_YER021W	2	RPN3:  Essential, non-ATPase regulatory subunit of the 26S proteasome lid, similar to the p58 subunit of the human 26S proteasome; temperature-sensitive alleles cause metaphase arrest, suggesting a role for the proteasome in cell cycle control	E[EV]..[KLD]FT	36									0.004	8
protein_40_YER018C	2	SPC25:  Component of the evolutionarily conserved kinetochore-associated Ndc80 complex (Ndc80p-Nuf2p-Spc24p-Spc25p); involved in chromosome segregation, spindle checkpoint activity and kinetochore clustering	K[EIF]ED[AN]	36	EDAIY	Abl kinase substrate motif							0.004	7
protein_40_YER018C	2	SPC25:  Component of the evolutionarily conserved kinetochore-associated Ndc80 complex (Ndc80p-Nuf2p-Spc24p-Spc25p); involved in chromosome segregation, spindle checkpoint activity and kinetochore clustering	Q..[QEH]E	36	[PSAT].[QE]E	LIG_TRAF2_1					transcription regulator activity (0.001)		0.007	10
protein_40_YER012W	2	PRE1:  Beta 4 subunit of the 20S proteasome; localizes to the nucleus throughout the cell cycle	L[GC][TM]P	36	[ST]P	LIG_WW_4	Y				proteasome regulatory particle (sensu Eukaryota) (0.01)		0.005	8
protein_40_YDR510W	2	SMT3:  Ubiquitin-like protein of the SUMO family, conjugated to lysine residues of target proteins; regulates chromatid cohesion, chromosome segregation, APC-mediated proteolysis, DNA replication and septin ring dynamics	V..V[GEQ]	36			Y				macromolecule biosynthetic process (0.01)		0.007	10
protein_40_YDR477W	2	SNF1:  AMP-activated serine/threonine protein kinase found in a complex containing Snf4p and members of the Sip1p/Sip2p/Gal83p family; required for transcription of glucose-repressed genes, thermotolerance, sporulation, and peroxisome biogenesis	[DFY]D.E[EVF]	36	D.E	Sec24p							0.007	10
protein_40_YDR418W	2	RPL12B:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl12Ap; rpl12a rpl12b double mutant exhibits slow growth and slow translation; has similarity to E. coli L11 and rat L12 ribosomal proteins	[NGE]K.[KQ]KV	36							cytosolic ribosome (sensu Eukaryota) (1e-06)		0.004	8
protein_40_YDR418W	2	RPL12B:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl12Ap; rpl12a rpl12b double mutant exhibits slow growth and slow translation; has similarity to E. coli L11 and rat L12 ribosomal proteins	A[RAG].[KYV]A	36							cytosolic ribosome (sensu Eukaryota) (1e-28)		0.007	10
protein_40_YDR388W	2	RVS167:  Actin-associated protein, subunit of a complex (Rvs161p-Rvs167p) involved in regulation of actin cytoskeleton, endocytosis, and viability following starvation or osmotic stress; homolog of mammalian amphiphysin	S[GTS]D	36	S[ST]	MDC1 BRCT domain binding motif					actin cortical patch (1e-04)		0.006	10
protein_40_YDR303C	2	RSC3:  Component of the RSC chromatin remodeling complex; essential gene required for maintenance of proper ploidy and regulation of ribosomal protein genes and the cell wall/stress response; highly similar to Rsc30p	P[VQA].[LH]T	36									0.005	8
protein_40_YDR224C	2	HTB1:  One of two nearly identical (see HTB2) histone H2B subtypes required for chromatin assembly and chromosome function; Rad6p-Bre1p-Lge1p mediated ubiquitination regulates transcriptional activation, meiotic DSB formation and H3 methylation	[DES][PQ].AVS	36									0.004	9
protein_40_YDR224C	2	HTB1:  One of two nearly identical (see HTB2) histone H2B subtypes required for chromatin assembly and chromosome function; Rad6p-Bre1p-Lge1p mediated ubiquitination regulates transcriptional activation, meiotic DSB formation and H3 methylation	[EDY]D.[THM]G	36	D..G	motif that binds phosphate in GDP and GTP binding proteins							0.006	9
protein_40_YDR174W	2	HMO1:  Chromatin associated high mobility group (HMG) family member involved in genome maintenance; rDNA-binding component of the Pol I transcription system; associates with a 5'-3' DNA helicase and Fpr1p, a prolyl isomerase	KL..[LFT][RYP]T	36									0.004	7
protein_40_YDR099W	2	BMH2:  14-3-3 protein, minor isoform; controls proteome at post-transcriptional level, binds proteins and DNA, involved in regulation of many processes including exocytosis, vesicle transport, Ras/MAPK signaling, and rapamycin-sensitive signaling	[KPR]A.[NCP]N	36									0.006	9
protein_40_YDR012W	2	RPL4B:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl4Ap and has similarity to E. coli L4 and rat L4 ribosomal proteins	R..[RAK]A	36	R..K	SH3 binding motif for GADS SH3 recognizing slp-76 motif (nonconventional)					cytosolic ribosome (sensu Eukaryota) (1e-21)	Y	0.007	10
protein_40_YDL213C	2	NOP6:  Putative RNA-binding protein implicated in ribosome biogenesis; contains an RNA recognition motif (RRM) and has similarity to hydrophilins; NOP6 may be a fungal-specific gene as no homologs have been yet identified in higher eukaryotes	AP..[KLR][KEM]	36							nucleolus (1e-07)	Y	0.007	9
protein_40_YDL147W	2	RPN5:  Essential, non-ATPase regulatory subunit of the 26S proteasome lid, similar to mammalian p55 subunit and to another S. cerevisiae regulatory subunit, Rpn7p	A[APE].I[AS]L	36									0.004	8
protein_40_YDL055C	2	PSA1:  GDP-mannose pyrophosphorylase (mannose-1-phosphate guanyltransferase), synthesizes GDP-mannose from GTP and mannose-1-phosphate in cell wall biosynthesis; required for normal cell wall structure	A[EAD].[ATF]G	36			Y					Y	0.007	9
protein_40_YDL055C	2	PSA1:  GDP-mannose pyrophosphorylase (mannose-1-phosphate guanyltransferase), synthesizes GDP-mannose from GTP and mannose-1-phosphate in cell wall biosynthesis; required for normal cell wall structure	G..V[TEK]	36	D[DE].G..[VI][TS]	DNA polymerase interaction motif in Cdc27					cytosol (1e-05)		0.007	10
protein_40_YDL047W	2	SIT4:  Type 2A-related serine-threonine phosphatase that functions in the G1/S transition of the mitotic cycle; cytoplasmic and nuclear protein that modulates functions mediated by Pkc1p including cell wall and actin cytoskeleton organization	K[IG]..K[PHM]	36									0.006	9
protein_40_YDL029W	2	ARP2:  Essential component of the Arp2/3 complex, which is a highly conserved actin nucleation center required for the motility and integrity of actin patches; involved in endocytosis and membrane growth and polarity	I[GHM]..[IPM]K	36									0.005	9
protein_40_YDL014W	2	NOP1:  Nucleolar protein, component of the small subunit processome complex, which is required for processing of pre-18S rRNA; has similarity to mammalian fibrillarin	[IVN]L.VD[ENA]	36	LEVD	Protease Caspase 4-stringent							0.004	8
protein_40_YCR009C	2	RVS161:  Amphiphysin-like lipid raft protein; subunit of a complex (Rvs161p-Rvs167p) that regulates polarization of the actin cytoskeleton, endocytosis, cell polarity, cell fusion and viability following starvation or osmotic stress	[EGM]A.[EVQ]Q	36									0.005	7
protein_40_YBR036C	2	CSG2:  Endoplasmic reticulum membrane protein, required for mannosylation of inositolphosphorylceramide and for growth at high calcium concentrations	II..[FTV][FYM]	36	D..SII.FF	CK I delta kinase phosphorylation site (peptide screen)							0.006	10
protein_40_YBR017C	2	KAP104:  Transportin, cytosolic karyopherin beta 2 involved in delivery of heterogeneous nuclear ribonucleoproteins to the nucleoplasm, binds rg-nuclear localization signals on Nab2p and Hrp1p, plays a role in cell-cycle progression	[EY]I..ES[KYM]	36									0.004	7
protein_40_YBL092W	2	RPL32:  Protein component of the large (60S) ribosomal subunit, has similarity to rat L32 ribosomal protein; overexpression disrupts telomeric silencing	RV.[RAD][RN]	36							cytosolic ribosome (sensu Eukaryota) (1e-08)		0.004	7
protein_40_YBL027W	2	RPL19B:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl19Ap and has similarity to rat L19 ribosomal protein; rpl19a and rpl19b single null mutations result in slow growth, while the double null mutation is lethal	[RGY]A.K[VGY]	36							cytosolic ribosome (sensu Eukaryota) (1e-19)		0.006	10
protein_40_YAL032C	2	PRP45:  Protein required for pre-mRNA splicing; associates with the spliceosome and interacts with splicing factors Prp22p and Prp46p; orthologous to human transcriptional coactivator SKIP and can activate transcription of a reporter gene	DP..[VNT][EPW]	36	DP[FW]	LIG_AP2alpha_2	Y				spliceosome (1e-04)	Y	0.006	10
protein_40_YAL032C	2	PRP45:  Protein required for pre-mRNA splicing; associates with the spliceosome and interacts with splicing factors Prp22p and Prp46p; orthologous to human transcriptional coactivator SKIP and can activate transcription of a reporter gene	I.[DQW]T	36							nuclear mRNA splicing, via spliceosome (1e-06)	Y	0.007	10
oshea_punctate_composite	2	oshea_punctate_composite	[LVD]TF[LFN]I	36									0.005	8
oshea_nuclear_periphery	2	oshea_nuclear_periphery	[STA]FT[KQA]	36							nuclear membrane part (1e-18)	Y	0.008	10
oshea_Golgi_or_Golgi_to_vacuole	2	oshea_Golgi_or_Golgi_to_vacuole	L..[EFQ]I	36	L...I...[IL]	Corepressor nuclear box motif binds to nuclear receptors					Golgi apparatus (1e-45)	Y	0.007	10
oshea_ER	2	oshea_ER	F[FLM].V[AVQ]	36							endoplasmic reticulum (1e-17)		0.007	10
oshea_cytoplasm	2	oshea_cytoplasm	K..S[SEA]	36	K..[ST]	PKA kinase substrate motif					regulation of cellular metabolism (1e-07)		0.007	10
oshea_cytoplasm	2	oshea_cytoplasm	L.P[NEQ]	36	P.L.P	motif for interaction with MYND domain of BS69					signal transduction (1e-04)		0.007	10
oshea_cell_periphery	2	oshea_cell_periphery	[GIM]G.I[ALT]	36							plasma membrane (1e-12)		0.007	10
oshea_bud	2	oshea_bud	R[ANK][SPV]S	36							site of polarized growth (1e-16)	Y	0.008	10
matsuyama_Spindle_or_SPB	2	matsuyama_Spindle_or_SPB	L[STE]P[SRW]K	36	[ST]P	LIG_WW_4					spindle (1e-10)		0.007	9
matsuyama_Cytosol	2	matsuyama_Cytosol	SK[HSD]	36	SKRKYRK	TP1 PATTERN					cell septum (1e-08)	Y	0.009	10
matsuyama_Cytoplasmic_dots	2	matsuyama_Cytoplasmic_dots	SS.[QLG][SQH]	36	S[ST]	MDC1 BRCT domain binding motif					cell septum (1e-13)		0.009	10
genetic_YPL055C	2	LGE1: Protein of unknown function; null mutant forms abnormally large cells, and homozygous diploid null mutant displays delayed premeiotic DNA synthesis and reduced efficiency of meiotic nuclear division	I[RL].LI[ECK]	36	R.L	Cyclin A motif that binds cdk2 complexes	Y						0.005	7
genetic_YNL153C	2	GIM3: Subunit of the heterohexameric cochaperone prefoldin complex which binds specifically to cytosolic chaperonin and transfers target proteins to it	S[EDQ]I	36	S[YILQP]II	BRCT domain of RAD9 binding motif, first Ser must be phosphorylated					cell cycle (1e-09)		0.007	10
genetic_YLR200W	2	YKE2: Subunit of the heterohexameric Gim/prefoldin protein complex involved in the folding of alpha-tubulin, beta-tubulin, and actin	[NSC]DF[SG]S	36	DF.DF	EF hand in gamma-synergin binding motif						Y	0.004	7
genetic_YLR200W	2	YKE2: Subunit of the heterohexameric Gim/prefoldin protein complex involved in the folding of alpha-tubulin, beta-tubulin, and actin	E..[NEG]N	36							cell cycle (1e-13)		0.006	10
genetic_YLR200W	2	YKE2: Subunit of the heterohexameric Gim/prefoldin protein complex involved in the folding of alpha-tubulin, beta-tubulin, and actin	S.[SLR]H	36	RSSLHL	Motif in beta-arrestin 2 for interaction with Jnk3					cell cycle (1e-14)	Y	0.007	10
genetic_YLR039C	2	RIC1: Protein involved in retrograde transport to the cis-Golgi network; forms heterodimer with Rgp1p that acts as a GTP exchange factor for Ypt6p; involved in transcription of rRNA and ribosomal protein genes	[VLN]T..L[EVY]	36	T..[IL]	FHA2 binding motif, Thr must be phosphorylated					vesicle-mediated transport (0.001)		0.007	10
genetic_YLR039C	2	RIC1: Protein involved in retrograde transport to the cis-Golgi network; forms heterodimer with Rgp1p that acts as a GTP exchange factor for Ypt6p; involved in transcription of rRNA and ribosomal protein genes	I..L[ITA]	36							endoplasmic reticulum (1e-10)	Y	0.006	10
genetic_YLR039C	2	RIC1: Protein involved in retrograde transport to the cis-Golgi network; forms heterodimer with Rgp1p that acts as a GTP exchange factor for Ypt6p; involved in transcription of rRNA and ribosomal protein genes	K.[LDG]E	36	G.[DN]F.K.DE	RUBISCO_LARGE PATTERN	Y				vesicle-mediated transport (1e-10)		0.007	10
genetic_YLR039C	2	RIC1: Protein involved in retrograde transport to the cis-Golgi network; forms heterodimer with Rgp1p that acts as a GTP exchange factor for Ypt6p; involved in transcription of rRNA and ribosomal protein genes	S.E[YGK]	36	LSQE	ATM kinase substrate motif					chromosome organization and biogenesis (sensu Eukaryota) (1e-05)		0.007	10
genetic_YEL003W	2	GIM4: Subunit of the heterohexameric cochaperone prefoldin complex which binds specifically to cytosolic chaperonin and transfers target proteins to it	K.L[EPG]	36	LLKIL	AP-2 binding motif in CXCR2 receptor					cytoskeleton organization and biogenesis (1e-07)		0.007	10
genetic_YEL003W	2	GIM4: Subunit of the heterohexameric cochaperone prefoldin complex which binds specifically to cytosolic chaperonin and transfers target proteins to it	T..[LKT]E	36	[ST]E	G protein-coupled receptor kinase 1 substrate motif					cytoskeleton (1e-06)	Y	0.006	10
genetic_YDL020C	2	RPN4: Transcription factor that stimulates expression of proteasome genes; Rpn4p levels are in turn regulated by the 26S proteasome in a negative feedback control mechanism; RPN4 is transcriptionally regulated by various stress responses	K[SGD]..[LKP]Q	36							chromosome organization and biogenesis (sensu Eukaryota) (1e-04)		0.006	10
ucsf_loc_k_means_G6	6	Sub-cellular localization, 6 clusters	Q.Q[QEL]	36			Y	 			nuclear lumen (1e-14)		0.022	10
protein_40_YBR160W	2	CDC28:  Catalytic subunit of the main cell cycle cyclin-dependent kinase (CDK); alternately associates with G1 cyclins (CLNs) and G2/M cyclins (CLBs) which direct the CDK to specific substrates	A[YPD]..[TDQ]G	36				Kinesin	1.E-03	1.9	cytoskeleton organization and biogenesis (0.001)		0.007	10
protein_40_YBR160W	2	CDC28:  Catalytic subunit of the main cell cycle cyclin-dependent kinase (CDK); alternately associates with G1 cyclins (CLNs) and G2/M cyclins (CLBs) which direct the CDK to specific substrates	K[LIQ].D[FAY]G	35				Pkinase	1.E-18	5	protein kinase activity (1e-17)		0.007	9
protein_40_YDR224C	2	HTB1:  One of two nearly identical (see HTB2) histone H2B subtypes required for chromatin assembly and chromosome function; Rad6p-Bre1p-Lge1p mediated ubiquitination regulates transcriptional activation, meiotic DSB formation and H3 methylation	G[GSR][KP]G	35	[ST]PG[ST]PGTP	CDK5 kinase substrate motif		Histone	1.E-05	-2.4	establishment and/or maintenance of chromatin architecture (1e-04)	Y	0.006	8
yeast-207_GO-0003677	2	DNA binding	Q[QIN]Q	35				zf-C2H2	1.E-07	-1.7	DNA binding (1e-09)		0.007	10
yeast-462_GO-0019222	2	regulation of metabolism	L.[SHN]L	35	L..L..L.L	Nuclear export signal		Zn_clus	1.E-07	-1.6	regulation of metabolism (10)	Y	0.007	10
protein_40_YMR125W	2	STO1:  Large subunit of the nuclear mRNA cap-binding protein complex, interacts with Npl3p to carry nuclear poly(A)+ mRNA to cytoplasm; also involved in nuclear mRNA degradation and telomere maintenance; orthologous to mammalian CBP80	[RTA]G..R[GY]	35				RRM_1	1.E-02	-1.6	RNA binding (1e-06)		0.006	9
protein_40_YKR001C	2	VPS1:  Dynamin-like GTPase required for vacuolar sorting; also involved in actin cytoskeleton organization, late Golgi-retention of some proteins, regulating peroxisome biogenesis	[DRH][PIF]..PK	35	P.[ST]PKK.KK	Cdc2 like protein kinase substrate motif		HMG_box	1.E-04	-1.6	chromatin remodeling (0.001)		0.005	10
yeast-631_GO-0050794	2	regulation of cellular process	H[TSD].E	35				zf-C2H2	1.E-11	-1.5	regulation of metabolism (1e-75)	Y	0.008	10
yeast-630_GO-0051244	2	regulation of cellular physiological process	H[TSD].E	35				zf-C2H2	1.E-11	-1.5	regulation of metabolism (1e-75)	Y	0.008	10
protein_40_YNL272C	2	SEC2:  Guanyl-nucleotide exchange factor for the small G-protein Sec4p, located on cytoplasmic vesicles; essential for post-Golgi vesicle transport	[SET]T..Q[NKR]	35				Pkinase	1.E-12	-1.4	protein serine/threonine kinase activity (1e-13)	Y	0.007	10
yeast-1115_GO-0006996	2	organelle organization and biogenesis	S.T[KIN]	35	RS.[ST].P	14-3-3 binding motif (Ser must be phosphorylated)(eta)		WD40	1.E-04	-1.3	chromosome organization and biogenesis (1e-92)	Y	0.007	10
protein_40_YCL059C	2	KRR1:  Essential nucleolar protein required for the synthesis of 18S rRNA and for the assembly of 40S ribosomal subunit	G[LIK]DI[PI]	35				DEAD	1.E-03	-1.2	nucleolus (1e-05)		0.004	7
protein_40_YPL043W	2	NOP4:  Nucleolar protein, essential for processing and maturation of 27S pre-rRNA and large ribosomal subunit biogenesis; constituent of 66S pre-ribosomal particles; contains four RNA recognition motifs (RRMs)	V[GWI]..[AHQ]R	35	[AG]R	Protease matriptase protease site		DEAD	1.E-02	-1.1	nucleolus (1e-05)		0.005	9
protein_40_YER102W	2	RPS8B:  Protein component of the small (40S) ribosomal subunit; identical to Rps8Ap and has similarity to rat S8 ribosomal protein	[ADT]A..LD[IQ]	35				DEAD	1.E-03	-1.1	nucleolus (0.01)		0.004	8
protein_40_YER102W	2	RPS8B:  Protein component of the small (40S) ribosomal subunit; identical to Rps8Ap and has similarity to rat S8 ribosomal protein	VAA[RTP][GK]	35				DEAD	1.E-03	-1.1	RNA helicase activity (0.01)		0.004	9
yeast-436_GO-0031323	2	regulation of cellular metabolism	H[TYV]G[ERV]K	35	G[KR][KR]	Amidation after cleavage after Gly (must be in secretory pathway)		zf-C2H2	1.E-12	-1	regulation of cellular metabolism (1e-08)		0.007	10
yeast-238_GO-0017111	2	nucleoside-triphosphatase activity	I[FDT].[ASL]T	35				Helicase_C	1.E-05	-1	nucleoside-triphosphatase activity (1e-58)	Y	0.008	10
protein_40_YNL002C	2	RLP7:  Nucleolar protein with similarity to large ribosomal subunit L7 proteins; constituent of 66S pre-ribosomal particles; plays an essential role in processing of precursors to the large ribosomal subunit RNAs	[ANV]R..[DEW]I	35	[AG]R	Protease matriptase protease site		DEAD	1.E-02	-1	ribosome biogenesis (1e-15)	Y	0.006	10
yeast-752_GO-0016787	2	hydrolase activity	V[LVR]D[EIL]	35				Helicase_C	1.E-04	-0.9	ATPase activity (1e-29)	Y	0.007	10
yeast-589_GO-0050896	2	response to stimulus	N.N[STP]	35				Pkinase	1.E-03	-0.9	response to stress (1e-12)		0.008	10
yeast-301_GO-0044451	2	nucleoplasm part	[KHQ]R.K[LER]	35	[KR]R	CLV_PCSK_KEX2_1		Bromodomain	1.E-02	-0.9	nucleoplasm part (1e-64)		0.007	10
yeast-388_GO-0007275	2	development	[QKS]E[LAK]E	35	[ST]E	G protein-coupled receptor kinase 1 substrate motif		SH3_1	1.E-02	-0.7	multicellular organismal development (1e-09)	Y	0.008	10
protein_40_YOL133W	2	HRT1:  RING finger containing subunit of Skp1-Cullin-F-box ubiquitin protein ligases (SCF); required for Gic2p, Far1p, Sic1p and Cln2p degradation; may tether Cdc34p (a ubiquitin conjugating enzyme or E2) and Cdc53p (a cullin) subunits of SCF	N.[GQF]E	35				F-box	1.E-05	-0.7	ubiquitin ligase complex (1e-05)	Y	0.006	10
protein_40_YML010W	2	SPT5:  Protein that forms a complex with Spt4p and mediates both activation and inhibition of transcription elongation; Spt4p-Spt5p complex also plays a role in pre-mRNA processing	R.K[DEA]	35	[KR][LIM]K[DE]K[LIM]PG	DEHYDRIN_2 PATTERN	Y	DEAD	1.E-04	-0.7	nuclear lumen (1e-19)		0.006	10
yeast-661_GO-0050789	2	regulation of biological process	[RSV]P..[LKE]K	35	[ST]P	LIG_WW_4	Y	GATA	1.E-02	-0.6	regulation of metabolism (1e-43)		0.008	9
protein_40_YOL133W	2	HRT1:  RING finger containing subunit of Skp1-Cullin-F-box ubiquitin protein ligases (SCF); required for Gic2p, Far1p, Sic1p and Cln2p degradation; may tether Cdc34p (a ubiquitin conjugating enzyme or E2) and Cdc53p (a cullin) subunits of SCF	L[LKS]..[VPQ]D	35			Y	F-box	1.E-03	-0.6	cullin-RING ubiquitin ligase complex (1e-06)		0.007	10
protein_40_YOL133W	2	HRT1:  RING finger containing subunit of Skp1-Cullin-F-box ubiquitin protein ligases (SCF); required for Gic2p, Far1p, Sic1p and Cln2p degradation; may tether Cdc34p (a ubiquitin conjugating enzyme or E2) and Cdc53p (a cullin) subunits of SCF	[NST]G[KAI]L	35	G[SA]LNK	GDP-mannose binding motif in transporter		F-box	1.E-02	-0.5	macromolecule catabolism (1e-04)	Y	0.007	10
protein_40_YLR293C	2	GSP1:  GTP binding protein (mammalian Ranp homolog) involved in the maintenance of nuclear organization, RNA processing and transport; regulated by Prp20p, Rna1p, Yrb1p, Yrb2p, Yrp4p, Yrb30p, Cse1p and Kap95p; yeast Gsp2p homolog	I[RQ][LFK]T	35				IBN_N	1.E-03	-0.5	protein carrier activity (1e-05)		0.005	8
yeast-235_GO-0000278	2	mitotic cell cycle	L.Q[DSH]	35				HEAT	1.E-02	-0.4	mitotic cell cycle (1e-13)	Y	0.008	10
protein_40_YGL207W	2	SPT16:  Subunit of the heterodimeric FACT complex (Spt16p-Pob3p), facilitates RNA Polymerase II transcription elongation through nucleosomes by destabilizing and then reassembling nucleosome structure	[SPG]K.P[ATP]	35	P[ST]	DNA dependent Protein kinase substrate motif		Pkinase	1.E-06	-0.4	protein kinase activity (1e-05)		0.007	9
yeast-752_GO-0016787	2	hydrolase activity	S..V[DNE]	35				Helicase_C	1.E-05	-0.3	pyrophosphatase activity (1e-65)		0.007	10
protein_40_YER082C	2	UTP7:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	DL[EKV]	35	WDL	Binding motif for AP-2 and clathrin heavy chain ear		WD40	1.E-04	-0.2	small nucleolar ribonucleoprotein complex (1e-28)		0.007	10
protein_40_YMR117C	2	SPC24:  Component of the evolutionarily conserved kinetochore-associated Ndc80 complex (Ndc80p-Nuf2p-Spc24p-Spc25p); involved in chromosome segregation, spindle checkpoint activity and kinetochore clustering	L..Q[RVE]	35			Y	SMC_N	1.E-02	0.1	chromosome segregation (1e-04)		0.006	10
protein_40_YLR197W	2	SIK1:  Essential evolutionarily-conserved nucleolar protein component of the box C/D snoRNP complexes that direct 2'-O-methylation of pre-rRNA during its maturation; overexpression causes spindle orientation defects	D..[ESR]D	35	DDDD..S	Casein kinase 1 phosphorylation motif		WD40	1.E-03	0.1	nucleolus (1e-33)		0.006	10
protein_40_YJL074C	2	SMC3:  Subunit of the multiprotein cohesin complex required for sister chromatid cohesion in mitotic cells; also required, with Rec8p, for cohesion and recombination during meiosis; phylogenetically conserved SMC chromosomal ATPase family member	K[TEV].A[VKL]	35	KTPAKEE	GSK-3, ERK1, ERK2, CDK5 substrate motif		SMC_N	1.E-03	0.2	cohesin complex (0.01)	Y	0.007	10
protein_40_YML069W	2	POB3:  Subunit of the heterodimeric FACT complex (Spt16p-Pob3p), which facilitates RNA Pol II transcription elongation through nucleosomes by destabilizing and then reassembling nucleosome structure; interacts with DNA polymerase alpha (Pol1p)	[LP][AE]..AAR	35	[AG]R	Protease matriptase protease site		Histone	1.E-04	0.4	nuclear chromatin (1e-04)		0.004	9
yeast-240_GO-0006807	2	nitrogen compound metabolism	VD.[LTK][YMF]	35	HAVDI	N-Cadherin ligand		Cys_Met_Meta_PP	1.E-02	0.5	amine metabolism (1e-43)	Y	0.008	10
yeast-980_GO-0051179	2	localization	VL[LRP]	35	LRT	LKB1 Kinase substrate motif		MFS_1	1.E-05	0.6	cellular localization (1e-11)		0.007	10
yeast-649_GO-0003676	2	nucleic acid binding	L[NPR]K	35	G[SA]LNK	GDP-mannose binding motif in transporter		RRM_1	1.E-06	0.6	nucleic acid binding (1e-28)		0.008	10
protein_40_YNL272C	2	SEC2:  Guanyl-nucleotide exchange factor for the small G-protein Sec4p, located on cytoplasmic vesicles; essential for post-Golgi vesicle transport	EI..[QAD][TIC]	35				Pkinase	1.E-07	0.6	protein kinase activity (1e-07)	Y	0.006	9
protein_40_YLR340W	2	RPP0:  Conserved ribosomal protein P0 similar to rat P0, human P0, and E. coli L10e; shown to be phosphorylated on serine 302	KE..[AVD]A[LED]	35	KEN	LIG_APCC_KENbox_2	Y	Ribosomal_60s	1.E-02	0.6			0.004	8
protein_40_YIL019W	2	FAF1:  Protein required for pre-rRNA processing and 40S ribosomal subunit assembly	K[LKP]L[AKP]	35	KKKLPATGDYMNMSPVGD	Insulin receptor kinase substrate motif		WD40	1.E-02	0.6	small nucleolar ribonucleoprotein complex (1e-27)		0.007	10
oshea_bud_neck	2	oshea_bud_neck	I.[IRD]D	35				PH	1.E-03	0.6	site of polarized growth (1e-49)	Y	0.007	10
yeast-470_GO-0006259	2	DNA metabolism	I..[LVI]K	35			Y	BRCT	1.E-03	0.7	DNA metabolism (1e-24)	Y	0.007	10
yeast-251_GO-0005886	2	plasma membrane	V..[CIL]V	35			Y	MFS_1	1.E-03	0.7	plasma membrane (1e-11)		0.008	10
protein_40_YKL065C	2	YET1:  Endoplasmic reticulum transmembrane protein; may interact with ribosomes, based on co-purification experiments; homolog of human BAP31 protein	F[AGF]..L	35	[FW]..L[FWY]	Regulatory motif in androgen receptors		Sugar_tr	1.E-03	0.9	endoplasmic reticulum (1e-06)		0.007	10
oshea_bud_neck	2	oshea_bud_neck	P..R[FYW]	35	P.[PA]..R	SH3 binding for binding CIN85/SETA/Ruk SH3 domains (nonconventional)		PH	1.E-03	0.9	site of polarized growth (1e-27)	Y	0.007	10
yeast-248_GO-0016072	2	rRNA metabolism	K.[LKA]A	35				DEAD	1.E-07	1	rRNA metabolism (1e-13)	Y	0.007	10
yeast-215_GO-0005694	2	chromosome	L..E[ILMV]	35			Y	Histone	1.E-07	1	chromosome (1e-20)		0.008	10
yeast-1721_GO-0016043	2	cell organization and biogenesis	T..[LEV]D	35	T..[IL]	FHA2 binding motif, Thr must be phosphorylated		WD40	1.E-04	1	cellular localization (1e-43)		0.007	10
protein_40_YPL153C	2	RAD53:  Protein kinase, required for cell-cycle arrest in response to DNA damage; activated by trans autophosphorylation when interacting with hyperphosphorylated Rad9p; also interacts with ARS1 and plays a role in initiation of DNA replication	G[NFI]G	35	G.G..G	Phosphate, FAD, NADH, binding motif		Septin	1.E-02	1	DNA integrity checkpoint (0.001)	Y	0.006	10
protein_40_YOL012C	2	HTZ1:  Histone variant H2AZ, exchanged for histone H2A in nucleosomes by the SWR1 complex; involved in transcriptional regulation through prevention of the spread of silent heterochromatin	I[TE].P[AG]I	35				Histone	1.E-02	1	nuclear chromatin (0.01)		0.004	9
oshea_bud_neck	2	oshea_bud_neck	R.L[EKT]	35	R.L	Cyclin A motif that binds cdk2 complexes		RhoGAP	1.E-04	1	site of polarized growth (1e-59)	Y	0.007	10
yeast-251_GO-0005886	2	plasma membrane	G..C	35				Sugar_tr	1.E-06	1.1	plasma membrane (1e-11)	Y	0.008	10
protein_40_YER012W	2	PRE1:  Beta 4 subunit of the 20S proteasome; localizes to the nucleus throughout the cell cycle	LY..[NEA][PDL]	35			Y	Proteasome	1.E-06	1.2	proteasome complex (sensu Eukaryota) (1e-10)		0.007	10
protein_40_YKR001C	2	VPS1:  Dynamin-like GTPase required for vacuolar sorting; also involved in actin cytoskeleton organization, late Golgi-retention of some proteins, regulating peroxisome biogenesis	IY[KP][VN]L	35	IY	cFGR and Csk kinase phosphorylation site (peptide screen)		Histone	1.E-02	1.3			0.004	9
matsuyama_nuclear_envelope_or_dots	2	matsuyama_nuclear_envelope_or_dots	N..P	35			Y	IBN_N	1.E-05	1.3	nuclear envelope (1e-47)	Y	0.009	10
protein_40_YAR019C	2	CDC15:  Protein kinase of the Mitotic Exit Network that is localized to the spindle pole bodies at late anaphase; promotes mitotic exit by directly switching on the kinase activity of Dbf2p	R..[KPR]P	35	R..RPLPPLP.P	SH3 binding motif for Lyn		Pkinase	1.E-22	1.5	protein kinase activity (1e-17)	Y	0.007	10
yeast-593_GO-0031981	2	nuclear lumen	A.[RGK]R	35	[KR]R	CLV_PCSK_KEX2_1		Helicase_C	1.E-04	1.6	nuclear lumen (1e-15)	Y	0.007	10
protein_40_YDL153C	2	SAS10:  Component of the small (ribosomal) subunit (SSU) processosome required for pre-18S rRNa processing; essential nucleolar protein that, when overproduced, disrupts silencing	KP...[LPF]	35	KP..[QK]	LIG_SH3_4	Y	Pkinase	1.E-25	1.6	protein kinase activity (1e-23)		0.006	10
yeast-565_GO-0006464	2	protein modification	L.[HIM]L	35	L..L..L.L	Nuclear export signal		Pkinase	1.E-11	1.7	protein modification (1e-24)		0.008	10
protein_40_YER148W	2	SPT15:  TATA-binding protein, general transcription factor that interacts with other factors to form the preinitiation complex at promoters, essential for viability	K[RVA][LTV]K	35	KR	CLV_PCSK_PC1ET2_1		Bromodomain	1.E-04	1.7	nuclear lumen (1e-11)		0.007	10
yeast-1036_GO-0005739	2	mitochondrion	[KPG]TR[LIC]Q	35				Mito_carr	1.E-18	2	mitochondrial envelope (1e-09)		0.008	10
yeast-281_GO-0016788	2	hydrolase activity, acting on ester bonds	[GK]NHE	35	[LIVMN][KR]GNHE	SER_THR_PHOSPHATASE PATTERN		Metallophos	1.E-07	2.2	hydrolase activity, acting on ester bonds (1e-12)	Y	0.006	9
protein_40_YJR002W	2	MPP10:  Component of the SSU processome, which is required for pre-18S rRNA processing, interacts with and controls the stability of Imp3p and Imp4p, essential for viability; similar to human Mpp10p	D[KGF].V[KRT]	35			Y	WD40	1.E-05	2.3	snoRNA binding (1e-20)		0.007	10
yeast-630_GO-0051244	2	regulation of cellular physiological process	H..[INT]I	35			Y	Cyclin	1.E-02	2.4	regulation of cellular metabolism (1e-57)		0.008	10
protein_40_YPL126W	2	NAN1:  U3 snoRNP protein, component of the small (ribosomal) subunit (SSU) processosome containing U3 snoRNA; required for the biogenesis of18S rRNA	D[GKS].[VDT]K	35				WD40	1.E-08	2.4	small nucleolar ribonucleoprotein complex (1e-22)	Y	0.007	10
yeast-631_GO-0050794	2	regulation of cellular process	H..[INT]I	35			Y	Cyclin	1.E-02	2.5	regulation of cellular metabolism (1e-57)		0.008	10
protein_40_YJR145C	2	RPS4A:  Protein component of the small (40S) ribosomal subunit; mutation affects 20S pre-rRNA processing; identical to Rps4Bp and has similarity to rat S4 ribosomal protein	R..[AKR]A	35	R..K	SH3 binding motif for GADS SH3 recognizing slp-76 motif (nonconventional)		Helicase_C	1.E-03	2.9	ribonucleoprotein complex (1e-18)	Y	0.007	10
protein_40_YLL008W	2	DRS1:  Nucleolar DEAD-box protein required for ribosome assembly and function, including synthesis of 60S ribosomal subunits; constituent of 66S pre-ribosomal particles	[TIS]DF[GRY]	35	DF.DF	EF hand in gamma-synergin binding motif		Pkinase	1.E-11	3.2	protein kinase activity (1e-10)	Y	0.006	10
protein_40_YNL002C	2	RLP7:  Nucleolar protein with similarity to large ribosomal subunit L7 proteins; constituent of 66S pre-ribosomal particles; plays an essential role in processing of precursors to the large ribosomal subunit RNAs	R[EK][LIE]A	35	MR[DE][IL]	TUBULIN_B_AUTOREG PATTERN		DEAD	1.E-03	3.3	cytoplasm organization and biogenesis (1e-19)		0.007	10
yeast-335_GO-0016772	2	transferase activity, transferring phosphorus-containing groups	VY[LKY][PAV]	35	Y[LI]	SH2 ligand for PLCgamma1 N-term.)group 3(phospho-peptide)		Pkinase	1.E-14	3.4	transferase activity, transferring phosphorus-containing groups (1e-32)	Y	0.007	10
yeast-244_GO-0000279	2	M phase	L[SLN]Q	35	LSQE	ATM kinase substrate motif		MutS_III	1.E-05	3.5	M phase (1e-18)		0.008	9
protein_40_YGL111W	2	NSA1:  Constituent of 66S pre-ribosomal particles, involved in 60S ribosomal subunit biogenesis	L[FM]SA	35	WLNS	Lipid binding motif in C-terminus of Apolipoprotein AII		DEAD	1.E-05	3.5	nucleolus (1e-07)	Y	0.004	8
protein_40_YDR060W	2	MAK21:  Constituent of 66S pre-ribosomal particles, required for large (60S) ribosomal subunit biogenesis; involved in nuclear export of pre-ribosomes; required for maintenance of dsRNA virus; homolog of human CAATT-binding protein	[REW]E[LDY]A	35	EDAIY	Abl kinase substrate motif		DEAD	1.E-07	3.5	cytoplasm organization and biogenesis (1e-17)	Y	0.007	9
yeast-299_GO-0005730	2	nucleolus	[PTG][TSD]REL	35	RE..E	Iron binding motif in ferritin L-chain and yeast Iron transport protein		DEAD	1.E-13	3.8	ATP-dependent RNA helicase activity (1e-15)		0.006	10
Oshea_mcl	13	Oshea_mcl	K[KPR].K	35	K[KR].[KR]	Nuclear localization motif		Zn_clus	1.E-07	4.1	nuclear lumen (1e-52)		0.035	10
yeast-335_GO-0016772	2	transferase activity, transferring phosphorus-containing groups	I..[RQI]D	35				Pkinase	1.E-47	4.9	transferase activity, transferring phosphorus-containing groups (1e-12)	Y	0.007	10
yeast-565_GO-0006464	2	protein modification	[KNA]PE[NVR]	35				Pkinase	1.E-26	5.5	protein modification (1e-51)	Y	0.007	9
yeast-706_GO-0043412	2	biopolymer modification	D[LIK]KP	35	FKPY	TLA binding motif in Brinker transcription factor for binding TLA domain in Groucho		Pkinase	1.E-39	5.6	protein amino acid phosphorylation (1e-47)		0.008	10
yeast-238_GO-0017111	2	nucleoside-triphosphatase activity	[RTI]V.[RLQ]T	35				Helicase_C	1.E-11	5.8	nucleoside-triphosphatase activity (1e-43)		0.008	10
yeast-1547_GO-0043283	2	biopolymer metabolism	[IVD]H[RPN]D	35			Y	Pkinase	1.E-24	6	protein amino acid phosphorylation (1e-29)		0.007	10
yeast-207_GO-0003677	2	DNA binding	C..C[RGL]	35	C..C	Motif on TIM mitochondrial translocation proteins	Y	Zn_clus	1.E-15	13.8	DNA binding (1e-59)		0.008	10
yeast-460_GO-0006351	2	transcription, DNA-dependent	[AMH]C..C[RIP]	35	C..C	Motif on TIM mitochondrial translocation proteins	Y	Zn_clus	1.E-19	16.9	transcription, DNA-dependent (1e-21)		0.008	10
yeast-856_GO-0009059	2	macromolecule biosynthesis	A[ATG].K[AKT]	35							macromolecule biosynthetic process (1e-77)		0.008	10
yeast-752_GO-0016787	2	hydrolase activity	D[AEH]..[FCR]F	35							hydrolase activity, acting on ester bonds (1e-07)		0.007	10
yeast-661_GO-0050789	2	regulation of biological process	E[IGD]..T[FNH]	35							regulation of metabolism (1e-28)	Y	0.007	10
yeast-648_GO-0050791	2	regulation of physiological process	E[IGD]..T[FNH]	35							regulation of metabolism (1e-29)	Y	0.007	10
yeast-648_GO-0050791	2	regulation of physiological process	E[VKN]L[LEV]	35							regulation of metabolism (1e-72)		0.008	10
yeast-544_GO-0016070	2	RNA metabolism	[GKF]KVS[SY]	35	S[ST]	MDC1 BRCT domain binding motif					RNA metabolism (1e-09)		0.007	10
yeast-462_GO-0019222	2	regulation of metabolism	[DNP]AT[NLQ]	35							regulation of metabolism (1e-56)		0.008	10
yeast-388_GO-0007275	2	development	E[NMD].I[ENC]	35							multicellular organismal development (1e-57)		0.007	10
yeast-341_GO-0045449	2	regulation of transcription	[SLG]S.R[LPQ]E	35	S.R	PKC phosphorylation motif					regulation of transcription (1e-14)		0.008	10
yeast-322_GO-0005654	2	nucleoplasm	[LVA]ENN[DMG]	35	KEN	LIG_APCC_KENbox_2					nucleoplasm part (1e-11)		0.007	9
yeast-248_GO-0016072	2	rRNA metabolism	R[KAE]..Q[KW]	35							rRNA processing (1e-28)		0.008	10
yeast-244_GO-0000279	2	M phase	[LEN]D.D[LVM]K	35	D.D	Ribose moiety of UDP and manganese binding site in glucuronyl transferase					M phase (1e-15)		0.007	9
yeast-244_GO-0000279	2	M phase	S[PQI].S[KMR]	35	SQ	ATM kinase substrate motif					M phase (1e-66)		0.008	10
yeast-235_GO-0000278	2	mitotic cell cycle	SP.[NRH][DSK]	35	SP	ERK1, ERK2 Kinase substrate motif					mitotic cell cycle (1e-51)	Y	0.007	10
yeast-233_GO-0006629	2	lipid metabolism	[AHF]F[IAC]Y	35	F[MLVI]Y	PTPRJ phosphatase substrate motif					lipid metabolism (1e-22)		0.008	9
yeast-223_GO-0003735	2	structural constituent of ribosome	LK[KDN]	35	F.F.LK...K.R	Phosphatidylserine binding motif in PKC							0.007	10
yeast-216_GO-0006325	2	establishment and/or maintenance of chromatin architecture	[AIF]I.Q[EG]L	35							establishment and/or maintenance of chromatin architecture (1e-10)		0.006	9
yeast-216_GO-0006323	2	DNA packaging	[AIF]I.Q[EG]L	35							establishment and/or maintenance of chromatin architecture (1e-10)		0.006	9
yeast-215_GO-0005694	2	chromosome	EL.K[LQI][LQG]	35	LLKIL	AP-2 binding motif in CXCR2 receptor					chromosome (1e-26)		0.008	10
yeast-207_GO-0006974	2	response to DNA damage stimulus	R[IRV].[STM]R	35	[KR].R..[ST]	p70s6k phosphorylation site					response to DNA damage stimulus (1e-41)	Y	0.008	10
yeast-1547_GO-0043283	2	biopolymer metabolism	[YND]G..E[EIS]	35	Q[MLVI]DG..[DE]	CLV_TASPASE1					DNA metabolism (1e-16)		0.007	10
protein_40_YPR182W	2	SMX3:  Core Sm protein Sm F; part of heteroheptameric complex (with Smb1p, Smd1p, Smd2p, Smd3p, Sme1p, and Smx2p) that is part of the spliceosomal U1, U2, U4, and U5 snRNPs; homolog of human Sm F	[TF][ST].MDL	35							U2-dependent spliceosome (1e-04)		0.004	7
protein_40_YPR161C	2	SGV1:  Cyclin (Bur2p)-dependent protein kinase that functions in transcriptional regulation; phosphorylates the carboxy-terminal domain of Rpo21p, which is the largest subunit of RNA polymerase II; regulated by Cak1p	E[EIY][AER]E	35	EEEEYFELV	EGFR kinase substrate motif					nucleolus (1e-10)		0.007	10
protein_40_YPR120C	2	CLB5:  B-type cyclin involved in DNA replication during S phase; activates Cdc28p to promote initiation of DNA synthesis; functions in formation of mitotic spindles along with Clb3p and Clb4p; most abundant during late G1 phase	S[SKP]K[SKI]	35	S[ST]	MDC1 BRCT domain binding motif							0.007	10
protein_40_YPR119W	2	CLB2:  B-type cyclin involved in cell cycle progression; activates Cdc28p to promote the transition from G2 to M phase; accumulates during G2 and M, then targeted via a destruction box motif for ubiquitin-mediated degradation by the proteasome	EY[LHI][EKQ]D	35	Y[LI]	SH2 ligand for PLCgamma1 N-term.)group 3(phospho-peptide)	Y						0.004	9
protein_40_YPR080W	2	TEF1:  Translational elongation factor EF-1 alpha; also encoded by TEF2; functions in the binding reaction of aminoacyl-tRNA (AA-tRNA) to ribosomes	R[DTV]A[IPC]	35	GR.A	Protease tPA proteolytic site	Y						0.006	9
protein_40_YPR034W	2	ARP7:  Component of both the SWI/SNF and RSC chromatin remodeling complexes; actin-related protein involved in transcriptional regulation	[AYH]Q.Q[LFA]	35			Y				chromatin remodeling complex (1e-08)		0.004	8
protein_40_YPR034W	2	ARP7:  Component of both the SWI/SNF and RSC chromatin remodeling complexes; actin-related protein involved in transcriptional regulation	E[NAI]M[NLG]	35							chromatin remodeling complex (0.001)		0.005	9
protein_40_YPL240C	2	HSP82:  Hsp90 chaperone required for pheromone signaling and negative regulation of Hsf1p; docks with Tom70p for mitochondrial preprotein delivery; promotes telomerase DNA binding and nucleotide addition; interacts with Cns1p, Cpr6p, Cpr7p, Sti1p	[PKM]T.[DAY]E	35	YE	TPK-IIB/P38Syk kinase phosphorylation site (peptide screen)							0.006	10
protein_40_YPL204W	2	HRR25:  Protein kinase involved in regulating diverse events including vesicular trafficking, DNA repair, and chromosome segregation; binds the CTD of RNA pol II; homolog of mammalian casein kinase 1delta (CK1delta)	[QAR][LGQ]LDI	35	GTALL	Receptor recycling motif							0.004	9
protein_40_YPL203W	2	TPK2:  cAMP-dependent protein kinase catalytic subunit; promotes vegetative growth in response to nutrients via the Ras-cAMP signaling pathway; inhibited by regulatory subunit Bcy1p in the absence of cAMP; partially redundant with Tpk1p and Tpk3p	[SNA]Q.[EQD]S	35	[ST]Q	ATM kinase phosphorylation site							0.006	10
protein_40_YPL146C	2	NOP53:  Nucleolar protein; involved in biogenesis of the 60S subunit of the ribosome; interacts with rRNA processing factors Cbf5p and Nop2p; null mutant is viable but growth is severely impaired	S[PV]F[LM]D	35	SP	ERK1, ERK2 Kinase substrate motif						Y	0.004	9
protein_40_YPL043W	2	NOP4:  Nucleolar protein, essential for processing and maturation of 27S pre-rRNA and large ribosomal subunit biogenesis; constituent of 66S pre-ribosomal particles; contains four RNA recognition motifs (RRMs)	[TSK]E..E[DEF]	35	[ST]E	G protein-coupled receptor kinase 1 substrate motif					cytoplasm organization and biogenesis (1e-21)		0.007	10
protein_40_YPL031C	2	PHO85:  Cyclin-dependent kinase, with ten cyclin partners; involved in regulating the cellular response to nutrient levels and environmental conditions and progression through the cell cycle	F[KNH].[EC]D	35									0.005	9
protein_40_YOR326W	2	MYO2:  One of two type V myosin motors (along with MYO4) involved in actin-based transport of cargos; required for the polarized delivery of secretory vesicles, the vacuole, late Golgi elements, peroxisomes, and the mitotic spindle	D[IAE][ENF]V	35	SEDEE	CKII kinase phosphorylation site (peptide screen)						Y	0.007	10
protein_40_YOR310C	2	NOP58:  Protein involved in pre-rRNA processing, 18S rRNA synthesis, and snoRNA synthesis; component of the small subunit processome complex, which is required for processing of pre-18S rRNA	S[NGP]..L[KQP]I	35	LLKIL	AP-2 binding motif in CXCR2 receptor					snoRNA binding (1e-07)		0.004	8
protein_40_YOR294W	2	RRS1:  Essential protein that binds ribosomal protein L11 and is required for nuclear export of the 60S pre-ribosomal subunit during ribosome biogenesis; mouse homolog shows altered expression in Huntington's disease model mice	[SEA]K..[KTY]K	35	K..[ST]	PKA kinase substrate motif	Y				nucleolus (1e-12)		0.007	10
protein_40_YOL127W	2	RPL25:  Primary rRNA-binding ribosomal protein component of the large (60S) ribosomal subunit, has similarity to E. coli L23 and rat L23a ribosomal proteins; binds to 26S rRNA via a conserved C-terminal motif	RA.[KRA][VAE]	35							cytosolic ribosome (sensu Eukaryota) (1e-12)		0.007	10
protein_40_YOL120C	2	RPL18A:  Protein component of the large (60S) ribosomal subunit, identical to Rpl18Bp and has similarity to rat L18 ribosomal protein; intron of RPL18A pre-mRNA forms stem-loop structures that are a target for Rnt1p cleavage leading to degradation	R..A[GRF]	35			Y				cytosolic large ribosomal subunit (sensu Eukaryota) (1e-10)		0.007	10
protein_40_YOL013C	2	HRD1:  Ubiquitin-protein ligase required for endoplasmic reticulum-associated degradation (ERAD) of misfolded proteins; genetically linked to the unfolded protein response (UPR); regulated through association with Hrd3p; contains an H2 ring finger	E.A[EVW]	35							amino acid and derivative metabolism (0.01)		0.007	10
protein_40_YOL013C	2	HRD1:  Ubiquitin-protein ligase required for endoplasmic reticulum-associated degradation (ERAD) of misfolded proteins; genetically linked to the unfolded protein response (UPR); regulated through association with Hrd3p; contains an H2 ring finger	LL[LWD][YV]L	35	LLDLL	Clathrin binding motif in AP1							0.004	8
protein_40_YNL301C	2	RPL18B:  Protein component of the large (60S) ribosomal subunit, identical to Rpl18Ap and has similarity to rat L18 ribosomal protein	AR..[AR]	35	AR..R[RK]RSFRR	PKC eta kinase substrate motif					cytosolic ribosome (sensu Eukaryota) (1e-30)	Y	0.007	10
protein_40_YNL289W	2	PCL1:  Pho85 cyclin of the Pcl1,2-like subfamily, involved in entry into the mitotic cell cycle and regulation of morphogenesis, localizes to sites of polarized cell growth	E[NLP][ESA]N	35								Y	0.006	10
protein_40_YNL209W	2	SSB2:  Cytoplasmic ATPase that is a ribosome-associated molecular chaperone, functions with J-protein partner Zuo1p; may be involved in the folding of newly-synthesized polypeptide chains; member of the HSP70 family; homolog of SSB1	[SNL][SE].FGS	35	LFG	Protease Papain substrate, a prototype cysteine proteinase							0.004	8
protein_40_YNL178W	2	RPS3:  Protein component of the small (40S) ribosomal subunit, has apurinic/apyrimidinic (AP) endonuclease activity; essential for viability; has similarity to E. coli S3 and rat S3 ribosomal proteins	R[VAT].[GRQ]G	35							cytosolic ribosome (sensu Eukaryota) (1e-17)		0.007	9
protein_40_YNL124W	2	NAF1:  Protein required for the assembly of box H/ACA snoRNPs and for pre-rRNA processing, forms a complex with Shq1p and interacts with H/ACA snoRNP components Nhp2p and Cbf5p; has similarity to Gar1p and other RNA-binding proteins	[GQP]G.[RMT]G	35	GGRGG	Arginine methyl transferease substrate motif (PRMT1)					ribonucleoprotein complex (1e-07)		0.006	10
protein_40_YNL118C	2	DCP2:  Catalytic subunit of the Dcp1p-Dcp2p decapping enzyme complex, which removes the 5' cap structure from mRNAs prior to their degradation; member of the Nudix hydrolase family	DI..[LR][EHW]	35								Y	0.005	8
protein_40_YNL031C	2	HHT2:  One of two identical histone H3 proteins (see also HHT1); core histone required for chromatin assembly, involved in heterochromatin-mediated telomeric and HM silencing; regulated by acetylation, methylation, and mitotic phosphorylation	[NPE]P..E[LIP]	35							chromatin modification (1e-05)		0.006	10
protein_40_YMR216C	2	SKY1:  SR protein kinase (SRPK) involved in regulating proteins involved in mRNA metabolism and cation homeostasis; similar to human SRPK1	[RGF]R.[GWA]R	35	[AG]R	Protease matriptase protease site					ATP-dependent helicase activity (0.001)		0.005	9
protein_40_YMR125W	2	STO1:  Large subunit of the nuclear mRNA cap-binding protein complex, interacts with Npl3p to carry nuclear poly(A)+ mRNA to cytoplasm; also involved in nuclear mRNA degradation and telomere maintenance; orthologous to mammalian CBP80	AD.[KWY][RWM]	35									0.004	7
protein_40_YMR093W	2	UTP15:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	[IKF]E..[EIL]G	35							rRNA processing (1e-20)		0.007	10
protein_40_YML085C	2	TUB1:  Alpha-tubulin; associates with beta-tubulin (Tub2p) to form tubulin dimer, which polymerizes to form microtubules	I[KTV]..G[VMN]	35								Y	0.007	10
protein_40_YML073C	2	RPL6A:  N-terminally acetylated protein component of the large (60S) ribosomal subunit, has similarity to Rpl6Bp and to rat L6 ribosomal protein; binds to 5.8S rRNA	RA[AGP][RKS]	35							cytosolic ribosome (sensu Eukaryota) (1e-17)	Y	0.007	10
protein_40_YML069W	2	POB3:  Subunit of the heterodimeric FACT complex (Spt16p-Pob3p), which facilitates RNA Pol II transcription elongation through nucleosomes by destabilizing and then reassembling nucleosome structure; interacts with DNA polymerase alpha (Pol1p)	D[EYH]..D[ECN]	35	D..D...D	Protein phosphatase 1 binding motif	Y				RNA elongation from RNA polymerase II promoter (1e-18)		0.007	10
protein_40_YML049C	2	RSE1:  Protein involved in pre-mRNA splicing; component of the pre-spliceosome; associates with U2 snRNA; involved in ER to Golgi transport	[YWV]D..[IQW]K	35							RNA splicing (1e-15)		0.006	9
protein_40_YML010W	2	SPT5:  Protein that forms a complex with Spt4p and mediates both activation and inhibition of transcription elongation; Spt4p-Spt5p complex also plays a role in pre-mRNA processing	[LEV]L..K[LHP]	35							nuclear lumen (1e-05)	Y	0.007	10
protein_40_YLR448W	2	RPL6B:  Protein component of the large (60S) ribosomal subunit, has similarity to Rpl6Ap and to rat L6 ribosomal protein; binds to 5.8S rRNA	K..[AKW]A	35							cytosolic ribosome (sensu Eukaryota) (1e-32)	Y	0.006	10
protein_40_YLR432W	2	IMD3:  Inosine monophosphate dehydrogenase, catalyzes the first step of GMP biosynthesis, member of a four-gene family in S. cerevisiae, constitutively expressed	K[KPD][RQS]K	35			Y				rRNA metabolism (0.01)		0.006	10
protein_40_YLR432W	2	IMD3:  Inosine monophosphate dehydrogenase, catalyzes the first step of GMP biosynthesis, member of a four-gene family in S. cerevisiae, constitutively expressed	NL[NA][ETR]E	35	[ST]E	G protein-coupled receptor kinase 1 substrate motif							0.004	7
protein_40_YLR372W	2	SUR4:  Elongase, involved in fatty acid and sphingolipid biosynthesis; synthesizes very long chain 20-26-carbon fatty acids from C18-CoA primers; involved in regulation of sphingolipid biosynthesis	[IF]TL[IMC]	35	T[LF]CGT	PDK1 phosphorylation site on AGC kinase activation loop					endoplasmic reticulum (0.001)		0.006	10
protein_40_YLR197W	2	SIK1:  Essential evolutionarily-conserved nucleolar protein component of the box C/D snoRNP complexes that direct 2'-O-methylation of pre-rRNA during its maturation; overexpression causes spindle orientation defects	[KSD]T.LL[NAK]	35	DLL	Binding motif for clathrin heavy chain ear					nucleolus (0.001)		0.005	8
protein_40_YLR180W	2	SAM1:  S-adenosylmethionine synthetase, catalyzes transfer of the adenosyl group of ATP to the sulfur atom of methionine; one of two differentially regulated isozymes (Sam1p and Sam2p)	[PV]L..[EAQ]L	35	L..LL	Motif for interaction with nuclear receptors, docking motif for p300 on p53 to promote acetylation					carboxylic acid metabolism (0.001)		0.007	10
protein_40_YLR180W	2	SAM1:  S-adenosylmethionine synthetase, catalyzes transfer of the adenosyl group of ATP to the sulfur atom of methionine; one of two differentially regulated isozymes (Sam1p and Sam2p)	G..T[IEN]	35							carboxylic acid metabolism (1e-04)	Y	0.007	9
protein_40_YLR180W	2	SAM1:  S-adenosylmethionine synthetase, catalyzes transfer of the adenosyl group of ATP to the sulfur atom of methionine; one of two differentially regulated isozymes (Sam1p and Sam2p)	VL[RAV]	35	LRT	LKB1 Kinase substrate motif	Y				cytosol (0.001)	Y	0.006	10
protein_40_YLR175W	2	CBF5:  Pseudouridine synthase catalytic subunit of box H/ACA small nucleolar ribonucleoprotein particles (snoRNPs), acts on both large and small rRNAs and on snRNA U2	A[KDE][RKG]D	35							ribosome biogenesis (1e-05)		0.007	10
protein_40_YLR106C	2	MDN1:  Huge dynein-related AAA-type ATPase (midasin), forms extended pre-60S particle with the Rix1 complex (Rix1p-Ipi1p-Ipi3p), may mediate ATP-dependent remodeling of 60S subunits and subsequent export from nucleoplasm to cytoplasm	[IDM]E.[LMQ]A	35			Y				ribosome assembly (0.001)	Y	0.006	9
protein_40_YKR001C	2	VPS1:  Dynamin-like GTPase required for vacuolar sorting; also involved in actin cytoskeleton organization, late Golgi-retention of some proteins, regulating peroxisome biogenesis	[SHQ]Q.S[MPI]	35	[ST]Q	ATM kinase phosphorylation site							0.006	8
protein_40_YKL203C	2	TOR2:  PIK-related protein kinase and rapamycin target; subunit of TORC1, a complex that regulates growth in response to nutrients and TORC2, a complex that regulates cell-cycle dependent polarization of the actin cytoskeleton; involved in meiosis	L.L[MAW]	35	DALDL	14-3-3 binding motif in ExoS					plasma membrane (1e-19)	Y	0.006	10
protein_40_YKL172W	2	EBP2:  Essential protein required for the maturation of 25S rRNA and 60S ribosomal subunit assembly, localizes to the nucleolus; constituent of 66S pre-ribosomal particles	D[DVW]E[EGM]	35	SD.E	Casein kinase II substrate motif					cytoplasm organization and biogenesis (1e-20)	Y	0.007	10
protein_40_YJR059W	2	PTK2:  Putative serine/threonine protein kinase involved in regulation of ion transport across plasma membrane; enhances spermine uptake	EK..[SEV][RAY]S	35	K..[ST]	PKA kinase substrate motif							0.005	9
protein_40_YJL203W	2	PRP21:  Subunit of the SF3a splicing factor complex, required for spliceosome assembly	[TIH]PL[LP]E	35	[DET]E[RK].PL[LI]	TRG_LysEnd_APsAcLL_3					small nuclear ribonucleoprotein complex (1e-05)		0.004	7
protein_40_YJL164C	2	TPK1:  cAMP-dependent protein kinase catalytic subunit; promotes vegetative growth in response to nutrients via the Ras-cAMP signaling pathway; inhibited by regulatory subunit Bcy1p in the absence of cAMP; partially redundant with Tpk2p and Tpk3p	Q..P	35							phosphotransferase activity, alcohol group as acceptor (0.01)		0.006	10
protein_40_YJL106W	2	IME2:  Serine/threonine protein kinase involved in activation of meiosis, associates with Ime1p and mediates its stability, activates Ndt80p; IME2 expression is positively regulated by Ime1p	[QER]P.[PHA]H	35	P.P	motif in interleukin 5 receptor necessary for signaling							0.004	8
protein_40_YJL095W	2	BCK1:  Mitogen-activated protein (MAP) kinase kinase kinase acting in the protein kinase C signaling pathway, which controls cell integrity; upon activation by Pkc1p phosphorylates downstream kinases Mkk1p and Mkk2p	[LI]L.V[LCP]G	35									0.004	7
protein_40_YJL092W	2	SRS2:  DNA helicase and DNA-dependent ATPase involved in DNA repair, needed for proper timing of commitment to meiotic recombination and transition from Meiosis I to II; affects genome stability by suppressing unscheduled homologous recombination	E.[ETQ]N	35	Y.E.E	Src phosphorylation site					DNA metabolism (1e-05)		0.007	10
protein_40_YIL094C	2	LYS12:  Homo-isocitrate dehydrogenase, an NAD-linked mitochondrial enzyme required for the fourth step in the biosynthesis of lysine, in which homo-isocitrate is oxidatively decarboxylated to alpha-ketoadipate	[AEW]T.[EID]G	35								Y	0.006	10
protein_40_YIL061C	2	SNP1:  Component of U1 snRNP required for mRNA splicing via spliceosome; may interact with poly(A) polymerase to regulate polyadenylation; homolog of human U1 70K protein	R[SPF][RQV]D	35	YRSVDE	Branched chain alpha-ketoacid dehydrogenase kinase substrate motif							0.006	10
protein_40_YIL035C	2	CKA1:  Alpha catalytic subunit of casein kinase 2, a Ser/Thr protein kinase with roles in cell growth and proliferation; the holoenzyme also contains CKA2, CKB1 and CKB2, the many substrates include transcription factors and all RNA polymerases	K[KPF]KS[KQV]	35	KKKKKK[ST]	TGF beta receptor kinase substrate motif					nuclear lumen (0.01)	Y	0.006	9
protein_40_YHR196W	2	UTP9:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	A.[GFK]K	35	VPGKARKKSSCQLL	Calmodulin-dependent protein kinase IV substrate motif					nucleolus (1e-21)		0.007	10
protein_40_YHR196W	2	UTP9:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	E[KIM][KVL]D	35							rRNA processing (1e-16)	Y	0.007	10
protein_40_YHR169W	2	DBP8:  Putative ATP-dependent RNA helicase of the DEAD-box family involved in biogenesis of the 40S ribosomal subunit	E..A[AFK]	35							cytosol (1e-05)		0.006	10
protein_40_YHR148W	2	IMP3:  Component of the SSU processome, which is required for pre-18S rRNA processing, essential protein that interacts with Mpp10p and mediates interactions of Imp4p and Mpp10p with U3 snoRNA	[LE]K..G[LN]T	35							processing of 20S pre-rRNA (1e-04)		0.004	7
protein_40_YHR141C	2	RPL42B:  Protein component of the large (60S) ribosomal subunit, identical to Rpl42Ap and has similarity to rat L44; required for propagation of the killer toxin-encoding M1 double-stranded RNA satellite of the L-A double-stranded RNA virus	S.L[STF]	35									0.006	10
protein_40_YHR082C	2	KSP1:  Nonessential putative serine/threonine protein kinase of unknown cellular role; overproduction causes allele-specific suppression of the prp20-10 mutation	N.E[GYC]	35									0.006	10
protein_40_YHR079C	2	IRE1:  Serine-threonine kinase and endoribonuclease; transmembrane protein that mediates the unfolded protein response (UPR) by regulating Hac1p synthesis through HAC1 mRNA splicing; Kar2p binds inactive Ire1p and releases from it upon ER stress	PA[SEH][PRS]	35	APAP	Motif for hydroxylation of Pro residues, which can further be modified with arabinogalactan							0.007	10
protein_40_YHR030C	2	SLT2:  Serine/threonine MAP kinase involved in regulating the maintenance of cell wall integrity and progression through the cell cycle; regulated by the PKC1-mediated signaling pathway	E[GQW]..D[ASY]	35									0.006	10
protein_40_YHL001W	2	RPL14B:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl14Ap and has similarity to rat L14 ribosomal protein	S..[SNL]S	35	S..[ST]	Casein Kinase I consensus phosphorylation site (N-term Ser must first be phosphorylated)							0.007	10
protein_40_YGR252W	2	GCN5:  Histone acetyltransferase, acetylates N-terminal lysines on histones H2B and H3; catalytic subunit of the ADA and SAGA histone acetyltransferase complexes; founding member of the Gcn5p-related N-acetyltransferase superfamily	EL..[LQG]L[GIA]	35	L..LL	Motif for interaction with nuclear receptors, docking motif for p300 on p53 to promote acetylation							0.004	8
protein_40_YGR218W	2	CRM1:  Major karyopherin, involved in export of proteins, RNAs, and ribosomal subunits from the nucleus	[LIN]A[AGV]L	35							rRNA export from nucleus (0.001)	Y	0.007	10
protein_40_YGR218W	2	CRM1:  Major karyopherin, involved in export of proteins, RNAs, and ribosomal subunits from the nucleus	[SKT]T[PMC]A	35	KTPAKEE	GSK-3, ERK1, ERK2, CDK5 substrate motif	Y				rRNA export from nucleus (0.01)		0.007	10
protein_40_YGR218W	2	CRM1:  Major karyopherin, involved in export of proteins, RNAs, and ribosomal subunits from the nucleus	GS[TDM][GHR]	35	KSGST	eIF4 motif phosphorylation motif					protein import into nucleus (1e-05)		0.007	10
protein_40_YGR103W	2	NOP7:  Nucleolar protein involved in rRNA processing and 60S ribosomal subunit biogenesis; constituent of several different pre-ribosomal particles; required for exit from G<sub>0</sub> and the initiation of cell proliferation	[KGV]KK[KAV]	35	KKKKKK[ST]	TGF beta receptor kinase substrate motif	Y				cytoplasm organization and biogenesis (1e-21)	Y	0.007	10
protein_40_YGR074W	2	SMD1:  Core Sm protein Sm D1; part of heteroheptameric complex (with Smb1p, Smd2p, Smd3p, Sme1p, Smx3p, and Smx2p) that is part of the spliceosomal U1, U2, U4, and U5 snRNPs; homolog of human Sm D1	[DIE]GQ[LRT]	35	GGQ	N-methylation motif in E. coli, Gln residue in methylated, mimics CCA motif at the end of tRNA molecule					nuclear mRNA splicing, via spliceosome (1e-14)		0.006	10
protein_40_YGL173C	2	KEM1:  Evolutionarily-conserved 5'-3' exonuclease component of cytoplasmic processing (P) bodies involved in mRNA decay; plays a role in microtubule-mediated processes, filamentous growth, ribosomal RNA maturation, and telomere maintenance	QQ[PAH][SYM]	35							cytoplasmic mRNA processing body (1e-05)		0.005	8
protein_40_YGL076C	2	RPL7A:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl7Bp and has similarity to E. coli L30 and rat L7 ribosomal proteins; contains a conserved C-terminal Nucleic acid Binding Domain (NDB2)	K..[KAR]A	35	K[KR].[KR]	Nuclear localization motif					cytosolic ribosome (sensu Eukaryota) (1e-26)		0.006	10
protein_40_YGL031C	2	RPL24A:  Ribosomal protein L30 of the large (60S) ribosomal subunit, nearly identical to Rpl24Bp and has similarity to rat L24 ribosomal protein; not essential for translation but may be required for normal translation rate	RA.[KRG][VGT]	35							cytosolic ribosome (sensu Eukaryota) (1e-11)		0.006	10
protein_40_YER165W	2	PAB1:  Poly(A) binding protein, part of the 3'-end RNA-processing complex, mediates interactions between the 5' cap structure and the 3' mRNA poly(A) tail, involved in control of poly(A) tail length, interacts with translation factor eIF-4G	[LF]F[GF]AK	35	GAKRH	HISTONE_H4 PATTERN	Y				snRNP protein import into nucleus (0.01)		0.004	7
protein_40_YER146W	2	LSM5:  Lsm (Like Sm) protein; part of heteroheptameric complexes (Lsm2p-7p and either Lsm1p or 8p): cytoplasmic Lsm1p complex involved in mRNA decay; nuclear Lsm8p complex part of U6 snRNP and possibly involved in processing tRNA, snoRNA, and rRNA	[LWV]S..[GAK]Y	35							U4/U6 x U5 tri-snRNP complex (1e-04)		0.006	10
protein_40_YDR477W	2	SNF1:  AMP-activated serine/threonine protein kinase found in a complex containing Snf4p and members of the Sip1p/Sip2p/Gal83p family; required for transcription of glucose-repressed genes, thermotolerance, sporulation, and peroxisome biogenesis	TP[EFK]	35	LTP	RAF1 kinase substrate motif							0.006	10
protein_40_YDR450W	2	RPS18A:  Protein component of the small (40S) ribosomal subunit; nearly identical to Rps18Bp and has similarity to E. coli S13 and rat S18 ribosomal proteins	[KRD][EA]YQ	35	[DE]Y	EGFR kinase substrate motif							0.004	9
protein_40_YDR449C	2	UTP6:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	[LIS]TSK[LAD]	35							small nucleolar ribonucleoprotein complex (1e-04)		0.004	8
protein_40_YDR418W	2	RPL12B:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl12Ap; rpl12a rpl12b double mutant exhibits slow growth and slow translation; has similarity to E. coli L11 and rat L12 ribosomal proteins	S.L[STQ]	35									0.007	10
protein_40_YDR394W	2	RPT3:  One of six ATPases of the 19S regulatory particle of the 26S proteasome involved in the degradation of ubiquitinated substrates; substrate of N-acetyltransferase B	[IMC]D[QPI]Y	35	IY	cFGR and Csk kinase phosphorylation site (peptide screen)							0.004	9
protein_40_YDR388W	2	RVS167:  Actin-associated protein, subunit of a complex (Rvs161p-Rvs167p) involved in regulation of actin cytoskeleton, endocytosis, and viability following starvation or osmotic stress; homolog of mammalian amphiphysin	[IF]..AK	35	GAKRH	HISTONE_H4 PATTERN					bipolar bud site selection (1e-05)		0.007	10
protein_40_YDR388W	2	RVS167:  Actin-associated protein, subunit of a complex (Rvs161p-Rvs167p) involved in regulation of actin cytoskeleton, endocytosis, and viability following starvation or osmotic stress; homolog of mammalian amphiphysin	S[NVG]K	35	RRK.S.KR	PKCgamma kinase phosphorylation site (peptide screen)					bipolar bud site selection (1e-05)		0.006	10
protein_40_YDR365C	2	ESF1:  Nucleolar protein involved in pre-rRNA processing; depletion causes severely decreased 18S rRNA levels	K..[KNQ]K	35	P.[ST]PKK.KK	Cdc2 like protein kinase substrate motif					nucleolus (1e-14)	Y	0.006	9
protein_40_YDR303C	2	RSC3:  Component of the RSC chromatin remodeling complex; essential gene required for maintenance of proper ploidy and regulation of ribosomal protein genes and the cell wall/stress response; highly similar to Rsc30p	[LDK][LCG].EC	35							RSC complex (1e-05)		0.004	7
protein_40_YDR025W	2	RPS11A:  Protein component of the small (40S) ribosomal subunit; identical to Rps11Bp and has similarity to E. coli S17 and rat S11 ribosomal proteins	[GRE]AA[KRS]	35							translation (1e-11)	Y	0.007	10
protein_40_YDL213C	2	NOP6:  Putative RNA-binding protein implicated in ribosome biogenesis; contains an RNA recognition motif (RRM) and has similarity to hydrophilins; NOP6 may be a fungal-specific gene as no homologs have been yet identified in higher eukaryotes	E[AEK]..[GEA]S	35							nucleolus (1e-15)	Y	0.007	10
protein_40_YDL213C	2	NOP6:  Putative RNA-binding protein implicated in ribosome biogenesis; contains an RNA recognition motif (RRM) and has similarity to hydrophilins; NOP6 may be a fungal-specific gene as no homologs have been yet identified in higher eukaryotes	EG.[ESR][EAN]	35	IEGR	Protease Protease Factor X a					nucleolus (1e-10)		0.007	10
protein_40_YDL213C	2	NOP6:  Putative RNA-binding protein implicated in ribosome biogenesis; contains an RNA recognition motif (RRM) and has similarity to hydrophilins; NOP6 may be a fungal-specific gene as no homologs have been yet identified in higher eukaryotes	F[LTV]..LE[SDK]	35	F..LL	A nuclear receptor box in the FF domain which binds nuclear receptors and are components of transcriptional coactivators					ribosome biogenesis (0.01)	Y	0.004	8
protein_40_YDL148C	2	NOP14:  Nucleolar protein, forms a complex with Noc4p that mediates maturation and nuclear export of 40S ribosomal subunits; also present in the small subunit processome complex, which is required for processing of pre-18S rRNA	[ST]L[DHP]AT	35	PLTLP	RAF1 kinase substrate motif					snoRNA binding (1e-07)		0.004	8
protein_40_YDL148C	2	NOP14:  Nucleolar protein, forms a complex with Noc4p that mediates maturation and nuclear export of 40S ribosomal subunits; also present in the small subunit processome complex, which is required for processing of pre-18S rRNA	DE[ESR][DFK]	35	SEDEE	CKII kinase phosphorylation site (peptide screen)					nucleolus (1e-21)		0.007	10
protein_40_YDL148C	2	NOP14:  Nucleolar protein, forms a complex with Noc4p that mediates maturation and nuclear export of 40S ribosomal subunits; also present in the small subunit processome complex, which is required for processing of pre-18S rRNA	LSV[VKI][SNK]	35							small nucleolar ribonucleoprotein complex (1e-05)		0.004	8
protein_40_YDL055C	2	PSA1:  GDP-mannose pyrophosphorylase (mannose-1-phosphate guanyltransferase), synthesizes GDP-mannose from GTP and mannose-1-phosphate in cell wall biosynthesis; required for normal cell wall structure	[TGP]K..L[EAM]	35								Y	0.007	10
protein_40_YDL055C	2	PSA1:  GDP-mannose pyrophosphorylase (mannose-1-phosphate guanyltransferase), synthesizes GDP-mannose from GTP and mannose-1-phosphate in cell wall biosynthesis; required for normal cell wall structure	V.[VGY]E	35	YE	TPK-IIB/P38Syk kinase phosphorylation site (peptide screen)					ATPase activity (0.01)	Y	0.007	10
protein_40_YDL029W	2	ARP2:  Essential component of the Arp2/3 complex, which is a highly conserved actin nucleation center required for the motility and integrity of actin patches; involved in endocytosis and membrane growth and polarity	[HMA]R.I[KAY]	35	[AG]R	Protease matriptase protease site							0.005	9
protein_40_YDL015C	2	TSC13:  Enoyl reductase that catalyzes the last step in each cycle of very long chain fatty acid elongation, localizes to the ER, highly enriched in a structure marking nuclear-vacuolar junctions, coimmunoprecipitates with elongases Fen1p and Sur4p	F[VLH].V[ISN]	35									0.006	10
protein_40_YCR057C	2	PWP2:  Conserved 90S pre-ribosomal component essential for proper endonucleolytic cleavage of the 35 S rRNA precursor at A0, A1, and A2 sites; contains eight WD-repeats; PWP2 deletion leads to defects in cell cycle and bud morphogenesis	[KAV]K..K[RHF]	35	KR	CLV_PCSK_PC1ET2_1					rRNA processing (1e-22)		0.007	10
protein_40_YBR154C	2	RPB5:  RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III; contacts DNA and affects transactivation	[GWV]R[LVG]P	35	[AG]R	Protease matriptase protease site					transcription (1e-06)		0.005	10
protein_40_YBR109C	2	CMD1:  Calmodulin; Ca++ binding protein that regulates Ca++ independent processes (mitosis, bud growth, actin organization, endocytosis, etc.) and Ca++ dependent processes (stress-activated pathways), targets include Nuf1p, Myo2p and calcineurin	[GIQ][ID]DLG	35									0.004	7
protein_40_YBR009C	2	HHF1:  One of two identical histone H4 proteins (see also HHF2); core histone required for chromatin assembly and chromosome function; contributes to telomeric silencing; N-terminal domain involved in maintaining genomic integrity	[IWP]L..[FQY]E	35	YE	TPK-IIB/P38Syk kinase phosphorylation site (peptide screen)						Y	0.007	10
protein_40_YBL003C	2	HTA2:  One of two nearly identical (see also HTA1) histone H2A subtypes; core histone required for chromatin assembly and chromosome function; DNA damage-dependent phosphorylation by Mec1p facilitates DNA repair; acetylated by Nat4p	ED.[SAT][LAQ]	35	YEDP	Fyn SH2 domain binding motif					establishment and/or maintenance of chromatin architecture (0.001)	Y	0.007	10
protein_40_YBL003C	2	HTA2:  One of two nearly identical (see also HTA1) histone H2A subtypes; core histone required for chromatin assembly and chromosome function; DNA damage-dependent phosphorylation by Mec1p facilitates DNA repair; acetylated by Nat4p	R[KFH]R	35	HHH[RK]SPR[RK]R	Cdc2 kinase substrate motif					establishment and/or maintenance of chromatin architecture (1e-10)		0.006	9
protein_40_YBL002W	2	HTB2:  One of two nearly identical (see HTB1) histone H2B subtypes required for chromatin assembly and chromosome function; Rad6p-Bre1p-Lge1p mediated ubiquitination regulates transcriptional activation, meiotic DSB formation and H3 methylation	DE[ELA][ERV]	35	SEDEE	CKII kinase phosphorylation site (peptide screen)					nucleoplasm (0.001)	Y	0.007	10
protein_40_YAL032C	2	PRP45:  Protein required for pre-mRNA splicing; associates with the spliceosome and interacts with splicing factors Prp22p and Prp46p; orthologous to human transcriptional coactivator SKIP and can activate transcription of a reporter gene	E..[LSA]N	35							nuclear mRNA splicing, via spliceosome (1e-09)	Y	0.007	10
protein_40_YAL032C	2	PRP45:  Protein required for pre-mRNA splicing; associates with the spliceosome and interacts with splicing factors Prp22p and Prp46p; orthologous to human transcriptional coactivator SKIP and can activate transcription of a reporter gene	I.[AGS]K	35			Y				nuclear mRNA splicing, via spliceosome (1e-12)	Y	0.006	9
oshea_punctate_composite	2	oshea_punctate_composite	PI[SMA]S[TE]	35	S[ST]	MDC1 BRCT domain binding motif							0.004	7
oshea_nuclear_periphery	2	oshea_nuclear_periphery	N..N[TLN]	35			Y				nuclear pore (1e-43)	Y	0.007	10
oshea_bud_neck	2	oshea_bud_neck	[IEW]LM[NKY]	35	LFDLM	Binding motif in Clint for clathrin TD domain					establishment of cell polarity (sensu Fungi) (1e-13)	Y	0.007	10
oshea_ambiguous	2	oshea_ambiguous	S[FNV].QL[EQD]	35			Y				receptor activity (0.01)		0.006	10
matsuyama_Spindle_or_SPB	2	matsuyama_Spindle_or_SPB	L[QDL]..[KRV]E	35							spindle (1e-67)	Y	0.009	10
matsuyama_Spindle_or_SPB	2	matsuyama_Spindle_or_SPB	P.N[ALH]	35							spindle (1e-92)	Y	0.009	10
matsuyama_Spindle_or_SPB	2	matsuyama_Spindle_or_SPB	Q..L[KVR]	35							spindle (1e-12)		0.009	10
matsuyama_periphery	2	matsuyama_periphery	[FAW]F..L[FTN]	35	F..LF	Androgen receptor motif that interacts with AF2					barrier septum (1e-09)		0.009	10
matsuyama_ER	2	matsuyama_ER	K.[KLI]R	35	[KR]R	CLV_PCSK_KEX2_1							0.009	10
genetic_YLR200W	2	YKE2: Subunit of the heterohexameric Gim/prefoldin protein complex involved in the folding of alpha-tubulin, beta-tubulin, and actin	[KLR]E..L[TPD]	35							microtubule-based process (1e-08)	Y	0.006	9
genetic_YLR200W	2	YKE2: Subunit of the heterohexameric Gim/prefoldin protein complex involved in the folding of alpha-tubulin, beta-tubulin, and actin	[RYQ]TI[KRE]	35							establishment of organelle localization (0.001)		0.007	10
genetic_YLR039C	2	RIC1: Protein involved in retrograde transport to the cis-Golgi network; forms heterodimer with Rgp1p that acts as a GTP exchange factor for Ypt6p; involved in transcription of rRNA and ribosomal protein genes	TE.[QIK][KSF]	35	[ST]E	G protein-coupled receptor kinase 1 substrate motif							0.006	10
genetic_YGL058W	2	RAD6: Ubiquitin-conjugating enzyme (E2), involved in postreplication repair (with Rad18p), sporulation, telomere silencing, and ubiquitin-mediated N-end rule protein degradation (with Ubr1p)	D[LEV]L	35	DLL	Binding motif for clathrin heavy chain ear					DNA metabolism (1e-19)	Y	0.007	10
genetic_YGL058W	2	RAD6: Ubiquitin-conjugating enzyme (E2), involved in postreplication repair (with Rad18p), sporulation, telomere silencing, and ubiquitin-mediated N-end rule protein degradation (with Ubr1p)	I..[LYA]K	35							DNA metabolism (1e-16)		0.006	10
genetic_YER083C	2	GET2: Subunit of the GET complex; required for meiotic nuclear division and for the retrieval of HDEL proteins from the Golgi to the ER in an ERD2 dependent fashion; may be involved in cell wall function	[AQ]E[SGE]S	35	[ED]GSG[DE]	Glycosaminoglycan attachment site					telomere organization and biogenesis (0.01)		0.006	10
genetic_YER083C	2	GET2: Subunit of the GET complex; required for meiotic nuclear division and for the retrieval of HDEL proteins from the Golgi to the ER in an ERD2 dependent fashion; may be involved in cell wall function	[NFP]L[KFD]D	35	LFDLM	Binding motif in Clint for clathrin TD domain					Golgi apparatus part (1e-04)		0.007	10
genetic_YAL024C	2	LTE1: Putative GDP/GTP exchange factor required for mitotic exit at low temperatures; acts as a guanine nucleotide exchange factor (GEF) for Tem1p, which is a key regulator of mitotic exit; physically associates with Ras2p-GTP	E..T[LEI]	35							mitotic cell cycle (1e-11)		0.007	10
protein_40_YBL002W	2	HTB2:  One of two nearly identical (see HTB1) histone H2B subtypes required for chromatin assembly and chromosome function; Rad6p-Bre1p-Lge1p mediated ubiquitination regulates transcriptional activation, meiotic DSB formation and H3 methylation	G[GSM]K[GWH]	34				Histone	1.E-07	-2.8	chromatin assembly or disassembly (1e-04)	Y	0.006	8
yeast-207_GO-0006974	2	response to DNA damage stimulus	I[SRC]..[EDI]S	34				SMC_N	1.E-02	-2.3	response to DNA damage stimulus (1e-59)		0.007	10
protein_40_YLL045C	2	RPL8B:  Ribosomal protein L4 of the large (60S) ribosomal subunit, nearly identical to Rpl8Ap and has similarity to rat L7a ribosomal protein; mutation results in decreased amounts of free 60S subunits	A.[GAI]K	34				Brix	1.E-02	-2.2	cytosolic ribosome (sensu Eukaryota) (1e-22)		0.006	10
yeast-544_GO-0016070	2	RNA metabolism	[HIK]..GR	34	[AG]R	Protease matriptase protease site		DEAD	1.E-10	-2	RNA metabolism (1e-11)		0.007	10
yeast-436_GO-0031323	2	regulation of cellular metabolism	L.S[LKQ]	34	WLNS	Lipid binding motif in C-terminus of Apolipoprotein AII	Y	Zn_clus	1.E-10	-1.6	regulation of cellular metabolism (10)		0.007	10
yeast-460_GO-0006351	2	transcription, DNA-dependent	L..P[SN]	34	P[ST]	DNA dependent Protein kinase substrate motif		zf-C2H2	1.E-05	-1.4	transcription, DNA-dependent (1e-16)		0.007	10
protein_40_YHR196W	2	UTP9:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	R[RLE]K[EQY]	34				WD40	1.E-03	-1.4	nucleolus (1e-16)		0.007	10
protein_40_YKL014C	2	URB1:  Nucleolar protein required for the normal accumulation of 25S and 5.8S rRNAs, associated with the 27SA2 pre-ribosomal particle; proposed to be involved in the biogenesis of the 60S ribosomal subunit	DV[AH][AS]R	34	[AG]R	Protease matriptase protease site		DEAD	1.E-06	-1.3	ATP-dependent RNA helicase activity (1e-06)		0.004	8
protein_40_YIL019W	2	FAF1:  Protein required for pre-rRNA processing and 40S ribosomal subunit assembly	[DMV]E[ES]D	34	EED	Ankyrin B C-terminal motif that binds internal Ankyrin repeats		WD40	1.E-05	-1.3	snoRNA binding (1e-26)	Y	0.007	10
yeast-462_GO-0019222	2	regulation of metabolism	H[TS].E[KRN]P	34				zf-C2H2	1.E-20	-1.2	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism (1e-14)		0.008	10
yeast-222_GO-0009308	2	amine metabolism	L..[KGD]A	34				tRNA-synt_2b	1.E-03	-1.2	amine metabolism (1e-14)	Y	0.007	10
protein_40_YML010W	2	SPT5:  Protein that forms a complex with Spt4p and mediates both activation and inhibition of transcription elongation; Spt4p-Spt5p complex also plays a role in pre-mRNA processing	[RP]T.R[KGR]	34				DEAD	1.E-03	-1.2	nuclear lumen (0.001)		0.007	10
oshea_bud_neck	2	oshea_bud_neck	E[HLF]S	34	R[RH][RH][RE]RE[RH]SR[RD]L	CLK2 kinase substrate motif		RhoGAP	1.E-03	-1.2	bud (1e-59)	Y	0.007	10
yeast-460_GO-0006351	2	transcription, DNA-dependent	K.[DKR]S	34	[NT]K.D	Motif for binding guanine nucleotides		Zn_clus	1.E-06	-1.1	transcription, DNA-dependent (1e-24)		0.007	10
yeast-460_GO-0006351	2	transcription, DNA-dependent	LP[PDK]	34	LPDEL	Motif in CBP for interaction with PPARg-LBD (secondary site)		Zn_clus	1.E-05	-1.1	transcription, DNA-dependent (1e-22)		0.007	10
protein_40_YOL133W	2	HRT1:  RING finger containing subunit of Skp1-Cullin-F-box ubiquitin protein ligases (SCF); required for Gic2p, Far1p, Sic1p and Cln2p degradation; may tether Cdc34p (a ubiquitin conjugating enzyme or E2) and Cdc53p (a cullin) subunits of SCF	I.[NDV]N	34				F-box	1.E-11	-1.1	ubiquitin ligase complex (1e-08)	Y	0.006	10
matsuyama_nucleolus	2	matsuyama_nucleolus	T[GN][SMF]GK	34	[SAG]GGTG[SA]G	TUBULIN PATTERN		Helicase_C	1.E-14	-1.1	ATP-dependent RNA helicase activity (1e-15)		0.008	9
protein_40_YNL175C	2	NOP13:  Protein of unknown function, localizes to the nucleolus and nucleoplasm; contains an RNA recognition motif (RRM) and has similarity to Nop12p, which is required for processing of pre-18S rRNA	E[EKA]..[KSL]D	34				DEAD	1.E-02	-1	ribosome biogenesis (1e-13)		0.007	10
yeast-1166_GO-0005488	2	binding	S..[QTN]E	34	S..[ST]	Casein Kinase I consensus phosphorylation site (N-term Ser must first be phosphorylated)		RRM_1	1.E-08	-0.8	nucleic acid binding (1e-96)		0.007	10
protein_40_YOL133W	2	HRT1:  RING finger containing subunit of Skp1-Cullin-F-box ubiquitin protein ligases (SCF); required for Gic2p, Far1p, Sic1p and Cln2p degradation; may tether Cdc34p (a ubiquitin conjugating enzyme or E2) and Cdc53p (a cullin) subunits of SCF	[FKC]D.L	34	DLL	Binding motif for clathrin heavy chain ear		F-box	1.E-09	-0.8	protein catabolism (1e-07)	Y	0.007	10
protein_40_YLR293C	2	GSP1:  GTP binding protein (mammalian Ranp homolog) involved in the maintenance of nuclear organization, RNA processing and transport; regulated by Prp20p, Rna1p, Yrb1p, Yrb2p, Yrp4p, Yrb30p, Cse1p and Kap95p; yeast Gsp2p homolog	D..E[TAW]	34				IBN_N	1.E-11	-0.8	nuclear transport (1e-18)	Y	0.006	9
yeast-216_GO-0006325	2	establishment and/or maintenance of chromatin architecture	[SFG]N.[NPE]N	34				Myb_DNA-binding	1.E-04	-0.7	establishment and/or maintenance of chromatin architecture (1e-68)		0.007	9
yeast-216_GO-0006323	2	DNA packaging	[SFG]N.[NPE]N	34				Myb_DNA-binding	1.E-04	-0.7	establishment and/or maintenance of chromatin architecture (1e-68)		0.007	9
protein_40_YJR002W	2	MPP10:  Component of the SSU processome, which is required for pre-18S rRNA processing, interacts with and controls the stability of Imp3p and Imp4p, essential for viability; similar to human Mpp10p	[DHM]E[ESK]D	34	E[ST]D	Ankyrin G binding motif in KNCQ2 and KNCQ3 potaqssium channels		WD40	1.E-04	-0.7	nucleolus (1e-24)		0.007	10
protein_40_YGR090W	2	UTP22:  Possible U3 snoRNP protein involved in maturation of pre-18S rRNA, based on computational analysis of large-scale protein-protein interaction data	K[KHP].[SNF]G	34			Y	Helicase_C	1.E-02	-0.7	ribosome biogenesis (1e-04)	Y	0.007	10
protein_40_YDL031W	2	DBP10:  Putative ATP-dependent RNA helicase of the DEAD-box protein family, constituent of 66S pre-ribosomal particles; essential protein involved in ribosome biogenesis	T[GEH][SK]GK	34	[SAG]GGTG[SA]G	TUBULIN PATTERN		Helicase_C	1.E-04	-0.7	ribosomal large subunit assembly and maintenance (1e-06)		0.004	8
yeast-238_GO-0017111	2	nucleoside-triphosphatase activity	I[NML].I[DGQ]	34				ABC_tran	1.E-06	-0.6	nucleoside-triphosphatase activity (1e-46)		0.008	10
matsuyama_Mitochondria	2	matsuyama_Mitochondria	I[DSI]L	34	YIDL	SH2 ligand for Syp (also tyr is phosphorylated by the insulin receptor)		HEAT	1.E-05	-0.6	ATP binding (0.001)		0.008	10
protein_40_YOL133W	2	HRT1:  RING finger containing subunit of Skp1-Cullin-F-box ubiquitin protein ligases (SCF); required for Gic2p, Far1p, Sic1p and Cln2p degradation; may tether Cdc34p (a ubiquitin conjugating enzyme or E2) and Cdc53p (a cullin) subunits of SCF	[IVQ]D[APR]L	34	DALDL	14-3-3 binding motif in ExoS		F-box	1.E-02	-0.5	ubiquitin ligase complex (0.001)		0.007	10
protein_40_YJL130C	2	URA2:  Bifunctional carbamoylphosphate synthetase (CPSase)-aspartate transcarbamylase (ATCase), catalyzes the first two enzymatic steps in the de novo biosynthesis of pyrimidines; both activities are subject to feedback inhibition by UTP	I[DLC].[EHC]E	34				IBN_N	1.E-03	-0.5	protein carrier activity (1e-05)		0.006	10
protein_40_YHR196W	2	UTP9:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	F[TNQ].K[YEF]	34				WD40	1.E-02	-0.4	rRNA processing (1e-11)		0.006	9
protein_40_YOR310C	2	NOP58:  Protein involved in pre-rRNA processing, 18S rRNA synthesis, and snoRNA synthesis; component of the small subunit processome complex, which is required for processing of pre-18S rRNA	K..K[RLV]	34	KR	CLV_PCSK_PC1ET2_1	Y	WD40	1.E-04	-0.2	nucleolus (1e-46)		0.007	10
protein_40_YML010W	2	SPT5:  Protein that forms a complex with Spt4p and mediates both activation and inhibition of transcription elongation; Spt4p-Spt5p complex also plays a role in pre-mRNA processing	G..[GPM]R	34	[AG]R	Protease matriptase protease site	Y	DEAD	1.E-03	-0.2	nuclear lumen (1e-06)		0.006	10
yeast-631_GO-0050794	2	regulation of cellular process	I..[LPI]K	34				Zn_clus	1.E-05	-0.1	regulation of cellular metabolism (1e-15)		0.007	10
yeast-630_GO-0051244	2	regulation of cellular physiological process	I..[LPI]K	34				Zn_clus	1.E-05	-0.1	regulation of cellular metabolism (1e-15)		0.007	9
yeast-301_GO-0044451	2	nucleoplasm part	KR[KRE]	34	KR	CLV_PCSK_PC1ET2_1		Bromodomain	1.E-04	-0.1	nucleoplasm part (1e-17)		0.007	10
yeast-256_GO-0016462	2	pyrophosphatase activity	[TDG]I[GKD]V	34				Ras	1.E-04	0	pyrophosphatase activity (1e-46)	Y	0.008	10
protein_40_YKL101W	2	HSL1:  Nim1p-related protein kinase that regulates the morphogenesis and septin checkpoints; associates with the assembled septin filament; required along with Hsl7p for bud neck recruitment, phosphorylation, and degradation of Swe1p	E[NQ]..K[KAI]	34				DnaJ_C	1.E-03	0.1			0.007	9
yeast-388_GO-0007275	2	development	E..T[DPS]	34			Y	SH3_1	1.E-02	0.2	multicellular organismal development (1e-16)	Y	0.007	10
protein_40_YJL074C	2	SMC3:  Subunit of the multiprotein cohesin complex required for sister chromatid cohesion in mitotic cells; also required, with Rec8p, for cohesion and recombination during meiosis; phylogenetically conserved SMC chromosomal ATPase family member	D[AFR][GAN]L	34				SMC_N	1.E-03	0.2	cohesin complex (1e-05)		0.006	9
protein_40_YJL074C	2	SMC3:  Subunit of the multiprotein cohesin complex required for sister chromatid cohesion in mitotic cells; also required, with Rec8p, for cohesion and recombination during meiosis; phylogenetically conserved SMC chromosomal ATPase family member	VS.[KEN][LEQ]	34				SMC_N	1.E-03	0.2	cohesin complex (1e-05)		0.007	10
protein_40_YER082C	2	UTP7:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	G.E[KDM]	34				WD40	1.E-04	0.2	small nucleolar ribonucleoprotein complex (1e-24)		0.007	10
yeast-630_GO-0051244	2	regulation of cellular physiological process	T..[RIN]R	34	[KR]R	CLV_PCSK_KEX2_1		Zn_clus	1.E-02	0.6	regulation of metabolism (1e-76)		0.007	10
yeast-462_GO-0019222	2	regulation of metabolism	G..N[GSD]	34				Zn_clus	1.E-02	0.6	regulation of metabolism (1e-17)		0.007	10
protein_40_YPL240C	2	HSP82:  Hsp90 chaperone required for pheromone signaling and negative regulation of Hsf1p; docks with Tom70p for mitochondrial preprotein delivery; promotes telomerase DNA binding and nucleotide addition; interacts with Cns1p, Cpr6p, Cpr7p, Sti1p	F..[LAT]K	34			Y	Pkinase	1.E-03	0.6	protein amino acid phosphorylation (0.01)		0.006	10
protein_40_YLR340W	2	RPP0:  Conserved ribosomal protein P0 similar to rat P0, human P0, and E. coli L10e; shown to be phosphorylated on serine 302	A[GQV]..A[EAQ]	34				Ribosomal_60s	1.E-03	0.6	cytosolic ribosome (sensu Eukaryota) (1e-09)	Y	0.007	10
protein_40_YLR293C	2	GSP1:  GTP binding protein (mammalian Ranp homolog) involved in the maintenance of nuclear organization, RNA processing and transport; regulated by Prp20p, Rna1p, Yrb1p, Yrb2p, Yrp4p, Yrb30p, Cse1p and Kap95p; yeast Gsp2p homolog	L.D[ESL]	34	LPDEL	Motif in CBP for interaction with PPARg-LBD (secondary site)	Y	IBN_N	1.E-13	0.6	nucleocytoplasmic transport (1e-19)		0.006	10
protein_40_YLR276C	2	DBP9:  ATP-dependent RNA helicase of the DEAD-box family involved in biogenesis of the 60S ribosomal subunit	E..[ELN]D	34				Pkinase	1.E-02	0.6	cytoplasm organization and biogenesis (1e-18)		0.006	9
yeast-1166_GO-0005488	2	binding	D..L[LSP]	34	D..LL	Di-Leu motif for receptor endocytosis (recognized by VHS domain of GGA proteins)		IBN_N	1.E-02	0.7	nucleic acid binding (1e-10)		0.007	10
protein_40_YDR388W	2	RVS167:  Actin-associated protein, subunit of a complex (Rvs161p-Rvs167p) involved in regulation of actin cytoskeleton, endocytosis, and viability following starvation or osmotic stress; homolog of mammalian amphiphysin	[GVC]S..E[EHT]	34	[ST]..E	Casien kinase II consensus phosphorylation site		HEAT	1.E-02	1			0.007	10
protein_40_YOL018C	2	TLG2:  Syntaxin-like t-SNARE that forms a complex with Tlg1p and Vti1p and mediates fusion of endosome-derived vesicles with the late Golgi; binds Vps45p, which prevents Tlg2p degradation and also facilitates t-SNARE complex formation	[DRN]T[ARE]G	34			Y	Ras	1.E-04	1.1	GTPase activity (1e-04)		0.006	9
yeast-752_GO-0016787	2	hydrolase activity	T..E	34	[DE]AT..[DE]PWG[PA]	PI(4,5)P2 binding motif in epsin		UCH	1.E-08	1.2	hydrolase activity, acting on ester bonds (1e-12)		0.007	10
yeast-256_GO-0016462	2	pyrophosphatase activity	E..S[AVG]	34	[LIVMA].EG[DN]SA.[STAG]	TOPOISOMERASE_II PATTERN		Helicase_C	1.E-14	1.2	pyrophosphatase activity (1e-13)	Y	0.007	10
protein_40_YER012W	2	PRE1:  Beta 4 subunit of the 20S proteasome; localizes to the nucleus throughout the cell cycle	A[RIQ].[ALK]A	34	EAIYAAPF	Abl kinase substrate motif		Proteasome	1.E-03	1.2	proteasome complex (sensu Eukaryota) (1e-09)		0.007	10
yeast-589_GO-0050896	2	response to stimulus	K..S[ESP]	34	K..[ST]	PKA kinase substrate motif		BRCT	1.E-02	1.3	response to stress (1e-17)	Y	0.007	10
protein_40_YLR293C	2	GSP1:  GTP binding protein (mammalian Ranp homolog) involved in the maintenance of nuclear organization, RNA processing and transport; regulated by Prp20p, Rna1p, Yrb1p, Yrb2p, Yrp4p, Yrb30p, Cse1p and Kap95p; yeast Gsp2p homolog	[KAD]K..[NIM]D	34				IBN_N	1.E-02	1.3	nuclear transport (1e-04)		0.007	10
yeast-437_GO-0044429	2	mitochondrial part	LD..[KAR][TVM]R	34				Mito_carr	1.E-20	1.5	mitochondrial part (1e-16)		0.008	9
yeast-274_GO-0005840	2	ribosome	A[ARG].[KPY]A	34				Ribosomal_60s	1.E-02	1.5	ribosome (1e-49)		0.007	10
protein_40_YFR052W	2	RPN12:  Subunit of the 19S regulatory particle of the 26S proteasome lid; synthetically lethal with RPT1, which is an ATPase component of the 19S regulatory particle; physically interacts with Nob1p and Rpn3p	[ARQ]A.G[LRM]	34			Y	HEAT	1.E-02	1.5	proteasome complex (sensu Eukaryota) (0.01)		0.006	10
yeast-752_GO-0016787	2	hydrolase activity	E[IRC]L	34	GFRGE[AG]L	DNA_MISMATCH_REPAIR_1 PATTERN		ABC_tran	1.E-05	1.6	pyrophosphatase activity (1e-70)	Y	0.007	10
yeast-256_GO-0016462	2	pyrophosphatase activity	N.[ISC]D	34	N.[TS]	N-linked glycosylation site	Y	Ras	1.E-08	1.6	pyrophosphatase activity (1e-10)	Y	0.007	10
yeast-980_GO-0051179	2	localization	[LFS]D..K[TVC]R	34				Mito_carr	1.E-32	2	transporter activity (1e-14)		0.008	10
protein_40_YNL272C	2	SEC2:  Guanyl-nucleotide exchange factor for the small G-protein Sec4p, located on cytoplasmic vesicles; essential for post-Golgi vesicle transport	[GKM][DKV]DT	34	[ASL][FY]SGG[LV]DT[ST]	ARGININOSUCCIN_SYN_1 PATTERN	Y	Pkinase	1.E-09	2.2	protein kinase activity (1e-09)		0.006	9
protein_40_YHR148W	2	IMP3:  Component of the SSU processome, which is required for pre-18S rRNA processing, essential protein that interacts with Mpp10p and mediates interactions of Imp4p and Mpp10p with U3 snoRNA	D[KGW].[VTA]K	34			Y	WD40	1.E-04	2.3	rRNA processing (1e-18)	Y	0.007	8
yeast-1939_GO-0003824	2	catalytic activity	WD.A[GQK][QPE]	34	WDL	Binding motif for AP-2 and clathrin heavy chain ear		Ras	1.E-27	2.4	GTPase activity (1e-21)		0.008	10
protein_40_YNL186W	2	UBP10:  Ubiquitin-specific protease that deubiquitinates ubiquitin-protein moieties; may regulate silencing by acting on Sir4p; involved in posttranscriptionally regulating Gap1p and possibly other transporters; primarily located in the nucleus	E..[LIC]L	34	[DE]...L[LI]	AP complex deleucine sorting motif		Pkinase	1.E-21	2.6	protein kinase activity (1e-21)	Y	0.006	9
protein_40_YPL093W	2	NOG1:  Putative GTPase that associates with free 60S ribosomal subunits in the nucleolus and is required for 60S ribosomal subunit biogenesis; constituent of 66S pre-ribosomal particles; member of the ODN family of nucleolar G-proteins	P[TNV].I[QC]	34			Y	DEAD	1.E-09	3.2	RNA helicase activity (1e-08)		0.005	9
protein_40_YML007W	2	YAP1:  Basic leucine zipper (bZIP) transcription factor required for oxidative stress tolerance; activated by H2O2 through the multistep formation of disulfide bonds and transit from the cytoplasm to the nucleus; mediates resistance to cadmium	N[IN][NEL]T	34	IETD	Protease Caspase 8-stringent		Bromodomain	1.E-03	3.2	nucleoplasm part (1e-11)	Y	0.007	10
yeast-376_GO-0019219	2	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism	L.Q[DHE]	34	LSQE	ATM kinase substrate motif		zf-C2H2	1.E-06	3.4	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism (1e-15)	Y	0.007	9
protein_40_YMR093W	2	UTP15:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	D[GDS].I[KRA]	34				WD40	1.E-04	3.9	nucleolus (1e-19)	Y	0.007	10
yeast-593_GO-0031981	2	nuclear lumen	[RNK]E[LTN]A	34				DEAD	1.E-08	4	nuclear lumen (1e-72)	Y	0.007	10
yeast-1974_GO-0005634	2	nucleus	WY..[RSN][LFI]	34	PWY[ST][ST]RL	SRP1_TIP1 PATTERN		SRP1_TIP1	1.E-55	4	cell wall (0.001)		0.007	10
yeast-1340_GO-0044267	2	cellular protein metabolism	[ACM][DW]FG	34	LFG	Protease Papain substrate, a prototype cysteine proteinase	Y	Pkinase	1.E-26	4.1	protein amino acid phosphorylation (1e-35)		0.007	9
yeast-565_GO-0006464	2	protein modification	G[LMQ].Y[LDE]H	34	Y[AGSTDE]	Src kinase substrate motif		Pkinase	1.E-14	4.2	protein amino acid phosphorylation (1e-16)		0.007	10
protein_40_YAR019C	2	CDC15:  Protein kinase of the Mitotic Exit Network that is localized to the spindle pole bodies at late anaphase; promotes mitotic exit by directly switching on the kinase activity of Dbf2p	E[NIW].L[LIR]	34				Pkinase	1.E-22	4.2	protein kinase activity (1e-19)		0.007	10
protein_40_YGL245W	2	GUS1:  Glutamyl-tRNA synthetase (GluRS), forms a complex with methionyl-tRNA synthetase (Mes1p) and Arc1p; complex formation increases the catalytic efficiency of both tRNA synthetases and ensures their correct localization to the cytoplasm	[VFY]A[IVE]K	34				Pkinase	1.E-17	4.3	protein kinase activity (1e-17)	Y	0.007	10
yeast-1389_GO-0044260	2	cellular macromolecule metabolism	[ACV]D[FHT]G	34	[LIVMFGAC][LIVMTADN][LIVFSA]D[ST]G[STAV][STAPDENQ]	ASP_PROTEASE PATTERN		Pkinase	1.E-23	4.4	protein amino acid phosphorylation (1e-32)		0.007	10
yeast-345_GO-0006396	2	RNA processing	P[TDG]R[ENF]L	34	[AG]R	Protease matriptase protease site		DEAD	1.E-13	4.6	RNA helicase activity (1e-13)		0.006	9
protein_40_YER006W	2	NUG1:  GTPase that associates with nuclear 60S pre-ribosomes, required for export of 60S ribosomal subunits from the nucleus	R.[GKA]R	34	[AG]R	Protease matriptase protease site		Helicase_C	1.E-02	5	cytoplasm organization and biogenesis (1e-20)	Y	0.006	10
yeast-565_GO-0006464	2	protein modification	[KMT]P.N[ILMV]	34	[ST]P	LIG_WW_4	Y	Pkinase	1.E-32	5.2	protein modification (1e-56)	Y	0.007	8
yeast-631_GO-0050794	2	regulation of cellular process	F.[QRC]R	34	[KR]R	CLV_PCSK_KEX2_1		zf-C2H2	1.E-03	6	regulation of cellular metabolism (1e-58)		0.007	10
yeast-630_GO-0051244	2	regulation of cellular physiological process	F.[QRC]R	34	[KR]R	CLV_PCSK_KEX2_1		zf-C2H2	1.E-03	6	regulation of cellular metabolism (1e-59)		0.007	10
protein_40_YJR066W	2	TOR1:  PIK-related protein kinase and rapamycin target; subunit of TORC1, a complex that controls growth in response to nutrients by regulating translation, transcription, ribosome biogenesis, nutrient transport and autophagy; involved in meiosis	A[CIF].[LGV]F	34				GATA	1.E-05	6.8	regulation of nitrogen utilization (1e-05)	Y	0.007	10
protein_40_YJR066W	2	TOR1:  PIK-related protein kinase and rapamycin target; subunit of TORC1, a complex that controls growth in response to nutrients by regulating translation, transcription, ribosome biogenesis, nutrient transport and autophagy; involved in meiosis	L[MCQ][INL]A	34	YL[VMAY]I	Sorting nexin 1 (Binding motif), Lysosomal targeting motif in EGFR		GATA	1.E-04	6.8	plasma membrane (1e-06)	Y	0.007	10
yeast-792_GO-0006412	2	protein biosynthesis	N.[DSG]D	34	N.[TS]	N-linked glycosylation site							0.007	10
yeast-589_GO-0050896	2	response to stimulus	[ISN]S..[VTQ]T	34	S..[ST]	Casein Kinase I consensus phosphorylation site (N-term Ser must first be phosphorylated)					response to stress (1e-50)	Y	0.007	10
yeast-548_GO-0051641	2	cellular localization	[EMV]N..[KMS]E	34							cellular localization (1e-61)		0.007	10
yeast-548_GO-0051641	2	cellular localization	[QDE]L.Q[EFS]	34							cellular localization (1e-72)		0.007	10
yeast-470_GO-0006259	2	DNA metabolism	PS[TND][KVG]	34							DNA metabolism (1e-63)		0.007	9
yeast-437_GO-0044429	2	mitochondrial part	T..N[AHN]	34									0.007	10
yeast-336_GO-0005783	2	endoplasmic reticulum	[VIG]I..L[ILF]	34							endoplasmic reticulum (1e-96)		0.007	9
yeast-295_GO-0016192	2	vesicle-mediated transport	I[NDG].L[KMS]	34							vesicle-mediated transport (1e-81)		0.007	10
yeast-285_GO-0012505	2	endomembrane system	[FLI]SF[GNL]	34	RK.SF	PKCepsilon kinase phosphorylation site (peptide screen)					endomembrane system (1e-61)		0.007	10
yeast-284_GO-0005740	2	mitochondrial envelope	E.I[DNEQ]	34	YE.[IV]	SH2 ligand for Fes (Tyr must be phosphorylated)							0.007	10
yeast-262_GO-0031224	2	intrinsic to membrane	FG[SIT][GIK]	34	RRFGS[MLVIF]RR[MLVIF]	MEKK kinase substrate motif					integral to membrane (1e-49)	Y	0.007	10
yeast-256_GO-0016021	2	integral to membrane	FG[SIT][GIK]	34	RRFGS[MLVIF]RR[MLVIF]	MEKK kinase substrate motif	Y				integral to membrane (1e-49)	Y	0.008	10
yeast-251_GO-0005886	2	plasma membrane	W..[RVT]L	34							plasma membrane (1e-58)		0.007	10
yeast-248_GO-0031966	2	mitochondrial membrane	KR[KHR]	34	KR	CLV_PCSK_PC1ET2_1							0.007	10
yeast-235_GO-0000278	2	mitotic cell cycle	Q.[QLV]Q	34							mitotic cell cycle (1e-11)	Y	0.007	10
yeast-212_GO-0045045	2	secretory pathway	I[ALV]..L[ELD]	34			Y				secretory pathway (1e-89)	Y	0.007	10
yeast-205_GO-0005856	2	cytoskeleton	[LNT]DK[KDY]F	34							cytoskeleton (1e-09)		0.005	7
yeast-1115_GO-0006996	2	organelle organization and biogenesis	[LTK]QR[KQH]	34	[ST]Q	ATM kinase phosphorylation site					cytoplasm organization and biogenesis (1e-15)		0.007	10
yeast-1036_GO-0005739	2	mitochondrion	R.[YFM]S	34	R.[FY]S.P	14-3-3 binding motifs, Ser must be phosphorylated 	Y				mitochondrial part (1e-31)		0.007	10
protein_40_YPR120C	2	CLB5:  B-type cyclin involved in DNA replication during S phase; activates Cdc28p to promote initiation of DNA synthesis; functions in formation of mitotic spindles along with Clb3p and Clb4p; most abundant during late G1 phase	DD[EFN]	34	G[IVT][LVAC][LVAC][IVT]D[DE][FL][DNST]	MCM_1 PATTERN	Y						0.007	10
protein_40_YPL240C	2	HSP82:  Hsp90 chaperone required for pheromone signaling and negative regulation of Hsf1p; docks with Tom70p for mitochondrial preprotein delivery; promotes telomerase DNA binding and nucleotide addition; interacts with Cns1p, Cpr6p, Cpr7p, Sti1p	[KMW]S.G[TRF]	34	STG	EH(3) EF hand domain binding motif of EPS15, Class II							0.006	9
protein_40_YPL240C	2	HSP82:  Hsp90 chaperone required for pheromone signaling and negative regulation of Hsf1p; docks with Tom70p for mitochondrial preprotein delivery; promotes telomerase DNA binding and nucleotide addition; interacts with Cns1p, Cpr6p, Cpr7p, Sti1p	[PTW][QNE]..KV	34								Y	0.006	10
protein_40_YPL204W	2	HRR25:  Protein kinase involved in regulating diverse events including vesicular trafficking, DNA repair, and chromosome segregation; binds the CTD of RNA pol II; homolog of mammalian casein kinase 1delta (CK1delta)	[NF]IL[KPL]K	34	LLKIL	AP-2 binding motif in CXCR2 receptor							0.004	8
protein_40_YPL204W	2	HRR25:  Protein kinase involved in regulating diverse events including vesicular trafficking, DNA repair, and chromosome segregation; binds the CTD of RNA pol II; homolog of mammalian casein kinase 1delta (CK1delta)	[TRI]EF[PFV]D	34	F.D.F	LIG_AP2alpha_1							0.004	8
protein_40_YPL153C	2	RAD53:  Protein kinase, required for cell-cycle arrest in response to DNA damage; activated by trans autophosphorylation when interacting with hyperphosphorylated Rad9p; also interacts with ARS1 and plays a role in initiation of DNA replication	[AIN]TG[NEY]	34	LP.TG	C-terminal sorting signal which targets surface proteins of Staphylococcus aureus to the cell wall peptidoglycan; Sortase cleaves between Thr and Gly and C-termini is used for crosslinking in cell wall						Y	0.007	10
protein_40_YPL153C	2	RAD53:  Protein kinase, required for cell-cycle arrest in response to DNA damage; activated by trans autophosphorylation when interacting with hyperphosphorylated Rad9p; also interacts with ARS1 and plays a role in initiation of DNA replication	[TDE]N..[SKH]H	34								Y	0.006	10
protein_40_YPL018W	2	CTF19:  Outer kinetochore protein, required for accurate mitotic chromosome segregation; component of the kinetochore sub-complex COMA (Ctf19p, Okp1p, Mcm21p, Ame1p) that functions as a platform for kinetochore assembly	L[LSD][EIL]E	34	S[LW]LD[DE]EL[LM]	TRG_LysEnd_GGAAcLL_2	Y				chromosome, pericentric region (1e-11)		0.007	9
protein_40_YOR310C	2	NOP58:  Protein involved in pre-rRNA processing, 18S rRNA synthesis, and snoRNA synthesis; component of the small subunit processome complex, which is required for processing of pre-18S rRNA	SD..S[SED][GIK]	34	SD.E	Casein kinase II substrate motif					nucleolus (1e-04)		0.005	8
protein_40_YOR133W	2	EFT1:  Elongation factor 2 (EF-2), also encoded by EFT2; catalyzes ribosomal translocation during protein synthesis; contains diphthamide, the unique posttranslationally modified histidine residue specifically ADP-ribosylated by diphtheria toxin	[VGH]G..[ATS]G	34							carboxylic acid metabolism (0.01)		0.007	10
protein_40_YOR133W	2	EFT1:  Elongation factor 2 (EF-2), also encoded by EFT2; catalyzes ribosomal translocation during protein synthesis; contains diphthamide, the unique posttranslationally modified histidine residue specifically ADP-ribosylated by diphtheria toxin	L..[ART]G	34	LP.TG	C-terminal sorting signal which targets surface proteins of Staphylococcus aureus to the cell wall peptidoglycan; Sortase cleaves between Thr and Gly and C-termini is used for crosslinking in cell wall					translation elongation factor activity (0.001)		0.006	10
protein_40_YOR061W	2	CKA2:  Alpha' catalytic subunit of casein kinase 2, a Ser/Thr protein kinase with roles in cell growth and proliferation; the holoenzyme also contains CKA1, CKB1 and CKB2, the many substrates include transcription factors and all RNA polymerases	K[PEY]..AK[AKI]	34	[PT]GKHG.AK	IF5A_HYPUSINE PATTERN							0.004	8
protein_40_YOR039W	2	CKB2:  Beta' regulatory subunit of casein kinase 2, a Ser/Thr protein kinase with roles in cell growth and proliferation; the holoenzyme also contains CKA1, CKA2 and CKB1, the many substrates include transcription factors and all RNA polymerases	[SY][LI].RLR	34			Y						0.004	7
protein_40_YOR039W	2	CKB2:  Beta' regulatory subunit of casein kinase 2, a Ser/Thr protein kinase with roles in cell growth and proliferation; the holoenzyme also contains CKA1, CKA2 and CKB1, the many substrates include transcription factors and all RNA polymerases	R[ARI].L[KN]S	34	R.L	Cyclin A motif that binds cdk2 complexes							0.004	7
protein_40_YOR016C	2	ERP4:  Protein with similarity to Emp24p and Erv25p, member of the p24 family involved in ER to Golgi transport	II..[ITV][IFA]	34									0.007	10
protein_40_YOL086C	2	ADH1:  Alcohol dehydrogenase, fermentative isozyme active as homo- or heterotetramers; required for the reduction of acetaldehyde to ethanol, the last step in the glycolytic pathway	[KDM]TQ[KNR]	34	[ST]Q	ATM kinase phosphorylation site							0.005	8
protein_40_YNL289W	2	PCL1:  Pho85 cyclin of the Pcl1,2-like subfamily, involved in entry into the mitotic cell cycle and regulation of morphogenesis, localizes to sites of polarized cell growth	G.G	34	G.G..G	Phosphate, FAD, NADH, binding motif							0.006	10
protein_40_YNL154C	2	YCK2:  Palmitoylated, plasma membrane-bound casein kinase I isoform; shares redundant functions with Yck1p in morphogenesis, proper septin assembly, endocytic trafficking; provides an essential function overlapping with that of Yck1p	[IDT]K.V[KSG]	34								Y	0.006	10
protein_40_YNL154C	2	YCK2:  Palmitoylated, plasma membrane-bound casein kinase I isoform; shares redundant functions with Yck1p in morphogenesis, proper septin assembly, endocytic trafficking; provides an essential function overlapping with that of Yck1p	E[GNQ]..[PIE]K	34								Y	0.006	10
protein_40_YNL118C	2	DCP2:  Catalytic subunit of the Dcp1p-Dcp2p decapping enzyme complex, which removes the 5' cap structure from mRNAs prior to their degradation; member of the Nudix hydrolase family	L[DNC]..N[FQP]	34							cytoplasmic mRNA processing body (1e-05)		0.006	9
protein_40_YNL118C	2	DCP2:  Catalytic subunit of the Dcp1p-Dcp2p decapping enzyme complex, which removes the 5' cap structure from mRNAs prior to their degradation; member of the Nudix hydrolase family	R[RN]S[KP]R	34	SPRK	CDK2 kinase phosphorylation site (peptide screen)						Y	0.004	8
protein_40_YNL096C	2	RPS7B:  Protein component of the small (40S) ribosomal subunit, nearly identical to Rps7Ap; interacts with Kti11p; deletion causes hypersensitivity to zymocin; has similarity to rat S7 and Xenopus S8 ribosomal proteins	R[RAH].[AGF]R	34	[AG]R	Protease matriptase protease site					cytosolic ribosome (sensu Eukaryota) (1e-16)		0.006	10
protein_40_YMR216C	2	SKY1:  SR protein kinase (SRPK) involved in regulating proteins involved in mRNA metabolism and cation homeostasis; similar to human SRPK1	[DSQ]A.[QAP]E	34			Y						0.006	9
protein_40_YMR049C	2	ERB1:  Protein required for maturation of the 25S and 5.8S ribosomal RNAs; constituent of 66S pre-ribosomal particles; homologous to mammalian Bop1	A.[GRE]K	34	KAPRK[QH][LI]	HISTONE_H3_1 PATTERN					nucleolus (1e-21)		0.006	9
protein_40_YMR047C	2	NUP116:  Subunit of the nuclear pore complex (NPC) that is localized to both sides of the pore; contains a repetitive GLFG motif that interacts with mRNA export factor Mex67p and with karyopherin Kap95p; homologous to Nup100p	SG..[FNC][GKP]	34	SG.G	Glycosaminoglycan attachment site	Y				protein export from nucleus (1e-22)	Y	0.007	9
protein_40_YML085C	2	TUB1:  Alpha-tubulin; associates with beta-tubulin (Tub2p) to form tubulin dimer, which polymerizes to form microtubules	L[VCE][GQH]G	34									0.006	9
protein_40_YML085C	2	TUB1:  Alpha-tubulin; associates with beta-tubulin (Tub2p) to form tubulin dimer, which polymerizes to form microtubules	T[RDW]..[VLK]E	34									0.007	10
protein_40_YML010W	2	SPT5:  Protein that forms a complex with Spt4p and mediates both activation and inhibition of transcription elongation; Spt4p-Spt5p complex also plays a role in pre-mRNA processing	V.R[TEY]	34			Y				nuclear lumen (1e-11)		0.006	10
protein_40_YLR423C	2	ATG17:  Scaffold potein responsible for pre-autophagosomal structure organization; interacts with and is required for activation of Apg1p protein kinase; involved in autophagy but not in the Cvt (cytoplasm to vacuole targeting) pathway	[RF]I.[KQ]AQ	34									0.004	7
protein_40_YLR249W	2	YEF3:  Translational elongation factor 3, stimulates the binding of aminoacyl-tRNA (AA-tRNA) to ribosomes by releasing EF-1 alpha from the ribosomal complex; contains two ABC cassettes; binds and hydrolyses ATP	D[SAE].R[EFG]	34			Y					Y	0.007	10
protein_40_YLR197W	2	SIK1:  Essential evolutionarily-conserved nucleolar protein component of the box C/D snoRNP complexes that direct 2'-O-methylation of pre-rRNA during its maturation; overexpression causes spindle orientation defects	D[TIY]LL[TFP]	34	LLTP	WD40 domain of Cdc4 binding motif, Thr must be phosphorylated, CPD motif					snoRNA binding (1e-04)	Y	0.004	8
protein_40_YLR129W	2	DIP2:  Nucleolar protein, specifically associated with the U3 snoRNA, part of the large ribonucleoprotein complex known as the small subunit (SSU) processome, required for 18S rRNA biogenesis, part of the active pre-rRNA processing complex	[IQC]I..[TMQ]P	34	[ST]P	LIG_WW_4					rRNA processing (1e-08)		0.004	8
protein_40_YLR075W	2	RPL10:  Protein component of the large (60S) ribosomal subunit, responsible for joining the 40S and 60S subunits; regulates translation initiation; has similarity to rat L10 ribosomal protein and to members of the QM gene family	R..A[RGN]	34			Y				cytosolic ribosome (sensu Eukaryota) (1e-19)		0.006	10
protein_40_YLL034C	2	RIX7:  Putative ATPase of the AAA family, required for export of pre-ribosomal large subunits from the nucleus; distributed between the nucleolus, nucleoplasm, and nuclear periphery depending on growth conditions	[KAT]EK[KIM]	34	[ST]E	G protein-coupled receptor kinase 1 substrate motif					nucleolus (1e-07)		0.007	10
protein_40_YKL014C	2	URB1:  Nucleolar protein required for the normal accumulation of 25S and 5.8S rRNAs, associated with the 27SA2 pre-ribosomal particle; proposed to be involved in the biogenesis of the 60S ribosomal subunit	[QV]T.L[SE]K	34									0.004	9
protein_40_YJR145C	2	RPS4A:  Protein component of the small (40S) ribosomal subunit; mutation affects 20S pre-rRNA processing; identical to Rps4Bp and has similarity to rat S4 ribosomal protein	K..[KAE]A	34							ribonucleoprotein complex (1e-24)	Y	0.006	9
protein_40_YJR066W	2	TOR1:  PIK-related protein kinase and rapamycin target; subunit of TORC1, a complex that controls growth in response to nutrients by regulating translation, transcription, ribosome biogenesis, nutrient transport and autophagy; involved in meiosis	F.[IAV]A	34							plasma membrane (1e-15)		0.006	9
protein_40_YJL177W	2	RPL17B:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl17Ap and has similarity to E. coli L22 and rat L17 ribosomal proteins	RA.[KRG][VYG]	34							cytosolic ribosome (sensu Eukaryota) (1e-18)		0.007	10
protein_40_YJL095W	2	BCK1:  Mitogen-activated protein (MAP) kinase kinase kinase acting in the protein kinase C signaling pathway, which controls cell integrity; upon activation by Pkc1p phosphorylates downstream kinases Mkk1p and Mkk2p	[KQW][TYS].SP	34	SP	ERK1, ERK2 Kinase substrate motif							0.007	10
protein_40_YJL092W	2	SRS2:  DNA helicase and DNA-dependent ATPase involved in DNA repair, needed for proper timing of commitment to meiotic recombination and transition from Meiosis I to II; affects genome stability by suppressing unscheduled homologous recombination	Q..E[KQV]	34									0.006	10
protein_40_YJL074C	2	SMC3:  Subunit of the multiprotein cohesin complex required for sister chromatid cohesion in mitotic cells; also required, with Rec8p, for cohesion and recombination during meiosis; phylogenetically conserved SMC chromosomal ATPase family member	EV..[IVG][EKL]	34			Y					Y	0.007	10
protein_40_YJL074C	2	SMC3:  Subunit of the multiprotein cohesin complex required for sister chromatid cohesion in mitotic cells; also required, with Rec8p, for cohesion and recombination during meiosis; phylogenetically conserved SMC chromosomal ATPase family member	F[TRH][VYI]K	34	FTY	mTOR kinase substrate motif					cohesin complex (0.001)	Y	0.005	10
protein_40_YIL094C	2	LYS12:  Homo-isocitrate dehydrogenase, an NAD-linked mitochondrial enzyme required for the fourth step in the biosynthesis of lysine, in which homo-isocitrate is oxidatively decarboxylated to alpha-ketoadipate	F[IKM].G[DQY]	34									0.005	8
protein_40_YIL035C	2	CKA1:  Alpha catalytic subunit of casein kinase 2, a Ser/Thr protein kinase with roles in cell growth and proliferation; the holoenzyme also contains CKA2, CKB1 and CKB2, the many substrates include transcription factors and all RNA polymerases	[VG][LFK]..TSA	34									0.004	7
protein_40_YHR196W	2	UTP9:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	[DIE][TAK]LLT	34	LLTP	WD40 domain of Cdc4 binding motif, Thr must be phosphorylated, CPD motif					rRNA processing (1e-06)		0.004	10
protein_40_YHR196W	2	UTP9:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	[SRA]VA[QDC]	34							rRNA processing (1e-06)	Y	0.006	10
protein_40_YHR196W	2	UTP9:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	E.[SVQ]G	34			Y				nucleolus (1e-22)		0.006	9
protein_40_YHR082C	2	KSP1:  Nonessential putative serine/threonine protein kinase of unknown cellular role; overproduction causes allele-specific suppression of the prp20-10 mutation	[IRT]G.S	34								Y	0.006	10
protein_40_YHR064C	2	SSZ1:  Hsp70 protein that interacts with Zuo1p (a DnaJ homolog) to form a ribosome-associated complex that binds the ribosome via the Zuo1p subunit; also involved in pleiotropic drug resistance via sequential activation of PDR1 and PDR5; binds ATP	A..[APC]K	34							translation (1e-04)		0.006	10
protein_40_YHR064C	2	SSZ1:  Hsp70 protein that interacts with Zuo1p (a DnaJ homolog) to form a ribosome-associated complex that binds the ribosome via the Zuo1p subunit; also involved in pleiotropic drug resistance via sequential activation of PDR1 and PDR5; binds ATP	G.[KYR]A	34	G[KR][KR]	Amidation after cleavage after Gly (must be in secretory pathway)					cytosolic ribosome (sensu Eukaryota) (1e-04)	Y	0.006	9
protein_40_YHL033C	2	RPL8A:  Ribosomal protein L4 of the large (60S) ribosomal subunit, nearly identical to Rpl8Bp and has similarity to rat L7a ribosomal protein; mutation results in decreased amounts of free 60S subunits	S[LSI]S	34	R.S.S.P	14-3-3 binding motifs, Ser must be phosphorylated							0.006	10
protein_40_YGR218W	2	CRM1:  Major karyopherin, involved in export of proteins, RNAs, and ribosomal subunits from the nucleus	[PFG]K[PQC]L	34								Y	0.007	10
protein_40_YGR218W	2	CRM1:  Major karyopherin, involved in export of proteins, RNAs, and ribosomal subunits from the nucleus	A[GNA].T[GSM]	34							snRNP protein import into nucleus (1e-08)	Y	0.007	10
protein_40_YGR218W	2	CRM1:  Major karyopherin, involved in export of proteins, RNAs, and ribosomal subunits from the nucleus	D[IPE]A	34	[LIVMF][LIVMF]DEAD[RKEN].[LIVMFYGSTN]	DEAD_ATP_HELICASE PATTERN					rRNA export from nucleus (1e-06)		0.006	10
protein_40_YGL120C	2	PRP43:  RNA helicase in the DEAH-box family, functions in both RNA polymerase I and polymerase II transcript metabolism, involved in release of the lariat-intron from the spliceosome	AK.[LTV][ASN]S	34							RNA processing (0.01)		0.005	9
protein_40_YGL031C	2	RPL24A:  Ribosomal protein L30 of the large (60S) ribosomal subunit, nearly identical to Rpl24Bp and has similarity to rat L24 ribosomal protein; not essential for translation but may be required for normal translation rate	G[KIM]K[VAY]	34							cytosolic ribosome (sensu Eukaryota) (1e-17)		0.006	10
protein_40_YFL039C	2	ACT1:  Actin, structural protein involved in cell polarization, endocytosis, and other cytoskeletal functions	P[PSK]..PA	34	P[ST]	DNA dependent Protein kinase substrate motif					cortical cytoskeleton (1e-08)	Y	0.006	9
protein_40_YER110C	2	KAP123:  Karyopherin beta, mediates nuclear import of ribosomal proteins prior to assembly into ribosomes and import of histones H3 and H4; localizes to the nuclear pore, nucleus, and cytoplasm; exhibits genetic interactions with RAI1	[SGM]F[GDI]A	34	[DE][DES][DEGAS]F[SGAD][DEAP][LVIMFD]	LIG_AP_GAE_1					rRNA export from nucleus (1e-09)		0.006	9
protein_40_YER074W	2	RPS24A:  Protein component of the small (40S) ribosomal subunit; identical to Rps24Bp and has similarity to rat S24 ribosomal protein	RA.[KRQ][VGK]	34			Y				cytosolic ribosome (sensu Eukaryota) (1e-18)		0.006	10
protein_40_YER036C	2	ARB1:  ATPase of the ATP-binding cassette (ABC) family involved in 40S and 60S ribosome biogenesis, has similarity to Gcn20p; shuttles from nucleus to cytoplasm, physically interacts with Tif6p, Lsg1p	AA.[KGS][KVD]	34							translation (1e-08)		0.007	10
protein_40_YER018C	2	SPC25:  Component of the evolutionarily conserved kinetochore-associated Ndc80 complex (Ndc80p-Nuf2p-Spc24p-Spc25p); involved in chromosome segregation, spindle checkpoint activity and kinetochore clustering	A.[NVE]N	34							microtubule associated complex (0.001)	Y	0.006	9
protein_40_YER018C	2	SPC25:  Component of the evolutionarily conserved kinetochore-associated Ndc80 complex (Ndc80p-Nuf2p-Spc24p-Spc25p); involved in chromosome segregation, spindle checkpoint activity and kinetochore clustering	Q[RN].K[TFW]	34								Y	0.005	10
protein_40_YEL037C	2	RAD23:  Protein with ubiquitin-like N terminus, recognizes and binds damaged DNA (with Rad4p) during nucleotide excision repair; regulates Rad4p levels, subunit of Nuclear Excision Repair Factor 2 (NEF2); homolog of human HR23A and HR23B proteins	AA.[GFW][LTH]	34	[LIV]..[LM]L.AA.[FY][LI]	LIG_Sin3_1							0.006	9
protein_40_YDR510W	2	SMT3:  Ubiquitin-like protein of the SUMO family, conjugated to lysine residues of target proteins; regulates chromatid cohesion, chromosome segregation, APC-mediated proteolysis, DNA replication and septin ring dynamics	[HMR]H..H[HPE]	34									0.006	10
protein_40_YDR471W	2	RPL27B:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl27Ap and has similarity to rat L27 ribosomal protein	[KQR]..AA	34							cytosolic ribosome (sensu Eukaryota) (1e-38)	Y	0.006	10
protein_40_YDR388W	2	RVS167:  Actin-associated protein, subunit of a complex (Rvs161p-Rvs167p) involved in regulation of actin cytoskeleton, endocytosis, and viability following starvation or osmotic stress; homolog of mammalian amphiphysin	K.[TLA]D	34	RKK.[ST]	ZIP kinase phosphorylation motif					cell cortex part (1e-04)	Y	0.006	10
protein_40_YDR324C	2	UTP4:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	L[DE]..[DTE]DA	34							snoRNA binding (0.01)	Y	0.004	8
protein_40_YDL082W	2	RPL13A:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl13Bp; not essential for viability; has similarity to rat L13 ribosomal protein	[RKI][ARG]AR	34	[AG]R	Protease matriptase protease site					cytosolic ribosome (sensu Eukaryota) (1e-18)		0.007	9
protein_40_YDL015C	2	TSC13:  Enoyl reductase that catalyzes the last step in each cycle of very long chain fatty acid elongation, localizes to the ER, highly enriched in a structure marking nuclear-vacuolar junctions, coimmunoprecipitates with elongases Fen1p and Sur4p	L[IYW].[SVF]Y	34	[ILV][ILV][IFV]Y[TV][IL][ILVP]	SH2 ligand for SHP-2N (PTP11n)(Tyr must be phosphorylated)					fatty acid biosynthetic process (0.01)		0.006	9
protein_40_YCR009C	2	RVS161:  Amphiphysin-like lipid raft protein; subunit of a complex (Rvs161p-Rvs167p) that regulates polarization of the actin cytoskeleton, endocytosis, cell polarity, cell fusion and viability following starvation or osmotic stress	KS.[ED][EP]I	34	S.D	CAMKII phosphorylation site							0.004	8
protein_40_YBR217W	2	ATG12:  Ubiquitin-like modifier, conjugated via an isopeptide bond to a lysine residue of Atg5p by the E1 enzyme, Atg7p, and the E2 enzyme, Atg10p, a step that is essential for autophagy	V[KIE]..G[TIS]	34			Y						0.007	10
protein_40_YBR109C	2	CMD1:  Calmodulin; Ca++ binding protein that regulates Ca++ independent processes (mitosis, bud growth, actin organization, endocytosis, etc.) and Ca++ dependent processes (stress-activated pathways), targets include Nuf1p, Myo2p and calcineurin	LK[KGP]F[TEK]	34									0.004	8
protein_40_YBR055C	2	PRP6:  Splicing factor, component of the U4/U6-U5 snRNP complex	T[PIA].E[AFV]	34	[ST]..E	Casien kinase II consensus phosphorylation site					spliceosome (1e-04)	Y	0.007	10
protein_40_YBR010W	2	HHT1:  One of two identical histone H3 proteins (see also HHT2); core histone required for chromatin assembly, involved in heterochromatin-mediated telomeric and HM silencing; regulated by acetylation, methylation, and mitotic phosphorylation	[LNE][LY].TSS	34	S[ST]	MDC1 BRCT domain binding motif					regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism (1e-06)		0.004	8
protein_40_YBL026W	2	LSM2:  Lsm (Like Sm) protein; part of heteroheptameric complexes (Lsm2p-7p and either Lsm1p or 8p): cytoplasmic Lsm1p complex involved in mRNA decay; nuclear Lsm8p complex part of U6 snRNP and possibly involved in processing tRNA, snoRNA, and rRNA	[ILD]G..A[TAY]G	34	GR.A	Protease tPA proteolytic site							0.004	7
protein_40_YAR007C	2	RFA1:  Subunit of heterotrimeric Replication Protein A (RPA), which is a highly conserved single-stranded DNA binding protein involved in DNA replication, repair, and recombination	D..[LEF]G	34	DH[YF]LGK[EQK]	G6P_DEHYDROGENASE PATTERN					response to DNA damage stimulus (1e-06)		0.006	10
protein_40_YAL035W	2	FUN12:  GTPase, required for general translation initiation by promoting Met-tRNAiMet binding to ribosomes and ribosomal subunit joining; homolog of bacterial IF2	G[KNI][KYC]V	34			Y				cytosolic ribosome (sensu Eukaryota) (1e-07)		0.006	10
protein_40_YAL032C	2	PRP45:  Protein required for pre-mRNA splicing; associates with the spliceosome and interacts with splicing factors Prp22p and Prp46p; orthologous to human transcriptional coactivator SKIP and can activate transcription of a reporter gene	[KYR][KRQ]..SR	34							spliceosome (1e-06)	Y	0.007	10
protein_40_YAL032C	2	PRP45:  Protein required for pre-mRNA splicing; associates with the spliceosome and interacts with splicing factors Prp22p and Prp46p; orthologous to human transcriptional coactivator SKIP and can activate transcription of a reporter gene	AI..[LYP][LYT]	34							nuclear mRNA splicing, via spliceosome (0.01)		0.007	10
protein_40_YAL032C	2	PRP45:  Protein required for pre-mRNA splicing; associates with the spliceosome and interacts with splicing factors Prp22p and Prp46p; orthologous to human transcriptional coactivator SKIP and can activate transcription of a reporter gene	E..I[QIN]	34							spliceosome (1e-05)	Y	0.006	10
protein_40_YAL032C	2	PRP45:  Protein required for pre-mRNA splicing; associates with the spliceosome and interacts with splicing factors Prp22p and Prp46p; orthologous to human transcriptional coactivator SKIP and can activate transcription of a reporter gene	E[SIY]R	34	[LIVM][ST][KR][LIVMF]E[ST]RP	PREPHENATE_DEHYDR_2 PATTERN	Y				nuclear mRNA splicing, via spliceosome (1e-11)	Y	0.006	10
protein_40_YAL032C	2	PRP45:  Protein required for pre-mRNA splicing; associates with the spliceosome and interacts with splicing factors Prp22p and Prp46p; orthologous to human transcriptional coactivator SKIP and can activate transcription of a reporter gene	KI[VPI]	34	IP[IV]	Crystallin motif for dimerization					nuclear mRNA splicing, via spliceosome (1e-11)		0.006	10
oshea_nuclear_periphery	2	oshea_nuclear_periphery	N[KYQ]..N[ITF]	34							nucleocytoplasmic transport (1e-12)	Y	0.007	9
oshea_nuclear_periphery	2	oshea_nuclear_periphery	Q[KSA]S	34	RQ.SFD	CAM Kinase II kinase phosphorylation site (peptide screen)					nuclear pore (1e-40)	Y	0.007	10
oshea_Golgi	2	oshea_Golgi	[LV][LI]..PNL	34	P.L	Motif in C-Fos for protein instability					Golgi apparatus (1e-04)		0.004	8
oshea_endosome	2	oshea_endosome	RK..[ECW][NWR]	34	RRK.[ST]	ZIP kinase phosphorylation motif					vacuolar transport (1e-11)		0.006	10
matsuyama_vacuole	2	matsuyama_vacuole	[VQY][SD]NTL	34	N.LY	Dok1 PTB domain binding motif					vacuole (0.001)		0.006	9
matsuyama_Spindle_or_SPB	2	matsuyama_Spindle_or_SPB	E..N[NLM]	34							spindle (1e-10)		0.009	10
matsuyama_Spindle_or_SPB	2	matsuyama_Spindle_or_SPB	S..[LKH]N	34							spindle (1e-13)	Y	0.008	10
matsuyama_Nucleus	2	matsuyama_Nucleus	D.[EMW]E	34	D.[WF]EH[STA][FY][FY]	SOD_MN PATTERN					DNA metabolism (1e-17)		0.008	10
matsuyama_Golgi	2	matsuyama_Golgi	[LVM]L.[TGV]V	34							Golgi apparatus (1e-51)	Y	0.009	9
matsuyama_Cytosol	2	matsuyama_Cytosol	[TIE]V.[SET]V	34									0.008	10
matsuyama_Cytosol	2	matsuyama_Cytosol	S.[QVM]R	34	R.DSPVR	14-3-3 binding motif on N-terminal domain of Nitrate Reductase necessary for 14-3-3 binding for inactivation in the dark	Y				purine nucleotide binding (1e-04)	Y	0.008	10
genetic_YPL055C	2	LGE1: Protein of unknown function; null mutant forms abnormally large cells, and homozygous diploid null mutant displays delayed premeiotic DNA synthesis and reduced efficiency of meiotic nuclear division	F.[KTR]D	34							DNA metabolism (1e-04)	Y	0.006	10
genetic_YNL153C	2	GIM3: Subunit of the heterohexameric cochaperone prefoldin complex which binds specifically to cytosolic chaperonin and transfers target proteins to it	[NEG]I..N[SCV]L	34							telomere organization and biogenesis (0.01)		0.005	10
genetic_YLR200W	2	YKE2: Subunit of the heterohexameric Gim/prefoldin protein complex involved in the folding of alpha-tubulin, beta-tubulin, and actin	PP..[SKN][SVH]	34	PP.Y	LIG_WW_1					asexual reproduction (0.01)	Y	0.006	10
genetic_YGL058W	2	RAD6: Ubiquitin-conjugating enzyme (E2), involved in postreplication repair (with Rad18p), sporulation, telomere silencing, and ubiquitin-mediated N-end rule protein degradation (with Ubr1p)	E.[KFR]T	34							DNA metabolism (1e-12)	Y	0.006	10
genetic_YGL020C	2	GET1: Subunit of the GET complex; required for the retrieval of HDEL proteins from the Golgi to the ER in an ERD2 dependent fashion and for normal mitochondrial morphology and inheritance	E.L	34	ENLYFQ[GS]	Protease TEV - stringent					chromosome organization and biogenesis (sensu Eukaryota) (1e-26)	Y	0.006	10
genetic_YER083C	2	GET2: Subunit of the GET complex; required for meiotic nuclear division and for the retrieval of HDEL proteins from the Golgi to the ER in an ERD2 dependent fashion; may be involved in cell wall function	I..L[KQN]	34							chromosome organization and biogenesis (sensu Eukaryota) (1e-16)		0.006	10
genetic_YER083C	2	GET2: Subunit of the GET complex; required for meiotic nuclear division and for the retrieval of HDEL proteins from the Golgi to the ER in an ERD2 dependent fashion; may be involved in cell wall function	I.K[NFP]	34							telomere organization and biogenesis (1e-06)	Y	0.006	10
genetic_YEL003W	2	GIM4: Subunit of the heterohexameric cochaperone prefoldin complex which binds specifically to cytosolic chaperonin and transfers target proteins to it	S[TNR]N	34	S[ST]	MDC1 BRCT domain binding motif					cytoskeleton organization and biogenesis (1e-06)	Y	0.006	10
genetic_YAL024C	2	LTE1: Putative GDP/GTP exchange factor required for mitotic exit at low temperatures; acts as a guanine nucleotide exchange factor (GEF) for Tem1p, which is a key regulator of mitotic exit; physically associates with Ras2p-GTP	E[ELN]..[QWY]L	34							cell cycle (1e-06)		0.006	9
yeast-589_GO-0050896	2	response to stimulus	[PVN]S..[SNP]S	33	S..[ST]	Casein Kinase I consensus phosphorylation site (N-term Ser must first be phosphorylated)		Pkinase	1.E-02	-3.2	response to stress (1e-66)		0.007	10
protein_40_YLR074C	2	BUD20:  Protein involved in bud-site selection; diploid mutants display a random budding pattern instead of the wild-type bipolar pattern	K[KPR].A[KFE]	33	KR	CLV_PCSK_PC1ET2_1		Histone	1.E-02	-1.9	cytoplasm organization and biogenesis (1e-04)	Y	0.007	10
protein_40_YML069W	2	POB3:  Subunit of the heterodimeric FACT complex (Spt16p-Pob3p), which facilitates RNA Pol II transcription elongation through nucleosomes by destabilizing and then reassembling nucleosome structure; interacts with DNA polymerase alpha (Pol1p)	[GH]S..KA[SI]	33				Histone	1.E-02	-1.6	establishment and/or maintenance of chromatin architecture (0.001)		0.004	8
yeast-341_GO-0045449	2	regulation of transcription	H[TFS].E	33	F.E	DNA binding motif in MutS	Y	zf-C2H2	1.E-15	-1.5	regulation of transcription (1e-91)		0.007	10
half_life_belle_q3	3	half_life_belle quantized 3	L...Q	33	[DE][DE][FL][FL][DE][LM][IL]...Q[GS].R[LM][DE][DE]QR	GoLoco motif, a G alpha binding motif		Zn_clus	1.E-03	-1.5	cell cycle (0.001)	Y	0.014	9
protein_40_YDR324C	2	UTP4:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	[KDN]ED[DEG]	33	EDAIY	Abl kinase substrate motif	Y	WD40	1.E-04	-1.4	nucleolus (1e-29)	Y	0.006	10
yeast-544_GO-0016070	2	RNA metabolism	T[GNC].[GLN]KT	33				Helicase_C	1.E-22	-1.3	RNA helicase activity (1e-25)		0.008	10
protein_40_YDR496C	2	PUF6:  Pumilio-homology domain protein that binds ASH1 mRNA at PUF consensus sequences in the 3' UTR and represses its translation, resulting in proper asymmetric localization of ASH1 mRNA	[HNR]R.[GAP]R	33	[AG]R	Protease matriptase protease site	Y	DEAD	1.E-05	-1.3	cytoplasm organization and biogenesis (1e-10)		0.006	10
matsuyama_periphery	2	matsuyama_periphery	RK[FSP]	33			Y	Pkinase	1.E-03	-1.3	barrier septum (1e-53)		0.008	10
yeast-752_GO-0016787	2	hydrolase activity	DK..[TLG][LEW]T	33	K..[ST]	PKA kinase substrate motif		E1-E2_ATPase	1.E-11	-1.2	ATPase activity, coupled to transmembrane movement of ions, phosphorylative mechanism (1e-12)	Y	0.008	10
yeast-752_GO-0016787	2	hydrolase activity	GG..L[NCY][LY]	33	GGQ	N-methylation motif in E. coli, Gln residue in methylated, mimics CCA motif at the end of tRNA molecule		SNF2_N	1.E-03	-1.2			0.006	8
yeast-661_GO-0050789	2	regulation of biological process	T[AST]A	33	KTPAKEE	GSK-3, ERK1, ERK2, CDK5 substrate motif		Zn_clus	1.E-04	-1.2	regulation of metabolism (1e-13)	Y	0.007	10
protein_40_YOR181W	2	LAS17:  Actin assembly factor, activates the Arp2/3 protein complex that nucleates branched actin filaments; localizes with the Arp2/3 complex to actin patches; homolog of the human Wiskott-Aldrich syndrome protein (WASP)	A[IQT]..[ASL]G	33			Y	SH3_1	1.E-10	-1.1	endocytosis (1e-04)		0.006	10
protein_40_YHR148W	2	IMP3:  Component of the SSU processome, which is required for pre-18S rRNA processing, essential protein that interacts with Mpp10p and mediates interactions of Imp4p and Mpp10p with U3 snoRNA	D[ELI]E[DIR]	33	WLDLE	14-3-3 binding motif from peptide screen		WD40	1.E-03	-1.1	rRNA processing (1e-26)		0.007	10
protein_40_YPL153C	2	RAD53:  Protein kinase, required for cell-cycle arrest in response to DNA damage; activated by trans autophosphorylation when interacting with hyperphosphorylated Rad9p; also interacts with ARS1 and plays a role in initiation of DNA replication	Q..L[PKS]	33				PH	1.E-02	-1			0.006	10
protein_40_YKL021C	2	MAK11:  Protein involved in an early, nucleolar step of 60S ribosomal subunit biogenesis; essential for cell growth and replication of killer M1 dsRNA virus; contains four beta-transducin repeats	R[TLW]..A[GQK]	33				DEAD	1.E-02	-1	cytoplasm organization and biogenesis (1e-11)		0.005	9
yeast-470_GO-0006259	2	DNA metabolism	[IDV]ID[LEG]	33	VEID	Protease Caspase 6 -stringent		Helicase_C	1.E-03	-0.9	DNA metabolism (1e-79)	Y	0.007	10
protein_40_YPL153C	2	RAD53:  Protein kinase, required for cell-cycle arrest in response to DNA damage; activated by trans autophosphorylation when interacting with hyperphosphorylated Rad9p; also interacts with ARS1 and plays a role in initiation of DNA replication	I...P	33				Septin	1.E-02	-0.8	DNA damage response, signal transduction (1e-04)	Y	0.006	10
protein_40_YNR054C	2	ESF2:  Essential nucleolar protein involved in pre-18S rRNA processing; component of the small subunit (SSU) processome; has sequence similarity to mABT1, a mouse transcription activator	K[KVI].K[LAH]	33	K[KR].[KR]	Nuclear localization motif		Helicase_C	1.E-02	-0.8	rRNA processing (1e-12)	Y	0.006	10
protein_40_YOL133W	2	HRT1:  RING finger containing subunit of Skp1-Cullin-F-box ubiquitin protein ligases (SCF); required for Gic2p, Far1p, Sic1p and Cln2p degradation; may tether Cdc34p (a ubiquitin conjugating enzyme or E2) and Cdc53p (a cullin) subunits of SCF	D..[AVK]T	33				F-box	1.E-07	-0.7	cullin-RING ubiquitin ligase complex (1e-10)	Y	0.006	10
matsuyama_nuclear_envelope_or_dots	2	matsuyama_nuclear_envelope_or_dots	Y..Q	33	Y..Q	LIG_SH2_STAT3		IBN_N	1.E-04	-0.7	nuclear envelope (1e-38)	Y	0.008	9
half_life_belle_q3	3	half_life_belle quantized 3	I.P	33	YIPP	AT(1) receptor motif necessary for activation of Jak/Stat pathway		Zn_clus	1.E-02	-0.7	transcription regulator activity (1e-05)		0.014	10
yeast-548_GO-0051641	2	cellular localization	N[ENK]..E[DAM]	33				IBN_N	1.E-03	-0.6	cellular localization (1e-65)		0.007	10
yeast-320_GO-0006355	2	regulation of transcription, DNA-dependent	Q..I[NPY]	33	IY	cFGR and Csk kinase phosphorylation site (peptide screen)	Y	Zn_clus	1.E-02	-0.6	regulation of transcription, DNA-dependent (1e-10)		0.007	10
yeast-312_GO-0006414	2	translational elongation	RE..[LA][LK]A	33				GTP_EFTU_D2	1.E-02	-0.6	translational elongation (1e-07)		0.004	8
protein_40_YOL133W	2	HRT1:  RING finger containing subunit of Skp1-Cullin-F-box ubiquitin protein ligases (SCF); required for Gic2p, Far1p, Sic1p and Cln2p degradation; may tether Cdc34p (a ubiquitin conjugating enzyme or E2) and Cdc53p (a cullin) subunits of SCF	Y[GVK][SEC]N	33	KEN	LIG_APCC_KENbox_2		F-box	1.E-05	-0.6	ubiquitin ligase complex (1e-04)	Y	0.006	9
protein_40_YMR047C	2	NUP116:  Subunit of the nuclear pore complex (NPC) that is localized to both sides of the pore; contains a repetitive GLFG motif that interacts with mRNA export factor Mex67p and with karyopherin Kap95p; homologous to Nup100p	SN[PKQ]	33	NPC	N-glycosylation site- aberrant		IBN_N	1.E-03	-0.6	nucleocytoplasmic transport (1e-25)	Y	0.006	10
oshea_bud_neck	2	oshea_bud_neck	K[LSP][GSP]T	33	LPTSY	SMAD interacting motif- FM1 in motif for binding in XFoxH1		PH	1.E-03	-0.6	bud neck (1e-25)		0.007	10
protein_40_YOL133W	2	HRT1:  RING finger containing subunit of Skp1-Cullin-F-box ubiquitin protein ligases (SCF); required for Gic2p, Far1p, Sic1p and Cln2p degradation; may tether Cdc34p (a ubiquitin conjugating enzyme or E2) and Cdc53p (a cullin) subunits of SCF	[DNC]I..[AIQ]V	33				F-box	1.E-04	-0.5	cullin-RING ubiquitin ligase complex (1e-04)		0.006	10
protein_40_YLR293C	2	GSP1:  GTP binding protein (mammalian Ranp homolog) involved in the maintenance of nuclear organization, RNA processing and transport; regulated by Prp20p, Rna1p, Yrb1p, Yrb2p, Yrp4p, Yrb30p, Cse1p and Kap95p; yeast Gsp2p homolog	[APR]F[GAW]S	33				IBN_N	1.E-03	-0.5	nuclear transport (1e-14)	Y	0.006	10
protein_40_YJL092W	2	SRS2:  DNA helicase and DNA-dependent ATPase involved in DNA repair, needed for proper timing of commitment to meiotic recombination and transition from Meiosis I to II; affects genome stability by suppressing unscheduled homologous recombination	S[DKP].I[NTS]	33	SP	ERK1, ERK2 Kinase substrate motif		IBN_N	1.E-02	-0.5			0.006	10
protein_40_YIL094C	2	LYS12:  Homo-isocitrate dehydrogenase, an NAD-linked mitochondrial enzyme required for the fourth step in the biosynthesis of lysine, in which homo-isocitrate is oxidatively decarboxylated to alpha-ketoadipate	[DVQ]V..[IDG]E	33				IBN_N	1.E-03	-0.5	protein carrier activity (0.01)	Y	0.007	10
protein_40_YBL003C	2	HTA2:  One of two nearly identical (see also HTA1) histone H2A subtypes; core histone required for chromatin assembly and chromosome function; DNA damage-dependent phosphorylation by Mec1p facilitates DNA repair; acetylated by Nat4p	AV.[KFR][SYP]	33			Y	Histone	1.E-04	-0.5	nuclear nucleosome (1e-05)		0.007	9
protein_40_YOL133W	2	HRT1:  RING finger containing subunit of Skp1-Cullin-F-box ubiquitin protein ligases (SCF); required for Gic2p, Far1p, Sic1p and Cln2p degradation; may tether Cdc34p (a ubiquitin conjugating enzyme or E2) and Cdc53p (a cullin) subunits of SCF	DE.[QSR][RSG]	33	LPDEL	Motif in CBP for interaction with PPARg-LBD (secondary site)		F-box	1.E-02	-0.4	protein catabolism (0.01)	Y	0.006	10
protein_40_YDR328C	2	SKP1:  Evolutionarily conserved kinetochore protein that is part of multiple protein complexes, including the SCF ubiquitin ligase complex, the CBF3 complex that binds centromeric DNA, and the RAVE complex that regulates assembly of the V-ATPase	L[LGN].RL[VFE]	33			Y	F-box	1.E-04	-0.4	ubiquitin ligase complex (0.001)		0.004	7
protein_40_YBR159W	2	IFA38: Microsomal beta-keto-reductase; contains oleate response element (ORE) sequence in the promoter region; mutants exhibit reduced VLCFA synthesis, accumulate high levels of dihydrosphingosine, phytosphingosine and medium-chain ceramides	L[PAI].[ITY]A	33				MFS_1	1.E-02	-0.3	transporter activity (1e-07)		0.006	10
protein_40_YOR272W	2	YTM1:  Constituent of 66S pre-ribosomal particles, required for maturation of the large ribosomal subunit	K.[ARW]K	33	SKRKYRK	TP1 PATTERN		Brix	1.E-02	-0.2	cytoplasm organization and biogenesis (1e-32)	Y	0.006	10
protein_40_YJL074C	2	SMC3:  Subunit of the multiprotein cohesin complex required for sister chromatid cohesion in mitotic cells; also required, with Rec8p, for cohesion and recombination during meiosis; phylogenetically conserved SMC chromosomal ATPase family member	[RLT]E.L[VQT]	33	[ST]E	G protein-coupled receptor kinase 1 substrate motif		SMC_N	1.E-03	0.1	nuclear chromosome part (0.001)		0.006	9
protein_40_YJL074C	2	SMC3:  Subunit of the multiprotein cohesin complex required for sister chromatid cohesion in mitotic cells; also required, with Rec8p, for cohesion and recombination during meiosis; phylogenetically conserved SMC chromosomal ATPase family member	K[LTI]..[MCL]E	33	L..[LM]E	Sec24p	Y	SMC_N	1.E-03	0.2	cohesin complex (0.01)	Y	0.007	10
yeast-215_GO-0005694	2	chromosome	Q.D[LDY]	33	GIQVD	dynein light chain LC8 interacting motif -alternative		SMC_N	1.E-06	0.3	chromosome (1e-97)		0.007	10
yeast-470_GO-0006259	2	DNA metabolism	V[SKQ].[KQP]D	33				SMC_N	1.E-02	0.4	DNA metabolism (1e-48)	Y	0.007	10
yeast-335_GO-0016772	2	transferase activity, transferring phosphorus-containing groups	[KDA]K..KR[EAD]	33	KR	CLV_PCSK_PC1ET2_1		Pkinase	1.E-04	0.4	transferase activity, transferring phosphorus-containing groups (1e-15)		0.007	9
matsuyama_K_G15	15	matsuyama_K_G15	IF.[VIY]	33	F.[YF]P	DEF motif for ERK docking		MFS_1	1.E-05	0.5	Golgi apparatus (1e-35)		0.030	10
yeast-631_GO-0050794	2	regulation of cellular process	T..[RIN]R	33	[KR]R	CLV_PCSK_KEX2_1		Zn_clus	1.E-02	0.6	regulation of metabolism (1e-76)		0.007	10
protein_40_YOR181W	2	LAS17:  Actin assembly factor, activates the Arp2/3 protein complex that nucleates branched actin filaments; localizes with the Arp2/3 complex to actin patches; homolog of the human Wiskott-Aldrich syndrome protein (WASP)	[NEA]T..V[PY]	33	VP	Interleukin converting enzyme protease	Y	SH3_1	1.E-04	0.6	actin cortical patch (1e-07)		0.005	9
protein_40_YDL014W	2	NOP1:  Nucleolar protein, component of the small subunit processome complex, which is required for processing of pre-18S rRNA; has similarity to mammalian fibrillarin	V..[KNV]D	33			Y	WD40	1.E-02	0.6	nucleolus (1e-34)		0.006	10
protein_40_YLR372W	2	SUR4:  Elongase, involved in fatty acid and sphingolipid biosynthesis; synthesizes very long chain 20-26-carbon fatty acids from C18-CoA primers; involved in regulation of sphingolipid biosynthesis	II..[ILMV][GWI]	33				Sugar_tr	1.E-02	0.8	integral to membrane (0.01)		0.007	10
protein_40_YGL106W	2	MLC1:  Essential light chain for Myo1p, light chain for Myo2p; stabilizes Myo2p by binding to the neck region; interacts with Myo1p, Iqg1p, and Myo2p to coordinate formation and contraction of the actomyosin ring with targeted membrane deposition	[ENC]Q.A[ENT]	33				UCH	1.E-02	0.8	ubiquitin-specific protease activity (0.01)	Y	0.005	9
yeast-457_GO-0007001	2	chromosome organization and biogenesis (sensu Eukaryota)	[AG]Q[ANM]Q	33				Helicase_C	1.E-02	1	chromosome organization and biogenesis (sensu Eukaryota) (1e-24)	Y	0.007	10
yeast-255_GO-0042254	2	ribosome biogenesis and assembly	G..[ENG]K	33	Q[MLVI]DG..[DE]	CLV_TASPASE1		WD40	1.E-05	1	cytoplasm organization and biogenesis (1e-12)		0.007	10
yeast-255_GO-0007028	2	cytoplasm organization and biogenesis	G..[ENG]K	33	Q[MLVI]DG..[DE]	CLV_TASPASE1		WD40	1.E-05	1	cytoplasm organization and biogenesis (1e-12)		0.007	10
yeast-1433_GO-0006139	2	nucleobase, nucleoside, nucleotide and nucleic acid metabolism	L[LAV]N	33	HLVNK	Motif for targeting CD44 to basolateral membranes		BRCT	1.E-03	1	DNA metabolism (1e-09)		0.007	10
protein_40_YNL189W	2	SRP1:  Karyopherin alpha homolog, forms a dimer with karyopherin beta Kap95p to mediate import of nuclear proteins, binds the nuclear localization signal of the substrate during import; may also play a role in regulation of protein degradation	[NMG]S[LEF]EE	33	EEEYF	EGFR kinase phosphorylation site (peptide screen)		RNase_PH_C	1.E-02	1			0.005	9
protein_40_YMR093W	2	UTP15:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	[KRQ]L[LYR]A	33				WD40	1.E-05	1	rRNA processing (1e-23)	Y	0.007	10
protein_40_YMR047C	2	NUP116:  Subunit of the nuclear pore complex (NPC) that is localized to both sides of the pore; contains a repetitive GLFG motif that interacts with mRNA export factor Mex67p and with karyopherin Kap95p; homologous to Nup100p	Q..E[QNR]	33				IBN_N	1.E-05	1.1	nucleocytoplasmic transport (1e-24)	Y	0.006	10
protein_40_YBR159W	2	IFA38: Microsomal beta-keto-reductase; contains oleate response element (ORE) sequence in the promoter region; mutants exhibit reduced VLCFA synthesis, accumulate high levels of dihydrosphingosine, phytosphingosine and medium-chain ceramides	L[LWM]G	33	LLG	Beta2-Integrin binding motif	Y	MFS_1	1.E-02	1.1	transporter activity (1e-09)	Y	0.006	10
protein_40_YML007W	2	YAP1:  Basic leucine zipper (bZIP) transcription factor required for oxidative stress tolerance; activated by H2O2 through the multistep formation of disulfide bonds and transit from the cytoplasm to the nucleus; mediates resistance to cadmium	LT.[QLP][QYG]	33	LLTP	WD40 domain of Cdc4 binding motif, Thr must be phosphorylated, CPD motif		Bromodomain	1.E-03	1.3	nucleoplasm part (1e-13)	Y	0.007	10
genetic_YNL153C	2	GIM3: Subunit of the heterohexameric cochaperone prefoldin complex which binds specifically to cytosolic chaperonin and transfers target proteins to it	S.[RSM]H	33	S.R	PKC phosphorylation motif		Kinesin	1.E-02	1.3	cell cycle (1e-07)	Y	0.006	10
yeast-921_GO-0006810	2	transport	V..[VFI]V	33				MFS_1	1.E-04	1.4	intracellular transport (1e-75)	Y	0.007	10
yeast-290_GO-0009057	2	macromolecule catabolism	GP..T[PED][YSA]	33	GP	Protease TTP cleavage site	Y	UQ_con	1.E-08	1.4	macromolecule catabolism (1e-08)		0.005	7
yeast-921_GO-0006810	2	transport	A..F[GFW]	33				MFS_1	1.E-08	1.5	transporter activity (1e-52)	Y	0.007	10
protein_40_YLR222C	2	UTP13:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	[FID]K.[FWY]D	33				WD40	1.E-02	1.5	small nucleolar ribonucleoprotein complex (1e-15)		0.006	10
protein_40_YMR304W	2	UBP15:  Ubiquitin-specific protease that may play a role in ubiquitin precursor processing	S[NLM]G	33	STG	EH(3) EF hand domain binding motif of EPS15, Class II		Pkinase	1.E-03	1.6	protein kinase activity (0.01)		0.006	10
oshea_spindle_pole	2	oshea_spindle_pole	DL..[SPQ][EMI]	33	DLL	Binding motif for clathrin heavy chain ear		Kinesin	1.E-03	1.6	microtubule cytoskeleton (1e-35)		0.007	10
Oshea_mcl	13	Oshea_mcl	I..[FLV]I	33				MFS_1	1.E-11	1.6	endoplasmic reticulum (1e-39)		0.034	10
yeast-939_GO-0051234	2	establishment of localization	[LQV]Y[RTW]G	33	YIGPY	PTB binding motif for NUMB-PTB domain (does not need to be Tyr phosphorylated)	Y	Mito_carr	1.E-14	1.7	transporter activity (1e-20)	Y	0.007	10
protein_40_YLL008W	2	DRS1:  Nucleolar DEAD-box protein required for ribosome assembly and function, including synthesis of 60S ribosomal subunits; constituent of 66S pre-ribosomal particles	[IKS]G..S[FED]	33	DSG..S	WD40 binding motif, Ser residues must be phosphorylated	Y	Pkinase	1.E-11	1.7	protein kinase activity (1e-10)	Y	0.007	10
yeast-706_GO-0043412	2	biopolymer modification	H[PEY]N[IVH]	33			Y	UQ_con	1.E-16	1.8	protein modification (1e-26)		0.007	10
protein_40_YOL133W	2	HRT1:  RING finger containing subunit of Skp1-Cullin-F-box ubiquitin protein ligases (SCF); required for Gic2p, Far1p, Sic1p and Cln2p degradation; may tether Cdc34p (a ubiquitin conjugating enzyme or E2) and Cdc53p (a cullin) subunits of SCF	L[PCH]N	33	[IL].NP.Y	PTB of Shc interaction motif, Must be Tyr phosphorylated, motif on autophosphorylated NGFR recognized by PI domain of Src- stringent		F-box	1.E-14	1.8	ubiquitin ligase complex (1e-11)	Y	0.006	9
protein_40_YMR093W	2	UTP15:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	[TIA]G..[DYM]K	33				WD40	1.E-04	1.8	rRNA processing (1e-14)		0.006	9
protein_40_YKR001C	2	VPS1:  Dynamin-like GTPase required for vacuolar sorting; also involved in actin cytoskeleton organization, late Golgi-retention of some proteins, regulating peroxisome biogenesis	GK..[QY]T[IS]	33				SNF2_N	1.E-02	2.3	ATPase activity (0.001)		0.004	7
protein_40_YJR002W	2	MPP10:  Component of the SSU processome, which is required for pre-18S rRNA processing, interacts with and controls the stability of Imp3p and Imp4p, essential for viability; similar to human Mpp10p	[DGM]G..K[VYN]	33	G..G..K	Sulfonate donor binding site in sulfotransferases		WD40	1.E-07	2.5	snoRNA binding (1e-16)		0.006	9
matsuyama_Cytosol	2	matsuyama_Cytosol	R[LQD]L	33	R[RH][RH][RE]RE[RH]SR[RD]L	CLK2 kinase substrate motif	Y	Pkinase	1.E-04	2.5	ATP binding (1e-11)		0.008	10
yeast-565_GO-0006464	2	protein modification	I...D	33				Pkinase	1.E-19	2.7	protein modification (10)	Y	0.007	10
protein_40_YLL008W	2	DRS1:  Nucleolar DEAD-box protein required for ribosome assembly and function, including synthesis of 60S ribosomal subunits; constituent of 66S pre-ribosomal particles	[GW]S[FCD]G	33	R.GSF	PKCdelta kinase phosphorylation site (peptide screen)		Pkinase	1.E-10	2.9	protein kinase activity (1e-10)		0.005	10
yeast-1721_GO-0016043	2	cell organization and biogenesis	V[RQV].[WYN]D	33				WD40	1.E-10	3.1	chromosome organization and biogenesis (sensu Eukaryota) (1e-07)		0.007	10
protein_40_YBR031W	2	RPL4A:  N-terminally acetylated protein component of the large (60S) ribosomal subunit, nearly identical to Rpl4Bp and has similarity to E. coli L4 and rat L4 ribosomal proteins	[LFR]DE[AK]D	33	[LIVMF][LIVMF]DEAD[RKEN].[LIVMFYGSTN]	DEAD_ATP_HELICASE PATTERN		DEAD	1.E-07	3.3	RNA helicase activity (1e-07)		0.004	7
protein_40_YPL043W	2	NOP4:  Nucleolar protein, essential for processing and maturation of 27S pre-rRNA and large ribosomal subunit biogenesis; constituent of 66S pre-ribosomal particles; contains four RNA recognition motifs (RRMs)	[RNE]E[LEW]A	33	[KRHQSA][DENQ]EL	ER_TARGET PATTERN	Y	DEAD	1.E-03	3.4	cytoplasm organization and biogenesis (1e-16)		0.007	10
protein_40_YNL186W	2	UBP10:  Ubiquitin-specific protease that deubiquitinates ubiquitin-protein moieties; may regulate silencing by acting on Sir4p; involved in posttranscriptionally regulating Gap1p and possibly other transporters; primarily located in the nucleus	[LIM]K.[EHD]N	33	[VILMAFP]K.E	MOD_SUMO	Y	Pkinase	1.E-24	3.7	protein kinase activity (1e-22)	Y	0.007	9
protein_40_YER165W	2	PAB1:  Poly(A) binding protein, part of the 3'-end RNA-processing complex, mediates interactions between the 5' cap structure and the 3' mRNA poly(A) tail, involved in control of poly(A) tail length, interacts with translation factor eIF-4G	KG[TYC][GAH]	33				RRM_1	1.E-05	3.9	mRNA metabolism (0.001)	Y	0.006	10
yeast-410_GO-0007049	2	cell cycle	K[LEY].DF[GSN]	33				Pkinase	1.E-15	4.1	cell cycle (1e-19)		0.008	10
protein_40_YCR057C	2	PWP2:  Conserved 90S pre-ribosomal component essential for proper endonucleolytic cleavage of the 35 S rRNA precursor at A0, A1, and A2 sites; contains eight WD-repeats; PWP2 deletion leads to defects in cell cycle and bud morphogenesis	[RHG]R.[AGQ]R	33	[AG]R	Protease matriptase protease site		Helicase_C	1.E-04	5.2	rRNA processing (1e-10)	Y	0.007	10
yeast-376_GO-0019219	2	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism	C[VQA]K	33	CKPCLK.TC	CLUSTERIN_1 PATTERN		Zn_clus	1.E-11	8.4	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism (1e-60)		0.007	10
yeast-752_GO-0016787	2	hydrolase activity	[DVT]E.[KC]LT	33	[ST]E	G protein-coupled receptor kinase 1 substrate motif					ATPase activity (0.01)		0.007	9
yeast-649_GO-0003676	2	nucleic acid binding	[IKY]K..DE[LN]	33							nucleic acid binding (1e-18)		0.008	10
yeast-548_GO-0051641	2	cellular localization	S[SWQ].F[GTM]	33	S..F	LIG_BRCT_BRCA1_1					cellular localization (1e-45)		0.007	10
yeast-523_GO-0030529	2	ribonucleoprotein complex	[KQA]K..K[KRV]	33	KR	CLV_PCSK_PC1ET2_1					ribonucleoprotein complex (1e-09)		0.007	10
yeast-470_GO-0006259	2	DNA metabolism	G[GEY][TNP]TS	33	FRGGT	Phosphoinositide binding motif in ATG18 and ATG21					DNA metabolism (1e-08)		0.006	10
yeast-437_GO-0044429	2	mitochondrial part	F[QIN]I	33	F.[IV][WFY][WFY][IL][ILM]	EH1 motif binds to groucho/TLE corepressors							0.007	10
yeast-436_GO-0031323	2	regulation of cellular metabolism	QD.[TNY]	33	GQDQTKQQI	43_KD_POSTSYNAPTIC PATTERN					regulation of cellular metabolism (1e-10)		0.007	10
yeast-424_GO-0006950	2	response to stress	S[KFQ].R[KSQ]	33							response to stress (1e-69)		0.007	10
yeast-424_GO-0006950	2	response to stress	VS.[IGA]E	33	[ST]..E	Casien kinase II consensus phosphorylation site	Y				response to stress (1e-34)	Y	0.007	10
yeast-271_GO-0045184	2	establishment of protein localization	[LTP]FGS[KNP]	33	LFG	Protease Papain substrate, a prototype cysteine proteinase					rRNA export from nucleus (1e-13)		0.006	8
yeast-267_GO-0000003	2	reproduction	S[GHQ].S[THN]	33	S[ST]	MDC1 BRCT domain binding motif					reproduction (1e-65)	Y	0.007	10
yeast-256_GO-0016021	2	integral to membrane	[TIG]S..F[TGL]	33	S..F	LIG_BRCT_BRCA1_1					integral to membrane (1e-56)		0.007	8
yeast-244_GO-0000279	2	M phase	Q[DIC]D	33	Q[MLVI]DG..[DE]	CLV_TASPASE1					M phase (1e-89)		0.007	9
yeast-213_GO-0009719	2	response to endogenous stimulus	[IEQ]D.F[NIK]	33	DPF	AP2 binding motif in Synaptojanin 1 and EPS15	Y				response to endogenous stimulus (1e-45)		0.007	10
yeast-213_GO-0009719	2	response to endogenous stimulus	[KIR][SER]TI	33							response to endogenous stimulus (1e-60)	Y	0.007	9
yeast-1974_GO-0005634	2	nucleus	G[AGR].[FLY]A	33							plasma membrane (0.01)		0.007	9
ubiquitin_peng2003	2	ubiquitin_peng2003	I[AYM]..[SVF]NG	33	IY	cFGR and Csk kinase phosphorylation site (peptide screen)							0.006	10
ubiquitin_peng2003	2	ubiquitin_peng2003	IL.[LCW][VAL]P	33	VP	Interleukin converting enzyme protease							0.006	9
protein_40_YPR144C	2	NOC4:  Nucleolar protein, forms a complex with Nop14p that mediates maturation and nuclear export of 40S ribosomal subunits	ES.[IVE][EWD]	33	YESP	Vav SH2 domain binding motif					nucleolus (1e-14)	Y	0.007	10
protein_40_YPR120C	2	CLB5:  B-type cyclin involved in DNA replication during S phase; activates Cdc28p to promote initiation of DNA synthesis; functions in formation of mitotic spindles along with Clb3p and Clb4p; most abundant during late G1 phase	KM..[IPT][DVQ]	33								Y	0.004	8
protein_40_YPR119W	2	CLB2:  B-type cyclin involved in cell cycle progression; activates Cdc28p to promote the transition from G2 to M phase; accumulates during G2 and M, then targeted via a destruction box motif for ubiquitin-mediated degradation by the proteasome	LN..[VRN]E[ESM]	33									0.005	10
protein_40_YPR010C	2	RPA135:  RNA polymerase I subunit A135	[YHW]G.A[SYN]	33									0.004	7
protein_40_YPL240C	2	HSP82:  Hsp90 chaperone required for pheromone signaling and negative regulation of Hsf1p; docks with Tom70p for mitochondrial preprotein delivery; promotes telomerase DNA binding and nucleotide addition; interacts with Cns1p, Cpr6p, Cpr7p, Sti1p	D[SGV][KWV]S	33								Y	0.006	10
protein_40_YPL209C	2	IPL1:  Aurora kinase involved in regulating kinetochore-microtubule attachments; helps maintain condensed chromosomes during anaphase and early telophase; associates with Sli15p, which promotes Ipl1p association with mitotic spindle	GA..[ERC][NQH]	33									0.004	8
protein_40_YPL153C	2	RAD53:  Protein kinase, required for cell-cycle arrest in response to DNA damage; activated by trans autophosphorylation when interacting with hyperphosphorylated Rad9p; also interacts with ARS1 and plays a role in initiation of DNA replication	[EYP]T..[KWA]P	33	T..[SA]	FHA of KAPP binding motif, Thr must be phosphorylated							0.006	9
protein_40_YPL153C	2	RAD53:  Protein kinase, required for cell-cycle arrest in response to DNA damage; activated by trans autophosphorylation when interacting with hyperphosphorylated Rad9p; also interacts with ARS1 and plays a role in initiation of DNA replication	[LIC]PQ[AMK]	33	HPQ	Biotin binding motif in streptavidin	Y						0.006	10
protein_40_YPL153C	2	RAD53:  Protein kinase, required for cell-cycle arrest in response to DNA damage; activated by trans autophosphorylation when interacting with hyperphosphorylated Rad9p; also interacts with ARS1 and plays a role in initiation of DNA replication	D[TMW][KLN]T	33									0.006	10
protein_40_YPL146C	2	NOP53:  Nucleolar protein; involved in biogenesis of the 60S subunit of the ribosome; interacts with rRNA processing factors Cbf5p and Nop2p; null mutant is viable but growth is severely impaired	L[LWV].[EGI]H	33								Y	0.005	10
protein_40_YPL131W	2	RPL5:  Protein component of the large (60S) ribosomal subunit with similarity to E. coli L18 and rat L5 ribosomal proteins; binds 5S rRNA and is required for 60S subunit assembly	AR..[ART]	33	[AG]R	Protease matriptase protease site	Y				cytoplasm organization and biogenesis (1e-17)		0.006	9
protein_40_YPL004C	2	LSP1:  Primary component of eisosomes, which are large immobile patch structures at the cell cortex associated with endocytosis, along with Pil1p and Sur7p; null mutants show activation of Pkc1p/Ypk1p stress resistance pathways	[IGR][SH]..GE	33								Y	0.005	7
protein_40_YOR181W	2	LAS17:  Actin assembly factor, activates the Arp2/3 protein complex that nucleates branched actin filaments; localizes with the Arp2/3 complex to actin patches; homolog of the human Wiskott-Aldrich syndrome protein (WASP)	L[AM]..L[AR]A	33	[LV][DE].[LM][LM]..L	LIG_PXL							0.004	7
protein_40_YOR133W	2	EFT1:  Elongation factor 2 (EF-2), also encoded by EFT2; catalyzes ribosomal translocation during protein synthesis; contains diphthamide, the unique posttranslationally modified histidine residue specifically ADP-ribosylated by diphtheria toxin	G[VGI]E[TLC]	33	EGGELGY	PHOSPHOKETOLASE_1 PATTERN						Y	0.006	8
protein_40_YOL139C	2	CDC33:  Cytoplasmic mRNA cap binding protein; the eIF4E-cap complex is responsible for mediating cap-dependent mRNA translation via interactions with the translation initiation factor eIF4G (Tif4631p or Tif4632p)	K[NRI]..T[GAT]	33	KR	CLV_PCSK_PC1ET2_1							0.007	10
protein_40_YOL135C	2	MED7:  Subunit of the RNA polymerase II mediator complex; associates with core polymerase subunits to form the RNA polymerase II holoenzyme; essential for transcriptional regulation	[MIG]N..[NMT]N	33			Y				RNA polymerase II transcription mediator activity (1e-14)		0.006	10
protein_40_YOL133W	2	HRT1:  RING finger containing subunit of Skp1-Cullin-F-box ubiquitin protein ligases (SCF); required for Gic2p, Far1p, Sic1p and Cln2p degradation; may tether Cdc34p (a ubiquitin conjugating enzyme or E2) and Cdc53p (a cullin) subunits of SCF	E[TWI][VFK]K	33								Y	0.007	10
protein_40_YNL308C	2	KRI1:  Essential nucleolar protein required for 40S ribosome biogenesis; physically and functionally interacts with Krr1p	[AIL][LPV].DLD	33	D.D	Ribose moiety of UDP and manganese binding site in glucuronyl transferase					cytoplasm organization and biogenesis (0.01)		0.004	7
protein_40_YNL308C	2	KRI1:  Essential nucleolar protein required for 40S ribosome biogenesis; physically and functionally interacts with Krr1p	[VDH]K..[RKI]K	33	K[KR].[KR]	Nuclear localization motif					nucleolus (1e-08)		0.007	10
protein_40_YNL289W	2	PCL1:  Pho85 cyclin of the Pcl1,2-like subfamily, involved in entry into the mitotic cell cycle and regulation of morphogenesis, localizes to sites of polarized cell growth	P.[NDY]A	33	NP.Y	LIG_PTB_1							0.006	10
protein_40_YNL244C	2	SUI1:  Translation initiation factor eIF1; component of a complex involved in recognition of the initiator codon; modulates translation accuracy at the initiation phase	QVN[ECQ]	33									0.004	7
protein_40_YNL154C	2	YCK2:  Palmitoylated, plasma membrane-bound casein kinase I isoform; shares redundant functions with Yck1p in morphogenesis, proper septin assembly, endocytic trafficking; provides an essential function overlapping with that of Yck1p	L.E[GNE]	33									0.006	10
protein_40_YNL118C	2	DCP2:  Catalytic subunit of the Dcp1p-Dcp2p decapping enzyme complex, which removes the 5' cap structure from mRNAs prior to their degradation; member of the Nudix hydrolase family	F[IRP]..L[RM]	33	DFR..L	Actin binding motif on Myosin light chain kinase						Y	0.004	9
protein_40_YNL096C	2	RPS7B:  Protein component of the small (40S) ribosomal subunit, nearly identical to Rps7Ap; interacts with Kti11p; deletion causes hypersensitivity to zymocin; has similarity to rat S7 and Xenopus S8 ribosomal proteins	S.L[SPF]	33									0.006	10
protein_40_YNL069C	2	RPL16B:  N-terminally acetylated protein component of the large (60S) ribosomal subunit, binds to 5.8 S rRNA; has similarity to Rpl16Ap, E. coli L13 and rat L13a ribosomal proteins; transcriptionally regulated by Rap1p	SL[SLG]	33	S[LW]LD[DE]EL[LM]	TRG_LysEnd_GGAAcLL_2							0.006	10
protein_40_YNL055C	2	POR1:  Mitochondrial porin (voltage-dependent anion channel), outer membrane protein required for the maintenance of mitochondrial osmotic stability and mitochondrial membrane permeability; phosphorylated	[EHS]P..[NHF]E	33	[ST]P	LIG_WW_4							0.005	8
protein_40_YMR308C	2	PSE1:  Karyopherin/importin that interacts with the nuclear pore complex; acts as the nuclear import receptor for specific proteins, including Pdr1p, Yap1p, Ste12p, and Aft1p	[TGA]G..F[GQP]	33	[AC]GL.FPV	HISTONE_H2A PATTERN					snRNP protein import into nucleus (1e-04)		0.006	10
protein_40_YMR128W	2	ECM16:  Essential DEAH-box ATP-dependent RNA helicase specific to the U3 snoRNP, predominantly nucleolar in distribution, required for 18S rRNA synthesis	E[KEI]K[DM]	33			Y				rRNA processing (1e-13)		0.006	10
protein_40_YMR047C	2	NUP116:  Subunit of the nuclear pore complex (NPC) that is localized to both sides of the pore; contains a repetitive GLFG motif that interacts with mRNA export factor Mex67p and with karyopherin Kap95p; homologous to Nup100p	[TMN]T..F[GVW]	33							nucleocytoplasmic transport (1e-10)	Y	0.006	10
protein_40_YMR001C	2	CDC5:  Polo-like kinase with similarity to Xenopus Plx1 and S. pombe Plo1p; found at bud neck, nucleus and SPBs; has multiple functions in mitosis and cytokinesis through phosphorylation of substrates; may be a Cdc28p substrate	DT..[APM][KQF]	33	T..[SA]	FHA of KAPP binding motif, Thr must be phosphorylated					mitotic cell cycle (0.01)		0.005	9
protein_40_YML069W	2	POB3:  Subunit of the heterodimeric FACT complex (Spt16p-Pob3p), which facilitates RNA Pol II transcription elongation through nucleosomes by destabilizing and then reassembling nucleosome structure; interacts with DNA polymerase alpha (Pol1p)	[ESM]E[DKT]E	33	[ST]E	G protein-coupled receptor kinase 1 substrate motif					RNA elongation from RNA polymerase II promoter (1e-19)		0.007	10
protein_40_YML056C	2	IMD4:  Inosine monophosphate dehydrogenase, catalyzes the first step of GMP biosynthesis, member of a four-gene family in S. cerevisiae, constitutively expressed	G[SAK][RF]P	33	[RHQ][ST]W[GSA]GARPE	NODA PATTERN							0.004	8
protein_40_YLR441C	2	RPS1A:  Ribosomal protein 10 (rp10) of the small (40S) subunit; nearly identical to Rps1Bp and has similarity to rat S3a ribosomal protein	[AKG]A..[ADC]E	33							cytosolic ribosome (sensu Eukaryota) (1e-17)		0.007	9
protein_40_YLR429W	2	CRN1:  Coronin, cortical actin cytoskeletal component that associates with the Arp2p/Arp3p complex to regulate its activity; plays a role in regulation of actin patch assembly	L[SLI]R[AGK]	33									0.006	10
protein_40_YLR197W	2	SIK1:  Essential evolutionarily-conserved nucleolar protein component of the box C/D snoRNP complexes that direct 2'-O-methylation of pre-rRNA during its maturation; overexpression causes spindle orientation defects	[DTI]S[LKR]D	33	S.D	CAMKII phosphorylation site					nucleolus (1e-16)		0.006	10
protein_40_YLR074C	2	BUD20:  Protein involved in bud-site selection; diploid mutants display a random budding pattern instead of the wild-type bipolar pattern	[KRA]P..[KRC]A	33	KP..[QK]	LIG_SH3_4							0.005	9
protein_40_YLR009W	2	RLP24:  Essential protein with similarity to Rpl24Ap and Rpl24Bp, associated with pre-60S ribosomal subunits and required for ribosomal large subunit biogenesis	KQ.[RKH][LER]	33							cytoplasm organization and biogenesis (1e-11)		0.006	10
protein_40_YKL203C	2	TOR2:  PIK-related protein kinase and rapamycin target; subunit of TORC1, a complex that regulates growth in response to nutrients and TORC2, a complex that regulates cell-cycle dependent polarization of the actin cytoskeleton; involved in meiosis	[AIM]LA[EYA]	33							plasma membrane (1e-07)		0.006	10
protein_40_YKL203C	2	TOR2:  PIK-related protein kinase and rapamycin target; subunit of TORC1, a complex that regulates growth in response to nutrients and TORC2, a complex that regulates cell-cycle dependent polarization of the actin cytoskeleton; involved in meiosis	[LQV]T..Q[DCA]	33							actin cytoskeleton organization and biogenesis (1e-04)		0.005	9
protein_40_YKL203C	2	TOR2:  PIK-related protein kinase and rapamycin target; subunit of TORC1, a complex that regulates growth in response to nutrients and TORC2, a complex that regulates cell-cycle dependent polarization of the actin cytoskeleton; involved in meiosis	V[INF]..[NYW]V	33			Y				plasma membrane (1e-05)		0.005	9
protein_40_YKL180W	2	RPL17A:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl17Bp and has similarity to E. coli L22 and rat L17 ribosomal proteins; copurifies with the Dam1 complex (aka DASH complex)	[AK]A..[ACD]E	33							cytosolic ribosome (sensu Eukaryota) (1e-17)	Y	0.006	10
protein_40_YKL166C	2	TPK3:  cAMP-dependent protein kinase catalytic subunit; promotes vegetative growth in response to nutrients via the Ras-cAMP signaling pathway; inhibited by regulatory subunit Bcy1p in the absence of cAMP; partially redundant with Tpk1p and Tpk2p	M[KY]..A[LVK]	33							endocytosis (0.01)		0.005	9
protein_40_YKL104C	2	GFA1:  Glutamine-fructose-6-phosphate amidotransferase, catalyzes the formation of glucosamine-6-P and glutamate from fructose-6-P and glutamine in the first step of chitin biosynthesis	A[AGC].[LVC]K	33							translational elongation (0.01)		0.006	8
protein_40_YKL065C	2	YET1:  Endoplasmic reticulum transmembrane protein; may interact with ribosomes, based on co-purification experiments; homolog of human BAP31 protein	[FIG]I..[IYV]I	33							endoplasmic reticulum (0.001)		0.007	10
protein_40_YKL009W	2	MRT4:  Protein involved in mRNA turnover and ribosome assembly, localizes to the nucleolus	KR..[VTE][EKD]	33	KR	CLV_PCSK_PC1ET2_1	Y				cytoplasm organization and biogenesis (1e-14)		0.006	10
protein_40_YJR145C	2	RPS4A:  Protein component of the small (40S) ribosomal subunit; mutation affects 20S pre-rRNA processing; identical to Rps4Bp and has similarity to rat S4 ribosomal protein	[HER]R.[GAL]R	33	[AG]R	Protease matriptase protease site					ribonucleoprotein complex (1e-07)		0.007	10
protein_40_YJR066W	2	TOR1:  PIK-related protein kinase and rapamycin target; subunit of TORC1, a complex that controls growth in response to nutrients by regulating translation, transcription, ribosome biogenesis, nutrient transport and autophagy; involved in meiosis	A[LGF].G[EFV]	33							plasma membrane (1e-13)		0.006	9
protein_40_YJR002W	2	MPP10:  Component of the SSU processome, which is required for pre-18S rRNA processing, interacts with and controls the stability of Imp3p and Imp4p, essential for viability; similar to human Mpp10p	Q[ITG]..K[KL]	33							nucleolus (1e-12)		0.006	9
protein_40_YJL138C	2	TIF2:  Translation initiation factor eIF4A, identical to Tif1p; DEA(D/H)-box RNA helicase that couples ATPase activity to RNA binding and unwinding; forms a dumbbell structure of two compact domains connected by a linker; interacts with eIF4G	[TWC]N..D[LMC]	33	NK.D	Motif for specificity of guanine in purine binding proteins							0.004	8
protein_40_YJL095W	2	BCK1:  Mitogen-activated protein (MAP) kinase kinase kinase acting in the protein kinase C signaling pathway, which controls cell integrity; upon activation by Pkc1p phosphorylates downstream kinases Mkk1p and Mkk2p	[DNW]E..[EKG]E	33			Y						0.006	10
protein_40_YJL092W	2	SRS2:  DNA helicase and DNA-dependent ATPase involved in DNA repair, needed for proper timing of commitment to meiotic recombination and transition from Meiosis I to II; affects genome stability by suppressing unscheduled homologous recombination	RK[LY]Q[EVS]	33	[RK]R[RK]L	Cyclin/CDK2 binding motif							0.004	7
protein_40_YJL074C	2	SMC3:  Subunit of the multiprotein cohesin complex required for sister chromatid cohesion in mitotic cells; also required, with Rec8p, for cohesion and recombination during meiosis; phylogenetically conserved SMC chromosomal ATPase family member	R[GF][KED]D	33	RGD	LIG_RGD							0.005	9
protein_40_YIL133C	2	RPL16A:  N-terminally acetylated protein component of the large (60S) ribosomal subunit, binds to 5.8 S rRNA; has similarity to Rpl16Bp, E. coli L13 and rat L13a ribosomal proteins; transcriptionally regulated by Rap1p	AG[KR]	33	G[KR][KR]	Amidation after cleavage after Gly (must be in secretory pathway)					cytosolic ribosome (sensu Eukaryota) (1e-18)		0.006	10
protein_40_YIL075C	2	RPN2:  Subunit of the 26S proteasome, substrate of the N-acetyltransferase Nat1p	[LQM]K.[YC]E	33	YE	TPK-IIB/P38Syk kinase phosphorylation site (peptide screen)					protein modification (0.01)		0.004	8
protein_40_YIL061C	2	SNP1:  Component of U1 snRNP required for mRNA splicing via spliceosome; may interact with poly(A) polymerase to regulate polyadenylation; homolog of human U1 70K protein	[AYC]E..G[DHP]	33	YE	TPK-IIB/P38Syk kinase phosphorylation site (peptide screen)							0.005	10
protein_40_YIL035C	2	CKA1:  Alpha catalytic subunit of casein kinase 2, a Ser/Thr protein kinase with roles in cell growth and proliferation; the holoenzyme also contains CKA2, CKB1 and CKB2, the many substrates include transcription factors and all RNA polymerases	KEL[IRM][SRA]	33	L[IVLMF].[IVLMF][DE]	LIG_Clathr_ClatBox_1					establishment and/or maintenance of chromatin architecture (1e-04)		0.005	9
protein_40_YIL018W	2	RPL2B:  Protein component of the large (60S) ribosomal subunit, identical to Rpl2Ap and has similarity to E. coli L2 and rat L8 ribosomal proteins; expression is upregulated at low temperatures	[ALH][GVC]..RG	33							cytosolic large ribosomal subunit (sensu Eukaryota) (1e-05)		0.005	10
protein_40_YIL018W	2	RPL2B:  Protein component of the large (60S) ribosomal subunit, identical to Rpl2Ap and has similarity to E. coli L2 and rat L8 ribosomal proteins; expression is upregulated at low temperatures	S[SNK]S	33	R.S.S.P	14-3-3 binding motifs, Ser must be phosphorylated							0.006	10
protein_40_YHR079C	2	IRE1:  Serine-threonine kinase and endoribonuclease; transmembrane protein that mediates the unfolded protein response (UPR) by regulating Hac1p synthesis through HAC1 mRNA splicing; Kar2p binds inactive Ire1p and releases from it upon ER stress	[SDH][SLP]..ED	33	EED	Ankyrin B C-terminal motif that binds internal Ankyrin repeats							0.006	9
protein_40_YHR079C	2	IRE1:  Serine-threonine kinase and endoribonuclease; transmembrane protein that mediates the unfolded protein response (UPR) by regulating Hac1p synthesis through HAC1 mRNA splicing; Kar2p binds inactive Ire1p and releases from it upon ER stress	S[AKI]S	33	R.S.S.P	14-3-3 binding motifs, Ser must be phosphorylated						Y	0.006	9
protein_40_YHR041C	2	SRB2:  Subunit of the RNA polymerase II mediator complex; associates with core polymerase subunits to form the RNA polymerase II holoenzyme; general transcription factor involved in telomere maintenance	TI..[TV]S[IP]	33	SP	ERK1, ERK2 Kinase substrate motif							0.004	7
protein_40_YHR010W	2	RPL27A:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl27Bp and has similarity to rat L27 ribosomal protein	[IMG]E.V[ECV]	33							ribosome biogenesis (1e-05)		0.006	10
protein_40_YHL007C	2	STE20:  Signal transducing kinase of the PAK (p21-activated kinase) family, involved in pheromone response and pseudohyphal/invasive growth pathways, activated by Cdc42p; binds Ste4p at a GBB motif present in noncatalytic domains of PAK kinases	S..[APR]K	33							bud (0.01)		0.006	10
protein_40_YGR274C	2	TAF1:  TFIID subunit (145 kDa), involved in RNA polymerase II transcription initiation, has histone acetyltransferase activity, involved in promoter binding and G1/S progression	[INQ]Q.[LFS]Q	33	[ST]Q	ATM kinase phosphorylation site	Y				nucleoplasm part (1e-11)		0.007	10
protein_40_YGR274C	2	TAF1:  TFIID subunit (145 kDa), involved in RNA polymerase II transcription initiation, has histone acetyltransferase activity, involved in promoter binding and G1/S progression	QT..[SHD][KVN]	33	T..[SA]	FHA of KAPP binding motif, Thr must be phosphorylated					transcription factor TFIID complex (1e-08)		0.006	7
protein_40_YGR218W	2	CRM1:  Major karyopherin, involved in export of proteins, RNAs, and ribosomal subunits from the nucleus	R.S[EQH]	33	RRR.S	MAPKAPK1 kinase substrate motif						Y	0.006	9
protein_40_YGR162W	2	TIF4631:  Translation initiation factor eIF4G, subunit of the mRNA cap-binding protein complex (eIF4F) that also contains eIF4E (Cdc33p); associates with the poly(A)-binding protein Pab1p, also interacts with eIF4A (Tif1p); homologous to Tif4632p	GR[GKV][GKY]	33	[AG]R	Protease matriptase protease site							0.006	10
protein_40_YGR040W	2	KSS1:  Mitogen-activated protein kinase (MAPK) involved in signal transduction pathways that control filamentous growth and pheromone response; the KSS1 gene is nonfunctional in S288C strains and functional in W303 strains	E[GEQ][TDE]D	33	EED	Ankyrin B C-terminal motif that binds internal Ankyrin repeats						Y	0.006	10
protein_40_YGR040W	2	KSS1:  Mitogen-activated protein kinase (MAPK) involved in signal transduction pathways that control filamentous growth and pheromone response; the KSS1 gene is nonfunctional in S288C strains and functional in W303 strains	K.[DAQ]V	33	[NT]K.D	Motif for binding guanine nucleotides							0.006	10
protein_40_YGL180W	2	ATG1:  Protein serine/threonine kinase, required for vesicle formation during autophagy and the cytoplasm-to-vacuole targeting (Cvt) pathway; structurally required for pre-autophagosome formation; forms a complex with Atg13p and Atg17p	T..K	33	D.G.T..K.I	Pyrophosphate binding motif, active site for S-Adenosylmethionine (AdoMet) synthetase							0.006	10
protein_40_YGL137W	2	SEC27:  Essential beta'-coat protein of the COPI coatomer, involved in ER-to-Golgi and Golgi-to-ER transport; contains WD40 domains that mediate cargo selective interactions; 45% sequence identity to mammalian beta'-COP	SAG[DA][DNM]	33									0.004	8
protein_40_YGL112C	2	TAF6:  Subunit (60 kDa) of TFIID and SAGA complexes, involved in transcription initiation of RNA polymerase II and in chromatin modification, similar to histone H4	D[EPW]..[DVR]E	33			Y				transcription factor complex (1e-19)		0.007	10
protein_40_YGL106W	2	MLC1:  Essential light chain for Myo1p, light chain for Myo2p; stabilizes Myo2p by binding to the neck region; interacts with Myo1p, Iqg1p, and Myo2p to coordinate formation and contraction of the actomyosin ring with targeted membrane deposition	P[VMY]I[INQ]	33	PWI	Motif in SRM160 for binding DNA and RNA						Y	0.006	9
protein_40_YGL031C	2	RPL24A:  Ribosomal protein L30 of the large (60S) ribosomal subunit, nearly identical to Rpl24Bp and has similarity to rat L24 ribosomal protein; not essential for translation but may be required for normal translation rate	[NKC][KQN]TR	33							cytosolic large ribosomal subunit (sensu Eukaryota) (1e-09)		0.005	9
protein_40_YFR037C	2	RSC8:  Component of the RSC chromatin remodeling complex; essential for viability and mitotic growth; homolog of SWI/SNF subunit Swi3p, but unlike Swi3p, does not activate transcription of reporters	[FMY]E..[FGA]Q	33	YE	TPK-IIB/P38Syk kinase phosphorylation site (peptide screen)					chromatin remodeling complex (1e-06)		0.004	8
protein_40_YFR031C-A	2	RPL2A:  Protein component of the large (60S) ribosomal subunit, identical to Rpl2Bp and has similarity to E. coli L2 and rat L8 ribosomal proteins	R[AGP][APR]R	33	[KR]R	CLV_PCSK_KEX2_1					cytosolic ribosome (sensu Eukaryota) (1e-15)		0.006	10
protein_40_YFR028C	2	CDC14:  Protein phosphatase required for mitotic exit; located in the nucleolus until liberated by the FEAR and Mitotic Exit Network in anaphase, enabling it to act on key substrates to effect a decrease in CDK/B-cyclin activity and mitotic exit	[VHR]L.[PAE]P	33							mitotic cell cycle (1e-04)		0.006	10
protein_40_YFL037W	2	TUB2:  Beta-tubulin; associates with alpha-tubulin (Tub1p and Tub3p) to form tubulin dimer, which polymerizes to form microtubules	K[YFQ].[KQL]M	33								Y	0.004	7
protein_40_YER177W	2	BMH1:  14-3-3 protein, major isoform; controls proteome at post-transcriptional level, binds proteins and DNA, involved in regulation of many processes including exocytosis, vesicle transport, Ras/MAPK signaling, and rapamycin-sensitive signaling	S.P[QNP]	33	KSPP	ERK1, ERK2, SAPK, CDK5 and GSK3 kinase substrate motif					bud (0.01)		0.006	10
protein_40_YER165W	2	PAB1:  Poly(A) binding protein, part of the 3'-end RNA-processing complex, mediates interactions between the 5' cap structure and the 3' mRNA poly(A) tail, involved in control of poly(A) tail length, interacts with translation factor eIF-4G	N..[GML]N	33			Y				mRNA metabolism (1e-11)	Y	0.006	10
protein_40_YER125W	2	RSP5:  Ubiquitin-protein ligase involved in ubiquitin-mediated protein degradation; functions in multivesicular body sorting, heat shock response and ubiquitylation of arrested RNAPII; contains a hect (homologous to E6-AP carboxyl terminus) domain	ES[PK][RM]Y	33	YESP	Vav SH2 domain binding motif							0.004	8
protein_40_YER082C	2	UTP7:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	A[ERA]E	33	A[EA]EEY[FV]F[LFMIV]F	FGFR kinase substrate motif					cytoplasm organization and biogenesis (1e-18)	Y	0.006	10
protein_40_YER082C	2	UTP7:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	KA[RVQ][IGD]	33							small nucleolar ribonucleoprotein complex (1e-08)		0.007	10
protein_40_YER006W	2	NUG1:  GTPase that associates with nuclear 60S pre-ribosomes, required for export of 60S ribosomal subunits from the nucleus	[EW]I..[SCG]T	33			Y				ribosome biogenesis (1e-07)		0.005	10
protein_40_YER006W	2	NUG1:  GTPase that associates with nuclear 60S pre-ribosomes, required for export of 60S ribosomal subunits from the nucleus	Y[KAN].[IT]KS	33									0.004	7
protein_40_YDR510W	2	SMT3:  Ubiquitin-like protein of the SUMO family, conjugated to lysine residues of target proteins; regulates chromatid cohesion, chromosome segregation, APC-mediated proteolysis, DNA replication and septin ring dynamics	A[RAI]R	33	[KR]R	CLV_PCSK_KEX2_1	Y				cytosol (1e-07)	Y	0.006	10
protein_40_YDR477W	2	SNF1:  AMP-activated serine/threonine protein kinase found in a complex containing Snf4p and members of the Sip1p/Sip2p/Gal83p family; required for transcription of glucose-repressed genes, thermotolerance, sporulation, and peroxisome biogenesis	D.[EFT]V	33	D.D.[TV]	Motif in PRS1 and PRS-2 required for phosphatase activity and salt stress response	Y						0.006	9
protein_40_YDR414C	2	ERD1:  Predicted membrane protein required for the retention of lumenal endoplasmic reticulum proteins; mutants secrete the endogenous ER protein, BiP (Kar2p)	[NFT]V.[LD]F	33									0.006	8
protein_40_YDR388W	2	RVS167:  Actin-associated protein, subunit of a complex (Rvs161p-Rvs167p) involved in regulation of actin cytoskeleton, endocytosis, and viability following starvation or osmotic stress; homolog of mammalian amphiphysin	K.[LEG]L	33	[VILMAFP]K.E	MOD_SUMO					cell cortex part (1e-04)	Y	0.006	10
protein_40_YDR365C	2	ESF1:  Nucleolar protein involved in pre-rRNA processing; depletion causes severely decreased 18S rRNA levels	[AS]P.[VE]K	33	SP	ERK1, ERK2 Kinase substrate motif					nucleolus (0.001)		0.005	10
protein_40_YDR365C	2	ESF1:  Nucleolar protein involved in pre-rRNA processing; depletion causes severely decreased 18S rRNA levels	EE..[EAR][ENF]	33	EED	Ankyrin B C-terminal motif that binds internal Ankyrin repeats					rRNA metabolism (1e-09)		0.007	10
protein_40_YDR365C	2	ESF1:  Nucleolar protein involved in pre-rRNA processing; depletion causes severely decreased 18S rRNA levels	I[SN].F[DI]N	33								Y	0.004	7
protein_40_YDR356W	2	SPC110:  Inner plaque spindle pole body (SPB) component, ortholog of human kendrin; involved in connecting nuclear microtubules to SPB; interacts with Tub4p-complex and calmodulin; phosphorylated by Mps1p in cell cycle-dependent manner	[DYE]Q..[VEG]I	33							microtubule cytoskeleton organization and biogenesis (1e-13)	Y	0.005	9
protein_40_YDR091C	2	RLI1:  Essential iron-sulfur protein required for ribosome biogenesis and translation initiation; facilitates binding of a multifactor complex (MFC) of translation initiation factors to the small ribosomal subunit; predicted ABC family ATPase	[AME][LA]..PA	33							cytosolic ribosome (sensu Eukaryota) (1e-04)		0.005	8
protein_40_YDR025W	2	RPS11A:  Protein component of the small (40S) ribosomal subunit; identical to Rps11Bp and has similarity to E. coli S17 and rat S11 ribosomal proteins	[KGI]RA[IFD]	33	FGRA	DNA binding motif in ssDNA binding proteins					ribonucleoprotein complex (1e-04)		0.007	10
protein_40_YDL213C	2	NOP6:  Putative RNA-binding protein implicated in ribosome biogenesis; contains an RNA recognition motif (RRM) and has similarity to hydrophilins; NOP6 may be a fungal-specific gene as no homologs have been yet identified in higher eukaryotes	E[FEM].[EKD]A	33							nucleolus (1e-13)		0.007	10
protein_40_YDL212W	2	SHR3:  Endoplasmic reticulum packaging chaperone, required for incorporation of amino acid permeases into COPII coated vesicles for transport to the cell surface	[FIY]I..I[IPC]	33							amine transporter activity (0.001)		0.006	10
protein_40_YDL185W	2	TFP1:  Vacuolar ATPase V1 domain subunit A containing the catalytic nucleotide binding sites; protein precursor undergoes self-catalyzed splicing to yield the extein Tfp1p and the intein Vde (PI-SceI), which is a site-specific endonuclease	QE.[SAD][LVI]	33							hydrogen ion homeostasis (1e-04)		0.006	10
protein_40_YDL136W	2	RPL35B:  Protein component of the large (60S) ribosomal subunit, identical to Rpl35Ap and has similarity to rat L35 ribosomal protein	G[KIP]K[VAK]	33	GP	Protease TTP cleavage site	Y				cytosolic ribosome (sensu Eukaryota) (1e-25)		0.007	10
protein_40_YDL082W	2	RPL13A:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl13Bp; not essential for viability; has similarity to rat L13 ribosomal protein	G[KIY]K[VAY]	33	G[KR][KR]	Amidation after cleavage after Gly (must be in secretory pathway)					cytosolic ribosome (sensu Eukaryota) (1e-22)		0.007	10
protein_40_YDL047W	2	SIT4:  Type 2A-related serine-threonine phosphatase that functions in the G1/S transition of the mitotic cycle; cytoplasmic and nuclear protein that modulates functions mediated by Pkc1p including cell wall and actin cytoskeleton organization	G[GYR][NLM]S	33									0.006	10
protein_40_YBR247C	2	ENP1:  Protein associated with U3 and U14 snoRNAs, required for pre-rRNA processing and 40S ribosomal subunit synthesis; localized in the nucleus and concentrated in the nucleolus	R[AIE].R[ICT]	33	R.[RK]R	CLV_PCSK_FUR_1					rRNA processing (1e-11)		0.007	9
protein_40_YBR245C	2	ISW1:  Member of the imitation-switch (ISWI) class of ATP-dependent chromatin remodeling complexes; ATPase that forms a complex with Ioc2p and Ioc4p to regulate transcription elongation, and a complex with Ioc3p to repress transcription initiation	[EH]V..[QFL]V	33							chromatin modification (0.001)		0.004	9
protein_40_YBR217W	2	ATG12:  Ubiquitin-like modifier, conjugated via an isopeptide bond to a lysine residue of Atg5p by the E1 enzyme, Atg7p, and the E2 enzyme, Atg10p, a step that is essential for autophagy	VR..[REF][REP]	33			Y						0.005	7
protein_40_YBR154C	2	RPB5:  RNA polymerase subunit ABC27, common to RNA polymerases I, II, and III; contacts DNA and affects transactivation	[DW]VD[MPS]	33	AEVD	Protease Caspase 10					RNA polymerase complex (1e-10)		0.005	10
protein_40_YBR109C	2	CMD1:  Calmodulin; Ca++ binding protein that regulates Ca++ independent processes (mitosis, bud growth, actin organization, endocytosis, etc.) and Ca++ dependent processes (stress-activated pathways), targets include Nuf1p, Myo2p and calcineurin	[ST]EL[SG]N	33	[ST]E	G protein-coupled receptor kinase 1 substrate motif							0.004	7
protein_40_YBL027W	2	RPL19B:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl19Ap and has similarity to rat L19 ribosomal protein; rpl19a and rpl19b single null mutations result in slow growth, while the double null mutation is lethal	A[RAG].[KRY]A	33							cytosolic ribosome (sensu Eukaryota) (1e-23)		0.006	10
protein_40_YBL002W	2	HTB2:  One of two nearly identical (see HTB1) histone H2B subtypes required for chromatin assembly and chromosome function; Rad6p-Bre1p-Lge1p mediated ubiquitination regulates transcriptional activation, meiotic DSB formation and H3 methylation	P[SAV][KET]K	33	P[ST]	DNA dependent Protein kinase substrate motif					chromatin assembly or disassembly (1e-04)		0.006	10
protein_40_YAR007C	2	RFA1:  Subunit of heterotrimeric Replication Protein A (RPA), which is a highly conserved single-stranded DNA binding protein involved in DNA replication, repair, and recombination	Q[LVQ][SRD]P	33	[ST]P	LIG_WW_4							0.005	8
protein_40_YAL032C	2	PRP45:  Protein required for pre-mRNA splicing; associates with the spliceosome and interacts with splicing factors Prp22p and Prp46p; orthologous to human transcriptional coactivator SKIP and can activate transcription of a reporter gene	FE[EIM][LRD]	33			Y				nuclear mRNA splicing, via spliceosome (0.001)		0.006	10
protein_40_YAL032C	2	PRP45:  Protein required for pre-mRNA splicing; associates with the spliceosome and interacts with splicing factors Prp22p and Prp46p; orthologous to human transcriptional coactivator SKIP and can activate transcription of a reporter gene	IP[DHN]	33	PL[ST]PIP[KRH]	CDK4 kinase substrate motif					nuclear mRNA splicing, via spliceosome (1e-09)	Y	0.006	10
oshea_mitochondrion	2	oshea_mitochondrion	RF[YNK]S	33	RRF.SLR	SLK1 kinase phosphorylation site (peptide screen)	Y				mitochondrial part (1e-06)		0.007	10
oshea_cytoplasm	2	oshea_cytoplasm	[LQH][LQT]RP	33	FRPW	TLA domain binding motif in Hkb transcription factor							0.006	10
oshea_cytoplasm	2	oshea_cytoplasm	[SED]LT[DQM]	33	[PG][LVIPME][DENS]L[VASTRGE]	LIG_CtBP							0.006	10
oshea_ambiguous	2	oshea_ambiguous	E.[NDC]S	33	[LIVMA].EG[DN]SA.[STAG]	TOPOISOMERASE_II PATTERN	Y				site of polarized growth (0.001)	Y	0.006	10
matsuyama_vacuole	2	matsuyama_vacuole	L[GLI]PS[LSF]	33	P[ST]	DNA dependent Protein kinase substrate motif					vacuole (1e-13)		0.007	10
matsuyama_Spindle_or_SPB	2	matsuyama_Spindle_or_SPB	K[YRA]..S	33	KKR..S	Phosphorylation site for MLCK	Y				spindle (1e-13)		0.008	10
matsuyama_Spindle_or_SPB	2	matsuyama_Spindle_or_SPB	N[RNK]..D[DYF]	33							spindle (1e-32)		0.008	10
matsuyama_nuclear_envelope_or_dots	2	matsuyama_nuclear_envelope_or_dots	QQ.[VYC][EKH]	33							nuclear envelope (1e-06)	Y	0.009	10
matsuyama_Cytosol	2	matsuyama_Cytosol	N..[TYD]P	33	[ST]P	LIG_WW_4					ligase activity, forming aminoacyl-tRNA and related compounds (0.01)	Y	0.008	10
matsuyama_Cytosol	2	matsuyama_Cytosol	RY	33	DRY	Binding motif for interaction of G-proteins or Phospholipase D with G-alpha	Y				barrier septum (1e-08)	Y	0.008	10
matsuyama_Cytoplasmic_dots	2	matsuyama_Cytoplasmic_dots	E[NMC]L	33	ENLYFQ[GS]	Protease TEV - stringent					vesicle-mediated transport (1e-05)		0.008	10
matsuyama_Cytoplasmic_dots	2	matsuyama_Cytoplasmic_dots	Q.[QEM]L	33							cell cortex (1e-09)	Y	0.008	10
matsuyama_Cytoplasmic_dots	2	matsuyama_Cytoplasmic_dots	T[ED]I[LTQ]	33								Y	0.008	10
genetic_YNL153C	2	GIM3: Subunit of the heterohexameric cochaperone prefoldin complex which binds specifically to cytosolic chaperonin and transfers target proteins to it	P[ITG]P	33	TPTP	Motif for hydroxylation of Pro residues, which can further be modified with arabinogalactan	Y				chromosome organization and biogenesis (0.001)	Y	0.006	10
genetic_YLR262C	2	YPT6: GTPase, Ras-like GTP binding protein involved in the secretory pathway, required for fusion of endosome-derived vesicles with the late Golgi, maturation of the vacuolar carboxypeptidase Y; has similarity to the human GTPase, Rab6	KN.V[LNP][TGR]	33	VP	Interleukin converting enzyme protease							0.005	8
genetic_YLR262C	2	YPT6: GTPase, Ras-like GTP binding protein involved in the secretory pathway, required for fusion of endosome-derived vesicles with the late Golgi, maturation of the vacuolar carboxypeptidase Y; has similarity to the human GTPase, Rab6	TT[ADS]	33	GRART[ST]SFAE	Akt kinase substrate motif					establishment and/or maintenance of chromatin architecture (1e-14)		0.006	10
genetic_YLR200W	2	YKE2: Subunit of the heterohexameric Gim/prefoldin protein complex involved in the folding of alpha-tubulin, beta-tubulin, and actin	I.[LDG]Q	33	INPISGQ	N-Cadherin ligand	Y				microtubule-based process (1e-10)		0.006	10
genetic_YLR200W	2	YKE2: Subunit of the heterohexameric Gim/prefoldin protein complex involved in the folding of alpha-tubulin, beta-tubulin, and actin	KR[ELI]	33	KR	CLV_PCSK_PC1ET2_1					DNA metabolism (1e-07)		0.006	9
genetic_YDL020C	2	RPN4: Transcription factor that stimulates expression of proteasome genes; Rpn4p levels are in turn regulated by the 26S proteasome in a negative feedback control mechanism; RPN4 is transcriptionally regulated by various stress responses	D[MNR]D[DET]	33	D.D	Ribose moiety of UDP and manganese binding site in glucuronyl transferase					DNA metabolism (1e-09)		0.006	10
ucsf_loc_k_means_G6	6	Sub-cellular localization, 6 clusters	F...[FVY]I	33				MFS_1	1.E-04	1	endoplasmic reticulum (1e-19)		0.020	10
protein_40_YBR160W	2	CDC28:  Catalytic subunit of the main cell cycle cyclin-dependent kinase (CDK); alternately associates with G1 cyclins (CLNs) and G2/M cyclins (CLBs) which direct the CDK to specific substrates	M..T[TPQ]	32							cellular morphogenesis (0.01)	Y	0.006	9
protein_40_YBR009C	2	HHF1:  One of two identical histone H4 proteins (see also HHF2); core histone required for chromatin assembly and chromosome function; contributes to telomeric silencing; N-terminal domain involved in maintaining genomic integrity	K.[SEP]A	32	RKK.[ST]	ZIP kinase phosphorylation motif		Histone	1.E-02	-3.6	nuclear chromatin (1e-04)	Y	0.006	10
protein_40_YOL012C	2	HTZ1:  Histone variant H2AZ, exchanged for histone H2A in nucleosomes by the SWR1 complex; involved in transcriptional regulation through prevention of the spread of silent heterochromatin	[GVH]G[KYQ]G	32	GGQ	N-methylation motif in E. coli, Gln residue in methylated, mimics CCA motif at the end of tRNA molecule	Y	Histone	1.E-05	-2.5	nuclear chromatin (1e-06)		0.005	9
yeast-649_GO-0003676	2	nucleic acid binding	P.P[SHP]	32	P.P	motif in interleukin 5 receptor necessary for signaling		RRM_1	1.E-08	-2.3	nucleic acid binding (1e-12)	Y	0.007	10
protein_40_YHR196W	2	UTP9:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	[EDF]E...E	32				WD40	1.E-02	-2.1	nucleolus (1e-34)	Y	0.006	10
yeast-248_GO-0016072	2	rRNA metabolism	[ASF]R..D[IVA]	32	[AG]R	Protease matriptase protease site		DEAD	1.E-12	-2	rRNA metabolism (1e-40)	Y	0.007	10
protein_40_YFR037C	2	RSC8:  Component of the RSC chromatin remodeling complex; essential for viability and mitotic growth; homolog of SWI/SNF subunit Swi3p, but unlike Swi3p, does not activate transcription of reporters	D[PMD]..[PGE]K	32				HMG_box	1.E-03	-1.9	chromosome organization and biogenesis (sensu Eukaryota) (1e-05)		0.006	10
protein_40_YER110C	2	KAP123:  Karyopherin beta, mediates nuclear import of ribosomal proteins prior to assembly into ribosomes and import of histones H3 and H4; localizes to the nuclear pore, nucleus, and cytoplasm; exhibits genetic interactions with RAI1	[GSM]AK[PRA]	32	GAKRH	HISTONE_H4 PATTERN		Histone	1.E-05	-1.9	rRNA export from nucleus (1e-08)	Y	0.006	10
yeast-255_GO-0042254	2	ribosome biogenesis and assembly	D[VLK].AR[GRE]	32	[AG]R	Protease matriptase protease site		DEAD	1.E-08	-1.7	ribosome biogenesis (1e-12)		0.006	9
yeast-255_GO-0007028	2	cytoplasm organization and biogenesis	D[VLK].AR[GRE]	32	[AG]R	Protease matriptase protease site		DEAD	1.E-08	-1.7	ribosome biogenesis (1e-12)		0.006	9
yeast-255_GO-0042254	2	ribosome biogenesis and assembly	VIN[YGV][DRS]	32				DEAD	1.E-02	-1.3	cytoplasm organization and biogenesis (1e-07)		0.005	8
yeast-255_GO-0007028	2	cytoplasm organization and biogenesis	VIN[YGV][DRS]	32				DEAD	1.E-02	-1.3	cytoplasm organization and biogenesis (1e-07)		0.005	8
protein_40_YPL126W	2	NAN1:  U3 snoRNP protein, component of the small (ribosomal) subunit (SSU) processosome containing U3 snoRNA; required for the biogenesis of18S rRNA	SK.[IAL][QAP]	32				WD40	1.E-02	-1.3	nucleolus (1e-20)		0.006	10
protein_40_YMR093W	2	UTP15:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	E..E[DKE]	32	RE..E	Iron binding motif in ferritin L-chain and yeast Iron transport protein		WD40	1.E-07	-1.3	nucleolus (1e-35)		0.006	9
yeast-649_GO-0003676	2	nucleic acid binding	K.[QDL]E	32	G.[DN]F.K.DE	RUBISCO_LARGE PATTERN		RRM_1	1.E-05	-1.1	nucleic acid binding (1e-26)	Y	0.007	10
yeast-255_GO-0042254	2	ribosome biogenesis and assembly	T[GH].[GMY]K	32			Y	Helicase_C	1.E-12	-1.1	cytoplasm organization and biogenesis (1e-29)	Y	0.007	10
yeast-255_GO-0007028	2	cytoplasm organization and biogenesis	T[GH].[GMY]K	32			Y	Helicase_C	1.E-12	-1.1	cytoplasm organization and biogenesis (1e-29)	Y	0.007	10
yeast-1433_GO-0006139	2	nucleobase, nucleoside, nucleotide and nucleic acid metabolism	Q.P[TIA]	32	P[ST]	DNA dependent Protein kinase substrate motif		zf-C2H2	1.E-03	-1.1	transcription (1e-44)	Y	0.007	10
protein_40_YLR186W	2	EMG1:  Protein required for the maturation of the 18S rRNA and for 40S ribosome production; associated with spindle/microtubules; nuclear localization depends on physical interaction with Nop14p; may bind snoRNAs	D[EYL][ESY]D	32	P.DLS	Binding motif on TGIF for CtBP		WD40	1.E-02	-1.1	nucleolus (1e-18)		0.006	10
protein_40_YGL120C	2	PRP43:  RNA helicase in the DEAH-box family, functions in both RNA polymerase I and polymerase II transcript metabolism, involved in release of the lariat-intron from the spliceosome	GR[LDV]	32	[NS][TS]DAEGR[LVMI]	CYTOSOL_AP PATTERN		Helicase_C	1.E-02	-1.1	cytoplasm organization and biogenesis (1e-22)		0.006	10
protein_40_YMR047C	2	NUP116:  Subunit of the nuclear pore complex (NPC) that is localized to both sides of the pore; contains a repetitive GLFG motif that interacts with mRNA export factor Mex67p and with karyopherin Kap95p; homologous to Nup100p	SA[FLH]	32	[LIVMA].EG[DN]SA.[STAG]	TOPOISOMERASE_II PATTERN		IBN_N	1.E-07	-1	nuclear transport (1e-35)		0.006	10
protein_40_YGL120C	2	PRP43:  RNA helicase in the DEAH-box family, functions in both RNA polymerase I and polymerase II transcript metabolism, involved in release of the lariat-intron from the spliceosome	Q.K[QKF]	32	GQDQTKQQI	43_KD_POSTSYNAPTIC PATTERN		Helicase_C	1.E-02	-1	nucleolus (1e-27)	Y	0.006	9
protein_40_YDL014W	2	NOP1:  Nucleolar protein, component of the small subunit processome complex, which is required for processing of pre-18S rRNA; has similarity to mammalian fibrillarin	R.[TNL]A	32	R.[ST]	PKA consensus phosphorylation site		Helicase_C	1.E-02	-1	cytoplasm organization and biogenesis (1e-34)	Y	0.006	9
yeast-410_GO-0007049	2	cell cycle	F[DNEQ]K	32			Y	Pkinase	1.E-07	-0.8	cell cycle (1e-19)		0.007	10
yeast-238_GO-0017111	2	nucleoside-triphosphatase activity	LV.[VEN][GQM]	32				Helicase_C	1.E-03	-0.7	nucleoside-triphosphatase activity (1e-40)		0.007	10
yeast-205_GO-0005856	2	cytoskeleton	T..[QSM]E	32	T..[SA]	FHA of KAPP binding motif, Thr must be phosphorylated		SH3_1	1.E-02	-0.7	cytoskeleton (1e-10)	Y	0.007	10
oshea_cell_periphery	2	oshea_cell_periphery	[EIK]L..[FSC]V	32				RhoGAP	1.E-02	-0.7	bud (1e-06)		0.007	10
yeast-238_GO-0017111	2	nucleoside-triphosphatase activity	R.I[TMG]	32			Y	Ras	1.E-06	-0.6	nucleoside-triphosphatase activity (1e-86)	Y	0.007	10
protein_40_YPL153C	2	RAD53:  Protein kinase, required for cell-cycle arrest in response to DNA damage; activated by trans autophosphorylation when interacting with hyperphosphorylated Rad9p; also interacts with ARS1 and plays a role in initiation of DNA replication	K..[NPE]G	32				Ank	1.E-02	-0.6	protein kinase activity (0.001)		0.006	10
protein_40_YOL133W	2	HRT1:  RING finger containing subunit of Skp1-Cullin-F-box ubiquitin protein ligases (SCF); required for Gic2p, Far1p, Sic1p and Cln2p degradation; may tether Cdc34p (a ubiquitin conjugating enzyme or E2) and Cdc53p (a cullin) subunits of SCF	K[SFK]..[EVC]Y	32	[EDY]Y	TC-PTP phosphatase substrate motif		F-box	1.E-05	-0.6	ubiquitin ligase complex (1e-04)		0.006	10
protein_40_YML085C	2	TUB1:  Alpha-tubulin; associates with beta-tubulin (Tub2p) to form tubulin dimer, which polymerizes to form microtubules	VI[SQN][ENI]	32				IBN_N	1.E-02	-0.6			0.006	10
protein_40_YLR293C	2	GSP1:  GTP binding protein (mammalian Ranp homolog) involved in the maintenance of nuclear organization, RNA processing and transport; regulated by Prp20p, Rna1p, Yrb1p, Yrb2p, Yrp4p, Yrb30p, Cse1p and Kap95p; yeast Gsp2p homolog	[TWA]Q..E[LDA]	32	[ST]Q	ATM kinase phosphorylation site		IBN_N	1.E-05	-0.6	nucleocytoplasmic transport (1e-06)	Y	0.006	9
yeast-548_GO-0051641	2	cellular localization	QQ[IEG]	32	S[QT]Q	ATM phosphorylation of this motif on Chk2		IBN_N	1.E-02	-0.5	cellular localization (1e-11)		0.007	10
protein_40_YOR181W	2	LAS17:  Actin assembly factor, activates the Arp2/3 protein complex that nucleates branched actin filaments; localizes with the Arp2/3 complex to actin patches; homolog of the human Wiskott-Aldrich syndrome protein (WASP)	R[EFL]..[EDW]G	32				SH3_1	1.E-02	-0.5	endocytosis (0.001)		0.005	8
protein_40_YOL133W	2	HRT1:  RING finger containing subunit of Skp1-Cullin-F-box ubiquitin protein ligases (SCF); required for Gic2p, Far1p, Sic1p and Cln2p degradation; may tether Cdc34p (a ubiquitin conjugating enzyme or E2) and Cdc53p (a cullin) subunits of SCF	D[SIQ]..[KIN]F	32				F-box	1.E-04	-0.5	cullin-RING ubiquitin ligase complex (1e-04)	Y	0.006	10
protein_40_YLR293C	2	GSP1:  GTP binding protein (mammalian Ranp homolog) involved in the maintenance of nuclear organization, RNA processing and transport; regulated by Prp20p, Rna1p, Yrb1p, Yrb2p, Yrp4p, Yrb30p, Cse1p and Kap95p; yeast Gsp2p homolog	[ILA]K..[EYQ]N	32				IBN_N	1.E-03	-0.5	nuclear transport (1e-07)	Y	0.006	10
protein_40_YGL105W	2	ARC1:  Protein that binds tRNA and methionyl- and glutamyl-tRNA synthetases (Mes1p and Gus1p), delivering tRNA to them, stimulating catalysis, and ensuring their localization to the cytoplasm; also binds quadruplex nucleic acids	E..R[NSD]	32				Pkinase	1.E-10	-0.1	protein kinase activity (1e-11)	Y	0.006	10
protein_40_YDL153C	2	SAS10:  Component of the small (ribosomal) subunit (SSU) processosome required for pre-18S rRNa processing; essential nucleolar protein that, when overproduced, disrupts silencing	[NYQ]Q..E[KEH]	32				Pkinase	1.E-05	-0.1	protein kinase activity (1e-04)		0.005	7
yeast-648_GO-0050791	2	regulation of physiological process	I..[LPV]K	32				Zn_clus	1.E-06	0.1	regulation of metabolism (1e-14)	Y	0.007	10
protein_40_YJL074C	2	SMC3:  Subunit of the multiprotein cohesin complex required for sister chromatid cohesion in mitotic cells; also required, with Rec8p, for cohesion and recombination during meiosis; phylogenetically conserved SMC chromosomal ATPase family member	EI.[SLM][LKR]	32	VEID	Protease Caspase 6 -stringent		SMC_N	1.E-03	0.1	cohesin complex (0.01)		0.007	10
yeast-1062_GO-0016020	2	membrane	V.A[VYF]	32				E1-E2_ATPase	1.E-02	0.2	integral to membrane (1e-38)	Y	0.007	10
oshea_bud_neck	2	oshea_bud_neck	L[CSK]I	32	LLKIL	AP-2 binding motif in CXCR2 receptor	Y	RhoGAP	1.E-06	0.2	site of polarized growth (1e-51)		0.006	10
protein_40_YOL133W	2	HRT1:  RING finger containing subunit of Skp1-Cullin-F-box ubiquitin protein ligases (SCF); required for Gic2p, Far1p, Sic1p and Cln2p degradation; may tether Cdc34p (a ubiquitin conjugating enzyme or E2) and Cdc53p (a cullin) subunits of SCF	A..L[SNV]	32				F-box	1.E-08	0.5	ubiquitin ligase complex (1e-10)	Y	0.006	10
protein_40_YML048W	2	GSF2:  ER localized integral membrane protein that may promote secretion of certain hexose transporters, including Gal2p; involved in glucose-dependent repression	[FIG]I..[IVL]I	32				Sugar_tr	1.E-02	0.7	endoplasmic reticulum (0.001)	Y	0.006	10
protein_40_YER165W	2	PAB1:  Poly(A) binding protein, part of the 3'-end RNA-processing complex, mediates interactions between the 5' cap structure and the 3' mRNA poly(A) tail, involved in control of poly(A) tail length, interacts with translation factor eIF-4G	D..[ERP]E	32				RRM_1	1.E-05	0.7	RNA metabolism (1e-09)	Y	0.006	10
protein_40_YBR106W	2	PHO88:  Probable membrane protein, involved in phosphate transport; pho88 pho86 double null mutant exhibits enhanced synthesis of repressible acid phosphatase at high inorganic phosphate concentrations	L..[YIM]L	32				MFS_1	1.E-08	0.7	transporter activity (1e-11)	Y	0.006	10
yeast-512_GO-0046907	2	intracellular transport	L[ISD].L[IMF]	32	LLDLL	Clathrin binding motif in AP1		IBN_N	1.E-04	0.8	intracellular transport (1e-09)		0.007	9
oshea_bud_neck	2	oshea_bud_neck	E[DVM]L	32	DLL	Binding motif for clathrin heavy chain ear		RhoGAP	1.E-04	0.8	site of polarized growth (1e-44)	Y	0.006	10
yeast-413_GO-0005215	2	transporter activity	SV.[AQW][VTF]	32				Mito_carr	1.E-04	0.9	transporter activity (1e-44)	Y	0.007	10
protein_40_YLR180W	2	SAM1:  S-adenosylmethionine synthetase, catalyzes transfer of the adenosyl group of ATP to the sulfur atom of methionine; one of two differentially regulated isozymes (Sam1p and Sam2p)	L[REC]..G[LAS]	32				GATase	1.E-02	0.9			0.006	9
protein_40_YGR252W	2	GCN5:  Histone acetyltransferase, acetylates N-terminal lysines on histones H2B and H3; catalytic subunit of the ADA and SAGA histone acetyltransferase complexes; founding member of the Gcn5p-related N-acetyltransferase superfamily	[RT]A.L[KW]S	32	GTALL	Receptor recycling motif		Histone	1.E-02	0.9	SAGA complex (0.001)		0.004	8
yeast-468_GO-0051276	2	chromosome organization and biogenesis	[AG]Q[ANM]Q	32				Helicase_C	1.E-02	1	chromosome organization and biogenesis (sensu Eukaryota) (1e-24)	Y	0.007	9
protein_40_YOL133W	2	HRT1:  RING finger containing subunit of Skp1-Cullin-F-box ubiquitin protein ligases (SCF); required for Gic2p, Far1p, Sic1p and Cln2p degradation; may tether Cdc34p (a ubiquitin conjugating enzyme or E2) and Cdc53p (a cullin) subunits of SCF	VK[SFA]	32				F-box	1.E-05	1	ubiquitin ligase complex (1e-05)	Y	0.006	10
protein_40_YLR372W	2	SUR4:  Elongase, involved in fatty acid and sphingolipid biosynthesis; synthesizes very long chain 20-26-carbon fatty acids from C18-CoA primers; involved in regulation of sphingolipid biosynthesis	F..[FSL]A	32				MFS_1	1.E-03	1	endoplasmic reticulum (1e-07)	Y	0.006	7
protein_40_YGL105W	2	ARC1:  Protein that binds tRNA and methionyl- and glutamyl-tRNA synthetases (Mes1p and Gus1p), delivering tRNA to them, stimulating catalysis, and ensuring their localization to the cytoplasm; also binds quadruplex nucleic acids	G[GTD]..D[AKL]	32	T..D	FHA1 binding motif, Thr must be phosphorylated, binding motif of proteins binding to Chk2		Pkinase	1.E-04	1	protein kinase activity (0.001)		0.006	10
protein_40_YER112W	2	LSM4:  Lsm (Like Sm) protein; part of heteroheptameric complexes (Lsm2p-7p and either Lsm1p or 8p): cytoplasmic Lsm1p complex involved in mRNA decay; nuclear Lsm8p complex part of U6 snRNP and possibly involved in processing tRNA, snoRNA, and rRNA	[SQY]I..[NRH]G	32				LSM	1.E-02	1.1	U4/U6 x U5 tri-snRNP complex (1e-06)		0.006	10
yeast-980_GO-0051179	2	localization	V.T[LVW]	32				MFS_1	1.E-03	1.2	establishment of cellular localization (1e-76)		0.007	10
yeast-523_GO-0030529	2	ribonucleoprotein complex	[RKA]A..[VDR]A	32	LK[EAD]AE.RA[ET]	TROPOMYOSIN PATTERN		Ribosomal_60s	1.E-04	1.2	ribonucleoprotein complex (1e-54)		0.007	9
protein_40_YLL008W	2	DRS1:  Nucleolar DEAD-box protein required for ribosome assembly and function, including synthesis of 60S ribosomal subunits; constituent of 66S pre-ribosomal particles	D..[DPH]E	32				Pkinase	1.E-05	1.2	cytoplasm organization and biogenesis (1e-21)		0.006	10
protein_40_YDR099W	2	BMH2:  14-3-3 protein, minor isoform; controls proteome at post-transcriptional level, binds proteins and DNA, involved in regulation of many processes including exocytosis, vesicle transport, Ras/MAPK signaling, and rapamycin-sensitive signaling	[PRQ]P.[AKR]A	32	P..P.[KR]	LIG_SH3_2		Pkinase	1.E-02	1.2			0.005	9
protein_40_YBR159W	2	IFA38: Microsomal beta-keto-reductase; contains oleate response element (ORE) sequence in the promoter region; mutants exhibit reduced VLCFA synthesis, accumulate high levels of dihydrosphingosine, phytosphingosine and medium-chain ceramides	A.F[GVM]	32			Y	MFS_1	1.E-02	1.2	transporter activity (1e-09)	Y	0.006	10
oshea_bud_neck	2	oshea_bud_neck	G.L[KQY]	32	IYG.L	Lck kinase phosphorylation site (peptide screen)		RhoGAP	1.E-03	1.2	bud (1e-47)	Y	0.006	10
yeast-939_GO-0051234	2	establishment of localization	[ALE]S...A	32				IBN_N	1.E-04	1.3	establishment of cellular localization (1e-12)		0.007	10
yeast-939_GO-0051234	2	establishment of localization	[QGF]L.G[AFM]	32	LFG	Protease Papain substrate, a prototype cysteine proteinase		Mito_carr	1.E-04	1.3	intracellular transport (1e-19)		0.007	10
yeast-413_GO-0005215	2	transporter activity	A.[SYL]V	32	RPVSSAASVY	14-3-3 domain binding motif		MFS_1	1.E-12	1.4	transporter activity (1e-14)	Y	0.007	10
protein_40_YPR120C	2	CLB5:  B-type cyclin involved in DNA replication during S phase; activates Cdc28p to promote initiation of DNA synthesis; functions in formation of mitotic spindles along with Clb3p and Clb4p; most abundant during late G1 phase	LK.[EWT][NLS]	32				Pkinase	1.E-02	1.5			0.006	10
yeast-238_GO-0017111	2	nucleoside-triphosphatase activity	AR[AVS]	32	[AG]R	Protease matriptase protease site	Y	ABC_tran	1.E-16	1.6	nucleoside-triphosphatase activity (1e-95)		0.007	10
yeast-589_GO-0050896	2	response to stimulus	L.D	32	LPDEL	Motif in CBP for interaction with PPARg-LBD (secondary site)		Pkinase	1.E-02	1.7	response to stress (10)	Y	0.006	9
protein_40_YOL012C	2	HTZ1:  Histone variant H2AZ, exchanged for histone H2A in nucleosomes by the SWR1 complex; involved in transcriptional regulation through prevention of the spread of silent heterochromatin	DF[GI]LA	32				Pkinase	1.E-04	1.7	protein amino acid phosphorylation (0.001)		0.004	8
yeast-649_GO-0003676	2	nucleic acid binding	[VK].VK	32				RRM_1	1.E-06	2	nucleic acid binding (1e-16)		0.007	10
protein_40_YGL245W	2	GUS1:  Glutamyl-tRNA synthetase (GluRS), forms a complex with methionyl-tRNA synthetase (Mes1p) and Arc1p; complex formation increases the catalytic efficiency of both tRNA synthetases and ensures their correct localization to the cytoplasm	KP[ESP][NVA]	32	P[ST]	DNA dependent Protein kinase substrate motif		Pkinase	1.E-15	2.1	protein kinase activity (1e-12)		0.006	10
yeast-215_GO-0005694	2	chromosome	[IED]I..K[NWM]	32				HMG_box	1.E-02	2.4	chromosome (1e-43)		0.007	10
oshea_bud_neck	2	oshea_bud_neck	R[RSE]..L[EIS]	32	R..L	LIG_APCC_Dbox_1		PH	1.E-03	2.6	bud (1e-25)	Y	0.007	9
protein_40_YGL111W	2	NSA1:  Constituent of 66S pre-ribosomal particles, involved in 60S ribosomal subunit biogenesis	GK.[AS]A[FK]	32				DEAD	1.E-03	3.1	nucleolus (0.001)	Y	0.004	7
protein_40_YER012W	2	PRE1:  Beta 4 subunit of the 20S proteasome; localizes to the nucleus throughout the cell cycle	[EY]A..N[AHR]	32				PCI	1.E-03	3.2	proteasome complex (sensu Eukaryota) (1e-06)		0.005	8
protein_40_YNL272C	2	SEC2:  Guanyl-nucleotide exchange factor for the small G-protein Sec4p, located on cytoplasmic vesicles; essential for post-Golgi vesicle transport	Y.[ASK]P	32	E.Y.[QSG]	Protease TEV	Y	Pkinase	1.E-24	3.5	protein kinase activity (1e-24)	Y	0.006	9
protein_40_YLR002C	2	NOC3:  Protein that forms a nuclear complex with Noc2p that binds to 66S ribosomal precursors to mediate their intranuclear transport; also binds to chromatin to promote the association of DNA replication factors and replication initiation	T[PVD][GF]R	32	[AG]R	Protease matriptase protease site		DEAD	1.E-05	3.5	ribosomal large subunit assembly and maintenance (1e-08)		0.004	7
protein_40_YGL245W	2	GUS1:  Glutamyl-tRNA synthetase (GluRS), forms a complex with methionyl-tRNA synthetase (Mes1p) and Arc1p; complex formation increases the catalytic efficiency of both tRNA synthetases and ensures their correct localization to the cytoplasm	FG.[ACN][KAR]	32	FGRA	DNA binding motif in ssDNA binding proteins		Pkinase	1.E-13	3.8	protein kinase activity (1e-13)		0.006	9
matsuyama_nucleolus	2	matsuyama_nucleolus	[PNL]TRE[LR]	32	RE..E	Iron binding motif in ferritin L-chain and yeast Iron transport protein		DEAD	1.E-11	4.1	ATP-dependent RNA helicase activity (1e-11)		0.006	10
protein_40_YDL014W	2	NOP1:  Nucleolar protein, component of the small subunit processome complex, which is required for processing of pre-18S rRNA; has similarity to mammalian fibrillarin	[DHN]V..R[GAY]	32				Helicase_C	1.E-03	4.7	nucleolus (1e-12)		0.006	10
yeast-1115_GO-0006996	2	organelle organization and biogenesis	V[RKE].W[DI]	32				WD40	1.E-20	5.4	nuclear lumen (1e-05)		0.007	9
yeast-980_GO-0051179	2	localization	[AEG]F[SMT]FG	32	F..F[ST][FY]	Rsks are phosphorylated at this bulky ring site, Ser/Thr must be phosphorylated. This motif recruits PDK1 kinase					rRNA export from nucleus (1e-14)		0.007	9
yeast-856_GO-0009059	2	macromolecule biosynthesis	K[MFY][SVQ]KS	32	F..KY[DE]KSL	Nucletodie binding motif in Annexin 6 for ATP/GTP	Y				amino acid activation (1e-14)		0.007	10
yeast-649_GO-0003676	2	nucleic acid binding	[AEN]D.[DAK]E	32	D.D	Ribose moiety of UDP and manganese binding site in glucuronyl transferase					nucleic acid binding (1e-88)	Y	0.007	9
yeast-648_GO-0050791	2	regulation of physiological process	S[STA].[RDW]LE	32	S[ST]	MDC1 BRCT domain binding motif					regulation of metabolism (1e-04)		0.007	10
yeast-596_GO-0044425	2	membrane part	S[FIT]..Y[LVT]	32	Y[VLTFIC]	LIG_SH2_STAT5					endomembrane system (1e-26)		0.007	9
yeast-589_GO-0050896	2	response to stimulus	T..K[NLH]	32	TP.K	CDK5 kinase substrate motif					response to stress (1e-10)		0.007	10
yeast-544_GO-0016070	2	RNA metabolism	S[SQV].S[TPY]	32	S[ST]	MDC1 BRCT domain binding motif							0.007	10
yeast-521_GO-0051649	2	establishment of cellular localization	Q.[LQF]S	32							establishment of cellular localization (1e-17)	Y	0.007	10
yeast-513_GO-0005515	2	protein binding	KL.[QAN][FNI]	32	NKLY	LIM3 domain in enigma binds to this site in Ret	Y				protein binding (1e-80)		0.007	10
yeast-436_GO-0031323	2	regulation of cellular metabolism	[KQC]P..IK[KTA]	32							regulation of cellular metabolism (1e-08)		0.006	9
yeast-410_GO-0007049	2	cell cycle	K.T[NIR]	32	RKK.[ST]	ZIP kinase phosphorylation motif					cell cycle (1e-16)		0.007	10
yeast-388_GO-0007275	2	development	[TSN]H[KQL]K	32							multicellular organismal development (1e-45)		0.007	10
yeast-388_GO-0007275	2	development	G[AMG][NKL]S	32							multicellular organismal development (1e-56)	Y	0.007	10
yeast-388_GO-0007275	2	development	TT[KGT][IHM]	32	YTT[ILM]	Syk N-terminal SH2 domain binding motif					multicellular organismal development (1e-44)	Y	0.007	10
yeast-371_GO-0009056	2	catabolism	K[KMW]..K[SRI]	32	KR	CLV_PCSK_PC1ET2_1							0.007	10
yeast-345_GO-0006396	2	RNA processing	[NAL]D..[SM]ES	32	RSESEE	14-3-3 binding motif in inositol polyphosphate 5-phosphatase	Y				RNA processing (1e-11)		0.006	8
yeast-341_GO-0045449	2	regulation of transcription	[LDA]S[QDV]H	32	[PLIM].[LIDE]SQ	ATM kinase substrate motif					regulation of transcription (1e-35)		0.007	10
yeast-324_GO-0030528	2	transcription regulator activity	KA..L[SYM][VQT]	32							transcription regulator activity (1e-12)		0.006	10
yeast-294_GO-0006366	2	transcription from RNA polymerase II promoter	K[IRD].S[EDP]	32	[DE]S[DE].[DE]	Casein Kinase II substrate motif					transcription from RNA polymerase II promoter (1e-67)		0.007	10
yeast-267_GO-0000003	2	reproduction	S[DLQ]E[DAG]	32	LSQE	ATM kinase substrate motif					reproduction (1e-73)		0.007	10
yeast-261_GO-0016491	2	oxidoreductase activity	KR[KIR]	32	KR	CLV_PCSK_PC1ET2_1							0.007	10
yeast-244_GO-0000279	2	M phase	K.Q	32	GQDQTKQQI	43_KD_POSTSYNAPTIC PATTERN					M phase (1e-28)		0.007	10
yeast-235_GO-0009653	2	morphogenesis	Q[DTL][AQT]S	32							cellular morphogenesis (1e-47)		0.007	10
yeast-235_GO-0000902	2	cellular morphogenesis	Q[DTL][AQT]S	32							cellular morphogenesis (1e-47)		0.007	10
yeast-220_GO-0044255	2	cellular lipid metabolism	L..[HFC]F	32							cellular lipid metabolism (1e-09)		0.007	10
yeast-219_GO-0046903	2	secretion	[KGR]LI[TQW]	32							secretion (1e-47)		0.007	10
yeast-216_GO-0006325	2	establishment and/or maintenance of chromatin architecture	ND.E[LEK][SRY]	32	D.E	Sec24p					chromatin modification (1e-12)		0.006	9
yeast-216_GO-0006323	2	DNA packaging	ND.E[LEK][SRY]	32	D.E	Sec24p					chromatin modification (1e-12)		0.006	9
yeast-215_GO-0007010	2	cytoskeleton organization and biogenesis	P.[PNI]R	32	P..R..KP	SH3 binding motif for GRB2 C-term					cytoskeleton organization and biogenesis (1e-81)		0.007	10
yeast-205_GO-0005856	2	cytoskeleton	[LNC][NFC]LND	32							cytoskeletal part (1e-10)		0.005	7
yeast-200_GO-0006519	2	amino acid and derivative metabolism	[AHV]E..G[LAC]	32							amino acid and derivative metabolism (1e-35)		0.007	10
yeast-1721_GO-0016043	2	cell organization and biogenesis	R.N[VEP]	32							chromosome organization and biogenesis (1e-29)	Y	0.007	10
yeast-1433_GO-0006139	2	nucleobase, nucleoside, nucleotide and nucleic acid metabolism	[REK]D.[NEH]T	32	D.E	Sec24p					RNA metabolism (1e-14)	Y	0.007	10
yeast-1036_GO-0005739	2	mitochondrion	IR[TAP][LSV]	32	RPL	VEGFR and neuropilin binding peptide					nucleoside-triphosphatase activity (0.01)		0.007	10
protein_40_YPR144C	2	NOC4:  Nucleolar protein, forms a complex with Nop14p that mediates maturation and nuclear export of 40S ribosomal subunits	DIS[DY][DF]	32							snoRNA binding (0.01)	Y	0.004	8
protein_40_YPR144C	2	NOC4:  Nucleolar protein, forms a complex with Nop14p that mediates maturation and nuclear export of 40S ribosomal subunits	EE.[ERA][KFE]	32	EED	Ankyrin B C-terminal motif that binds internal Ankyrin repeats	Y				snoRNA binding (1e-16)	Y	0.006	10
protein_40_YPR119W	2	CLB2:  B-type cyclin involved in cell cycle progression; activates Cdc28p to promote the transition from G2 to M phase; accumulates during G2 and M, then targeted via a destruction box motif for ubiquitin-mediated degradation by the proteasome	[GSE]D.T[FYA]	32	D.D.[TV]	Motif in PRS1 and PRS-2 required for phosphatase activity and salt stress response					bud neck (0.001)	Y	0.006	10
protein_40_YPR119W	2	CLB2:  B-type cyclin involved in cell cycle progression; activates Cdc28p to promote the transition from G2 to M phase; accumulates during G2 and M, then targeted via a destruction box motif for ubiquitin-mediated degradation by the proteasome	R[GYM].P[RNA]	32			Y				cell cycle (0.01)	Y	0.006	10
protein_40_YPR110C	2	RPC40:  RNA polymerase subunit, common to RNA polymerase I and III	HG[VRN][ALD]	32								Y	0.005	8
protein_40_YPR110C	2	RPC40:  RNA polymerase subunit, common to RNA polymerase I and III	R.[LYK]G	32	G[FL]PGER..G	LIG_IBS_1					RNA polymerase complex (0.01)	Y	0.006	9
protein_40_YPR016C	2	TIF6:  Constituent of 66S pre-ribosomal particles, has similarity to human translation initiation factor 6 (eIF6); may be involved in the biogenesis and or stability of 60S ribosomal subunits	E.[KER]A	32	LK[EAD]AE.RA[ET]	TROPOMYOSIN PATTERN					cytoplasm organization and biogenesis (1e-18)		0.006	10
protein_40_YPL256C	2	CLN2:  G1 cyclin involved in regulation of the cell cycle; activates Cdc28p kinase to promote the G1 to S phase transition; late G1 specific expression depends on transcription factor complexes, MBF (Swi6p-Mbp1p) and SBF (Swi6p-Swi4p)	LI..G[LS][VY]	32									0.004	7
protein_40_YPL220W	2	RPL1A:  N-terminally acetylated protein component of the large (60S) ribosomal subunit, nearly identical to Rpl1Bp and has similarity to E. coli L1 and rat L10a ribosomal proteins; rpl1a rpl1b double null mutation is lethal	[GTV]K[KYN]V	32	G[VT][EK][FY]VCCP	A4_EXTRA PATTERN					ribonucleoprotein complex (1e-05)		0.006	9
protein_40_YPL209C	2	IPL1:  Aurora kinase involved in regulating kinetochore-microtubule attachments; helps maintain condensed chromosomes during anaphase and early telophase; associates with Sli15p, which promotes Ipl1p association with mitotic spindle	F[EAC]..[EGD]G	32								Y	0.005	10
protein_40_YPL204W	2	HRR25:  Protein kinase involved in regulating diverse events including vesicular trafficking, DNA repair, and chromosome segregation; binds the CTD of RNA pol II; homolog of mammalian casein kinase 1delta (CK1delta)	[NRY]SN[NLT]G	32	SNHG[AG]RQ	FMN_HYDROXY_ACID_DH_1 PATTERN							0.004	7
protein_40_YPL204W	2	HRR25:  Protein kinase involved in regulating diverse events including vesicular trafficking, DNA repair, and chromosome segregation; binds the CTD of RNA pol II; homolog of mammalian casein kinase 1delta (CK1delta)	DE..E[EKS][VNF]	32									0.005	8
protein_40_YPL204W	2	HRR25:  Protein kinase involved in regulating diverse events including vesicular trafficking, DNA repair, and chromosome segregation; binds the CTD of RNA pol II; homolog of mammalian casein kinase 1delta (CK1delta)	G[KEY]..A	32			Y						0.006	10
protein_40_YPL153C	2	RAD53:  Protein kinase, required for cell-cycle arrest in response to DNA damage; activated by trans autophosphorylation when interacting with hyperphosphorylated Rad9p; also interacts with ARS1 and plays a role in initiation of DNA replication	[IEQ]H..G[SEY]	32									0.005	9
protein_40_YPL153C	2	RAD53:  Protein kinase, required for cell-cycle arrest in response to DNA damage; activated by trans autophosphorylation when interacting with hyperphosphorylated Rad9p; also interacts with ARS1 and plays a role in initiation of DNA replication	[KRI]K[APY]P	32	K[ST]P.K	GSK-3, ERK1, ERK2, CDK5 substrate motif							0.006	9
protein_40_YPL153C	2	RAD53:  Protein kinase, required for cell-cycle arrest in response to DNA damage; activated by trans autophosphorylation when interacting with hyperphosphorylated Rad9p; also interacts with ARS1 and plays a role in initiation of DNA replication	A..[LSD]N	32								Y	0.006	9
protein_40_YPL153C	2	RAD53:  Protein kinase, required for cell-cycle arrest in response to DNA damage; activated by trans autophosphorylation when interacting with hyperphosphorylated Rad9p; also interacts with ARS1 and plays a role in initiation of DNA replication	PL.[DVP][FPY]	32	PPLP	LIG_WW_2						Y	0.006	10
protein_40_YPL153C	2	RAD53:  Protein kinase, required for cell-cycle arrest in response to DNA damage; activated by trans autophosphorylation when interacting with hyperphosphorylated Rad9p; also interacts with ARS1 and plays a role in initiation of DNA replication	S[AHY]P[NYE]	32	P[TS]AP	LIG_PTAP							0.007	10
protein_40_YPL153C	2	RAD53:  Protein kinase, required for cell-cycle arrest in response to DNA damage; activated by trans autophosphorylation when interacting with hyperphosphorylated Rad9p; also interacts with ARS1 and plays a role in initiation of DNA replication	TI[NIS][NTV]	32								Y	0.006	10
protein_40_YPL146C	2	NOP53:  Nucleolar protein; involved in biogenesis of the 60S subunit of the ribosome; interacts with rRNA processing factors Cbf5p and Nop2p; null mutant is viable but growth is severely impaired	K[KQV].K[SFN]	32	K[KR].[KR]	Nuclear localization motif					rRNA metabolism (1e-04)		0.006	10
protein_40_YPL141C	2	FRK1:  Putative protein kinase; similar to Kin4p; green fluorescent protein (GFP)-fusion protein localizes to the cytoplasm; YPL141C is not an essential gene	E[NDV]..D[DAY]	32			Y						0.006	10
protein_40_YOR326W	2	MYO2:  One of two type V myosin motors (along with MYO4) involved in actin-based transport of cargos; required for the polarized delivery of secretory vesicles, the vacuole, late Golgi elements, peroxisomes, and the mitotic spindle	[GHN]E.[GRM]V	32								Y	0.004	9
protein_40_YOR181W	2	LAS17:  Actin assembly factor, activates the Arp2/3 protein complex that nucleates branched actin filaments; localizes with the Arp2/3 complex to actin patches; homolog of the human Wiskott-Aldrich syndrome protein (WASP)	IV.[HRY][KVT]	32			Y				endocytosis (0.001)		0.005	10
protein_40_YOR133W	2	EFT1:  Elongation factor 2 (EF-2), also encoded by EFT2; catalyzes ribosomal translocation during protein synthesis; contains diphthamide, the unique posttranslationally modified histidine residue specifically ADP-ribosylated by diphtheria toxin	[SL]D..[PV]KE	32								Y	0.004	7
protein_40_YOR096W	2	RPS7A:  Protein component of the small (40S) ribosomal subunit, nearly identical to Rps7Bp; interacts with Kti11p; deletion causes hypersensitivity to zymocin; has similarity to rat S7 and Xenopus S8 ribosomal proteins	G[KRM]K[VGM]	32	G[KR][KR]	Amidation after cleavage after Gly (must be in secretory pathway)					ribonucleoprotein complex (1e-11)	Y	0.007	10
protein_40_YOL086C	2	ADH1:  Alcohol dehydrogenase, fermentative isozyme active as homo- or heterotetramers; required for the reduction of acetaldehyde to ethanol, the last step in the glycolytic pathway	[DIY]A.D[TIG]	32							secretory pathway (1e-04)	Y	0.006	10
protein_40_YOL041C	2	NOP12:  Nucleolar protein, required for pre-25S rRNA processing; contains an RNA recognition motif (RRM) and has similarity to Nop13p, Nsr1p, and putative orthologs in Drosophila and S. pombe	AF[TV][KTQ]	32							nucleolus (1e-04)		0.005	9
protein_40_YOL013C	2	HRD1:  Ubiquitin-protein ligase required for endoplasmic reticulum-associated degradation (ERAD) of misfolded proteins; genetically linked to the unfolded protein response (UPR); regulated through association with Hrd3p; contains an H2 ring finger	A..[LEY]G	32							carboxylic acid metabolism (1e-04)		0.006	10
protein_40_YNL307C	2	MCK1:  Protein serine/threonine/tyrosine (dual-specificity) kinase involved in control of chromosome segregation and in regulating entry into meiosis; related to mammalian glycogen synthase kinases of the GSK-3 family	[STF]P..[SAQ]P	32	[ST]P	LIG_WW_4	Y						0.006	10
protein_40_YNL289W	2	PCL1:  Pho85 cyclin of the Pcl1,2-like subfamily, involved in entry into the mitotic cell cycle and regulation of morphogenesis, localizes to sites of polarized cell growth	TP[RAN]	32	LTP	RAF1 kinase substrate motif	Y						0.006	10
protein_40_YNL154C	2	YCK2:  Palmitoylated, plasma membrane-bound casein kinase I isoform; shares redundant functions with Yck1p in morphogenesis, proper septin assembly, endocytic trafficking; provides an essential function overlapping with that of Yck1p	A..P[PKE]	32								Y	0.006	10
protein_40_YNL118C	2	DCP2:  Catalytic subunit of the Dcp1p-Dcp2p decapping enzyme complex, which removes the 5' cap structure from mRNAs prior to their degradation; member of the Nudix hydrolase family	[DNV]P.I[SWK]	32	PWI	Motif in SRM160 for binding DNA and RNA							0.006	10
protein_40_YNL118C	2	DCP2:  Catalytic subunit of the Dcp1p-Dcp2p decapping enzyme complex, which removes the 5' cap structure from mRNAs prior to their degradation; member of the Nudix hydrolase family	LV..[QL][TC]L	32									0.004	9
protein_40_YNL118C	2	DCP2:  Catalytic subunit of the Dcp1p-Dcp2p decapping enzyme complex, which removes the 5' cap structure from mRNAs prior to their degradation; member of the Nudix hydrolase family	QQ.[QND][NGS]	32	Q[MLVI]DG..[DE]	CLV_TASPASE1						Y	0.006	10
protein_40_YMR304W	2	UBP15:  Ubiquitin-specific protease that may play a role in ubiquitin precursor processing	[TPL][DHT]PF	32	DPF	AP2 binding motif in Synaptojanin 1 and EPS15							0.005	8
protein_40_YMR216C	2	SKY1:  SR protein kinase (SRPK) involved in regulating proteins involved in mRNA metabolism and cation homeostasis; similar to human SRPK1	P.[ESR]E	32	[DE]FPPPP.[DE][DE]	EVH1 binding site in ActA protein of Listeria monocytogenes	Y				helicase activity (0.01)	Y	0.006	10
protein_40_YMR194W	2	RPL36A:  N-terminally acetylated protein component of the large (60S) ribosomal subunit, nearly identical to Rpl36Bp and has similarity to rat L36 ribosomal protein; binds to 5.8 S rRNA	S.L[FST]	32									0.006	10
protein_40_YMR106C	2	YKU80:  Subunit of the telomeric Ku complex (Yku70p-Yku80p), involved in telomere length maintenance, structure and telomere position effect; relocates to sites of double-strand cleavage to promote nonhomologous end joining during DSB repair	A[SAN]..[KIR]P	32									0.006	10
protein_40_YML085C	2	TUB1:  Alpha-tubulin; associates with beta-tubulin (Tub2p) to form tubulin dimer, which polymerizes to form microtubules	[ADC]P.[IEL]A	32	P.L	Motif in C-Fos for protein instability						Y	0.006	10
protein_40_YML073C	2	RPL6A:  N-terminally acetylated protein component of the large (60S) ribosomal subunit, has similarity to Rpl6Bp and to rat L6 ribosomal protein; binds to 5.8S rRNA	R.[AHK]R	32	R.[RK]R	CLV_PCSK_FUR_1					cytosolic ribosome (sensu Eukaryota) (1e-25)	Y	0.006	9
protein_40_YML007W	2	YAP1:  Basic leucine zipper (bZIP) transcription factor required for oxidative stress tolerance; activated by H2O2 through the multistep formation of disulfide bonds and transit from the cytoplasm to the nucleus; mediates resistance to cadmium	GN.[NTS][NKF]	32	N.[TS]	N-linked glycosylation site					general RNA polymerase II transcription factor activity (1e-15)		0.006	10
protein_40_YML007W	2	YAP1:  Basic leucine zipper (bZIP) transcription factor required for oxidative stress tolerance; activated by H2O2 through the multistep formation of disulfide bonds and transit from the cytoplasm to the nucleus; mediates resistance to cadmium	SN[APG][NRE]	32							general RNA polymerase II transcription factor activity (1e-14)		0.006	10
protein_40_YLR372W	2	SUR4:  Elongase, involved in fatty acid and sphingolipid biosynthesis; synthesizes very long chain 20-26-carbon fatty acids from C18-CoA primers; involved in regulation of sphingolipid biosynthesis	I[AIV][ILMV]Y	32	[ILV][ILV][IFV]Y[TV][IL][ILVP]	SH2 ligand for SHP-2N (PTP11n)(Tyr must be phosphorylated)					endoplasmic reticulum (0.001)		0.006	10
protein_40_YLR249W	2	YEF3:  Translational elongation factor 3, stimulates the binding of aminoacyl-tRNA (AA-tRNA) to ribosomes by releasing EF-1 alpha from the ribosomal complex; contains two ABC cassettes; binds and hydrolyses ATP	E[VYG]K	32	[QGF][WLCF]GDE[GA]K[GA]	ADENYLOSUCCIN_SYN_1 PATTERN	Y						0.006	10
protein_40_YLR180W	2	SAM1:  S-adenosylmethionine synthetase, catalyzes transfer of the adenosyl group of ATP to the sulfur atom of methionine; one of two differentially regulated isozymes (Sam1p and Sam2p)	GK[TPG]	32	[GA]....GK[ST]	Purine nucleotide triphosphate binding motif					cytosol (0.01)		0.006	10
protein_40_YLR180W	2	SAM1:  S-adenosylmethionine synthetase, catalyzes transfer of the adenosyl group of ATP to the sulfur atom of methionine; one of two differentially regulated isozymes (Sam1p and Sam2p)	R.[TAE]V	32	R.[ST]	PKA consensus phosphorylation site					carboxylic acid metabolism (0.001)	Y	0.006	9
protein_40_YLR166C	2	SEC10:  Essential 100kDa subunit of the exocyst complex (Sec3p, Sec5p, Sec6p, Sec8p, Sec10p, Sec15p, Exo70p, and Exo84p), which has the essential function of mediating polarized targeting of secretory vesicles to active sites of exocytosis	[GVC]R..[ETN]D	32	R..[PA]DG	LIG_TNKBM							0.005	10
protein_40_YLR166C	2	SEC10:  Essential 100kDa subunit of the exocyst complex (Sec3p, Sec5p, Sec6p, Sec8p, Sec10p, Sec15p, Exo70p, and Exo84p), which has the essential function of mediating polarized targeting of secretory vesicles to active sites of exocytosis	E[SRC]F[ERG]	32	EEEYF	EGFR kinase phosphorylation site (peptide screen)					exocyst (0.01)		0.006	10
protein_40_YLR129W	2	DIP2:  Nucleolar protein, specifically associated with the U3 snoRNA, part of the large ribonucleoprotein complex known as the small subunit (SSU) processome, required for 18S rRNA biogenesis, part of the active pre-rRNA processing complex	GV..[TIH][KLM]	32							rRNA processing (1e-15)		0.005	9
protein_40_YLR002C	2	NOC3:  Protein that forms a nuclear complex with Noc2p that binds to 66S ribosomal precursors to mediate their intranuclear transport; also binds to chromatin to promote the association of DNA replication factors and replication initiation	[KPV]K..[KSM]K	32	K..[ST]	PKA kinase substrate motif	Y				cytoplasm organization and biogenesis (1e-20)		0.006	10
protein_40_YKR001C	2	VPS1:  Dynamin-like GTPase required for vacuolar sorting; also involved in actin cytoskeleton organization, late Golgi-retention of some proteins, regulating peroxisome biogenesis	[GN]L..N[VWK]V	32	PN[VA]V[AM]P[LP]	SMAD-interacting motif -FM2 in motif for binding in XFoxH1							0.004	7
protein_40_YKR001C	2	VPS1:  Dynamin-like GTPase required for vacuolar sorting; also involved in actin cytoskeleton organization, late Golgi-retention of some proteins, regulating peroxisome biogenesis	K[VFG].[KHS]Q	32	[ST]Q	ATM kinase phosphorylation site					establishment and/or maintenance of chromatin architecture (0.001)		0.006	10
protein_40_YKL180W	2	RPL17A:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl17Bp and has similarity to E. coli L22 and rat L17 ribosomal proteins; copurifies with the Dam1 complex (aka DASH complex)	K..[AKR]A	32	K[KR].[KR]	Nuclear localization motif					cytosolic ribosome (sensu Eukaryota) (1e-43)	Y	0.006	10
protein_40_YKL104C	2	GFA1:  Glutamine-fructose-6-phosphate amidotransferase, catalyzes the formation of glucosamine-6-P and glutamate from fructose-6-P and glutamine in the first step of chitin biosynthesis	[VDS]E..P[KA]	32	[ST]E	G protein-coupled receptor kinase 1 substrate motif							0.006	10
protein_40_YKL104C	2	GFA1:  Glutamine-fructose-6-phosphate amidotransferase, catalyzes the formation of glucosamine-6-P and glutamate from fructose-6-P and glutamine in the first step of chitin biosynthesis	V..[AYN]G	32							amino acid metabolism (1e-04)	Y	0.006	10
protein_40_YJR059W	2	PTK2:  Putative serine/threonine protein kinase involved in regulation of ion transport across plasma membrane; enhances spermine uptake	EQ[QAR]	32	[DE][DE][FL][FL][DE][LM][IL]...Q[GS].R[LM][DE][DE]QR	GoLoco motif, a G alpha binding motif							0.006	10
protein_40_YJR059W	2	PTK2:  Putative serine/threonine protein kinase involved in regulation of ion transport across plasma membrane; enhances spermine uptake	S..P[TSK]	32	P[ST]	DNA dependent Protein kinase substrate motif							0.006	10
protein_40_YJL177W	2	RPL17B:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl17Ap and has similarity to E. coli L22 and rat L17 ribosomal proteins	L..[SFD]I	32	L...I...[IL]	Corepressor nuclear box motif binds to nuclear receptors							0.006	10
protein_40_YJL177W	2	RPL17B:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl17Ap and has similarity to E. coli L22 and rat L17 ribosomal proteins	N..[LNM]L	32									0.006	10
protein_40_YJL092W	2	SRS2:  DNA helicase and DNA-dependent ATPase involved in DNA repair, needed for proper timing of commitment to meiotic recombination and transition from Meiosis I to II; affects genome stability by suppressing unscheduled homologous recombination	Q[EFP]S	32	QPS..E	Phosphorylation motif in alpha 3A, alpha 6A, alpha 7A Integrin tails							0.006	10
protein_40_YJL081C	2	ARP4:  Nuclear actin-related protein involved in chromatin remodeling, component of chromatin-remodeling enzyme complexes	E[EI].[LD]RI	32									0.004	7
protein_40_YJL074C	2	SMC3:  Subunit of the multiprotein cohesin complex required for sister chromatid cohesion in mitotic cells; also required, with Rec8p, for cohesion and recombination during meiosis; phylogenetically conserved SMC chromosomal ATPase family member	A[NDE]T[ERA]	32								Y	0.005	10
protein_40_YJL074C	2	SMC3:  Subunit of the multiprotein cohesin complex required for sister chromatid cohesion in mitotic cells; also required, with Rec8p, for cohesion and recombination during meiosis; phylogenetically conserved SMC chromosomal ATPase family member	V[NKT]..[GFH]G	32								Y	0.005	10
protein_40_YJL033W	2	HCA4:  Putative nucleolar DEAD box RNA helicase; high-copy number suppression of a U14 snoRNA processing mutant suggests an involvement in 18S rRNA synthesis	E..A[AEG]	32	LK[EAD]AE.RA[ET]	TROPOMYOSIN PATTERN					mRNA polyadenylylation (1e-07)	Y	0.006	9
protein_40_YIL095W	2	PRK1:  Protein serine/threonine kinase; regulates the organization and function of the actin cytoskeleton through the phosphorylation of the Pan1p-Sla1p-End3p protein complex	[SQN]PA[QVI]	32	[ST]P	LIG_WW_4					actin cortical patch assembly (0.01)		0.005	10
protein_40_YIL061C	2	SNP1:  Component of U1 snRNP required for mRNA splicing via spliceosome; may interact with poly(A) polymerase to regulate polyadenylation; homolog of human U1 70K protein	EA.[DIV][ATI]	32	IEAD	Protease Caspase 10					U2-dependent spliceosome (1e-08)		0.007	9
protein_40_YIL019W	2	FAF1:  Protein required for pre-rRNA processing and 40S ribosomal subunit assembly	[AQE]DG[VGY]	32			Y				nucleolus (1e-13)		0.005	9
protein_40_YHR196W	2	UTP9:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	E[ADW].[DMV]I	32							nucleolus (1e-06)		0.006	10
protein_40_YHR121W	2	LSM12:  Protein of unknown function that may function in RNA processing; interacts with Pbp1p and Pbp4p and associates with ribosomes; contains an RNA-binding LSM domain and an AD domain; GFP-fusion protein is induced by the DNA-damaging agent MMS	HE..[IRS][KQC]	32									0.004	9
protein_40_YHR082C	2	KSP1:  Nonessential putative serine/threonine protein kinase of unknown cellular role; overproduction causes allele-specific suppression of the prp20-10 mutation	S.[ADY]D	32	S.D	CAMKII phosphorylation site							0.006	10
protein_40_YHR041C	2	SRB2:  Subunit of the RNA polymerase II mediator complex; associates with core polymerase subunits to form the RNA polymerase II holoenzyme; general transcription factor involved in telomere maintenance	TL.[LH][ESF]S	32							RNA polymerase II transcription mediator activity (1e-05)		0.004	7
protein_40_YHL007C	2	STE20:  Signal transducing kinase of the PAK (p21-activated kinase) family, involved in pheromone response and pseudohyphal/invasive growth pathways, activated by Cdc42p; binds Ste4p at a GBB motif present in noncatalytic domains of PAK kinases	S..[TND]N	32	S..[ST]	Casein Kinase I consensus phosphorylation site (N-term Ser must first be phosphorylated)					bud (0.001)		0.006	10
protein_40_YHL007C	2	STE20:  Signal transducing kinase of the PAK (p21-activated kinase) family, involved in pheromone response and pseudohyphal/invasive growth pathways, activated by Cdc42p; binds Ste4p at a GBB motif present in noncatalytic domains of PAK kinases	S.[PLD]K	32	S.D	CAMKII phosphorylation site					regulation of conjugation with cellular fusion (0.01)		0.006	10
protein_40_YGR275W	2	RTT102:  Component of both the SWI/SNF and RSC chromatin remodeling complexes, suggested role in chromosome maintenance; possible weak regulator of Ty1 transposition	NS..K[RA][AK]	32	KR	CLV_PCSK_PC1ET2_1							0.004	9
protein_40_YGR218W	2	CRM1:  Major karyopherin, involved in export of proteins, RNAs, and ribosomal subunits from the nucleus	EE..[QKS][TAS]	32	EED	Ankyrin B C-terminal motif that binds internal Ankyrin repeats					cellular localization (0.01)		0.006	10
protein_40_YGR218W	2	CRM1:  Major karyopherin, involved in export of proteins, RNAs, and ribosomal subunits from the nucleus	EL[EPW]	32	S[LW]LD[DE]EL[LM]	TRG_LysEnd_GGAAcLL_2					rRNA export from nucleus (1e-05)	Y	0.006	10
protein_40_YGR218W	2	CRM1:  Major karyopherin, involved in export of proteins, RNAs, and ribosomal subunits from the nucleus	G[TNK]A[NLA]	32							rRNA export from nucleus (1e-08)		0.006	9
protein_40_YGR092W	2	DBF2:  Ser/Thr kinase involved in transcription and stress response; functions as part of a network of genes in exit from mitosis; localization is cell cycle regulated; activated by Cdc15p during the exit from mitosis	[LNK]E.E[DMY]E	32	SEDEE	CKII kinase phosphorylation site (peptide screen)							0.005	7
protein_40_YGR074W	2	SMD1:  Core Sm protein Sm D1; part of heteroheptameric complex (with Smb1p, Smd2p, Smd3p, Sme1p, Smx3p, and Smx2p) that is part of the spliceosomal U1, U2, U4, and U5 snRNPs; homolog of human Sm D1	IF[ITA][RQ]	32							small nuclear ribonucleoprotein complex (1e-13)		0.004	8
protein_40_YGL180W	2	ATG1:  Protein serine/threonine kinase, required for vesicle formation during autophagy and the cytoplasm-to-vacuole targeting (Cvt) pathway; structurally required for pre-autophagosome formation; forms a complex with Atg13p and Atg17p	R[PA][PDG]P	32	PPPGHRPPPGHR	SH3 binding motif- CD2 and Sm B/B' motif in C-terminus (potential Class 2 SH3 motif)							0.006	8
protein_40_YGL179C	2	TOS3:  Protein kinase, related to and functionally redundant with Elm1p and Sak1p for the phosphorylation and activation of Snf1p; functionally orthologous to LKB1, a mammalian kinase associated with Peutz-Jeghers cancer-susceptibility syndrome	[PKT][SKW].RA	32									0.006	10
protein_40_YFR031C-A	2	RPL2A:  Protein component of the large (60S) ribosomal subunit, identical to Rpl2Bp and has similarity to E. coli L2 and rat L8 ribosomal proteins	A[AKQ][LKF]R	32	[KR]R	CLV_PCSK_KEX2_1					cytosolic ribosome (sensu Eukaryota) (1e-18)		0.007	10
protein_40_YFL039C	2	ACT1:  Actin, structural protein involved in cell polarization, endocytosis, and other cytoskeletal functions	KR[RP][TMP]	32	KR	CLV_PCSK_PC1ET2_1					actin cortical patch (0.01)		0.006	9
protein_40_YFL037W	2	TUB2:  Beta-tubulin; associates with alpha-tubulin (Tub1p and Tub3p) to form tubulin dimer, which polymerizes to form microtubules	[GVE][SQI].PD	32	LPDEL	Motif in CBP for interaction with PPARg-LBD (secondary site)							0.005	10
protein_40_YFL037W	2	TUB2:  Beta-tubulin; associates with alpha-tubulin (Tub1p and Tub3p) to form tubulin dimer, which polymerizes to form microtubules	K[SPA].D[PRM]	32	S.D	CAMKII phosphorylation site	Y					Y	0.005	9
protein_40_YFL002C	2	SPB4:  Putative ATP-dependent RNA helicase, nucleolar protein required for synthesis of 60S ribosomal subunits at a late step in the pathway; sediments with 66S pre-ribosomes in sucrose gradients	KK.[SAE][KFW]	32	RKK.[ST]	ZIP kinase phosphorylation motif					cytoplasm organization and biogenesis (1e-12)		0.006	10
protein_40_YFL002C	2	SPB4:  Putative ATP-dependent RNA helicase, nucleolar protein required for synthesis of 60S ribosomal subunits at a late step in the pathway; sediments with 66S pre-ribosomes in sucrose gradients	P[NV].[GR]KS	32							cytoplasm organization and biogenesis (0.001)		0.004	7
protein_40_YER177W	2	BMH1:  14-3-3 protein, major isoform; controls proteome at post-transcriptional level, binds proteins and DNA, involved in regulation of many processes including exocytosis, vesicle transport, Ras/MAPK signaling, and rapamycin-sensitive signaling	[INQ]D.N[SGM]	32								Y	0.006	9
protein_40_YER177W	2	BMH1:  14-3-3 protein, major isoform; controls proteome at post-transcriptional level, binds proteins and DNA, involved in regulation of many processes including exocytosis, vesicle transport, Ras/MAPK signaling, and rapamycin-sensitive signaling	P[TAY].A[KGY]	32	P[ST]	DNA dependent Protein kinase substrate motif	Y						0.005	10
protein_40_YER172C	2	BRR2:  RNA-dependent ATPase RNA helicase (DEIH box); required for disruption of U4/U6 base-pairing in native snRNPs to activate the spliceosome for catalysis; homologous to human U5-200kD	[EGH][AVP].HK	32							spliceosome (1e-09)	Y	0.005	9
protein_40_YER133W	2	GLC7:  Catalytic subunit of type 1 serine/threonine protein phosphatase, involved in many processes including glycogen metabolism, sporulation, and mitosis; interacts with multiple regulatory subunits; predominantly isolated with Sds22p	VD.[PEA][EFS]	32	HAVDI	N-Cadherin ligand					phosphatase regulator activity (0.01)	Y	0.006	10
protein_40_YER102W	2	RPS8B:  Protein component of the small (40S) ribosomal subunit; identical to Rps8Ap and has similarity to rat S8 ribosomal protein	[SGQ][KH]KA	32							ribonucleoprotein complex (1e-06)		0.006	8
protein_40_YER102W	2	RPS8B:  Protein component of the small (40S) ribosomal subunit; identical to Rps8Ap and has similarity to rat S8 ribosomal protein	R[AGS][AKG]R	32	[AG]R	Protease matriptase protease site					ribonucleoprotein complex (1e-11)	Y	0.007	10
protein_40_YER025W	2	GCD11:  Gamma subunit of the translation initiation factor eIF2, involved in the identification of the start codon; binds GTP when forming the ternary complex with GTP and tRNAi-Met	FL.R[RT]L	32	R.L	Cyclin A motif that binds cdk2 complexes							0.004	7
protein_40_YDR510W	2	SMT3:  Ubiquitin-like protein of the SUMO family, conjugated to lysine residues of target proteins; regulates chromatid cohesion, chromosome segregation, APC-mediated proteolysis, DNA replication and septin ring dynamics	PS[GKQ]	32	QPS..E	Phosphorylation motif in alpha 3A, alpha 6A, alpha 7A Integrin tails							0.006	10
protein_40_YDR447C	2	RPS17B:  Ribosomal protein 51 (rp51) of the small (40s) subunit; nearly identical to Rps17Ap and has similarity to rat S17 ribosomal protein	G[KMI]K[VAG]	32							cytosolic ribosome (sensu Eukaryota) (1e-19)	Y	0.006	10
protein_40_YDR388W	2	RVS167:  Actin-associated protein, subunit of a complex (Rvs161p-Rvs167p) involved in regulation of actin cytoskeleton, endocytosis, and viability following starvation or osmotic stress; homolog of mammalian amphiphysin	R..[KGY]V	32	R..K	SH3 binding motif for GADS SH3 recognizing slp-76 motif (nonconventional)							0.006	10
protein_40_YDR356W	2	SPC110:  Inner plaque spindle pole body (SPB) component, ortholog of human kendrin; involved in connecting nuclear microtubules to SPB; interacts with Tub4p-complex and calmodulin; phosphorylated by Mps1p in cell cycle-dependent manner	R[RDI].I[PQE]	32							structural constituent of cytoskeleton (1e-07)		0.006	10
protein_40_YDR303C	2	RSC3:  Component of the RSC chromatin remodeling complex; essential gene required for maintenance of proper ploidy and regulation of ribosomal protein genes and the cell wall/stress response; highly similar to Rsc30p	PA..[SDQ][FCV]	32							RSC complex (1e-05)		0.004	7
protein_40_YDR174W	2	HMO1:  Chromatin associated high mobility group (HMG) family member involved in genome maintenance; rDNA-binding component of the Pol I transcription system; associates with a 5'-3' DNA helicase and Fpr1p, a prolyl isomerase	[EKS]A..K[RWL]	32	KR	CLV_PCSK_PC1ET2_1	Y					Y	0.006	10
protein_40_YDR167W	2	TAF10:  Subunit (145 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation and in chromatin modification	QI.[QHI][QNI]	32			Y				SAGA complex (1e-11)		0.005	8
protein_40_YDR064W	2	RPS13:  Protein component of the small (40S) ribosomal subunit; has similarity to E. coli S15 and rat S13 ribosomal proteins	[KYH][LIN]RA	32	Y[LIVAC]R[VA]S[ST]..Q	RECOMBINASES_1 PATTERN					ribonucleoprotein complex (1e-11)		0.006	10
protein_40_YDL148C	2	NOP14:  Nucleolar protein, forms a complex with Noc4p that mediates maturation and nuclear export of 40S ribosomal subunits; also present in the small subunit processome complex, which is required for processing of pre-18S rRNA	[EI]E[PLS]S	32	Y[MLE]EP	SH2 ligand for Vav1 (Tyr must be phosphorylated)					rRNA processing (1e-16)		0.006	10
protein_40_YDL136W	2	RPL35B:  Protein component of the large (60S) ribosomal subunit, identical to Rpl35Ap and has similarity to rat L35 ribosomal protein	[RK]A.[KTF]V	32							cytosolic ribosome (sensu Eukaryota) (1e-10)		0.005	10
protein_40_YDL055C	2	PSA1:  GDP-mannose pyrophosphorylase (mannose-1-phosphate guanyltransferase), synthesizes GDP-mannose from GTP and mannose-1-phosphate in cell wall biosynthesis; required for normal cell wall structure	E.[ATR]F	32								Y	0.006	10
protein_40_YDL055C	2	PSA1:  GDP-mannose pyrophosphorylase (mannose-1-phosphate guanyltransferase), synthesizes GDP-mannose from GTP and mannose-1-phosphate in cell wall biosynthesis; required for normal cell wall structure	RP[DEG]	32	P.RP.[RH][RH]	SH3 binding motif for amphiphysin-general						Y	0.006	10
protein_40_YDL029W	2	ARP2:  Essential component of the Arp2/3 complex, which is a highly conserved actin nucleation center required for the motility and integrity of actin patches; involved in endocytosis and membrane growth and polarity	[QYD]I.Q[VQY]	32									0.005	9
protein_40_YCR086W	2	CSM1:  Nucleolar protein that forms a complex with Lrs4p which binds Mam1p at kinetochores during meiosis I to mediate accurate chromosome segregation, may be involved in premeiotic DNA replication; possible role in telomere maintenance	G[PKQ].G[VSN]	32	GP	Protease TTP cleavage site						Y	0.006	9
protein_40_YCL059C	2	KRR1:  Essential nucleolar protein required for the synthesis of 18S rRNA and for the assembly of 40S ribosomal subunit	AR[IGE]	32	[AG]R	Protease matriptase protease site					nucleolus (1e-29)		0.006	9
protein_40_YBR189W	2	RPS9B:  Protein component of the small (40S) ribosomal subunit; nearly identical to Rps9Ap and has similarity to E. coli S4 and rat S9 ribosomal proteins	[ARG]K..[AKF]A	32							ribonucleoprotein complex (1e-11)		0.006	10
protein_40_YBR031W	2	RPL4A:  N-terminally acetylated protein component of the large (60S) ribosomal subunit, nearly identical to Rpl4Bp and has similarity to E. coli L4 and rat L4 ribosomal proteins	[LAK]G.K[AVM]	32							cytosolic large ribosomal subunit (sensu Eukaryota) (1e-13)		0.006	10
protein_40_YBR009C	2	HHF1:  One of two identical histone H4 proteins (see also HHF2); core histone required for chromatin assembly and chromosome function; contributes to telomeric silencing; N-terminal domain involved in maintaining genomic integrity	L[GPV]..[LKS]D	32								Y	0.006	9
protein_40_YBL026W	2	LSM2:  Lsm (Like Sm) protein; part of heteroheptameric complexes (Lsm2p-7p and either Lsm1p or 8p): cytoplasmic Lsm1p complex involved in mRNA decay; nuclear Lsm8p complex part of U6 snRNP and possibly involved in processing tRNA, snoRNA, and rRNA	V[QP]..L[LRT]S	32	VP	Interleukin converting enzyme protease					snRNP U5 (0.001)		0.004	7
protein_40_YBL016W	2	FUS3:  Mitogen-activated serine/threonine protein kinase involved in mating; phosphoactivated by Ste7p; substrates include Ste12p, Far1p, Bni1p, Sst2p; inhibits invasive growth during mating by phosphorylating Tec1p, promoting its degradation	E.[EFD]D	32	Y.E.E	Src phosphorylation site					regulation of conjugation with cellular fusion (1e-04)		0.006	10
protein_40_YAR007C	2	RFA1:  Subunit of heterotrimeric Replication Protein A (RPA), which is a highly conserved single-stranded DNA binding protein involved in DNA replication, repair, and recombination	A[VPE]K	32							response to DNA damage stimulus (0.001)		0.006	9
protein_40_YAL032C	2	PRP45:  Protein required for pre-mRNA splicing; associates with the spliceosome and interacts with splicing factors Prp22p and Prp46p; orthologous to human transcriptional coactivator SKIP and can activate transcription of a reporter gene	[NDC]IG[KMH]	32	EFYA.[VI]G[RKH]S	SHP2 phosphatase substrate motif	Y					Y	0.005	10
oshea_vacuole	2	oshea_vacuole	I..[FLH]I	32							vacuole (1e-25)		0.006	10
oshea_vacuole	2	oshea_vacuole	L..[AGW]S	32							vacuole (1e-31)		0.006	9
oshea_spindle_pole	2	oshea_spindle_pole	N[EML]..[ED]L	32							microtubule cytoskeleton (1e-24)		0.007	10
oshea_nuclear_periphery	2	oshea_nuclear_periphery	KE.[KAC][ILK]	32	KEN	LIG_APCC_KENbox_2					nuclear envelope (1e-22)	Y	0.007	10
oshea_nuclear_periphery	2	oshea_nuclear_periphery	S[TAY]S	32	R.S.S.P	14-3-3 binding motifs, Ser must be phosphorylated					nuclear pore (1e-44)	Y	0.006	10
oshea_cell_periphery	2	oshea_cell_periphery	[GPN]I.Q[ENP]	32			Y				site of polarized growth (1e-09)		0.007	9
oshea_cell_periphery	2	oshea_cell_periphery	[RAP]KP[SPY]	32	KP..[QK]	LIG_SH3_4					site of polarized growth (1e-06)		0.007	10
oshea_cell_periphery	2	oshea_cell_periphery	N..[DVW]R	32							site of polarized growth (1e-15)		0.007	10
matsuyama_Mitochondria	2	matsuyama_Mitochondria	N.[TQD]D	32	N.[TS]	N-linked glycosylation site	Y						0.008	10
matsuyama_ER	2	matsuyama_ER	[SIM]Y.V[FAV]	32	YTV	14-3-3 domain binding motif	Y				cellular lipid metabolism (1e-05)	Y	0.008	10
matsuyama_ER	2	matsuyama_ER	W..[GFC]T	32	W..[WFY]	AP1 binding site for endosomal trafficking					endoplasmic reticulum membrane (1e-08)	Y	0.008	10
genetic_YNL153C	2	GIM3: Subunit of the heterohexameric cochaperone prefoldin complex which binds specifically to cytosolic chaperonin and transfers target proteins to it	[SEL][LPG].ERI	32							cell cortex (0.01)	Y	0.005	9
genetic_YNL153C	2	GIM3: Subunit of the heterohexameric cochaperone prefoldin complex which binds specifically to cytosolic chaperonin and transfers target proteins to it	QE..[RSP][SNI]	32							establishment of cell polarity (sensu Fungi) (0.01)	Y	0.006	10
genetic_YNL153C	2	GIM3: Subunit of the heterohexameric cochaperone prefoldin complex which binds specifically to cytosolic chaperonin and transfers target proteins to it	S[ERN]..SL[EMH]	32	[ST]R..S	GSK3-BETA phosphorylation site						Y	0.005	8
genetic_YNL153C	2	GIM3: Subunit of the heterohexameric cochaperone prefoldin complex which binds specifically to cytosolic chaperonin and transfers target proteins to it	Y..[LED]Q	32	[DN].Y..[DE]	cCBl TKB domain binding motif, Tyr must be PO4					mitotic cell cycle (0.001)		0.006	10
genetic_YLR262C	2	YPT6: GTPase, Ras-like GTP binding protein involved in the secretory pathway, required for fusion of endosome-derived vesicles with the late Golgi, maturation of the vacuolar carboxypeptidase Y; has similarity to the human GTPase, Rab6	P.[KNY]K	32	[ST]P.[KR]	Cyclin D1/CDK1,2,4,5 phosphorylation site					DNA metabolism (1e-09)	Y	0.006	9
genetic_YLR200W	2	YKE2: Subunit of the heterohexameric Gim/prefoldin protein complex involved in the folding of alpha-tubulin, beta-tubulin, and actin	T[VHE].[LMG]M	32			Y						0.006	9
genetic_YGL020C	2	GET1: Subunit of the GET complex; required for the retrieval of HDEL proteins from the Golgi to the ER in an ERD2 dependent fashion and for normal mitochondrial morphology and inheritance	L.[LDI]I	32							chromosome organization and biogenesis (sensu Eukaryota) (1e-10)	Y	0.006	10
genetic_YGL020C	2	GET1: Subunit of the GET complex; required for the retrieval of HDEL proteins from the Golgi to the ER in an ERD2 dependent fashion and for normal mitochondrial morphology and inheritance	L[ETK]..[RSP]K	32							chromosome organization and biogenesis (sensu Eukaryota) (1e-07)		0.006	9
genetic_YDL020C	2	RPN4: Transcription factor that stimulates expression of proteasome genes; Rpn4p levels are in turn regulated by the 26S proteasome in a negative feedback control mechanism; RPN4 is transcriptionally regulated by various stress responses	[NLC]L.[EHV]E	32	S[LW]LD[DE]EL[LM]	TRG_LysEnd_GGAAcLL_2					chromosome organization and biogenesis (sensu Eukaryota) (0.001)		0.006	9
genetic_YAL024C	2	LTE1: Putative GDP/GTP exchange factor required for mitotic exit at low temperatures; acts as a guanine nucleotide exchange factor (GEF) for Tem1p, which is a key regulator of mitotic exit; physically associates with Ras2p-GTP	K..[ADR]S	32	KR.RS	ZIP kinase substrate motif	Y				telomere organization and biogenesis (1e-11)		0.006	10
genetic_YAL024C	2	LTE1: Putative GDP/GTP exchange factor required for mitotic exit at low temperatures; acts as a guanine nucleotide exchange factor (GEF) for Tem1p, which is a key regulator of mitotic exit; physically associates with Ras2p-GTP	KL	32	NKLY	LIM3 domain in enigma binds to this site in Ret					chromosome organization and biogenesis (sensu Eukaryota) (1e-19)		0.006	10
genetic_YAL024C	2	LTE1: Putative GDP/GTP exchange factor required for mitotic exit at low temperatures; acts as a guanine nucleotide exchange factor (GEF) for Tem1p, which is a key regulator of mitotic exit; physically associates with Ras2p-GTP	V.N[DKA]	32			Y				cell cycle (1e-09)	Y	0.006	9
protein_40_YER165W	2	PAB1:  Poly(A) binding protein, part of the 3'-end RNA-processing complex, mediates interactions between the 5' cap structure and the 3' mRNA poly(A) tail, involved in control of poly(A) tail length, interacts with translation factor eIF-4G	G.[PRT]G	31	IQ.RG.RG.RRR	Binding motif on Calmodulin		RRM_1	1.E-03	-4.1	RNA metabolism (1e-09)	Y	0.006	10
matsuyama_Cytoplasmic_dots	2	matsuyama_Cytoplasmic_dots	P.[SPM]S	31	P.P	motif in interleukin 5 receptor necessary for signaling		SH3_1	1.E-03	-2.1	site of polarized growth (1e-12)		0.007	10
yeast-217_GO-0007046	2	ribosome biogenesis	[ASF]R..D[IVA]	31	[AG]R	Protease matriptase protease site		DEAD	1.E-11	-1.9	ribosome biogenesis (1e-42)	Y	0.007	10
yeast-939_GO-0051234	2	establishment of localization	G.[ALM]S	31	GP[QM]SPI	JNK1 Kinase substrate motif		Mito_carr	1.E-06	-1.6	establishment of cellular localization (1e-95)	Y	0.006	10
protein_40_YLR186W	2	EMG1:  Protein required for the maturation of the 18S rRNA and for 40S ribosome production; associated with spindle/microtubules; nuclear localization depends on physical interaction with Nop14p; may bind snoRNAs	[KAG]K..K[RHL]	31	KR	CLV_PCSK_PC1ET2_1		WD40	1.E-02	-1.3	rRNA processing (1e-21)		0.006	10
matsuyama_Golgi	2	matsuyama_Golgi	VL[IFL]	31	E.IYGVLF	Lck kinase substrate motif		zf-DHHC	1.E-03	-1.3	Golgi apparatus (1e-12)	Y	0.008	10
protein_40_YML010W	2	SPT5:  Protein that forms a complex with Spt4p and mediates both activation and inhibition of transcription elongation; Spt4p-Spt5p complex also plays a role in pre-mRNA processing	EA.[TVA][PKS]	31	IEAD	Protease Caspase 10		DEAD	1.E-02	-1.2	nuclear lumen (1e-07)		0.006	10
protein_40_YML085C	2	TUB1:  Alpha-tubulin; associates with beta-tubulin (Tub2p) to form tubulin dimer, which polymerizes to form microtubules	E.I[GSH]	31	YE.[IV]	SH2 ligand for Fes (Tyr must be phosphorylated)		HEAT	1.E-02	-1.1	microtubule (0.01)	Y	0.006	10
protein_40_YLR340W	2	RPP0:  Conserved ribosomal protein P0 similar to rat P0, human P0, and E. coli L10e; shown to be phosphorylated on serine 302	[RGW]R.A[RCY]	31	GR.A	Protease tPA proteolytic site		DEAD	1.E-02	-1.1	cytosolic ribosome (sensu Eukaryota) (1e-04)		0.006	10
yeast-752_GO-0016787	2	hydrolase activity	H..P	31	QHR.P[PL]PP[GS]H[RH]	Motif recognized by GYF domains		UCH	1.E-04	-1	hydrolase activity, acting on ester bonds (1e-69)		0.006	10
yeast-661_GO-0050789	2	regulation of biological process	HT.[EHR]K[PLI]	31				zf-C2H2	1.E-11	-1	regulation of cellular metabolism (1e-09)	Y	0.007	10
yeast-648_GO-0050791	2	regulation of physiological process	HT.[EHR]K[PLI]	31				zf-C2H2	1.E-11	-1	regulation of cellular metabolism (1e-09)	Y	0.007	10
yeast-460_GO-0006351	2	transcription, DNA-dependent	E..L[LEQ]	31	[DE]..LL	Di-Leu acidic motif for receptor endocytosis (recognized by VHS domain of GGA proteins)		Zn_clus	1.E-06	-0.9	transcription, DNA-dependent (1e-26)		0.006	9
yeast-294_GO-0006366	2	transcription from RNA polymerase II promoter	T[GFT]E[KDI]P	31	[ST]E	G protein-coupled receptor kinase 1 substrate motif		zf-C2H2	1.E-06	-0.9	transcription from RNA polymerase II promoter (1e-09)		0.005	7
yeast-216_GO-0006325	2	establishment and/or maintenance of chromatin architecture	PS[TNV][KGV]	31	P[ST]	DNA dependent Protein kinase substrate motif		Bromodomain	1.E-02	-0.9	establishment and/or maintenance of chromatin architecture (1e-51)	Y	0.007	10
yeast-216_GO-0006323	2	DNA packaging	PS[TNV][KGV]	31	P[ST]	DNA dependent Protein kinase substrate motif		Bromodomain	1.E-02	-0.9	establishment and/or maintenance of chromatin architecture (1e-51)	Y	0.007	10
yeast-1464_GO-0019538	2	protein metabolism	S[FEH].S[SHA]	31	S[ST]	MDC1 BRCT domain binding motif		Zn_clus	1.E-02	-0.9	transcription regulator activity (1e-04)		0.006	8
protein_40_YPL126W	2	NAN1:  U3 snoRNP protein, component of the small (ribosomal) subunit (SSU) processosome containing U3 snoRNA; required for the biogenesis of18S rRNA	[WEY]D..S[GKE]	31	D..SII.FF	CK I delta kinase phosphorylation site (peptide screen)		WD40	1.E-05	-0.9	small nucleolar ribonucleoprotein complex (1e-12)		0.006	10
protein_40_YOL133W	2	HRT1:  RING finger containing subunit of Skp1-Cullin-F-box ubiquitin protein ligases (SCF); required for Gic2p, Far1p, Sic1p and Cln2p degradation; may tether Cdc34p (a ubiquitin conjugating enzyme or E2) and Cdc53p (a cullin) subunits of SCF	I.E[FTQ]	31	IYE	cFPS/FES kinase phosphorylation site (peptide screen)		F-box	1.E-11	-0.9	ubiquitin ligase complex (1e-09)	Y	0.006	10
protein_40_YJL095W	2	BCK1:  Mitogen-activated protein (MAP) kinase kinase kinase acting in the protein kinase C signaling pathway, which controls cell integrity; upon activation by Pkc1p phosphorylates downstream kinases Mkk1p and Mkk2p	P[VPI]..S[QSK]	31	S[ST]	MDC1 BRCT domain binding motif		Pkinase	1.E-02	-0.9			0.006	10
yeast-512_GO-0046907	2	intracellular transport	N[KTY]L	31	NKLY	LIM3 domain in enigma binds to this site in Ret		IBN_N	1.E-06	-0.8	intracellular transport (1e-23)		0.007	10
yeast-256_GO-0016462	2	pyrophosphatase activity	[ELR]I.D[TNA]	31				ABC_tran	1.E-06	-0.8	pyrophosphatase activity (1e-49)		0.007	10
protein_40_YJL092W	2	SRS2:  DNA helicase and DNA-dependent ATPase involved in DNA repair, needed for proper timing of commitment to meiotic recombination and transition from Meiosis I to II; affects genome stability by suppressing unscheduled homologous recombination	I[LAQ]S	31	K[AI][CL]SGK[FI].[PQ]	UBIQUITIN_ACTIVAT_1 PATTERN		Metallophos	1.E-02	-0.8	response to DNA damage stimulus (0.001)		0.006	10
yeast-213_GO-0009719	2	response to endogenous stimulus	[IVD]ID[LEG]	31	VEID	Protease Caspase 6 -stringent		Helicase_C	1.E-02	-0.7	response to DNA damage stimulus (1e-62)		0.007	10
protein_40_YPL129W	2	TAF14:  Subunit of TFIID, TFIIF, INO80, SWI/SNF, and NuA3 complexes, involved in RNA polymerase II transcription initiation and in chromatin modification; contains a YEATS domain	Q[QEF]Q	31	GQDQTKQQI	43_KD_POSTSYNAPTIC PATTERN		Actin	1.E-04	-0.7	nucleoplasm part (1e-35)		0.006	9
protein_40_YML010W	2	SPT5:  Protein that forms a complex with Spt4p and mediates both activation and inhibition of transcription elongation; Spt4p-Spt5p complex also plays a role in pre-mRNA processing	DV.[ASL][RME]	31				DEAD	1.E-04	-0.2	RNA processing (1e-08)		0.006	9
protein_40_YLL008W	2	DRS1:  Nucleolar DEAD-box protein required for ribosome assembly and function, including synthesis of 60S ribosomal subunits; constituent of 66S pre-ribosomal particles	KV..[SKE][AKE]	31				Pkinase	1.E-03	-0.2	cytoplasm organization and biogenesis (1e-11)		0.006	10
protein_40_YGL120C	2	PRP43:  RNA helicase in the DEAH-box family, functions in both RNA polymerase I and polymerase II transcript metabolism, involved in release of the lariat-intron from the spliceosome	RK[RME]	31	VRKRTLRRL	PAK1 kinase substrate motif		Brix	1.E-02	-0.2	cytoplasm organization and biogenesis (1e-29)		0.006	9
protein_40_YDL013W	2	SLX5:  Subunit of the Slx5-Slx8 substrate-specific ubiquitin ligase complex; stimulated by prior attachment of SUMO to the substrate	N[DNEQ]..[NWC]T	31				Pkinase	1.E-04	-0.2	protein kinase activity (0.01)		0.005	9
protein_40_YPL031C	2	PHO85:  Cyclin-dependent kinase, with ten cyclin partners; involved in regulating the cellular response to nutrient levels and environmental conditions and progression through the cell cycle	TP[PMA]	31	LTP	RAF1 kinase substrate motif		Cyclin_N	1.E-02	-0.1	kinase regulator activity (1e-05)		0.006	9
yeast-256_GO-0016462	2	pyrophosphatase activity	R.V[TRF]	31	[RK].V.F	PPI binding sites		Helicase_C	1.E-09	0	pyrophosphatase activity (1e-90)	Y	0.007	10
protein_40_YMR093W	2	UTP15:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	[GNY]K[TIM]K	31				WD40	1.E-02	0	rRNA processing (1e-16)	Y	0.006	9
protein_40_YHR148W	2	IMP3:  Component of the SSU processome, which is required for pre-18S rRNA processing, essential protein that interacts with Mpp10p and mediates interactions of Imp4p and Mpp10p with U3 snoRNA	K..K[LE]	31	K..K.K	Nuclear Localization		WD40	1.E-07	0	rRNA processing (1e-42)		0.006	10
yeast-215_GO-0005694	2	chromosome	K.R[KIE]	31	[IL]Q..C....K.R.W	Myosin light chain binding motifs Type 2B Ca independent		SMC_N	1.E-05	0.1	chromosome (1e-14)		0.007	10
yeast-1493_GO-0043234	2	protein complex	K.[RLA]K	31	SKRKYRK	TP1 PATTERN		SMC_N	1.E-02	0.1	ribonucleoprotein complex (1e-80)		0.007	10
protein_40_YMR117C	2	SPC24:  Component of the evolutionarily conserved kinetochore-associated Ndc80 complex (Ndc80p-Nuf2p-Spc24p-Spc25p); involved in chromosome segregation, spindle checkpoint activity and kinetochore clustering	K[TEH]D	31				SMC_N	1.E-02	0.1			0.006	10
protein_40_YGR128C	2	UTP8:  Nucleolar protein required for export of tRNAs from the nucleus; also copurifies with the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	SD[IDQ]	31	E[ST]D	Ankyrin G binding motif in KNCQ2 and KNCQ3 potaqssium channels		WD40	1.E-07	0.1	small nucleolar ribonucleoprotein complex (1e-32)	Y	0.006	8
yeast-222_GO-0009308	2	amine metabolism	K..[DYH]V	31				PALP	1.E-02	0.2	amine metabolism (1e-09)	Y	0.007	8
protein_40_YBL004W	2	UTP20:  Component of the small-subunit (SSU) processome, which is involved in the biogenesis of the 18S rRNA	K..K[RLW]	31	KR	CLV_PCSK_PC1ET2_1		WD40	1.E-05	0.2	nucleolus (1e-33)		0.006	9
yeast-213_GO-0009719	2	response to endogenous stimulus	I.[NTI]E	31	[ST]E	G protein-coupled receptor kinase 1 substrate motif		BRCT	1.E-05	0.3	response to endogenous stimulus (1e-13)		0.007	10
yeast-1974_GO-0005634	2	nucleus	Q[LKN]A	31				HEAT	1.E-03	0.3	nuclear lumen (1e-23)	Y	0.007	10
protein_40_YMR117C	2	SPC24:  Component of the evolutionarily conserved kinetochore-associated Ndc80 complex (Ndc80p-Nuf2p-Spc24p-Spc25p); involved in chromosome segregation, spindle checkpoint activity and kinetochore clustering	Q[RED]R	31	[KR]R	CLV_PCSK_KEX2_1	Y	SMC_N	1.E-03	0.3			0.006	10
protein_40_YJL109C	2	UTP10:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	A..[DRA]R	31	[KR]R	CLV_PCSK_KEX2_1		WD40	1.E-03	0.4	small nucleolar ribonucleoprotein complex (1e-32)		0.006	10
yeast-222_GO-0009308	2	amine metabolism	I..[TAD]G	31				Iso_dh	1.E-03	0.5	amine metabolism (1e-10)		0.007	10
yeast-513_GO-0005515	2	protein binding	AL[PTC][SNM]	31	GTALL	Receptor recycling motif		HEAT	1.E-03	0.7	protein binding (1e-49)		0.007	10
protein_40_YML048W	2	GSF2:  ER localized integral membrane protein that may promote secretion of certain hexose transporters, including Gal2p; involved in glucose-dependent repression	[PVQ]F..[GFQ]A	31				Sugar_tr	1.E-03	0.7			0.005	9
protein_40_YER165W	2	PAB1:  Poly(A) binding protein, part of the 3'-end RNA-processing complex, mediates interactions between the 5' cap structure and the 3' mRNA poly(A) tail, involved in control of poly(A) tail length, interacts with translation factor eIF-4G	EA[ERP]	31	E[ST][EA]REA[RK].[LI]	RIBOSOMAL_S28E PATTERN		RRM_1	1.E-03	0.7	RNA metabolism (1e-10)		0.006	10
matsuyama_Cytosol	2	matsuyama_Cytosol	N.L[QPI]	31			Y	RhoGEF	1.E-02	0.7	cell septum (1e-06)	Y	0.007	10
yeast-235_GO-0000278	2	mitotic cell cycle	R..[TKD]S	31	[KR].R..[ST]	p70s6k phosphorylation site		HEAT	1.E-02	0.8	mitotic cell cycle (1e-12)	Y	0.007	10
yeast-238_GO-0017111	2	nucleoside-triphosphatase activity	I[PIL]V[IMY]	31	IP[IV]	Crystallin motif for dimerization		E1-E2_ATPase	1.E-05	0.9	nucleoside-triphosphatase activity (1e-37)	Y	0.007	10
protein_40_YPL240C	2	HSP82:  Hsp90 chaperone required for pheromone signaling and negative regulation of Hsf1p; docks with Tom70p for mitochondrial preprotein delivery; promotes telomerase DNA binding and nucleotide addition; interacts with Cns1p, Cpr6p, Cpr7p, Sti1p	G.[IDC]I	31	VIG..G..I	KH domain, RNA binding motif		AA_permease	1.E-02	0.9			0.006	8
protein_40_YJL130C	2	URA2:  Bifunctional carbamoylphosphate synthetase (CPSase)-aspartate transcarbamylase (ATCase), catalyzes the first two enzymatic steps in the de novo biosynthesis of pyrimidines; both activities are subject to feedback inhibition by UTP	E[TRQ][AWC]L	31				HEAT	1.E-02	1	protein carrier activity (0.01)		0.005	9
yeast-205_GO-0005856	2	cytoskeleton	D[KQL]..[KRS]D	31			Y	SH3_1	1.E-02	1.1	cytoskeleton (1e-51)	Y	0.007	10
protein_40_YLR026C	2	SED5:  cis-Golgi t-SNARE syntaxin required for vesicular transport between the ER and the Golgi complex, binds at least 9 SNARE proteins	TA[GCF][QD]	31				Ras	1.E-05	1.1	vesicle-mediated transport (1e-08)		0.004	9
yeast-610_GO-0031090	2	organelle membrane	F[SFY].[FIG]V	31				Mito_carr	1.E-02	1.2	vacuolar membrane (1e-15)		0.006	10
yeast-335_GO-0016772	2	transferase activity, transferring phosphorus-containing groups	L[AHP]D	31	LPDEL	Motif in CBP for interaction with PPARg-LBD (secondary site)		Pkinase	1.E-43	1.2	transferase activity, transferring phosphorus-containing groups (1e-12)		0.006	10
protein_40_YMR128W	2	ECM16:  Essential DEAH-box ATP-dependent RNA helicase specific to the U3 snoRNP, predominantly nucleolar in distribution, required for 18S rRNA synthesis	[IPF]K.[WFP]D	31				WD40	1.E-02	1.4	snoRNA binding (1e-17)	Y	0.005	9
protein_40_YER012W	2	PRE1:  Beta 4 subunit of the 20S proteasome; localizes to the nucleus throughout the cell cycle	R[LPF].[QGY]V	31			Y	Proteasome	1.E-17	1.4	proteasome core complex (sensu Eukaryota) (1e-19)		0.006	10
yeast-256_GO-0016462	2	pyrophosphatase activity	[LAM]FA[ITM]	31			Y	E1-E2_ATPase	1.E-03	1.5	ATPase activity (1e-36)	Y	0.007	10
yeast-240_GO-0006807	2	nitrogen compound metabolism	V[GFE]G[GYC]	31				PALP	1.E-02	1.5	nitrogen compound metabolism (1e-36)		0.007	10
matsuyama_Nucleus	2	matsuyama_Nucleus	G.[VAF]F	31				MFS_1	1.E-02	1.5	endoplasmic reticulum (1e-16)		0.007	9
genetic_YPL240C	2	HSP82: Hsp90 chaperone required for pheromone signaling and negative regulation of Hsf1p; docks with Tom70p for mitochondrial preprotein delivery; promotes telomerase DNA binding and nucleotide addition; interacts with Cns1p, Cpr6p, Cpr7p, Sti1p	N[SLC]V[RSN]	31				RasGEF_N	1.E-02	1.5	signal transduction (0.01)		0.006	9
yeast-335_GO-0016772	2	transferase activity, transferring phosphorus-containing groups	Q[VGM]L[KEY]	31				Pkinase	1.E-21	1.6	transferase activity, transferring phosphorus-containing groups (1e-42)	Y	0.007	9
yeast-1721_GO-0016043	2	cell organization and biogenesis	I.D[FST]	31				HEAT	1.E-04	1.7	chromosome organization and biogenesis (1e-44)	Y	0.006	10
protein_40_YGL105W	2	ARC1:  Protein that binds tRNA and methionyl- and glutamyl-tRNA synthetases (Mes1p and Gus1p), delivering tRNA to them, stimulating catalysis, and ensuring their localization to the cytoplasm; also binds quadruplex nucleic acids	A.[EDP]V	31	IYA.P	c-Abl kinase phosphorylation site (peptide screen)		Pkinase	1.E-07	1.8	protein kinase activity (1e-07)	Y	0.006	10
protein_40_YDR510W	2	SMT3:  Ubiquitin-like protein of the SUMO family, conjugated to lysine residues of target proteins; regulates chromatid cohesion, chromosome segregation, APC-mediated proteolysis, DNA replication and septin ring dynamics	G.[PAD]G	31	G[FL]PGER..G	LIG_IBS_1		GTP_EFTU_D2	1.E-02	1.8	protein sumoylation (0.001)	Y	0.006	10
yeast-685_GO-0016740	2	transferase activity	C.L	31	VPGKARKKSSCQLL	Calmodulin-dependent protein kinase IV substrate motif		Pkinase	1.E-26	1.9	transferase activity, transferring phosphorus-containing groups (1e-84)		0.007	10
genetic_YLR200W	2	YKE2: Subunit of the heterohexameric Gim/prefoldin protein complex involved in the folding of alpha-tubulin, beta-tubulin, and actin	D.[GLP]T	31				SH3_1	1.E-02	2	cell cycle (1e-06)	Y	0.006	9
yeast-752_GO-0016787	2	hydrolase activity	Y.[NGQ]A	31	E.Y.[QSG]	Protease TEV		Ras	1.E-05	2.1	hydrolase activity, acting on acid anhydrides (1e-25)	Y	0.007	8
protein_40_YJR145C	2	RPS4A:  Protein component of the small (40S) ribosomal subunit; mutation affects 20S pre-rRNA processing; identical to Rps4Bp and has similarity to rat S4 ribosomal protein	G.[KRN]G	31	IQ.RG.RG.RRR	Binding motif on Calmodulin		KH_1	1.E-02	2.2	ribonucleoprotein complex (1e-09)		0.006	10
protein_40_YGL245W	2	GUS1:  Glutamyl-tRNA synthetase (GluRS), forms a complex with methionyl-tRNA synthetase (Mes1p) and Arc1p; complex formation increases the catalytic efficiency of both tRNA synthetases and ensures their correct localization to the cytoplasm	EN[ILE][LSW]	31	YEN[FIV]	SH2 ligand for Tns (Tyr must be phosphorylated)		Pkinase	1.E-15	2.5	protein kinase activity (1e-14)		0.006	8
protein_40_YJL010C	2	NOP9:  Essential component of pre-40S ribosomes that is required for early cleavages of 35S pre-rRNA and hence formation of 18S rRNA; binds RNA in vitro and contains multiple pumilio-like repeats	D[VKG]..R[GAI]	31				WD40	1.E-05	2.6	ribosome biogenesis (1e-15)		0.006	9
protein_40_YNL272C	2	SEC2:  Guanyl-nucleotide exchange factor for the small G-protein Sec4p, located on cytoplasmic vesicles; essential for post-Golgi vesicle transport	G[SAY][FYM]G	31	R.GSF	PKCdelta kinase phosphorylation site (peptide screen)	Y	Pkinase	1.E-12	2.8	protein kinase activity (1e-12)		0.005	8
protein_40_YDL013W	2	SLX5:  Subunit of the Slx5-Slx8 substrate-specific ubiquitin ligase complex; stimulated by prior attachment of SUMO to the substrate	YC..G[DS]L	31				Pkinase	1.E-04	2.8	protein serine/threonine kinase activity (1e-05)		0.004	7
matsuyama_periphery	2	matsuyama_periphery	D[LAE]..E[NWP]I	31				Pkinase	1.E-06	2.8	barrier septum (1e-10)		0.008	10
yeast-410_GO-0007049	2	cell cycle	[HAL]R.I[KSL]	31	[AG]R	Protease matriptase protease site	Y	Pkinase	1.E-11	3	cell cycle (1e-68)	Y	0.007	10
protein_40_YDR328C	2	SKP1:  Evolutionarily conserved kinetochore protein that is part of multiple protein complexes, including the SCF ubiquitin ligase complex, the CBF3 complex that binds centromeric DNA, and the RAVE complex that regulates assembly of the V-ATPase	D..[TPY]L	31				F-box	1.E-11	3	ubiquitin ligase complex (1e-09)		0.006	9
protein_40_YNL175C	2	NOP13:  Protein of unknown function, localizes to the nucleolus and nucleoplasm; contains an RNA recognition motif (RRM) and has similarity to Nop12p, which is required for processing of pre-18S rRNA	I[AG].PG[RA]	31				DEAD	1.E-06	3.6	RNA helicase activity (1e-05)	Y	0.004	8
yeast-1974_GO-0005634	2	nucleus	[GEM]V.W[YIF]	31				SRP1_TIP1	1.E-50	3.7	cell wall (1e-04)		0.006	10
protein_40_YKL021C	2	MAK11:  Protein involved in an early, nucleolar step of 60S ribosomal subunit biogenesis; essential for cell growth and replication of killer M1 dsRNA virus; contains four beta-transducin repeats	GS.KT[LA]	31	YIYGSFK	Src kinase substrate motif		DEAD	1.E-09	3.7	ATP-dependent RNA helicase activity (1e-10)	Y	0.004	7
oshea_cytoplasm	2	oshea_cytoplasm	V[PLR]W[YFK]	31	VP	Interleukin converting enzyme protease		SRP1_TIP1	1.E-50	3.9	cell wall (0.01)		0.006	10
yeast-706_GO-0043412	2	biopolymer modification	[GTP]L.Y[LID]H	31	Y[LI]	SH2 ligand for PLCgamma1 N-term.)group 3(phospho-peptide)		Pkinase	1.E-12	4	protein amino acid phosphorylation (1e-13)		0.007	9
matsuyama_nucleolus	2	matsuyama_nucleolus	[LVS]V.DE[AGM]	31				DEAD	1.E-10	4.3	nucleolus (1e-10)		0.007	10
yeast-238_GO-0017111	2	nucleoside-triphosphatase activity	Q[EAM]..R[ATS]	31				Helicase_C	1.E-06	5.2	nucleoside-triphosphatase activity (1e-32)	Y	0.007	10
yeast-942_GO-0043232	2	intracellular non-membrane-bound organelle	WY[SYA]	31	PWY[ST][ST]RL	SRP1_TIP1 PATTERN							0.007	10
yeast-942_GO-0043228	2	non-membrane-bound organelle	WY[SYA]	31	PWY[ST][ST]RL	SRP1_TIP1 PATTERN							0.007	10
yeast-921_GO-0006810	2	transport	[TKG]G..[FRE]GN	31							protein export from nucleus (0.001)		0.007	10
yeast-792_GO-0006412	2	protein biosynthesis	TT[TNR]	31	[DGH][IVSAC]T[ST]NP[STA][LIVMF][LIVMF]	TRANSALDOLASE_1 PATTERN							0.007	10
yeast-610_GO-0031090	2	organelle membrane	E[EFS].E[DGW]	31	F.E	DNA binding motif in MutS							0.007	10
yeast-548_GO-0051641	2	cellular localization	Q.[LQF]S	31							cellular localization (1e-18)	Y	0.007	10
yeast-470_GO-0006259	2	DNA metabolism	[KAG]S[EIM]S	31			Y				DNA metabolism (1e-84)		0.007	10
yeast-468_GO-0051276	2	chromosome organization and biogenesis	[KAI]R..[ENH]EE	31	[KR]R	CLV_PCSK_KEX2_1					chromosome organization and biogenesis (sensu Eukaryota) (1e-17)		0.007	10
yeast-436_GO-0031323	2	regulation of cellular metabolism	[SLQ]S.R[LQP]E	31	S.R	PKC phosphorylation motif	Y				regulation of cellular metabolism (1e-14)		0.007	10
yeast-424_GO-0006950	2	response to stress	D.D[EKV]	31	D.D	Ribose moiety of UDP and manganese binding site in glucuronyl transferase					response to stress (1e-20)		0.007	10
yeast-424_GO-0006950	2	response to stress	E[LEW].[NDK]L	31							response to stress (1e-09)		0.006	10
yeast-410_GO-0007049	2	cell cycle	R..[IEA]T	31			Y				cell cycle (1e-12)		0.007	10
yeast-341_GO-0045449	2	regulation of transcription	[KQH]IR[ESM]	31							regulation of transcription (1e-40)	Y	0.007	9
yeast-304_GO-0019752	2	carboxylic acid metabolism	PI[TAM]	31	IP[IV]	Crystallin motif for dimerization					carboxylic acid metabolism (1e-09)		0.007	10
yeast-304_GO-0006082	2	organic acid metabolism	PI[TAM]	31	IP[IV]	Crystallin motif for dimerization					carboxylic acid metabolism (1e-09)		0.007	10
yeast-267_GO-0044265	2	cellular macromolecule catabolism	LE.S[GFV][SHM]	31							cellular macromolecule catabolism (1e-09)		0.005	8
yeast-251_GO-0005886	2	plasma membrane	C..A[TIC]	31							plasma membrane (1e-44)		0.007	10
yeast-238_GO-0017111	2	nucleoside-triphosphatase activity	D[AR][QH]S	31							nucleoside-triphosphatase activity (1e-18)		0.006	9
yeast-238_GO-0017111	2	nucleoside-triphosphatase activity	E.[IRV]K	31	YE.[IV]	SH2 ligand for Fes (Tyr must be phosphorylated)					nucleoside-triphosphatase activity (1e-14)	Y	0.007	9
yeast-235_GO-0000278	2	mitotic cell cycle	K..[DLP]Q	31							mitotic cell cycle (1e-12)		0.007	10
yeast-233_GO-0006629	2	lipid metabolism	AF[IAS]	31	F[MLVI]Y	PTPRJ phosphatase substrate motif					lipid metabolism (1e-09)		0.007	10
yeast-222_GO-0009308	2	amine metabolism	T[ISQ]..EK[VPD]	31	[ST]..E	Casien kinase II consensus phosphorylation site					amino acid and derivative metabolism (1e-11)		0.005	9
yeast-216_GO-0006325	2	establishment and/or maintenance of chromatin architecture	[VI]Q..Q[QPI]	31							establishment and/or maintenance of chromatin architecture (1e-30)		0.007	10
yeast-216_GO-0006325	2	establishment and/or maintenance of chromatin architecture	L[LTM][EAG]Q	31	LLG	Beta2-Integrin binding motif					establishment and/or maintenance of chromatin architecture (1e-49)		0.007	10
yeast-216_GO-0006323	2	DNA packaging	[VI]Q..Q[QPI]	31							establishment and/or maintenance of chromatin architecture (1e-30)		0.007	10
yeast-216_GO-0006323	2	DNA packaging	L[LTM][EAG]Q	31	LLG	Beta2-Integrin binding motif					establishment and/or maintenance of chromatin architecture (1e-49)		0.007	10
yeast-215_GO-0007010	2	cytoskeleton organization and biogenesis	[ADC]P.[PSH]P	31	P.[ST]P	Erk p44 MAP kinase phosphorylation site	Y				cytoskeleton organization and biogenesis (1e-32)		0.007	10
yeast-215_GO-0007010	2	cytoskeleton organization and biogenesis	Q..E[ILP]	31							cytoskeleton organization and biogenesis (1e-10)		0.007	10
yeast-205_GO-0005856	2	cytoskeleton	K[REV]LN[DFN]	31	KR	CLV_PCSK_PC1ET2_1					cytoskeletal part (1e-15)	Y	0.006	10
yeast-1493_GO-0043234	2	protein complex	[SMP]L[SFC]S	31							signal transduction (0.01)		0.007	10
protein_40_YPR144C	2	NOC4:  Nucleolar protein, forms a complex with Nop14p that mediates maturation and nuclear export of 40S ribosomal subunits	[LE]K..G[LN]T	31							processing of 20S pre-rRNA (1e-04)		0.004	9
protein_40_YPR119W	2	CLB2:  B-type cyclin involved in cell cycle progression; activates Cdc28p to promote the transition from G2 to M phase; accumulates during G2 and M, then targeted via a destruction box motif for ubiquitin-mediated degradation by the proteasome	I[DSA]..LD[DKY]	31								Y	0.005	10
protein_40_YPR110C	2	RPC40:  RNA polymerase subunit, common to RNA polymerase I and III	[EIR]V[NAP]Q	31	VP	Interleukin converting enzyme protease					transcription from RNA polymerase III promoter (0.01)		0.006	10
protein_40_YPL217Cs	2	BMS1:  Essential conserved nucleolar GTP-binding protein required for synthesis of 40S ribosomal subunits and for processing of the 35S pre-rRNA at sites A0, A1, and A2; interacts with Rcl1p, has similarity to Tsr1p	K..D[FTV]	31							rRNA processing (1e-23)	Y	0.006	10
protein_40_YPL211W	2	NIP7:  Nucleolar protein required for 60S ribosome subunit biogenesis, constituent of 66S pre-ribosomal particles; physically interacts with Nop8p and the exosome subunit Rrp43p	[EWQ]I..[SG]T	31							cytoplasm organization and biogenesis (1e-11)		0.005	7
protein_40_YPL209C	2	IPL1:  Aurora kinase involved in regulating kinetochore-microtubule attachments; helps maintain condensed chromosomes during anaphase and early telophase; associates with Sli15p, which promotes Ipl1p association with mitotic spindle	[SIV]K..[KRG]K	31	K[KR].[KR]	Nuclear localization motif					spindle midzone (0.01)	Y	0.006	10
protein_40_YPL204W	2	HRR25:  Protein kinase involved in regulating diverse events including vesicular trafficking, DNA repair, and chromosome segregation; binds the CTD of RNA pol II; homolog of mammalian casein kinase 1delta (CK1delta)	DD[DVC][VSF]	31	Y[DQ]DV	SH2 ligand for Blnk (Tyr must be phosphorylated)							0.006	10
protein_40_YPL153C	2	RAD53:  Protein kinase, required for cell-cycle arrest in response to DNA damage; activated by trans autophosphorylation when interacting with hyperphosphorylated Rad9p; also interacts with ARS1 and plays a role in initiation of DNA replication	N[AYQ]..E[LIQ]	31								Y	0.006	9
protein_40_YPL126W	2	NAN1:  U3 snoRNP protein, component of the small (ribosomal) subunit (SSU) processosome containing U3 snoRNA; required for the biogenesis of18S rRNA	[KAF]R..[TMQ]G	31	[KR]R	CLV_PCSK_KEX2_1					rRNA processing (1e-08)		0.005	10
protein_40_YPL012W	2	RRP12:  Protein required for export of the ribosomal subunits; associates with the RNA components of the pre-ribosomes; contains HEAT-repeats	EK.[SMY][KAT]	31							nucleolus (1e-21)		0.006	9
protein_40_YPL004C	2	LSP1:  Primary component of eisosomes, which are large immobile patch structures at the cell cortex associated with endocytosis, along with Pil1p and Sur7p; null mutants show activation of Pkc1p/Ypk1p stress resistance pathways	G[NSQ]..S[RLF]	31	S..S	Casien kinase I phosphorylation site, 1st Ser must be phosphorylated	Y						0.006	10
protein_40_YOR308C	2	SNU66:  Component of the U4/U6.U5 snRNP complex involved in pre-mRNA splicing via spliceosome; has homology to human SART-1 and to an S. pombe protein; snu66 null mutation confers cold-sensitivity but is not lethal at normal growth temperatures	R[IHG].[KV]R	31	KR	CLV_PCSK_PC1ET2_1					U4/U6 x U5 tri-snRNP complex (0.001)		0.004	7
protein_40_YOR174W	2	MED4:  Subunit of the RNA polymerase II mediator complex; associates with core polymerase subunits to form the RNA polymerase II holoenzyme; essential for transcriptional regulation	[QMC]D[LSR]I	31							RNA polymerase II transcription mediator activity (1e-08)		0.005	8
protein_40_YOR174W	2	MED4:  Subunit of the RNA polymerase II mediator complex; associates with core polymerase subunits to form the RNA polymerase II holoenzyme; essential for transcriptional regulation	P[QPH]Y[INV]	31	NP.Y	LIG_PTB_1					general RNA polymerase II transcription factor activity (1e-06)		0.004	7
protein_40_YOR061W	2	CKA2:  Alpha' catalytic subunit of casein kinase 2, a Ser/Thr protein kinase with roles in cell growth and proliferation; the holoenzyme also contains CKA1, CKB1 and CKB2, the many substrates include transcription factors and all RNA polymerases	RG[SWH][KWT]	31	RGD	LIG_RGD	Y				establishment and/or maintenance of chromatin architecture (1e-04)		0.004	8
protein_40_YOR039W	2	CKB2:  Beta' regulatory subunit of casein kinase 2, a Ser/Thr protein kinase with roles in cell growth and proliferation; the holoenzyme also contains CKA1, CKA2 and CKB1, the many substrates include transcription factors and all RNA polymerases	[TQA]KP[AEY]	31	KP..[QK]	LIG_SH3_4					RNA polymerase II transcription elongation factor activity (1e-04)		0.005	9
protein_40_YOL133W	2	HRT1:  RING finger containing subunit of Skp1-Cullin-F-box ubiquitin protein ligases (SCF); required for Gic2p, Far1p, Sic1p and Cln2p degradation; may tether Cdc34p (a ubiquitin conjugating enzyme or E2) and Cdc53p (a cullin) subunits of SCF	[IND]LA[AFN]	31								Y	0.006	10
protein_40_YOL133W	2	HRT1:  RING finger containing subunit of Skp1-Cullin-F-box ubiquitin protein ligases (SCF); required for Gic2p, Far1p, Sic1p and Cln2p degradation; may tether Cdc34p (a ubiquitin conjugating enzyme or E2) and Cdc53p (a cullin) subunits of SCF	FT..[KAH][KFL]	31	FTY	mTOR kinase substrate motif						Y	0.006	8
protein_40_YOL133W	2	HRT1:  RING finger containing subunit of Skp1-Cullin-F-box ubiquitin protein ligases (SCF); required for Gic2p, Far1p, Sic1p and Cln2p degradation; may tether Cdc34p (a ubiquitin conjugating enzyme or E2) and Cdc53p (a cullin) subunits of SCF	I[RET][KSL]E	31	[ST]E	G protein-coupled receptor kinase 1 substrate motif					protein catabolism (0.001)	Y	0.006	10
protein_40_YNL289W	2	PCL1:  Pho85 cyclin of the Pcl1,2-like subfamily, involved in entry into the mitotic cell cycle and regulation of morphogenesis, localizes to sites of polarized cell growth	T.N[NDF]	31								Y	0.006	10
protein_40_YNL244C	2	SUI1:  Translation initiation factor eIF1; component of a complex involved in recognition of the initiator codon; modulates translation accuracy at the initiation phase	F..E[GIA]	31	GFRGE[AG]L	DNA_MISMATCH_REPAIR_1 PATTERN	Y				eukaryotic translation initiation factor 3 complex (0.01)		0.006	10
protein_40_YNL175C	2	NOP13:  Protein of unknown function, localizes to the nucleolus and nucleoplasm; contains an RNA recognition motif (RRM) and has similarity to Nop12p, which is required for processing of pre-18S rRNA	D[DSH]E[EQC]	31	SD.E	Casein kinase II substrate motif					nucleolus (1e-11)	Y	0.006	10
protein_40_YNL118C	2	DCP2:  Catalytic subunit of the Dcp1p-Dcp2p decapping enzyme complex, which removes the 5' cap structure from mRNAs prior to their degradation; member of the Nudix hydrolase family	K[INW]S[SMH]	31	S[ST]	MDC1 BRCT domain binding motif					cytoplasmic mRNA processing body (0.01)	Y	0.006	10
protein_40_YMR242C	2	RPL20A:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl20Bp and has similarity to rat L18a ribosomal protein	A.[GAK]K	31	VPGKARKKSSCQLL	Calmodulin-dependent protein kinase IV substrate motif					cytosolic ribosome (sensu Eukaryota) (1e-29)	Y	0.006	10
protein_40_YMR242C	2	RPL20A:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl20Bp and has similarity to rat L18a ribosomal protein	R.[QGA]K	31	GR.A	Protease tPA proteolytic site					cytosolic ribosome (sensu Eukaryota) (1e-19)	Y	0.006	9
protein_40_YMR236W	2	TAF9:  Subunit (17 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation and in chromatin modification, similar to histone H3	LT.[QLI][NQI]	31	LLTP	WD40 domain of Cdc4 binding motif, Thr must be phosphorylated, CPD motif					transcription factor complex (1e-15)	Y	0.006	9
protein_40_YMR229C	2	RRP5:  Protein required for the synthesis of both 18S and 5.8S rRNA; C-terminal region is crucial for the formation of 18S rRNA and N-terminal region is required for the 5.8S rRNA; component of small ribosomal subunit (SSU) processosome	[EPR]V.A[KLW]	31	FGPVVA	Zyxin motif that binds alpha-actinin					nucleolus (1e-13)		0.006	9
protein_40_YMR186W	2	HSC82:  Cytoplasmic chaperone of the Hsp90 family, redundant in function and nearly identical with Hsp82p, and together they are essential; expressed constitutively at 10-fold higher basal levels than HSP82 and induced 2-3 fold by heat shock	E.I[NEP]	31	YE.[IV]	SH2 ligand for Fes (Tyr must be phosphorylated)							0.006	10
protein_40_YMR186W	2	HSC82:  Cytoplasmic chaperone of the Hsp90 family, redundant in function and nearly identical with Hsp82p, and together they are essential; expressed constitutively at 10-fold higher basal levels than HSP82 and induced 2-3 fold by heat shock	PK[LVA][EVH]	31	LPKY	WW motif (non-conventional ) in spt23 for binding to WW domain of RSP5p, also for NEDD4 WW domain							0.006	8
protein_40_YMR117C	2	SPC24:  Component of the evolutionarily conserved kinetochore-associated Ndc80 complex (Ndc80p-Nuf2p-Spc24p-Spc25p); involved in chromosome segregation, spindle checkpoint activity and kinetochore clustering	[LIV]D..S[RKY]	31									0.006	9
protein_40_YMR116C	2	ASC1:  G-protein beta subunit and guanine nucleotide dissociation inhibitor for Gpa2p; ortholog of RACK1 that inhibits translation; core component of the small (40S) ribosomal subunit; represses Gcn4p in the absence of amino acid starvation	SE..[PSV]L[NEL]	31	[ST]E	G protein-coupled receptor kinase 1 substrate motif							0.004	7
protein_40_YMR106C	2	YKU80:  Subunit of the telomeric Ku complex (Yku70p-Yku80p), involved in telomere length maintenance, structure and telomere position effect; relocates to sites of double-strand cleavage to promote nonhomologous end joining during DSB repair	[GWY]F..[NH]K	31									0.004	9
protein_40_YMR106C	2	YKU80:  Subunit of the telomeric Ku complex (Yku70p-Yku80p), involved in telomere length maintenance, structure and telomere position effect; relocates to sites of double-strand cleavage to promote nonhomologous end joining during DSB repair	Q[IQM]..T[FRY]	31									0.005	9
protein_40_YMR093W	2	UTP15:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	[DV]K.[VTA]K	31							ribosome biogenesis (1e-14)	Y	0.006	10
protein_40_YMR001C	2	CDC5:  Polo-like kinase with similarity to Xenopus Plx1 and S. pombe Plo1p; found at bud neck, nucleus and SPBs; has multiple functions in mitosis and cytokinesis through phosphorylation of substrates; may be a Cdc28p substrate	KR..[LSA][LEN]	31	KR	CLV_PCSK_PC1ET2_1					cohesin complex (1e-05)		0.006	10
protein_40_YMR001C	2	CDC5:  Polo-like kinase with similarity to Xenopus Plx1 and S. pombe Plo1p; found at bud neck, nucleus and SPBs; has multiple functions in mitosis and cytokinesis through phosphorylation of substrates; may be a Cdc28p substrate	LQ.[NQS][IVS]	31							cell cycle (1e-06)		0.006	9
protein_40_YML010W	2	SPT5:  Protein that forms a complex with Spt4p and mediates both activation and inhibition of transcription elongation; Spt4p-Spt5p complex also plays a role in pre-mRNA processing	[KIQ]A.[AYE]D	31							nuclear lumen (1e-05)	Y	0.006	10
protein_40_YML010W	2	SPT5:  Protein that forms a complex with Spt4p and mediates both activation and inhibition of transcription elongation; Spt4p-Spt5p complex also plays a role in pre-mRNA processing	L.[DSH]D	31	LEHD	Protease Caspase 9	Y				nuclear lumen (1e-13)	Y	0.006	10
protein_40_YLR372W	2	SUR4:  Elongase, involved in fatty acid and sphingolipid biosynthesis; synthesizes very long chain 20-26-carbon fatty acids from C18-CoA primers; involved in regulation of sphingolipid biosynthesis	A[VY]F	31	AEV[IVLF]YAA[PF]F	Abl kinase substrate motif					lipid biosynthetic process (1e-04)	Y	0.006	10
protein_40_YLR249W	2	YEF3:  Translational elongation factor 3, stimulates the binding of aminoacyl-tRNA (AA-tRNA) to ribosomes by releasing EF-1 alpha from the ribosomal complex; contains two ABC cassettes; binds and hydrolyses ATP	V.[GVF]E	31	[RK].V.F	PPI binding sites							0.006	10
protein_40_YLR129W	2	DIP2:  Nucleolar protein, specifically associated with the U3 snoRNA, part of the large ribonucleoprotein complex known as the small subunit (SSU) processome, required for 18S rRNA biogenesis, part of the active pre-rRNA processing complex	RK..[EKH][SAD]	31	RRK.[ST]	ZIP kinase phosphorylation motif					rRNA processing (1e-20)		0.006	10
protein_40_YLL011W	2	SOF1:  Essential protein required for biogenesis of 40S (small) ribosomal subunit; has similarity to the beta subunit of trimeric G-proteins and the splicing factor Prp4p	LT.[DYC][GDK]	31	LLTP	WD40 domain of Cdc4 binding motif, Thr must be phosphorylated, CPD motif					snoRNA binding (1e-14)	Y	0.006	10
protein_40_YKL203C	2	TOR2:  PIK-related protein kinase and rapamycin target; subunit of TORC1, a complex that regulates growth in response to nutrients and TORC2, a complex that regulates cell-cycle dependent polarization of the actin cytoskeleton; involved in meiosis	SF[QEV]	31							plasma membrane (1e-17)	Y	0.006	10
protein_40_YJR066W	2	TOR1:  PIK-related protein kinase and rapamycin target; subunit of TORC1, a complex that controls growth in response to nutrients by regulating translation, transcription, ribosome biogenesis, nutrient transport and autophagy; involved in meiosis	N[KTN]I[FCT]	31							plasma membrane (1e-10)	Y	0.006	9
protein_40_YJR002W	2	MPP10:  Component of the SSU processome, which is required for pre-18S rRNA processing, interacts with and controls the stability of Imp3p and Imp4p, essential for viability; similar to human Mpp10p	[EKP]K.S[RKE]	31	RKK.[ST]	ZIP kinase phosphorylation motif					small nucleolar ribonucleoprotein complex (1e-29)	Y	0.006	9
protein_40_YJL164C	2	TPK1:  cAMP-dependent protein kinase catalytic subunit; promotes vegetative growth in response to nutrients via the Ras-cAMP signaling pathway; inhibited by regulatory subunit Bcy1p in the absence of cAMP; partially redundant with Tpk2p and Tpk3p	[FPR]P..[KLI]D	31									0.006	10
protein_40_YJL164C	2	TPK1:  cAMP-dependent protein kinase catalytic subunit; promotes vegetative growth in response to nutrients via the Ras-cAMP signaling pathway; inhibited by regulatory subunit Bcy1p in the absence of cAMP; partially redundant with Tpk2p and Tpk3p	S..[PRV]K	31									0.006	10
protein_40_YJL109C	2	UTP10:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	[DHP]E[ESK]D	31	E[ST]D	Ankyrin G binding motif in KNCQ2 and KNCQ3 potaqssium channels					rRNA processing (1e-24)		0.006	10
protein_40_YJL109C	2	UTP10:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	E[ETC].D[QMR]	31							rRNA processing (1e-14)		0.006	10
protein_40_YJL092W	2	SRS2:  DNA helicase and DNA-dependent ATPase involved in DNA repair, needed for proper timing of commitment to meiotic recombination and transition from Meiosis I to II; affects genome stability by suppressing unscheduled homologous recombination	F[KTL]K	31	S..F.K	LIG_BRCT_BRCA1_2					response to DNA damage stimulus (0.001)		0.006	10
protein_40_YJL092W	2	SRS2:  DNA helicase and DNA-dependent ATPase involved in DNA repair, needed for proper timing of commitment to meiotic recombination and transition from Meiosis I to II; affects genome stability by suppressing unscheduled homologous recombination	R.I[DGS]	31								Y	0.006	10
protein_40_YJL074C	2	SMC3:  Subunit of the multiprotein cohesin complex required for sister chromatid cohesion in mitotic cells; also required, with Rec8p, for cohesion and recombination during meiosis; phylogenetically conserved SMC chromosomal ATPase family member	DY.[DNR][LGY]	31	[DE]Y	EGFR kinase substrate motif						Y	0.005	10
protein_40_YJL074C	2	SMC3:  Subunit of the multiprotein cohesin complex required for sister chromatid cohesion in mitotic cells; also required, with Rec8p, for cohesion and recombination during meiosis; phylogenetically conserved SMC chromosomal ATPase family member	E.K[EQM]	31							cohesin complex (1e-04)	Y	0.006	10
protein_40_YJL074C	2	SMC3:  Subunit of the multiprotein cohesin complex required for sister chromatid cohesion in mitotic cells; also required, with Rec8p, for cohesion and recombination during meiosis; phylogenetically conserved SMC chromosomal ATPase family member	R[DSI].S[FM]	31	F.R..S[FM][FM]	PKC zeta kinase substrate motif							0.005	8
protein_40_YIL061C	2	SNP1:  Component of U1 snRNP required for mRNA splicing via spliceosome; may interact with poly(A) polymerase to regulate polyadenylation; homolog of human U1 70K protein	QF.[SPY][KQP]	31							nuclear mRNA splicing, via spliceosome (0.001)		0.005	9
protein_40_YIL035C	2	CKA1:  Alpha catalytic subunit of casein kinase 2, a Ser/Thr protein kinase with roles in cell growth and proliferation; the holoenzyme also contains CKA2, CKB1 and CKB2, the many substrates include transcription factors and all RNA polymerases	A[TPI][GEK]S	31			Y				nuclear lumen (0.001)		0.006	10
protein_40_YHR197W	2	RIX1:  Essential component of the Rix1 complex (Rix1p, Ipi1p, Ipi3p) that is required for processing of ITS2 sequences from 35S pre-rRNA; Rix1 complex associates with Mdn1p in pre-60S ribosomal particles	[SD][IY].NSF	31	Y.N	LIG_SH2_GRB2							0.004	7
protein_40_YHR165C	2	PRP8:  Component of the U4/U6-U5 snRNP complex, involved in the second catalytic step of splicing; mutations of human Prp8 cause retinitis pigmentosa	L[ESL]..[EAS]R	31	[AG]R	Protease matriptase protease site					RNA splicing (1e-21)	Y	0.006	10
protein_40_YHR135C	2	YCK1:  Palmitoylated, plasma membrane-bound casein kinase I isoform; shares redundant functions with Yck2p in morphogenesis, proper septin assembly, endocytic trafficking; provides an essential function overlapping with that of Yck2p	PV	31	CPV	Heme binding site in mitochondrial heme lyases							0.006	10
protein_40_YHR135C	2	YCK1:  Palmitoylated, plasma membrane-bound casein kinase I isoform; shares redundant functions with Yck2p in morphogenesis, proper septin assembly, endocytic trafficking; provides an essential function overlapping with that of Yck2p	V..[NKD]K	31							RNA processing (0.01)		0.006	10
protein_40_YHR082C	2	KSP1:  Nonessential putative serine/threonine protein kinase of unknown cellular role; overproduction causes allele-specific suppression of the prp20-10 mutation	K..[GVN]G	31								Y	0.006	9
protein_40_YHR052W	2	CIC1:  Essential protein that interacts with proteasome components and has a potential role in proteasome substrate specificity; also copurifies with 66S pre-ribosomal particles	EE..[DNG][GYI]	31	EED	Ankyrin B C-terminal motif that binds internal Ankyrin repeats					cytoplasm organization and biogenesis (1e-10)		0.006	9
protein_40_YHL007C	2	STE20:  Signal transducing kinase of the PAK (p21-activated kinase) family, involved in pheromone response and pseudohyphal/invasive growth pathways, activated by Cdc42p; binds Ste4p at a GBB motif present in noncatalytic domains of PAK kinases	[ELR]Q..Q[QKH]	31							bud (0.01)		0.006	9
protein_40_YHL001W	2	RPL14B:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl14Ap and has similarity to rat L14 ribosomal protein	[KDR]AG[KCM]	31							cytosolic ribosome (sensu Eukaryota) (1e-11)		0.005	9
protein_40_YGR218W	2	CRM1:  Major karyopherin, involved in export of proteins, RNAs, and ribosomal subunits from the nucleus	S.[QTF]Q	31							rRNA export from nucleus (1e-08)		0.006	10
protein_40_YGR103W	2	NOP7:  Nucleolar protein involved in rRNA processing and 60S ribosomal subunit biogenesis; constituent of several different pre-ribosomal particles; required for exit from G<sub>0</sub> and the initiation of cell proliferation	R[GEF]..I[PNK]	31							cytoplasm organization and biogenesis (1e-12)		0.006	10
protein_40_YGR086C	2	PIL1:  Primary component of eisosomes, which are large immobile cell cortex structures associated with endocytosis; null mutants show activation of Pkc1p/Ypk1p stress resistance pathways; detected in phosphorylated state in mitochondria	K..[EVF]V	31			Y				SWR1 complex (0.01)		0.006	10
protein_40_YGR040W	2	KSS1:  Mitogen-activated protein kinase (MAPK) involved in signal transduction pathways that control filamentous growth and pheromone response; the KSS1 gene is nonfunctional in S288C strains and functional in W303 strains	[KHW]T..F[LRY]	31									0.006	8
protein_40_YGR040W	2	KSS1:  Mitogen-activated protein kinase (MAPK) involved in signal transduction pathways that control filamentous growth and pheromone response; the KSS1 gene is nonfunctional in S288C strains and functional in W303 strains	A[STA]..N	31								Y	0.006	10
protein_40_YGR040W	2	KSS1:  Mitogen-activated protein kinase (MAPK) involved in signal transduction pathways that control filamentous growth and pheromone response; the KSS1 gene is nonfunctional in S288C strains and functional in W303 strains	T.E	31	CP[LP]T.E[ST].C	GM_CSF PATTERN					invasive growth (sensu Saccharomyces) (1e-04)		0.006	10
protein_40_YGL179C	2	TOS3:  Protein kinase, related to and functionally redundant with Elm1p and Sak1p for the phosphorylation and activation of Snf1p; functionally orthologous to LKB1, a mammalian kinase associated with Peutz-Jeghers cancer-susceptibility syndrome	D.E[DTY]	31	SD.E	Casein kinase II substrate motif	Y						0.006	10
protein_40_YGL179C	2	TOS3:  Protein kinase, related to and functionally redundant with Elm1p and Sak1p for the phosphorylation and activation of Snf1p; functionally orthologous to LKB1, a mammalian kinase associated with Peutz-Jeghers cancer-susceptibility syndrome	E[DTW].H[ETY]	31	HE.GH	Protease AAA proteases - cut membrane proteins metal binding site							0.005	9
protein_40_YGL179C	2	TOS3:  Protein kinase, related to and functionally redundant with Elm1p and Sak1p for the phosphorylation and activation of Snf1p; functionally orthologous to LKB1, a mammalian kinase associated with Peutz-Jeghers cancer-susceptibility syndrome	N.N[ESQ]	31									0.006	9
protein_40_YGL120C	2	PRP43:  RNA helicase in the DEAH-box family, functions in both RNA polymerase I and polymerase II transcript metabolism, involved in release of the lariat-intron from the spliceosome	P[NER].[KAV]A	31							nucleolus (1e-18)	Y	0.006	10
protein_40_YGL106W	2	MLC1:  Essential light chain for Myo1p, light chain for Myo2p; stabilizes Myo2p by binding to the neck region; interacts with Myo1p, Iqg1p, and Myo2p to coordinate formation and contraction of the actomyosin ring with targeted membrane deposition	S[QE]F[ICW]	31	SQ	ATM kinase substrate motif							0.004	9
protein_40_YGL030W	2	RPL30:  Protein component of the large (60S) ribosomal subunit, has similarity to rat L30 ribosomal protein; involved in pre-rRNA processing in the nucleolus; autoregulates splicing of its transcript	A.[GAK]K	31	VPGKARKKSSCQLL	Calmodulin-dependent protein kinase IV substrate motif					cytosolic ribosome (sensu Eukaryota) (1e-27)	Y	0.006	10
protein_40_YFR034C	2	PHO4:  Basic helix-loop-helix (bHLH) transcription factor of the myc-family; binds cooperatively with Pho2p to the PHO5 promoter; function is regulated by phosphorylation at multiple sites and by phosphate availability	[PTS]P[PGD]H	31	[ST]P	LIG_WW_4							0.006	10
protein_40_YFL039C	2	ACT1:  Actin, structural protein involved in cell polarization, endocytosis, and other cytoskeletal functions	E.[EYV]I	31	EEEIYEEIE	cFPS/FES kinase phosphorylation site					cell cortex (1e-16)		0.006	10
protein_40_YFL037W	2	TUB2:  Beta-tubulin; associates with alpha-tubulin (Tub1p and Tub3p) to form tubulin dimer, which polymerizes to form microtubules	[KQT]R.[TWF]V	31	[KR]R	CLV_PCSK_KEX2_1						Y	0.004	9
protein_40_YER177W	2	BMH1:  14-3-3 protein, major isoform; controls proteome at post-transcriptional level, binds proteins and DNA, involved in regulation of many processes including exocytosis, vesicle transport, Ras/MAPK signaling, and rapamycin-sensitive signaling	S[TPA].N[LDF]	31	S[ST]	MDC1 BRCT domain binding motif							0.006	10
protein_40_YER082C	2	UTP7:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	I..A[RGV]	31							small nucleolar ribonucleoprotein complex (1e-21)	Y	0.006	10
protein_40_YER036C	2	ARB1:  ATPase of the ATP-binding cassette (ABC) family involved in 40S and 60S ribosome biogenesis, has similarity to Gcn20p; shuttles from nucleus to cytoplasm, physically interacts with Tif6p, Lsg1p	V[EQI].[EGQ]K	31							translation (0.01)		0.006	10
protein_40_YEL037C	2	RAD23:  Protein with ubiquitin-like N terminus, recognizes and binds damaged DNA (with Rad4p) during nucleotide excision repair; regulates Rad4p levels, subunit of Nuclear Excision Repair Factor 2 (NEF2); homolog of human HR23A and HR23B proteins	D[PMW][AME]L	31							protein catabolism (0.001)		0.005	8
protein_40_YDR510W	2	SMT3:  Ubiquitin-like protein of the SUMO family, conjugated to lysine residues of target proteins; regulates chromatid cohesion, chromosome segregation, APC-mediated proteolysis, DNA replication and septin ring dynamics	K.[DVQ]G	31	[EDQH].K.[DN]G.R[GACIVM]	DNA_LIGASE_A1 PATTERN							0.006	10
protein_40_YDR448W	2	ADA2:  Transcription coactivator, component of the ADA and SAGA transcriptional adaptor/HAT (histone acetyltransferase) complexes	[PTM]P.N[ELQ]	31	[ST]P	LIG_WW_4	Y				SAGA complex (0.001)		0.005	8
protein_40_YDR448W	2	ADA2:  Transcription coactivator, component of the ADA and SAGA transcriptional adaptor/HAT (histone acetyltransferase) complexes	R..Q[LGT]	31							SAGA complex (1e-17)		0.006	9
protein_40_YDR448W	2	ADA2:  Transcription coactivator, component of the ADA and SAGA transcriptional adaptor/HAT (histone acetyltransferase) complexes	R[SLR].P[NY]	31							SLIK (SAGA-like) complex (1e-07)		0.004	9
protein_40_YDR414C	2	ERD1:  Predicted membrane protein required for the retention of lumenal endoplasmic reticulum proteins; mutants secrete the endogenous ER protein, BiP (Kar2p)	[TF]N.W[IA]	31									0.004	7
protein_40_YDR365C	2	ESF1:  Nucleolar protein involved in pre-rRNA processing; depletion causes severely decreased 18S rRNA levels	EE.[SEF][DKL]	31	EED	Ankyrin B C-terminal motif that binds internal Ankyrin repeats					nucleolus (1e-13)		0.006	10
protein_40_YDR324C	2	UTP4:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	[IFV]E..[ELT]G	31							small nucleolar ribonucleoprotein complex (1e-12)		0.006	10
protein_40_YDR303C	2	RSC3:  Component of the RSC chromatin remodeling complex; essential gene required for maintenance of proper ploidy and regulation of ribosomal protein genes and the cell wall/stress response; highly similar to Rsc30p	[NYD][KNL]..DA	31							chromosome organization and biogenesis (sensu Eukaryota) (1e-04)		0.006	9
protein_40_YDR225W	2	HTA1:  One of two nearly identical (see also HTA2) histone H2A subtypes; core histone required for chromatin assembly and chromosome function; DNA damage-dependent phosphorylation by Mec1p facilitates DNA repair; acetylated by Nat4p	A[DGP]..A[EKQ]	31							nuclear lumen (0.001)		0.006	10
protein_40_YDR145W	2	TAF12:  Subunit (61/68 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation and in chromatin modification, similar to histone H2A	ST[QPH]	31	[KR]STQT	Light chain 8 of dynein binding motif					transcription factor complex (1e-16)		0.005	9
protein_40_YDR099W	2	BMH2:  14-3-3 protein, minor isoform; controls proteome at post-transcriptional level, binds proteins and DNA, involved in regulation of many processes including exocytosis, vesicle transport, Ras/MAPK signaling, and rapamycin-sensitive signaling	ID..[DFA][SVP]	31									0.006	9
protein_40_YDR012W	2	RPL4B:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl4Ap and has similarity to E. coli L4 and rat L4 ribosomal proteins	[RSK]A.R[AVK]	31							cytosolic ribosome (sensu Eukaryota) (1e-05)		0.006	10
protein_40_YDL213C	2	NOP6:  Putative RNA-binding protein implicated in ribosome biogenesis; contains an RNA recognition motif (RRM) and has similarity to hydrophilins; NOP6 may be a fungal-specific gene as no homologs have been yet identified in higher eukaryotes	[GFR]T..[ICH]G	31	T..[IL]	FHA2 binding motif, Thr must be phosphorylated					rRNA metabolism (1e-04)		0.005	9
protein_40_YDL213C	2	NOP6:  Putative RNA-binding protein implicated in ribosome biogenesis; contains an RNA recognition motif (RRM) and has similarity to hydrophilins; NOP6 may be a fungal-specific gene as no homologs have been yet identified in higher eukaryotes	[VPE]G.R[VGA]	31							nucleolus (1e-04)		0.005	10
protein_40_YDL213C	2	NOP6:  Putative RNA-binding protein implicated in ribosome biogenesis; contains an RNA recognition motif (RRM) and has similarity to hydrophilins; NOP6 may be a fungal-specific gene as no homologs have been yet identified in higher eukaryotes	E[KFP]..A[AQP]	31							ribosome biogenesis (1e-05)		0.006	10
protein_40_YDL213C	2	NOP6:  Putative RNA-binding protein implicated in ribosome biogenesis; contains an RNA recognition motif (RRM) and has similarity to hydrophilins; NOP6 may be a fungal-specific gene as no homologs have been yet identified in higher eukaryotes	R..L[TPI]	31	R..L	LIG_APCC_Dbox_1					nucleolus (1e-19)		0.006	10
protein_40_YDL055C	2	PSA1:  GDP-mannose pyrophosphorylase (mannose-1-phosphate guanyltransferase), synthesizes GDP-mannose from GTP and mannose-1-phosphate in cell wall biosynthesis; required for normal cell wall structure	GE..[KSF][PVI]	31								Y	0.006	10
protein_40_YDL047W	2	SIT4:  Type 2A-related serine-threonine phosphatase that functions in the G1/S transition of the mitotic cycle; cytoplasmic and nuclear protein that modulates functions mediated by Pkc1p including cell wall and actin cytoskeleton organization	[DIT]..IG	31	FIGQY	Ankryn G binding motif in neurofascin							0.006	9
protein_40_YDL047W	2	SIT4:  Type 2A-related serine-threonine phosphatase that functions in the G1/S transition of the mitotic cycle; cytoplasmic and nuclear protein that modulates functions mediated by Pkc1p including cell wall and actin cytoskeleton organization	A[SHY].[SCW]N	31			Y						0.005	9
protein_40_YBR251W	2	MRPS5:  Mitochondrial ribosomal protein of the small subunit	I[PMR].[NPW]L	31									0.006	9
protein_40_YBR181C	2	RPS6B:  Protein component of the small (40S) ribosomal subunit; identical to Rps6Ap and has similarity to rat S6 ribosomal protein	L.[NSY]L	31	L..L..L.L	Nuclear export signal							0.006	9
protein_40_YBR159W	2	IFA38: Microsomal beta-keto-reductase; contains oleate response element (ORE) sequence in the promoter region; mutants exhibit reduced VLCFA synthesis, accumulate high levels of dihydrosphingosine, phytosphingosine and medium-chain ceramides	F..[STF]L	31			Y				endoplasmic reticulum (1e-12)	Y	0.006	10
protein_40_YBR142W	2	MAK5:  Essential nucleolar protein, putative DEAD-box RNA helicase required for maintenance of M1 dsRNA virus; involved in biogenesis of large (60S) ribosomal subunits	A.[GRP]K	31	IYA.P	c-Abl kinase phosphorylation site (peptide screen)					nucleolus (1e-13)		0.006	10
protein_40_YBR109C	2	CMD1:  Calmodulin; Ca++ binding protein that regulates Ca++ independent processes (mitosis, bud growth, actin organization, endocytosis, etc.) and Ca++ dependent processes (stress-activated pathways), targets include Nuf1p, Myo2p and calcineurin	[IKH]PE[FN]	31								Y	0.006	10
protein_40_YBR010W	2	HHT1:  One of two identical histone H3 proteins (see also HHT2); core histone required for chromatin assembly, involved in heterochromatin-mediated telomeric and HM silencing; regulated by acetylation, methylation, and mitotic phosphorylation	[ETN]N..[KD]S	31							regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism (1e-07)		0.006	9
protein_40_YBL092W	2	RPL32:  Protein component of the large (60S) ribosomal subunit, has similarity to rat L32 ribosomal protein; overexpression disrupts telomeric silencing	S.L[SLT]	31									0.006	10
protein_40_YAL032C	2	PRP45:  Protein required for pre-mRNA splicing; associates with the spliceosome and interacts with splicing factors Prp22p and Prp46p; orthologous to human transcriptional coactivator SKIP and can activate transcription of a reporter gene	[NAD]K..[LQN]L	31							nuclear mRNA splicing, via spliceosome (1e-04)		0.006	9
protein_40_YAL032C	2	PRP45:  Protein required for pre-mRNA splicing; associates with the spliceosome and interacts with splicing factors Prp22p and Prp46p; orthologous to human transcriptional coactivator SKIP and can activate transcription of a reporter gene	L[KSP].D[FER]	31	S.D	CAMKII phosphorylation site					mRNA processing (1e-08)		0.006	10
oshea_vacuole	2	oshea_vacuole	FF[VYI]	31	F[MLVI]Y	PTPRJ phosphatase substrate motif					storage vacuole (1e-16)		0.006	10
oshea_spindle_pole	2	oshea_spindle_pole	D[STF]..[LGE]M	31							microtubule cytoskeleton (1e-12)		0.005	10
oshea_punctate_composite	2	oshea_punctate_composite	ND[LRC]	31	DRY	Binding motif for interaction of G-proteins or Phospholipase D with G-alpha					vesicle-mediated transport (1e-05)		0.006	10
oshea_nuclear_periphery	2	oshea_nuclear_periphery	[FST][GDL].KP	31	FKPY	TLA binding motif in Brinker transcription factor for binding TLA domain in Groucho					nuclear pore (1e-16)	Y	0.007	10
oshea_nuclear_periphery	2	oshea_nuclear_periphery	A[NQI]S	31	RPVSSAASVY	14-3-3 domain binding motif					nuclear membrane part (1e-38)		0.006	10
oshea_nuclear_periphery	2	oshea_nuclear_periphery	FG..[PAM][ASF]	31							nuclear pore (1e-24)		0.006	8
oshea_cell_periphery	2	oshea_cell_periphery	P..A[GYR]	31							plasma membrane (1e-15)		0.006	10
oshea_cell_periphery	2	oshea_cell_periphery	V[LFM]..V[FGW]	31							plasma membrane (1e-12)		0.007	10
oshea_cell_periphery	2	oshea_cell_periphery	VF[AIG]	31	EEEEYVFI	PDGFR kinase substrate motif					plasma membrane (1e-15)		0.006	10
oshea_bud_neck	2	oshea_bud_neck	D.M[ERL]	31	LFDLM	Binding motif in Clint for clathrin TD domain					site of polarized growth (1e-26)		0.006	10
matsuyama_Spindle_or_SPB	2	matsuyama_Spindle_or_SPB	IS..E[SAC][LAR]	31	[ST]..E	Casien kinase II consensus phosphorylation site					spindle (1e-15)	Y	0.008	9
matsuyama_Spindle_or_SPB	2	matsuyama_Spindle_or_SPB	K.R[RET]	31	[IL]Q..C....K.R.W	Myosin light chain binding motifs Type 2B Ca independent					spindle (1e-10)		0.008	10
matsuyama_periphery	2	matsuyama_periphery	I[EMC]..[EH]E	31							barrier septum (1e-13)		0.008	10
matsuyama_nuclear_envelope_or_dots	2	matsuyama_nuclear_envelope_or_dots	A..[PSQ]Q	31	[ST]Q	ATM kinase phosphorylation site	Y				nuclear pore (1e-13)	Y	0.008	10
matsuyama_nuclear_envelope_or_dots	2	matsuyama_nuclear_envelope_or_dots	E[TLS]K	31	ES[RK][FY][YST]FH[PS][IV][ES]D	LIG_WH1					nuclear envelope (1e-28)	Y	0.008	10
matsuyama_nuclear_envelope_or_dots	2	matsuyama_nuclear_envelope_or_dots	I[IQA][KLD]D	31							nuclear envelope (1e-10)		0.008	9
matsuyama_ER	2	matsuyama_ER	D..[KVH]R	31	[KR]R	CLV_PCSK_KEX2_1							0.008	10
matsuyama_Cytosol	2	matsuyama_Cytosol	R.[MVG]V	31	H.R.G	Motif for cell cycle arrest in SIV virus	Y				cytosolic ribosome (sensu Eukaryota) (1e-05)	Y	0.007	10
matsuyama_Cytoplasmic_dots	2	matsuyama_Cytoplasmic_dots	P..Q[VNQ]	31	KP..[QK]	LIG_SH3_4					vesicle-mediated transport (1e-04)	Y	0.008	10
genetic_YPL055C	2	LGE1: Protein of unknown function; null mutant forms abnormally large cells, and homozygous diploid null mutant displays delayed premeiotic DNA synthesis and reduced efficiency of meiotic nuclear division	[KNE]T.S	31	[RK].[RK][ST].S	Akt kinase substrate motif					chromosome organization and biogenesis (sensu Eukaryota) (1e-21)		0.006	10
genetic_YPL055C	2	LGE1: Protein of unknown function; null mutant forms abnormally large cells, and homozygous diploid null mutant displays delayed premeiotic DNA synthesis and reduced efficiency of meiotic nuclear division	R..K[RSN]	31	R..K	SH3 binding motif for GADS SH3 recognizing slp-76 motif (nonconventional)	Y				chromosome organization and biogenesis (sensu Eukaryota) (1e-11)		0.006	10
genetic_YNL153C	2	GIM3: Subunit of the heterohexameric cochaperone prefoldin complex which binds specifically to cytosolic chaperonin and transfers target proteins to it	P.[TQH]S	31	NPK[ST]SG.AR	PROK_SULFATE_BIND_2 PATTERN					cytoskeleton organization and biogenesis (1e-06)	Y	0.006	10
genetic_YNL153C	2	GIM3: Subunit of the heterohexameric cochaperone prefoldin complex which binds specifically to cytosolic chaperonin and transfers target proteins to it	Q.[GID]V	31							asexual reproduction (0.001)	Y	0.006	10
genetic_YLR200W	2	YKE2: Subunit of the heterohexameric Gim/prefoldin protein complex involved in the folding of alpha-tubulin, beta-tubulin, and actin	[FNL]AK	31	[PT]GKHG.AK	IF5A_HYPUSINE PATTERN					cell cycle (1e-09)	Y	0.006	10
genetic_YLR200W	2	YKE2: Subunit of the heterohexameric Gim/prefoldin protein complex involved in the folding of alpha-tubulin, beta-tubulin, and actin	K..[HDM]Q	31							cytoskeleton organization and biogenesis (0.001)	Y	0.005	10
genetic_YLR039C	2	RIC1: Protein involved in retrograde transport to the cis-Golgi network; forms heterodimer with Rgp1p that acts as a GTP exchange factor for Ypt6p; involved in transcription of rRNA and ribosomal protein genes	E..S[IYE]	31							chromosome organization and biogenesis (sensu Eukaryota) (1e-09)		0.006	10
genetic_YGL058W	2	RAD6: Ubiquitin-conjugating enzyme (E2), involved in postreplication repair (with Rad18p), sporulation, telomere silencing, and ubiquitin-mediated N-end rule protein degradation (with Ubr1p)	[LWP]TQ[EPN]	31	[ST]Q	ATM kinase phosphorylation site						Y	0.006	9
genetic_YGL058W	2	RAD6: Ubiquitin-conjugating enzyme (E2), involved in postreplication repair (with Rad18p), sporulation, telomere silencing, and ubiquitin-mediated N-end rule protein degradation (with Ubr1p)	Q.[LDS]L	31							DNA metabolism (1e-10)		0.006	9
genetic_YGL020C	2	GET1: Subunit of the GET complex; required for the retrieval of HDEL proteins from the Golgi to the ER in an ERD2 dependent fashion and for normal mitochondrial morphology and inheritance	D..[DIQ]D	31							chromosome organization and biogenesis (sensu Eukaryota) (1e-16)		0.006	10
genetic_YGL020C	2	GET1: Subunit of the GET complex; required for the retrieval of HDEL proteins from the Golgi to the ER in an ERD2 dependent fashion and for normal mitochondrial morphology and inheritance	L.D[ETH]	31	LPDEL	Motif in CBP for interaction with PPARg-LBD (secondary site)					chromosome organization and biogenesis (sensu Eukaryota) (1e-12)		0.006	10
genetic_YER083C	2	GET2: Subunit of the GET complex; required for meiotic nuclear division and for the retrieval of HDEL proteins from the Golgi to the ER in an ERD2 dependent fashion; may be involved in cell wall function	T..[DKQ]I	31	PT..[DI]	FHA binding motif					chromosome organization and biogenesis (sensu Eukaryota) (1e-14)	Y	0.006	10
genetic_YEL003W	2	GIM4: Subunit of the heterohexameric cochaperone prefoldin complex which binds specifically to cytosolic chaperonin and transfers target proteins to it	R...E	31	RE..E	Iron binding motif in ferritin L-chain and yeast Iron transport protein					chromosome organization and biogenesis (sensu Eukaryota) (1e-10)		0.006	10
genetic_YDL020C	2	RPN4: Transcription factor that stimulates expression of proteasome genes; Rpn4p levels are in turn regulated by the 26S proteasome in a negative feedback control mechanism; RPN4 is transcriptionally regulated by various stress responses	[LQK][KDN].LDV	31			Y					Y	0.006	10
genetic_YDL020C	2	RPN4: Transcription factor that stimulates expression of proteasome genes; Rpn4p levels are in turn regulated by the 26S proteasome in a negative feedback control mechanism; RPN4 is transcriptionally regulated by various stress responses	D..[QLP]N	31							chromosome organization and biogenesis (sensu Eukaryota) (1e-07)		0.006	9
genetic_YDL020C	2	RPN4: Transcription factor that stimulates expression of proteasome genes; Rpn4p levels are in turn regulated by the 26S proteasome in a negative feedback control mechanism; RPN4 is transcriptionally regulated by various stress responses	L..E[LEP]	31	S[LW]LD[DE]EL[LM]	TRG_LysEnd_GGAAcLL_2					chromosome organization and biogenesis (sensu Eukaryota) (1e-19)		0.006	10
genetic_YAL024C	2	LTE1: Putative GDP/GTP exchange factor required for mitotic exit at low temperatures; acts as a guanine nucleotide exchange factor (GEF) for Tem1p, which is a key regulator of mitotic exit; physically associates with Ras2p-GTP	K..N[TSP]	31	CK..NTF	RNASE_PANCREATIC PATTERN					cell cycle (1e-11)		0.006	10
protein_40_YBR160W	2	CDC28:  Catalytic subunit of the main cell cycle cyclin-dependent kinase (CDK); alternately associates with G1 cyclins (CLNs) and G2/M cyclins (CLBs) which direct the CDK to specific substrates	A..L[ARL]	31			Y	Pkinase	1.E-06	3.3	site of polarized growth (1e-10)		0.006	10
yeast-235_GO-0000278	2	mitotic cell cycle	T.[EDH]L	30	T..[IL]	FHA2 binding motif, Thr must be phosphorylated		Kinesin	1.E-03	-2.3	mitotic cell cycle (1e-13)		0.006	10
protein_40_YBR159W	2	IFA38: Microsomal beta-keto-reductase; contains oleate response element (ORE) sequence in the promoter region; mutants exhibit reduced VLCFA synthesis, accumulate high levels of dihydrosphingosine, phytosphingosine and medium-chain ceramides	V..[VFM]L	30			Y	MFS_1	1.E-04	-2.2	endoplasmic reticulum (1e-08)	Y	0.005	10
protein_40_YJR059W	2	PTK2:  Putative serine/threonine protein kinase involved in regulation of ion transport across plasma membrane; enhances spermine uptake	P..[PRE]R	30	[KR]R	CLV_PCSK_KEX2_1	Y	Pkinase	1.E-03	-2	protein kinase activity (0.01)		0.006	9
protein_40_YAR019C	2	CDC15:  Protein kinase of the Mitotic Exit Network that is localized to the spindle pole bodies at late anaphase; promotes mitotic exit by directly switching on the kinase activity of Dbf2p	S..[PWH]S	30	S...S	WD40 binding motif, Ser residues must be phosphorylated		Pkinase	1.E-18	-2	protein kinase activity (1e-14)		0.006	9
matsuyama_periphery	2	matsuyama_periphery	T..[PSL]N	30	T..[SA]	FHA of KAPP binding motif, Thr must be phosphorylated		Pkinase	1.E-04	-2	barrier septum (1e-54)		0.007	9
protein_40_YML010W	2	SPT5:  Protein that forms a complex with Spt4p and mediates both activation and inhibition of transcription elongation; Spt4p-Spt5p complex also plays a role in pre-mRNA processing	A..[KEF]R	30	[KR]R	CLV_PCSK_KEX2_1		DEAD	1.E-03	-1.8	nuclear lumen (1e-15)		0.005	10
yeast-324_GO-0030528	2	transcription regulator activity	[TNS][GHS]EK	30	[ST]E	G protein-coupled receptor kinase 1 substrate motif	Y	zf-C2H2	1.E-17	-1.6	transcription regulator activity (1e-53)		0.007	9
protein_40_YNL002C	2	RLP7:  Nucleolar protein with similarity to large ribosomal subunit L7 proteins; constituent of 66S pre-ribosomal particles; plays an essential role in processing of precursors to the large ribosomal subunit RNAs	AR[NKA]	30	[AG]R	Protease matriptase protease site		Brix	1.E-02	-1.6	cytoplasm organization and biogenesis (1e-30)		0.006	10
protein_40_YGL106W	2	MLC1:  Essential light chain for Myo1p, light chain for Myo2p; stabilizes Myo2p by binding to the neck region; interacts with Myo1p, Iqg1p, and Myo2p to coordinate formation and contraction of the actomyosin ring with targeted membrane deposition	LE.[ISV][SPE]	30				UCH	1.E-02	-1.6			0.006	10
protein_40_YDR087C	2	RRP1:  Essential evolutionarily conserved nucleolar protein necessary for biogenesis of 60S ribosomal subunits and processing of pre-rRNAs to mature rRNAs, associated with several distinct 66S pre-ribosomal particles	AR[AKW]	30	[AG]R	Protease matriptase protease site		Brix	1.E-02	-1.6	nucleolus (1e-14)		0.006	9
yeast-1216_GO-0009058	2	biosynthesis	Q.Q[QNE]	30				zf-C2H2	1.E-02	-1.5	transcription regulator activity (1e-11)		0.006	10
yeast-345_GO-0006396	2	RNA processing	T[PMQ]G[RTM]	30				Helicase_C	1.E-17	-1.4	RNA processing (1e-24)		0.007	10
yeast-1036_GO-0005739	2	mitochondrion	S[ANF]..[SNP]N	30				zf-C2H2	1.E-02	-1.4	transcriptional activator activity (1e-09)		0.006	9
protein_40_YNL069C	2	RPL16B:  N-terminally acetylated protein component of the large (60S) ribosomal subunit, binds to 5.8 S rRNA; has similarity to Rpl16Ap, E. coli L13 and rat L13a ribosomal proteins; transcriptionally regulated by Rap1p	K..[AKR]A	30	K[KR].[KR]	Nuclear localization motif		Ribosomal_60s	1.E-02	-1.4	cytosolic ribosome (sensu Eukaryota) (1e-48)	Y	0.006	9
protein_40_YGL105W	2	ARC1:  Protein that binds tRNA and methionyl- and glutamyl-tRNA synthetases (Mes1p and Gus1p), delivering tRNA to them, stimulating catalysis, and ensuring their localization to the cytoplasm; also binds quadruplex nucleic acids	LD[DLA]	30	S[LW]LD[DE]EL[LM]	TRG_LysEnd_GGAAcLL_2		Pkinase	1.E-13	-1.4	protein kinase activity (1e-15)		0.006	10
yeast-285_GO-0012505	2	endomembrane system	L.L[LGV]	30	DALDL	14-3-3 binding motif in ExoS		Adaptin_N	1.E-04	-1.3	endomembrane system (1e-24)		0.006	10
yeast-593_GO-0031981	2	nuclear lumen	Q.K[QRA]	30	KR	CLV_PCSK_PC1ET2_1		Helicase_C	1.E-06	-1.2	nuclear lumen (1e-13)		0.006	10
yeast-376_GO-0019219	2	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism	Q..S[HGD]	30				zf-C2H2	1.E-09	-1.2	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism (1e-11)	Y	0.006	9
yeast-294_GO-0006366	2	transcription from RNA polymerase II promoter	N..[TGL]T	30				bZIP_1	1.E-03	-1.2	transcription from RNA polymerase II promoter (1e-15)		0.006	10
protein_40_YML010W	2	SPT5:  Protein that forms a complex with Spt4p and mediates both activation and inhibition of transcription elongation; Spt4p-Spt5p complex also plays a role in pre-mRNA processing	AR[NGT]	30	[AG]R	Protease matriptase protease site		DEAD	1.E-05	-1.2	nuclear lumen (1e-15)	Y	0.005	10
protein_40_YLR009W	2	RLP24:  Essential protein with similarity to Rpl24Ap and Rpl24Bp, associated with pre-60S ribosomal subunits and required for ribosomal large subunit biogenesis	K.K[VQD]	30	KRKQISVR	Phosphorylase kinase substrate motif		Brix	1.E-03	-1.2	cytoplasm organization and biogenesis (1e-27)		0.006	10
protein_40_YHR196W	2	UTP9:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	K[EDI]K	30	[KR][LIM]K[DE]K[LIM]PG	DEHYDRIN_2 PATTERN		WD40	1.E-03	-1.2	rRNA processing (1e-35)	Y	0.006	10
protein_40_YOR272W	2	YTM1:  Constituent of 66S pre-ribosomal particles, required for maturation of the large ribosomal subunit	E..K[LKY]	30				Brix	1.E-02	-1.1	cytoplasm organization and biogenesis (1e-29)		0.005	10
protein_40_YAR019C	2	CDC15:  Protein kinase of the Mitotic Exit Network that is localized to the spindle pole bodies at late anaphase; promotes mitotic exit by directly switching on the kinase activity of Dbf2p	[LCG]S..P[TRF]	30	S.IP	EB1		Pkinase	1.E-12	-1.1	protein amino acid phosphorylation (1e-13)	Y	0.006	9
matsuyama_nuclear_envelope_or_dots	2	matsuyama_nuclear_envelope_or_dots	E.[DNF]E	30	EEEEYFELV	EGFR kinase substrate motif		IBN_N	1.E-04	-1	nuclear envelope (1e-29)	Y	0.007	10
yeast-648_GO-0050791	2	regulation of physiological process	[FTK]T...K	30			Y	Zn_clus	1.E-03	-0.9	regulation of metabolism (1e-13)	Y	0.006	10
protein_40_YOR181W	2	LAS17:  Actin assembly factor, activates the Arp2/3 protein complex that nucleates branched actin filaments; localizes with the Arp2/3 complex to actin patches; homolog of the human Wiskott-Aldrich syndrome protein (WASP)	[FCE]A.[NMT]L	30				SH3_1	1.E-06	-0.9			0.005	9
protein_40_YOL133W	2	HRT1:  RING finger containing subunit of Skp1-Cullin-F-box ubiquitin protein ligases (SCF); required for Gic2p, Far1p, Sic1p and Cln2p degradation; may tether Cdc34p (a ubiquitin conjugating enzyme or E2) and Cdc53p (a cullin) subunits of SCF	S..[KRA]I	30				F-box	1.E-09	-0.9	ubiquitin ligase complex (1e-08)	Y	0.006	10
protein_40_YMR047C	2	NUP116:  Subunit of the nuclear pore complex (NPC) that is localized to both sides of the pore; contains a repetitive GLFG motif that interacts with mRNA export factor Mex67p and with karyopherin Kap95p; homologous to Nup100p	S[EYN]L	30	S[LW]LD[DE]EL[LM]	TRG_LysEnd_GGAAcLL_2		IBN_N	1.E-05	-0.9	nuclear pore (1e-37)		0.006	10
protein_40_YDR060W	2	MAK21:  Constituent of 66S pre-ribosomal particles, required for large (60S) ribosomal subunit biogenesis; involved in nuclear export of pre-ribosomes; required for maintenance of dsRNA virus; homolog of human CAATT-binding protein	T[GAY].G[KVD]	30	[SAG]GGTG[SA]G	TUBULIN PATTERN		Helicase_C	1.E-06	-0.9	cytoplasm organization and biogenesis (1e-08)		0.006	10
oshea_nucleolus	2	oshea_nucleolus	TG[SLG][GIA]K	30	[SAG]GGTG[SA]G	TUBULIN PATTERN		Helicase_C	1.E-09	-0.9	ribosome biogenesis (1e-13)		0.005	9
yeast-649_GO-0003676	2	nucleic acid binding	S..A[NDT]	30			Y	RRM_1	1.E-10	-0.8	nucleic acid binding (1e-20)		0.006	9
matsuyama_Cytosol	2	matsuyama_Cytosol	P..L[RNT]	30			Y	Pkinase	1.E-02	-0.8	ATP binding (1e-11)	Y	0.008	9
protein_40_YLR293C	2	GSP1:  GTP binding protein (mammalian Ranp homolog) involved in the maintenance of nuclear organization, RNA processing and transport; regulated by Prp20p, Rna1p, Yrb1p, Yrb2p, Yrp4p, Yrb30p, Cse1p and Kap95p; yeast Gsp2p homolog	K[SDE]..S[NQK]	30	S..S	Casien kinase I phosphorylation site, 1st Ser must be phosphorylated		IBN_N	1.E-07	-0.7	nuclear transport (1e-08)		0.006	10
yeast-304_GO-0019752	2	carboxylic acid metabolism	F..[APH]K	30				tRNA-synt_2b	1.E-02	-0.6	carboxylic acid metabolism (1e-98)	Y	0.006	10
protein_40_YOL133W	2	HRT1:  RING finger containing subunit of Skp1-Cullin-F-box ubiquitin protein ligases (SCF); required for Gic2p, Far1p, Sic1p and Cln2p degradation; may tether Cdc34p (a ubiquitin conjugating enzyme or E2) and Cdc53p (a cullin) subunits of SCF	[EQL]S..S[LDC]	30	S..S	Casien kinase I phosphorylation site, 1st Ser must be phosphorylated		F-box	1.E-04	-0.6	catabolism (1e-08)	Y	0.006	10
protein_40_YMR128W	2	ECM16:  Essential DEAH-box ATP-dependent RNA helicase specific to the U3 snoRNP, predominantly nucleolar in distribution, required for 18S rRNA synthesis	R.M[KRM]	30				WD40	1.E-05	-0.6	ribosome biogenesis (1e-16)	Y	0.006	10
protein_40_YLR129W	2	DIP2:  Nucleolar protein, specifically associated with the U3 snoRNA, part of the large ribonucleoprotein complex known as the small subunit (SSU) processome, required for 18S rRNA biogenesis, part of the active pre-rRNA processing complex	SD.[EVG][ENL]	30	SD.E	Casein kinase II substrate motif		WD40	1.E-06	-0.6	rRNA processing (1e-24)		0.006	10
protein_40_YFL037W	2	TUB2:  Beta-tubulin; associates with alpha-tubulin (Tub1p and Tub3p) to form tubulin dimer, which polymerizes to form microtubules	[KED]L.E[DIT]	30			Y	IBN_N	1.E-02	-0.6			0.006	10
yeast-304_GO-0006082	2	organic acid metabolism	F..[APH]K	30				tRNA-synt_2b	1.E-02	-0.5	carboxylic acid metabolism (1e-98)	Y	0.006	10
yeast-256_GO-0016462	2	pyrophosphatase activity	T..I[DPL]	30	T..I	FHA domain bind this ligand in Chk2		ABC_tran	1.E-08	-0.4	pyrophosphatase activity (1e-12)	Y	0.007	10
yeast-295_GO-0016192	2	vesicle-mediated transport	S[KYQ]L	30	S[LW]LD[DE]EL[LM]	TRG_LysEnd_GGAAcLL_2		Adaptin_N	1.E-09	-0.2	vesicle-mediated transport (1e-20)	Y	0.006	9
yeast-295_GO-0016192	2	vesicle-mediated transport	NS[ISV]	30	RRR[RN]SII[FD]	PKA kinase substrate motif		Adaptin_N	1.E-03	-0.2	vesicle-mediated transport (1e-20)		0.007	10
protein_40_YLR129W	2	DIP2:  Nucleolar protein, specifically associated with the U3 snoRNA, part of the large ribonucleoprotein complex known as the small subunit (SSU) processome, required for 18S rRNA biogenesis, part of the active pre-rRNA processing complex	K..K[LET]	30				WD40	1.E-05	-0.2	rRNA processing (1e-45)		0.006	9
yeast-462_GO-0019222	2	regulation of metabolism	E..R	30				Zn_clus	1.E-07	-0.1	regulation of cellular metabolism (10)	Y	0.006	10
protein_40_YDL014W	2	NOP1:  Nucleolar protein, component of the small subunit processome complex, which is required for processing of pre-18S rRNA; has similarity to mammalian fibrillarin	SE[SKQ]	30	KEESEK	14-3-3 gamma, epsilon nonphosphorylated binding motif in Ammodytoxin C, not confirmed	Y	Helicase_C	1.E-04	0	nucleolus (1e-43)		0.005	10
yeast-413_GO-0005215	2	transporter activity	V[KFL]T[RVY]	30	FTYP	Docking motif on c-Fos for Erk	Y	Mito_carr	1.E-09	0.1	transporter activity (1e-40)	Y	0.007	10
yeast-256_GO-0016462	2	pyrophosphatase activity	K.[LVI]A	30				Helicase_C	1.E-19	0.1	pyrophosphatase activity (1e-13)	Y	0.007	9
protein_40_YOL139C	2	CDC33:  Cytoplasmic mRNA cap binding protein; the eIF4E-cap complex is responsible for mediating cap-dependent mRNA translation via interactions with the translation initiation factor eIF4G (Tif4631p or Tif4632p)	R[KDA]..[TMA]K	30				Pkinase	1.E-02	0.1			0.006	8
protein_40_YKL101W	2	HSL1:  Nim1p-related protein kinase that regulates the morphogenesis and septin checkpoints; associates with the assembled septin filament; required along with Hsl7p for bud neck recruitment, phosphorylation, and degradation of Swe1p	E[NEA]A	30	KEN	LIG_APCC_KENbox_2		DnaJ_C	1.E-02	0.1		Y	0.006	10
protein_40_YDR449C	2	UTP6:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	VG.[RTH][VFD]	30				WD40	1.E-03	0.1	nucleolus (1e-13)		0.005	10
protein_40_YDR388W	2	RVS167:  Actin-associated protein, subunit of a complex (Rvs161p-Rvs167p) involved in regulation of actin cytoskeleton, endocytosis, and viability following starvation or osmotic stress; homolog of mammalian amphiphysin	I[PKA]P	30	YIPP	AT(1) receptor motif necessary for activation of Jak/Stat pathway		Pkinase	1.E-03	0.1	cell cortex (1e-06)	Y	0.005	7
yeast-628_GO-0043037	2	translation	GK[KRY]	30	G[KR][KR]	Amidation after cleavage after Gly (must be in secretory pathway)		HGTP_anticodon	1.E-03	0.2	translation (1e-14)		0.007	10
oshea_bud_neck	2	oshea_bud_neck	I..E[TKM]	30				RhoGAP	1.E-05	0.2	site of polarized growth (1e-41)	Y	0.006	9
protein_40_YJL010C	2	NOP9:  Essential component of pre-40S ribosomes that is required for early cleavages of 35S pre-rRNA and hence formation of 18S rRNA; binds RNA in vitro and contains multiple pumilio-like repeats	SA[LIF][QR]	30	[RK].PNS[AR].R	RIBOSOMAL_S12 PATTERN		WD40	1.E-02	0.3	nucleolus (1e-13)	Y	0.005	8
protein_40_YGR252W	2	GCN5:  Histone acetyltransferase, acetylates N-terminal lysines on histones H2B and H3; catalytic subunit of the ADA and SAGA histone acetyltransferase complexes; founding member of the Gcn5p-related N-acetyltransferase superfamily	AA[AHR]	30	[LIV]..[LM]L.AA.[FY][LI]	LIG_Sin3_1		Histone	1.E-02	0.4	SAGA complex (1e-15)		0.006	10
yeast-596_GO-0044425	2	membrane part	I[GLV]A	30				Adaptin_N	1.E-05	0.5	intrinsic to membrane (1e-83)	Y	0.006	9
yeast-256_GO-0016462	2	pyrophosphatase activity	E.[YDG]R	30	[AG]R	Protease matriptase protease site		Helicase_C	1.E-12	0.5	pyrophosphatase activity (1e-91)	Y	0.007	9
matsuyama_ER	2	matsuyama_ER	M.F	30	Y[GD][WH]M[DR]F	GASTRIN PATTERN		MFS_1	1.E-02	0.6	nuclear envelope-endoplasmic reticulum network (1e-23)	Y	0.007	10
oshea_bud_neck	2	oshea_bud_neck	[INP]E..L[VYH]	30				RhoGAP	1.E-02	0.7	bud (1e-20)		0.007	9
protein_40_YPL126W	2	NAN1:  U3 snoRNP protein, component of the small (ribosomal) subunit (SSU) processosome containing U3 snoRNA; required for the biogenesis of18S rRNA	[IHF]K.[WEF]D	30	[VILAFP]K.E	Motif recognized for modification by SUMO-1		WD40	1.E-05	0.8	snoRNA binding (1e-22)		0.006	10
protein_40_YJR002W	2	MPP10:  Component of the SSU processome, which is required for pre-18S rRNA processing, interacts with and controls the stability of Imp3p and Imp4p, essential for viability; similar to human Mpp10p	KK[LVD]	30	KKKLPATGDYMNMSPVGD	Insulin receptor kinase substrate motif		WD40	1.E-04	0.8	rRNA processing (1e-46)	Y	0.006	10
yeast-980_GO-0051179	2	localization	LY[RTG][GAK]	30	Y[AGSTDE]	Src kinase substrate motif		Mito_carr	1.E-13	0.9	cellular localization (1e-17)		0.006	10
protein_40_YPR103W	2	PRE2:  Beta 5 subunit of the 20S proteasome, responsible for the chymotryptic activity of the proteasome	[GHA]V..[LG]I	30				Proteasome	1.E-21	0.9	proteasome core complex (sensu Eukaryota) (1e-23)	Y	0.006	9
protein_40_YPL153C	2	RAD53:  Protein kinase, required for cell-cycle arrest in response to DNA damage; activated by trans autophosphorylation when interacting with hyperphosphorylated Rad9p; also interacts with ARS1 and plays a role in initiation of DNA replication	R..[GED]D	30	R..[PA]DG	LIG_TNKBM		Ank	1.E-02	1.1	cell cycle (0.01)	Y	0.006	9
protein_40_YMR308C	2	PSE1:  Karyopherin/importin that interacts with the nuclear pore complex; acts as the nuclear import receptor for specific proteins, including Pdr1p, Yap1p, Ste12p, and Aft1p	A[NVR]..A	30				Proteasome	1.E-02	1.1	proteasome core complex, alpha-subunit complex (sensu Eukaryota) (0.001)		0.006	10
protein_40_YMR047C	2	NUP116:  Subunit of the nuclear pore complex (NPC) that is localized to both sides of the pore; contains a repetitive GLFG motif that interacts with mRNA export factor Mex67p and with karyopherin Kap95p; homologous to Nup100p	I..[AVY]Q	30				IBN_N	1.E-06	1.1	nuclear transport (1e-18)		0.006	10
protein_40_YGL245W	2	GUS1:  Glutamyl-tRNA synthetase (GluRS), forms a complex with methionyl-tRNA synthetase (Mes1p) and Arc1p; complex formation increases the catalytic efficiency of both tRNA synthetases and ensures their correct localization to the cytoplasm	P[LPH]K	30	P..P.K	SH3 binding motif for Crk, general		Pkinase	1.E-10	1.2	protein kinase activity (1e-10)		0.006	10
protein_40_YMR047C	2	NUP116:  Subunit of the nuclear pore complex (NPC) that is localized to both sides of the pore; contains a repetitive GLFG motif that interacts with mRNA export factor Mex67p and with karyopherin Kap95p; homologous to Nup100p	L..V[AES]	30				IBN_N	1.E-07	1.3	nucleocytoplasmic transport (1e-28)	Y	0.006	10
protein_40_YLR074C	2	BUD20:  Protein involved in bud-site selection; diploid mutants display a random budding pattern instead of the wild-type bipolar pattern	S[IR].NSF	30	R..SFF	Phosphorylase kinase phosphorylation site (peptide screen)		Histone	1.E-02	1.3			0.004	8
protein_40_YER082C	2	UTP7:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	D[IVY][SDF]F	30				WD40	1.E-04	1.3	snoRNA binding (1e-13)		0.006	10
yeast-939_GO-0051234	2	establishment of localization	Q.[LQF]S	30				Adaptin_N	1.E-02	1.4	establishment of cellular localization (1e-11)	Y	0.006	9
protein_40_YMR047C	2	NUP116:  Subunit of the nuclear pore complex (NPC) that is localized to both sides of the pore; contains a repetitive GLFG motif that interacts with mRNA export factor Mex67p and with karyopherin Kap95p; homologous to Nup100p	L[VAD]..[TEP]L	30			Y	IBN_N	1.E-02	1.4	nuclear pore (1e-15)	Y	0.006	9
protein_40_YBR159W	2	IFA38: Microsomal beta-keto-reductase; contains oleate response element (ORE) sequence in the promoter region; mutants exhibit reduced VLCFA synthesis, accumulate high levels of dihydrosphingosine, phytosphingosine and medium-chain ceramides	G[GLF]F	30	E.IYG.F	cSrc kinase phosphorylation site		MFS_1	1.E-06	1.4	transporter activity (1e-11)	Y	0.006	9
yeast-358_GO-0044248	2	cellular catabolism	G.A[TAE]	30	[ED].D[ST]EG.A[LI]	Motif in sodium channel that binds ankIryn G		Proteasome	1.E-06	1.5	cellular catabolism (1e-12)		0.006	10
protein_40_YNL031C	2	HHT2:  One of two identical histone H3 proteins (see also HHT1); core histone required for chromatin assembly, involved in heterochromatin-mediated telomeric and HM silencing; regulated by acetylation, methylation, and mitotic phosphorylation	LQ.[AMW][IAK]	30				Histone	1.E-02	1.5	nuclear chromatin (1e-07)		0.006	10
yeast-1340_GO-0044267	2	cellular protein metabolism	[DCF]D..[FHM]G	30			Y	Ribosomal_60s	1.E-07	1.6	protein modification (1e-15)		0.006	9
protein_40_YOL133W	2	HRT1:  RING finger containing subunit of Skp1-Cullin-F-box ubiquitin protein ligases (SCF); required for Gic2p, Far1p, Sic1p and Cln2p degradation; may tether Cdc34p (a ubiquitin conjugating enzyme or E2) and Cdc53p (a cullin) subunits of SCF	[KSR]L..[KFV]N	30				F-box	1.E-02	1.6	protein catabolism (0.001)		0.006	9
protein_40_YCL059C	2	KRR1:  Essential nucleolar protein required for the synthesis of 18S rRNA and for the assembly of 40S ribosomal subunit	G.K[VKG]	30				Helicase_C	1.E-02	1.6	cytoplasm organization and biogenesis (1e-25)		0.006	10
matsuyama_Cytosol	2	matsuyama_Cytosol	[GTS][LSF]FD	30	LFDLM	Binding motif in Clint for clathrin TD domain	Y	Ribosomal_60s	1.E-07	1.6	translational elongation (1e-06)		0.008	10
protein_40_YKL021C	2	MAK11:  Protein involved in an early, nucleolar step of 60S ribosomal subunit biogenesis; essential for cell growth and replication of killer M1 dsRNA virus; contains four beta-transducin repeats	KT[LNE][ARM]	30	[RDH][LY][LM][KA]T[QLMEV][KLIR]	FHA domain binding motif		DEAD	1.E-04	1.7	ribosome biogenesis (1e-11)		0.005	8
matsuyama_Microtubule	2	matsuyama_Microtubule	[NRV]KS[LFR]	30				Kinesin	1.E-03	1.7	microtubule cytoskeleton (1e-27)		0.008	9
yeast-238_GO-0017111	2	nucleoside-triphosphatase activity	E[TQD].[KMV]R	30	[KR]R	CLV_PCSK_KEX2_1		ABC_tran	1.E-03	1.8	nucleoside-triphosphatase activity (1e-35)	Y	0.007	10
yeast-413_GO-0005215	2	transporter activity	Y.G[VLW]	30	E.Y.[QSG]	Protease TEV		Mito_carr	1.E-27	1.9	transporter activity (1e-88)	Y	0.006	10
protein_40_YDL153C	2	SAS10:  Component of the small (ribosomal) subunit (SSU) processosome required for pre-18S rRNa processing; essential nucleolar protein that, when overproduced, disrupts silencing	EN[ICV][LIV]	30	YEN[FIV]	SH2 ligand for Tns (Tyr must be phosphorylated)		Pkinase	1.E-14	2.1	protein kinase activity (1e-12)		0.006	8
matsuyama_Cytosol	2	matsuyama_Cytosol	H..[VFE]V	30				Pkinase	1.E-02	2.1	kinase activity (1e-05)	Y	0.007	9
protein_40_YMR047C	2	NUP116:  Subunit of the nuclear pore complex (NPC) that is localized to both sides of the pore; contains a repetitive GLFG motif that interacts with mRNA export factor Mex67p and with karyopherin Kap95p; homologous to Nup100p	F.[SAT]Q	30	[ST]Q	ATM kinase phosphorylation site		IBN_N	1.E-08	2.2	protein import into nucleus (1e-30)		0.006	10
yeast-324_GO-0030528	2	transcription regulator activity	M..[EAD]E	30	M..E	Motif for targeting Arf1 to Golgi		Zn_clus	1.E-02	2.3	transcription regulator activity (1e-91)		0.007	10
yeast-207_GO-0006974	2	response to DNA damage stimulus	[IQA]ID	30	RRR[RN]SII[FD]	PKA kinase substrate motif		BRCT	1.E-02	2.3	response to DNA damage stimulus (1e-11)	Y	0.007	10
protein_40_YIL019W	2	FAF1:  Protein required for pre-rRNA processing and 40S ribosomal subunit assembly	A[TKV]..[YHA]D	30			Y	WD40	1.E-04	2.4	small nucleolar ribonucleoprotein complex (1e-17)	Y	0.005	8
yeast-1547_GO-0043283	2	biopolymer metabolism	PG[TWR][GEF]	30				AAA	1.E-02	2.5	DNA metabolism (1e-09)		0.006	9
yeast-513_GO-0005515	2	protein binding	E..L[RKA]	30				IBN_N	1.E-04	2.6	protein binding (1e-25)	Y	0.006	10
protein_40_YKR081C	2	RPF2:  Essential protein involved in the processing of pre-rRNA and the assembly of the 60S ribosomal subunit; interacts with ribosomal protein L11; localizes predominantly to the nucleolus; constituent of 66S pre-ribosomal particles	R[EKQ][LIE]A	30	MR[DE][IL]	TUBULIN_B_AUTOREG PATTERN		DEAD	1.E-05	2.8	nucleolus (1e-15)		0.006	10
protein_40_YGR128C	2	UTP8:  Nucleolar protein required for export of tRNAs from the nucleus; also copurifies with the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	VK[ILH][WIR]	30				WD40	1.E-06	2.8	snoRNA binding (1e-12)	Y	0.005	10
yeast-217_GO-0007046	2	ribosome biogenesis	A[LDI][DRI]L	30	DALDL	14-3-3 binding motif in ExoS		DEAD	1.E-06	3	ribosome biogenesis (1e-62)		0.006	8
protein_40_YHR030C	2	SLT2:  Serine/threonine MAP kinase involved in regulating the maintenance of cell wall integrity and progression through the cell cycle; regulated by the PKC1-mediated signaling pathway	E[YRP]..G[GRS]	30	G[FL]PGER..G	LIG_IBS_1		Pkinase	1.E-03	3.2	kinase activity (0.001)		0.005	8
yeast-685_GO-0016740	2	transferase activity	[FYG]G[KYT]V	30	FRGGT	Phosphoinositide binding motif in ATG18 and ATG21		Pkinase	1.E-10	3.3	transferase activity, transferring phosphorus-containing groups (1e-21)	Y	0.007	10
protein_40_YBL007C	2	SLA1:  Cytoskeletal protein binding protein required for assembly of the cortical actin cytoskeleton; interacts with proteins regulating actin dynamics and proteins required for endocytosis; found in the nucleus and cell cortex; has 3 SH3 domains	DFG[LIM]	30				Pkinase	1.E-10	3.3	protein kinase activity (1e-10)		0.004	8
yeast-706_GO-0043412	2	biopolymer modification	Y[RMC][AKH]P	30				Pkinase	1.E-14	3.4	protein modification (1e-19)		0.007	10
protein_40_YOR272W	2	YTM1:  Constituent of 66S pre-ribosomal particles, required for maturation of the large ribosomal subunit	A[TH].GRF	30	[AG]R	Protease matriptase protease site	Y	DEAD	1.E-04	3.4	ATP-dependent RNA helicase activity (0.001)		0.004	8
protein_40_YKL166C	2	TPK3:  cAMP-dependent protein kinase catalytic subunit; promotes vegetative growth in response to nutrients via the Ras-cAMP signaling pathway; inhibited by regulatory subunit Bcy1p in the absence of cAMP; partially redundant with Tpk1p and Tpk2p	R[DFW].K[PIC]	30			Y	Pkinase	1.E-10	3.6	protein kinase activity (1e-10)		0.006	10
yeast-565_GO-0006464	2	protein modification	[MRT]AP[EM]	30	P[TS]AP	LIG_PTAP		Pkinase	1.E-22	4	protein amino acid phosphorylation (1e-26)		0.007	10
yeast-335_GO-0016772	2	transferase activity, transferring phosphorus-containing groups	EL[LDF]	30	S[LW]LD[DE]EL[LM]	TRG_LysEnd_GGAAcLL_2		Pkinase	1.E-51	4.7	transferase activity, transferring phosphorus-containing groups (1e-18)	Y	0.007	9
yeast-942_GO-0043228	2	non-membrane-bound organelle	[TND]GS[GTQ]K	30	S[ST]	MDC1 BRCT domain binding motif	Y	DEAD	1.E-14	5.1	RNA helicase activity (1e-17)		0.007	10
yeast-942_GO-0043232	2	intracellular non-membrane-bound organelle	[TND]GS[GTQ]K	30	S[ST]	MDC1 BRCT domain binding motif	Y	DEAD	1.E-14	5.2	RNA helicase activity (1e-17)		0.007	10
yeast-1389_GO-0044260	2	cellular macromolecule metabolism	K[PTQ].N[ILK]L	30				Pkinase	1.E-33	5.6	protein amino acid phosphorylation (1e-43)		0.007	10
yeast-1340_GO-0044267	2	cellular protein metabolism	KP.N[ILF][LMD]	30				Pkinase	1.E-43	5.7	protein amino acid phosphorylation (1e-49)		0.006	9
yeast-324_GO-0030528	2	transcription regulator activity	FSR[SIH][DYN]	30	RR.SR	SRPK2 kinase phosphorylation site (peptide screen)		zf-C2H2	1.E-14	6.4	transcription regulator activity (1e-11)		0.006	9
yeast-324_GO-0030528	2	transcription regulator activity	L.[RQT]H	30			Y	zf-C2H2	1.E-33	9.5	transcription regulator activity (1e-09)		0.006	9
yeast-1974_GO-0005634	2	nucleus	C.[NIY]C	30	C..C	Motif on TIM mitochondrial translocation proteins		Zn_clus	1.E-12	16.4	transcription (1e-16)		0.006	9
yeast-939_GO-0051234	2	establishment of localization	TG.[VLA][EMS]	30	TGY	ERK6/SAPK3 activation sites for HOG/p38 activation	Y				cellular localization (1e-18)		0.007	10
yeast-856_GO-0009059	2	macromolecule biosynthesis	D[KDS]N	30	Y.D.NHKPE	PMI_I_1 PATTERN							0.006	10
yeast-856_GO-0009059	2	macromolecule biosynthesis	S[PNL]T	30	PTL	Motif in Fos for proteosome degredation							0.006	10
yeast-752_GO-0016787	2	hydrolase activity	S[NYF]A[VKI]	30							hydrolase activity, acting on ester bonds (1e-11)	Y	0.006	9
yeast-596_GO-0044425	2	membrane part	IG..[GWF][DAI]	30							integral to membrane (1e-12)	Y	0.007	9
yeast-589_GO-0050896	2	response to stimulus	D.[LRM]G	30	D..G	motif that binds phosphate in GDP and GTP binding proteins					response to stress (1e-90)		0.006	10
yeast-513_GO-0005515	2	protein binding	[RAT]I..F[FKT]	30							protein binding (1e-44)		0.006	9
yeast-513_GO-0005515	2	protein binding	PP.[PMD][PGQ]A	30	PPR	LIG_WW_3					protein binding (1e-11)		0.006	8
yeast-504_GO-0006350	2	transcription	A[QVS]..A[QGP]A	30							transcription (1e-14)		0.007	9
yeast-470_GO-0006259	2	DNA metabolism	Q[EDF][NGW]KK	30							DNA metabolism (1e-08)	Y	0.006	9
yeast-457_GO-0007001	2	chromosome organization and biogenesis (sensu Eukaryota)	L[LTK]..[QHM]Q	30							chromosome organization and biogenesis (sensu Eukaryota) (1e-45)		0.006	10
yeast-424_GO-0006950	2	response to stress	[PLD]E.P[KMG]	30							response to stress (1e-38)		0.007	10
yeast-413_GO-0005215	2	transporter activity	N..K[NRK]	30	KR	CLV_PCSK_PC1ET2_1							0.006	10
yeast-388_GO-0007275	2	development	K[KTM].[TQG]G	30			Y				multicellular organismal development (1e-44)		0.007	9
yeast-376_GO-0019219	2	regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism	KL.N[AHM][TLH]	30							regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolism (1e-12)		0.007	9
yeast-371_GO-0009056	2	catabolism	[AGF]A..G[FYE]	30							catabolism (1e-36)		0.006	10
yeast-358_GO-0044248	2	cellular catabolism	[LVC]E.[SQV]G	30							cellular catabolism (1e-41)		0.006	9
yeast-345_GO-0006396	2	RNA processing	KN..[LSD]I[GMY]	30	IY	cFGR and Csk kinase phosphorylation site (peptide screen)					RNA processing (1e-11)		0.006	10
yeast-284_GO-0005740	2	mitochondrial envelope	L[LFQ]Q	30	DLL	Binding motif for clathrin heavy chain ear							0.006	10
yeast-267_GO-0000003	2	reproduction	[LNT][LIT].VN	30	YVNI	SH2 ligand for Grb2					reproduction (1e-53)		0.007	10
yeast-262_GO-0031224	2	intrinsic to membrane	I[FYN]F	30	D..SII.FF	CK I delta kinase phosphorylation site (peptide screen)	Y				intrinsic to membrane (1e-96)		0.006	9
yeast-244_GO-0000279	2	M phase	[LAS]I[RMF]E	30	IYE	cFPS/FES kinase phosphorylation site (peptide screen)					M phase (1e-48)	Y	0.007	9
yeast-244_GO-0000279	2	M phase	[QT]D.L[VFH]	30	DLL	Binding motif for clathrin heavy chain ear					M phase (1e-32)		0.007	10
yeast-244_GO-0000279	2	M phase	T[LCM]Q[FGM]	30							M phase (1e-25)		0.007	10
yeast-238_GO-0017111	2	nucleoside-triphosphatase activity	[GAQ]TL[TGR]	30	PTL	Motif in Fos for proteosome degredation					nucleoside-triphosphatase activity (1e-45)	Y	0.007	10
yeast-217_GO-0007046	2	ribosome biogenesis	[EKQ]D.L[LFD]T	30	DLL	Binding motif for clathrin heavy chain ear					ribosome biogenesis (1e-12)		0.006	8
yeast-215_GO-0007010	2	cytoskeleton organization and biogenesis	[INY]..LR	30	Y..L	Motif for down regulation of the CD46 receptor					cytoskeleton organization and biogenesis (1e-11)	Y	0.006	10
yeast-213_GO-0009719	2	response to endogenous stimulus	[NYM]Q.[ESQ]A	30							response to endogenous stimulus (1e-25)		0.007	10
yeast-212_GO-0045045	2	secretory pathway	[ESC]N.IK[SLD]	30							secretory pathway (1e-12)	Y	0.005	9
yeast-207_GO-0006974	2	response to DNA damage stimulus	[LEA]D.[DRN]L	30	D..LL	Di-Leu motif for receptor endocytosis (recognized by VHS domain of GGA proteins)					response to DNA damage stimulus (1e-57)	Y	0.006	9
yeast-203_GO-0005975	2	carbohydrate metabolism	F..D[TYG]	30							carbohydrate metabolism (1e-87)		0.006	10
yeast-201_GO-0050876	2	reproductive physiological process	VN..[RVA][NLT]	30							reproductive physiological process (1e-42)		0.007	10
yeast-201_GO-0048610	2	reproductive cellular physiological process	VN..[RVA][NLT]	30							reproductive physiological process (1e-42)		0.007	10
protein_40_YPR144C	2	NOC4:  Nucleolar protein, forms a complex with Nop14p that mediates maturation and nuclear export of 40S ribosomal subunits	RG..[SK]K[IY]	30	RGD	LIG_RGD							0.004	7
protein_40_YPR120C	2	CLB5:  B-type cyclin involved in DNA replication during S phase; activates Cdc28p to promote initiation of DNA synthesis; functions in formation of mitotic spindles along with Clb3p and Clb4p; most abundant during late G1 phase	K.[NQA]S	30								Y	0.005	10
protein_40_YPR110C	2	RPC40:  RNA polymerase subunit, common to RNA polymerase I and III	T[PQW][QVE]E	30	[PSAT].[QE]E	LIG_TRAF2_1					RNA polymerase complex (1e-07)		0.006	10
protein_40_YPR010C	2	RPA135:  RNA polymerase I subunit A135	RA.[FE]E[EL]	30									0.004	8
protein_40_YPL240C	2	HSP82:  Hsp90 chaperone required for pheromone signaling and negative regulation of Hsf1p; docks with Tom70p for mitochondrial preprotein delivery; promotes telomerase DNA binding and nucleotide addition; interacts with Cns1p, Cpr6p, Cpr7p, Sti1p	N..[KIP]V	30									0.005	10
protein_40_YPL240C	2	HSP82:  Hsp90 chaperone required for pheromone signaling and negative regulation of Hsf1p; docks with Tom70p for mitochondrial preprotein delivery; promotes telomerase DNA binding and nucleotide addition; interacts with Cns1p, Cpr6p, Cpr7p, Sti1p	N..[NEI]T	30									0.005	10
protein_40_YPL240C	2	HSP82:  Hsp90 chaperone required for pheromone signaling and negative regulation of Hsf1p; docks with Tom70p for mitochondrial preprotein delivery; promotes telomerase DNA binding and nucleotide addition; interacts with Cns1p, Cpr6p, Cpr7p, Sti1p	S.V[LNG]	30	KKKLPATGDYMNMSPVGD	Insulin receptor kinase substrate motif	Y						0.006	10
protein_40_YPL213W	2	LEA1:  Component of U2 snRNP; disruption causes reduced U2 snRNP levels; physically interacts with Msl1p; invovled in telomere maintenance; putative homolog of human U2A' snRNP protein	[FRM][SHQ]..ED	30	EED	Ankyrin B C-terminal motif that binds internal Ankyrin repeats					nuclear mRNA splicing, via spliceosome (1e-19)		0.005	9
protein_40_YPL153C	2	RAD53:  Protein kinase, required for cell-cycle arrest in response to DNA damage; activated by trans autophosphorylation when interacting with hyperphosphorylated Rad9p; also interacts with ARS1 and plays a role in initiation of DNA replication	K..[ILMV]T	30			Y					Y	0.006	10
protein_40_YPL146C	2	NOP53:  Nucleolar protein; involved in biogenesis of the 60S subunit of the ribosome; interacts with rRNA processing factors Cbf5p and Nop2p; null mutant is viable but growth is severely impaired	D[RTE]..[EGM]E	30								Y	0.006	10
protein_40_YPL129W	2	TAF14:  Subunit of TFIID, TFIIF, INO80, SWI/SNF, and NuA3 complexes, involved in RNA polymerase II transcription initiation and in chromatin modification; contains a YEATS domain	ED.[EV][NVG]	30	SEDEE	CKII kinase phosphorylation site (peptide screen)					nucleoplasm part (1e-14)		0.006	10
protein_40_YPL042C	2	SSN3:  Cyclin-dependent protein kinase, component of RNA polymerase II holoenzyme; involved in phosphorylation of the RNA polymerase II C-terminal domain; involved in glucose repression	[KLM]N.S[SAT]	30	S[ST]	MDC1 BRCT domain binding motif	Y				transcription regulator activity (1e-11)		0.006	10
protein_40_YPL004C	2	LSP1:  Primary component of eisosomes, which are large immobile patch structures at the cell cortex associated with endocytosis, along with Pil1p and Sur7p; null mutants show activation of Pkc1p/Ypk1p stress resistance pathways	[RTK]AE[ANC]	30									0.005	9
protein_40_YPL004C	2	LSP1:  Primary component of eisosomes, which are large immobile patch structures at the cell cortex associated with endocytosis, along with Pil1p and Sur7p; null mutants show activation of Pkc1p/Ypk1p stress resistance pathways	Y[PNR]..[PYA]S	30								Y	0.005	8
protein_40_YOR326W	2	MYO2:  One of two type V myosin motors (along with MYO4) involved in actin-based transport of cargos; required for the polarized delivery of secretory vesicles, the vacuole, late Golgi elements, peroxisomes, and the mitotic spindle	EL[LAH][TQV]	30									0.006	10
protein_40_YOR326W	2	MYO2:  One of two type V myosin motors (along with MYO4) involved in actin-based transport of cargos; required for the polarized delivery of secretory vesicles, the vacuole, late Golgi elements, peroxisomes, and the mitotic spindle	K[PYC].E[PRL]	30								Y	0.005	10
protein_40_YOR312C	2	RPL20B:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl20Ap and has similarity to rat L18a ribosomal protein	R..[RAY]A	30							cytosolic ribosome (sensu Eukaryota) (1e-28)	Y	0.006	10
protein_40_YOR294W	2	RRS1:  Essential protein that binds ribosomal protein L11 and is required for nuclear export of the 60S pre-ribosomal subunit during ribosome biogenesis; mouse homolog shows altered expression in Huntington's disease model mice	[DLS]E..D[KQC]	30	[ST]E	G protein-coupled receptor kinase 1 substrate motif					ribosome biogenesis (1e-07)	Y	0.006	10
protein_40_YOR294W	2	RRS1:  Essential protein that binds ribosomal protein L11 and is required for nuclear export of the 60S pre-ribosomal subunit during ribosome biogenesis; mouse homolog shows altered expression in Huntington's disease model mice	EE[ELD]	30	EE[DE]IYFFFF	CSK kinase substrate motif					nucleolus (1e-14)		0.006	10
protein_40_YOR206W	2	NOC2:  Protein that forms a nucleolar complex with Mak21p that binds to 90S and 66S pre-ribosomes, as well as a nuclear complex with Noc3p that binds to 66S pre-ribosomes; both complexes mediate intranuclear transport of ribosomal precursors	[AGF]T.[KVG]K	30	[KG][AG][TID].[PVLS]K.[KR][HY]	PI(4,5)P2 binding motif					cytoplasm organization and biogenesis (1e-08)		0.006	10
protein_40_YOR174W	2	MED4:  Subunit of the RNA polymerase II mediator complex; associates with core polymerase subunits to form the RNA polymerase II holoenzyme; essential for transcriptional regulation	[NEV]S[TGM]N	30	S[ST]	MDC1 BRCT domain binding motif					RNA polymerase II transcription mediator activity (1e-12)		0.006	10
protein_40_YOR174W	2	MED4:  Subunit of the RNA polymerase II mediator complex; associates with core polymerase subunits to form the RNA polymerase II holoenzyme; essential for transcriptional regulation	[QDP]Q..[QYA]N	30							general RNA polymerase II transcription factor activity (1e-15)		0.005	9
protein_40_YOR133W	2	EFT1:  Elongation factor 2 (EF-2), also encoded by EFT2; catalyzes ribosomal translocation during protein synthesis; contains diphthamide, the unique posttranslationally modified histidine residue specifically ADP-ribosylated by diphtheria toxin	AA[LGW]	30	[LIV]..[LM]L.AA.[FY][LI]	LIG_Sin3_1					translation elongation factor activity (0.001)		0.006	10
protein_40_YOL127W	2	RPL25:  Primary rRNA-binding ribosomal protein component of the large (60S) ribosomal subunit, has similarity to E. coli L23 and rat L23a ribosomal proteins; binds to 26S rRNA via a conserved C-terminal motif	S..[LFY]L	30	S..F	LIG_BRCT_BRCA1_1							0.005	10
protein_40_YOL004W	2	SIN3:  Component of the Sin3p-Rpd3p histone deacetylase complex, involved in transcriptional repression and activation of diverse processes, including mating-type switching and meiosis; involved in the maintenance of chromosomal integrity	[GVK]S..[AM]R	30	[AG]R	Protease matriptase protease site					transcription (0.01)		0.004	7
protein_40_YNR054C	2	ESF2:  Essential nucleolar protein involved in pre-18S rRNA processing; component of the small subunit (SSU) processome; has sequence similarity to mABT1, a mouse transcription activator	[KFQ]I.[RNK]V	30			Y				nucleolus (1e-11)		0.005	10
protein_40_YNL289W	2	PCL1:  Pho85 cyclin of the Pcl1,2-like subfamily, involved in entry into the mitotic cell cycle and regulation of morphogenesis, localizes to sites of polarized cell growth	[DES]FN[NIT]	30									0.006	8
protein_40_YNL289W	2	PCL1:  Pho85 cyclin of the Pcl1,2-like subfamily, involved in entry into the mitotic cell cycle and regulation of morphogenesis, localizes to sites of polarized cell growth	D.D[TFI]	30	D.D	Ribose moiety of UDP and manganese binding site in glucuronyl transferase						Y	0.005	9
protein_40_YNL289W	2	PCL1:  Pho85 cyclin of the Pcl1,2-like subfamily, involved in entry into the mitotic cell cycle and regulation of morphogenesis, localizes to sites of polarized cell growth	ET..[FMW][GPI]	30									0.006	9
protein_40_YNL154C	2	YCK2:  Palmitoylated, plasma membrane-bound casein kinase I isoform; shares redundant functions with Yck1p in morphogenesis, proper septin assembly, endocytic trafficking; provides an essential function overlapping with that of Yck1p	E..[VTE]P	30								Y	0.006	10
protein_40_YNL154C	2	YCK2:  Palmitoylated, plasma membrane-bound casein kinase I isoform; shares redundant functions with Yck1p in morphogenesis, proper septin assembly, endocytic trafficking; provides an essential function overlapping with that of Yck1p	L.K[TED]	30	G[SA]LNK	GDP-mannose binding motif in transporter						Y	0.005	10
protein_40_YNL118C	2	DCP2:  Catalytic subunit of the Dcp1p-Dcp2p decapping enzyme complex, which removes the 5' cap structure from mRNAs prior to their degradation; member of the Nudix hydrolase family	[KDI]I.K[TFA]	30									0.006	10
protein_40_YNL055C	2	POR1:  Mitochondrial porin (voltage-dependent anion channel), outer membrane protein required for the maintenance of mitochondrial osmotic stability and mitochondrial membrane permeability; phosphorylated	T[SMQ].D[GH]	30	S.D	CAMKII phosphorylation site							0.004	7
protein_40_YMR186W	2	HSC82:  Cytoplasmic chaperone of the Hsp90 family, redundant in function and nearly identical with Hsp82p, and together they are essential; expressed constitutively at 10-fold higher basal levels than HSP82 and induced 2-3 fold by heat shock	GV[ELI]	30	E.IYGVLF	Lck kinase substrate motif	Y						0.006	10
protein_40_YMR116C	2	ASC1:  G-protein beta subunit and guanine nucleotide dissociation inhibitor for Gpa2p; ortholog of RACK1 that inhibits translation; core component of the small (40S) ribosomal subunit; represses Gcn4p in the absence of amino acid starvation	[VGR]E.[AIV]G	30									0.005	9
protein_40_YMR047C	2	NUP116:  Subunit of the nuclear pore complex (NPC) that is localized to both sides of the pore; contains a repetitive GLFG motif that interacts with mRNA export factor Mex67p and with karyopherin Kap95p; homologous to Nup100p	T[ALT].T[KFQ]	30							protein import into nucleus (1e-13)	Y	0.006	9
protein_40_YMR012W	2	CLU1:  eIF3 component of unknown function; deletion causes defects in mitochondrial organization but not in growth or translation initiation, can rescue cytokinesis and mitochondrial organization defects of the Dictyostelium cluA- mutant	GK..[LGM][ELM]	30									0.006	9
protein_40_YMR001C	2	CDC5:  Polo-like kinase with similarity to Xenopus Plx1 and S. pombe Plo1p; found at bud neck, nucleus and SPBs; has multiple functions in mitosis and cytokinesis through phosphorylation of substrates; may be a Cdc28p substrate	[TLD]D..[NID]S	30							cohesin complex (1e-05)		0.006	10
protein_40_YMR001C	2	CDC5:  Polo-like kinase with similarity to Xenopus Plx1 and S. pombe Plo1p; found at bud neck, nucleus and SPBs; has multiple functions in mitosis and cytokinesis through phosphorylation of substrates; may be a Cdc28p substrate	T..N[LEG]	30							mitosis (1e-04)		0.006	10
protein_40_YML010W	2	SPT5:  Protein that forms a complex with Spt4p and mediates both activation and inhibition of transcription elongation; Spt4p-Spt5p complex also plays a role in pre-mRNA processing	E..N[AIK]	30							nuclear lumen (1e-15)		0.005	7
protein_40_YML010W	2	SPT5:  Protein that forms a complex with Spt4p and mediates both activation and inhibition of transcription elongation; Spt4p-Spt5p complex also plays a role in pre-mRNA processing	V[IKY][NQD]L	30							nuclear lumen (1e-12)	Y	0.006	9
protein_40_YLR429W	2	CRN1:  Coronin, cortical actin cytoskeletal component that associates with the Arp2p/Arp3p complex to regulate its activity; plays a role in regulation of actin patch assembly	V..K[EGI]	30							cortical cytoskeleton (0.01)		0.006	9
protein_40_YLR423C	2	ATG17:  Scaffold potein responsible for pre-autophagosomal structure organization; interacts with and is required for activation of Apg1p protein kinase; involved in autophagy but not in the Cvt (cytoplasm to vacuole targeting) pathway	[LHQ]E.[KC]R	30	KR	CLV_PCSK_PC1ET2_1							0.005	8
protein_40_YLR276C	2	DBP9:  ATP-dependent RNA helicase of the DEAD-box family involved in biogenesis of the 60S ribosomal subunit	R[EKQ][LEV]A	30							cytoplasm organization and biogenesis (1e-11)		0.006	8
protein_40_YLR180W	2	SAM1:  S-adenosylmethionine synthetase, catalyzes transfer of the adenosyl group of ATP to the sulfur atom of methionine; one of two differentially regulated isozymes (Sam1p and Sam2p)	[TMQ]G[FNR]K	30	G[KR][KR]	Amidation after cleavage after Gly (must be in secretory pathway)							0.005	9
protein_40_YLR180W	2	SAM1:  S-adenosylmethionine synthetase, catalyzes transfer of the adenosyl group of ATP to the sulfur atom of methionine; one of two differentially regulated isozymes (Sam1p and Sam2p)	Y[EPF]A	30									0.006	10
protein_40_YJR145C	2	RPS4A:  Protein component of the small (40S) ribosomal subunit; mutation affects 20S pre-rRNA processing; identical to Rps4Bp and has similarity to rat S4 ribosomal protein	E..[AG]E	30							ribonucleoprotein complex (1e-13)	Y	0.006	10
protein_40_YJL177W	2	RPL17B:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl17Ap and has similarity to E. coli L22 and rat L17 ribosomal proteins	K[GVA].K[VAY]	30							cytosolic ribosome (sensu Eukaryota) (1e-28)	Y	0.006	10
protein_40_YJL164C	2	TPK1:  cAMP-dependent protein kinase catalytic subunit; promotes vegetative growth in response to nutrients via the Ras-cAMP signaling pathway; inhibited by regulatory subunit Bcy1p in the absence of cAMP; partially redundant with Tpk2p and Tpk3p	S[DKS]Q	30	[ST]Q	ATM kinase phosphorylation site							0.005	9
protein_40_YJL117W	2	PHO86:  Endoplasmic reticulum (ER) resident protein required for ER exit of the high-affinity phosphate transporter Pho84p, specifically required for packaging of Pho84p into COPII vesicles	II.[TIQ][IVH]	30									0.006	10
protein_40_YJL106W	2	IME2:  Serine/threonine protein kinase involved in activation of meiosis, associates with Ime1p and mediates its stability, activates Ndt80p; IME2 expression is positively regulated by Ime1p	[GHS][SVP].SE	30	[ST]E	G protein-coupled receptor kinase 1 substrate motif							0.006	10
protein_40_YJL106W	2	IME2:  Serine/threonine protein kinase involved in activation of meiosis, associates with Ime1p and mediates its stability, activates Ndt80p; IME2 expression is positively regulated by Ime1p	[KFR][SNG].KKN	30			Y						0.004	7
protein_40_YJL095W	2	BCK1:  Mitogen-activated protein (MAP) kinase kinase kinase acting in the protein kinase C signaling pathway, which controls cell integrity; upon activation by Pkc1p phosphorylates downstream kinases Mkk1p and Mkk2p	[TMS][EDG]..AS	30									0.006	10
protein_40_YJL092W	2	SRS2:  DNA helicase and DNA-dependent ATPase involved in DNA repair, needed for proper timing of commitment to meiotic recombination and transition from Meiosis I to II; affects genome stability by suppressing unscheduled homologous recombination	K[ALT]L	30	K[AI][CL]SGK[FI].[PQ]	UBIQUITIN_ACTIVAT_1 PATTERN					response to DNA damage stimulus (1e-05)	Y	0.005	10
protein_40_YJL092W	2	SRS2:  DNA helicase and DNA-dependent ATPase involved in DNA repair, needed for proper timing of commitment to meiotic recombination and transition from Meiosis I to II; affects genome stability by suppressing unscheduled homologous recombination	LK.[SQC]	30									0.005	10
protein_40_YJL074C	2	SMC3:  Subunit of the multiprotein cohesin complex required for sister chromatid cohesion in mitotic cells; also required, with Rec8p, for cohesion and recombination during meiosis; phylogenetically conserved SMC chromosomal ATPase family member	AI.[DFR][GVI]	30	EDAIY	Abl kinase substrate motif					cohesin complex (0.001)		0.006	10
protein_40_YIL133C	2	RPL16A:  N-terminally acetylated protein component of the large (60S) ribosomal subunit, binds to 5.8 S rRNA; has similarity to Rpl16Bp, E. coli L13 and rat L13a ribosomal proteins; transcriptionally regulated by Rap1p	A.[GKA]K	30	VPGKARKKSSCQLL	Calmodulin-dependent protein kinase IV substrate motif					cytosolic ribosome (sensu Eukaryota) (1e-29)	Y	0.006	10
protein_40_YIL094C	2	LYS12:  Homo-isocitrate dehydrogenase, an NAD-linked mitochondrial enzyme required for the fourth step in the biosynthesis of lysine, in which homo-isocitrate is oxidatively decarboxylated to alpha-ketoadipate	[LIE]E.[GVL]T	30								Y	0.006	10
protein_40_YIL094C	2	LYS12:  Homo-isocitrate dehydrogenase, an NAD-linked mitochondrial enzyme required for the fourth step in the biosynthesis of lysine, in which homo-isocitrate is oxidatively decarboxylated to alpha-ketoadipate	V[DGN].[AET]L	30								Y	0.006	10
protein_40_YIL075C	2	RPN2:  Subunit of the 26S proteasome, substrate of the N-acetyltransferase Nat1p	[FTD][LQW]IE	30							proteasome complex (sensu Eukaryota) (1e-10)		0.006	10
protein_40_YIL035C	2	CKA1:  Alpha catalytic subunit of casein kinase 2, a Ser/Thr protein kinase with roles in cell growth and proliferation; the holoenzyme also contains CKA2, CKB1 and CKB2, the many substrates include transcription factors and all RNA polymerases	E[TGQ]S[DIR]	30							RNA polymerase II transcription elongation factor activity (1e-08)		0.006	9
protein_40_YHR197W	2	RIX1:  Essential component of the Rix1 complex (Rix1p, Ipi1p, Ipi3p) that is required for processing of ITS2 sequences from 35S pre-rRNA; Rix1 complex associates with Mdn1p in pre-60S ribosomal particles	KR..[VEF][EKG]	30	KR	CLV_PCSK_PC1ET2_1					cytoplasm organization and biogenesis (1e-16)		0.006	10
protein_40_YHR196W	2	UTP9:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	[PMQ]V.K[LRW]	30	KR	CLV_PCSK_PC1ET2_1					small nucleolar ribonucleoprotein complex (1e-13)		0.005	9
protein_40_YHR169W	2	DBP8:  Putative ATP-dependent RNA helicase of the DEAD-box family involved in biogenesis of the 40S ribosomal subunit	G..G[ERF]	30	G.G..G	Phosphate, FAD, NADH, binding motif					ribosome (0.01)		0.006	9
protein_40_YHR082C	2	KSP1:  Nonessential putative serine/threonine protein kinase of unknown cellular role; overproduction causes allele-specific suppression of the prp20-10 mutation	V..[RVP]G	30									0.006	9
protein_40_YHR030C	2	SLT2:  Serine/threonine MAP kinase involved in regulating the maintenance of cell wall integrity and progression through the cell cycle; regulated by the PKC1-mediated signaling pathway	AG[GKH][SQY]	30	GGQ	N-methylation motif in E. coli, Gln residue in methylated, mimics CCA motif at the end of tRNA molecule							0.005	10
protein_40_YHL007C	2	STE20:  Signal transducing kinase of the PAK (p21-activated kinase) family, involved in pheromone response and pseudohyphal/invasive growth pathways, activated by Cdc42p; binds Ste4p at a GBB motif present in noncatalytic domains of PAK kinases	K.G[DQM]	30									0.005	10
protein_40_YGR274C	2	TAF1:  TFIID subunit (145 kDa), involved in RNA polymerase II transcription initiation, has histone acetyltransferase activity, involved in promoter binding and G1/S progression	Y[SL]S[IN]L	30	R.Y.S	14-3-3 binding motif (Ser must be phosphorylated)	Y						0.003	8
protein_40_YGR245C	2	SDA1:  Highly conserved nuclear protein required for actin cytoskeleton organization and passage through Start, plays a critical role in G1 events, binds Nap1p, also involved in 60S ribosome biogenesis	VK..[SMW][KGW]	30	K..[ST]	PKA kinase substrate motif					cytoplasm organization and biogenesis (0.001)	Y	0.005	8
protein_40_YGR218W	2	CRM1:  Major karyopherin, involved in export of proteins, RNAs, and ribosomal subunits from the nucleus	A[EAV][KSD]N	30							rRNA export from nucleus (1e-06)	Y	0.006	10
protein_40_YGR218W	2	CRM1:  Major karyopherin, involved in export of proteins, RNAs, and ribosomal subunits from the nucleus	EI[KEM][SMW]	30	VEID	Protease Caspase 6 -stringent							0.006	10
protein_40_YGR218W	2	CRM1:  Major karyopherin, involved in export of proteins, RNAs, and ribosomal subunits from the nucleus	LA.[PTD][DIE]	30									0.006	10
protein_40_YGR218W	2	CRM1:  Major karyopherin, involved in export of proteins, RNAs, and ribosomal subunits from the nucleus	Q..[PNQ]S	30							rRNA export from nucleus (1e-06)	Y	0.005	9
protein_40_YGR103W	2	NOP7:  Nucleolar protein involved in rRNA processing and 60S ribosomal subunit biogenesis; constituent of several different pre-ribosomal particles; required for exit from G<sub>0</sub> and the initiation of cell proliferation	KA..[ESI][LDF]	30							cytoplasm organization and biogenesis (1e-11)		0.006	9
protein_40_YGR086C	2	PIL1:  Primary component of eisosomes, which are large immobile cell cortex structures associated with endocytosis; null mutants show activation of Pkc1p/Ypk1p stress resistance pathways; detected in phosphorylated state in mitochondria	K[NVG][SDL]G	30							SWR1 complex (1e-04)		0.006	10
protein_40_YGR086C	2	PIL1:  Primary component of eisosomes, which are large immobile cell cortex structures associated with endocytosis; null mutants show activation of Pkc1p/Ypk1p stress resistance pathways; detected in phosphorylated state in mitochondria	P.P[KQN]	30	P.P	motif in interleukin 5 receptor necessary for signaling					SWR1 complex (0.001)		0.006	10
protein_40_YGR040W	2	KSS1:  Mitogen-activated protein kinase (MAPK) involved in signal transduction pathways that control filamentous growth and pheromone response; the KSS1 gene is nonfunctional in S288C strains and functional in W303 strains	[EGM]D.[ENG]T	30	D.E	Sec24p							0.006	9
protein_40_YGR040W	2	KSS1:  Mitogen-activated protein kinase (MAPK) involved in signal transduction pathways that control filamentous growth and pheromone response; the KSS1 gene is nonfunctional in S288C strains and functional in W303 strains	A[PDK]..[KAG]E	30									0.006	9
protein_40_YGR040W	2	KSS1:  Mitogen-activated protein kinase (MAPK) involved in signal transduction pathways that control filamentous growth and pheromone response; the KSS1 gene is nonfunctional in S288C strains and functional in W303 strains	V[ETV]..[STF]K	30									0.006	10
protein_40_YGR034W	2	RPL26B:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl26Ap and has similarity to E. coli L24 and rat L26 ribosomal proteins; binds to 5.8S rRNA	[KEH][IKL]RA	30	[KR]R	CLV_PCSK_KEX2_1					cytosolic ribosome (sensu Eukaryota) (1e-22)		0.006	9
protein_40_YGL207W	2	SPT16:  Subunit of the heterodimeric FACT complex (Spt16p-Pob3p), facilitates RNA Polymerase II transcription elongation through nucleosomes by destabilizing and then reassembling nucleosome structure	[RKY]K.[LQF]R	30							RNA polymerase II transcription elongation factor activity (1e-09)		0.006	8
protein_40_YGL103W	2	RPL28:  Ribosomal protein of the large (60S) ribosomal subunit, has similarity to E. coli L15 and rat L27a ribosomal proteins; may have peptidyl transferase activity; can mutate to cycloheximide resistance	R[VDR].[RDA]R	30	[KR]R	CLV_PCSK_KEX2_1					cytosolic ribosome (sensu Eukaryota) (1e-19)		0.006	10
protein_40_YGL048C	2	RPT6:  One of six ATPases of the 19S regulatory particle of the 26S proteasome involved in the degradation of ubiquitinated substrates; bound by ubiquitin-protein ligases Ubr1p and Ufd4p; localized mainly to the nucleus throughout the cell cycle	[VPG]D.[LER]A	30	D.E	Sec24p					proteasome complex (sensu Eukaryota) (1e-09)		0.006	10
protein_40_YFR034C	2	PHO4:  Basic helix-loop-helix (bHLH) transcription factor of the myc-family; binds cooperatively with Pho2p to the PHO5 promoter; function is regulated by phosphorylation at multiple sites and by phosphate availability	V[SEA].[AEG]AA	30			Y						0.004	8
protein_40_YFL037W	2	TUB2:  Beta-tubulin; associates with alpha-tubulin (Tub1p and Tub3p) to form tubulin dimer, which polymerizes to form microtubules	K[TEA]T	30	CKPCLK.TC	CLUSTERIN_1 PATTERN	Y					Y	0.006	10
protein_40_YFL037W	2	TUB2:  Beta-tubulin; associates with alpha-tubulin (Tub1p and Tub3p) to form tubulin dimer, which polymerizes to form microtubules	L[QHR]Q[IVN]	30	Y[MLVIF][PRKH]Q	STAT3 SH2 domain binding motif						Y	0.005	10
protein_40_YER177W	2	BMH1:  14-3-3 protein, major isoform; controls proteome at post-transcriptional level, binds proteins and DNA, involved in regulation of many processes including exocytosis, vesicle transport, Ras/MAPK signaling, and rapamycin-sensitive signaling	SN[SLG]	30	CP[ST]N[ILV]GT	GUANIDO_KINASE PATTERN							0.005	10
protein_40_YER172C	2	BRR2:  RNA-dependent ATPase RNA helicase (DEIH box); required for disruption of U4/U6 base-pairing in native snRNPs to activate the spliceosome for catalysis; homologous to human U5-200kD	L[ERA].E[EQR]	30							spliceosome (1e-14)		0.006	10
protein_40_YER118C	2	SHO1:  Transmembrane osmosensor, participates in activation of both the Cdc42p- and MAP kinase-dependent filamentous growth pathway and the high-osmolarity glycerol response pathway	V[RLH].[TRY]S	30	R.[FY]S.P	14-3-3 binding motifs, Ser must be phosphorylated 							0.006	10
protein_40_YER112W	2	LSM4:  Lsm (Like Sm) protein; part of heteroheptameric complexes (Lsm2p-7p and either Lsm1p or 8p): cytoplasmic Lsm1p complex involved in mRNA decay; nuclear Lsm8p complex part of U6 snRNP and possibly involved in processing tRNA, snoRNA, and rRNA	Q[EAQ]Q	30	GQDQTKQQI	43_KD_POSTSYNAPTIC PATTERN					mRNA metabolism (1e-07)		0.006	9
protein_40_YER110C	2	KAP123:  Karyopherin beta, mediates nuclear import of ribosomal proteins prior to assembly into ribosomes and import of histones H3 and H4; localizes to the nuclear pore, nucleus, and cytoplasm; exhibits genetic interactions with RAI1	[KP]S.[EHG]G	30									0.005	10
protein_40_YER082C	2	UTP7:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	[EDK]E.[IWA]A	30							cytoplasm organization and biogenesis (1e-10)	Y	0.006	10
protein_40_YER082C	2	UTP7:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	[VAT]LL[RDH]	30	[DE]..LL	Di-Leu acidic motif for receptor endocytosis (recognized by VHS domain of GGA proteins)	Y				small nucleolar ribonucleoprotein complex (1e-16)		0.006	9
protein_40_YER074W	2	RPS24A:  Protein component of the small (40S) ribosomal subunit; identical to Rps24Bp and has similarity to rat S24 ribosomal protein	L..I[LTF]	30									0.006	10
protein_40_YER018C	2	SPC25:  Component of the evolutionarily conserved kinetochore-associated Ndc80 complex (Ndc80p-Nuf2p-Spc24p-Spc25p); involved in chromosome segregation, spindle checkpoint activity and kinetochore clustering	DL.[LRS][KMD]	30	PWDLW	LIG_Clathr_ClatBox_2					microtubule cytoskeleton (0.001)		0.006	10
protein_40_YER018C	2	SPC25:  Component of the evolutionarily conserved kinetochore-associated Ndc80 complex (Ndc80p-Nuf2p-Spc24p-Spc25p); involved in chromosome segregation, spindle checkpoint activity and kinetochore clustering	EL[EQR][ELK]	30							microtubule cytoskeleton organization and biogenesis (0.01)		0.006	10
protein_40_YEL037C	2	RAD23:  Protein with ubiquitin-like N terminus, recognizes and binds damaged DNA (with Rad4p) during nucleotide excision repair; regulates Rad4p levels, subunit of Nuclear Excision Repair Factor 2 (NEF2); homolog of human HR23A and HR23B proteins	V[VSR]D[QPG]	30	DVAD	Protease Caspase 2 -stringent					proteasome regulatory particle (sensu Eukaryota) (1e-05)		0.005	10
protein_40_YDR510W	2	SMT3:  Ubiquitin-like protein of the SUMO family, conjugated to lysine residues of target proteins; regulates chromatid cohesion, chromosome segregation, APC-mediated proteolysis, DNA replication and septin ring dynamics	D[ILT]DA[DIP]	30									0.005	8
protein_40_YDR510W	2	SMT3:  Ubiquitin-like protein of the SUMO family, conjugated to lysine residues of target proteins; regulates chromatid cohesion, chromosome segregation, APC-mediated proteolysis, DNA replication and septin ring dynamics	DL[TEG]	30	WDL	Binding motif for AP-2 and clathrin heavy chain ear	Y				protein sumoylation (1e-04)	Y	0.005	10
protein_40_YDR477W	2	SNF1:  AMP-activated serine/threonine protein kinase found in a complex containing Snf4p and members of the Sip1p/Sip2p/Gal83p family; required for transcription of glucose-repressed genes, thermotolerance, sporulation, and peroxisome biogenesis	R[KPD]N	30									0.005	10
protein_40_YDR449C	2	UTP6:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	G[KNG]..K[LAT]	30							rRNA processing (1e-20)		0.006	10
protein_40_YDR448W	2	ADA2:  Transcription coactivator, component of the ADA and SAGA transcriptional adaptor/HAT (histone acetyltransferase) complexes	Q[QGY]L[QVC]	30	YL[VMAY]I	Sorting nexin 1 (Binding motif), Lysosomal targeting motif in EGFR					SAGA complex (1e-12)		0.006	10
protein_40_YDR447C	2	RPS17B:  Ribosomal protein 51 (rp51) of the small (40s) subunit; nearly identical to Rps17Ap and has similarity to rat S17 ribosomal protein	K.[RAK]A	30			Y				cytosolic ribosome (sensu Eukaryota) (1e-35)	Y	0.006	10
protein_40_YDR381W	2	YRA1:  Nuclear protein that binds to RNA and to Mex67p, required for export of poly(A)+ mRNA from the nucleus; member of the REF (RNA and export factor binding proteins) family; another family member, Yra2p, can substitute for Yra1p function	Q[ARI]A	30			Y				cytoplasm organization and biogenesis (1e-05)	Y	0.005	9
protein_40_YDR356W	2	SPC110:  Inner plaque spindle pole body (SPB) component, ortholog of human kendrin; involved in connecting nuclear microtubules to SPB; interacts with Tub4p-complex and calmodulin; phosphorylated by Mps1p in cell cycle-dependent manner	[RKE]KI[LME]	30							microtubule nucleation (1e-15)		0.006	10
protein_40_YDR328C	2	SKP1:  Evolutionarily conserved kinetochore protein that is part of multiple protein complexes, including the SCF ubiquitin ligase complex, the CBF3 complex that binds centromeric DNA, and the RAVE complex that regulates assembly of the V-ATPase	D[SG]..G[IMR]	30									0.005	9
protein_40_YDR328C	2	SKP1:  Evolutionarily conserved kinetochore protein that is part of multiple protein complexes, including the SCF ubiquitin ligase complex, the CBF3 complex that binds centromeric DNA, and the RAVE complex that regulates assembly of the V-ATPase	S[STE].[TGD]ID	30	S[ST]	MDC1 BRCT domain binding motif							0.004	8
protein_40_YDR303C	2	RSC3:  Component of the RSC chromatin remodeling complex; essential gene required for maintenance of proper ploidy and regulation of ribosomal protein genes and the cell wall/stress response; highly similar to Rsc30p	[SQD]T..N[GQ]	30							RSC complex (1e-07)		0.004	10
protein_40_YDR303C	2	RSC3:  Component of the RSC chromatin remodeling complex; essential gene required for maintenance of proper ploidy and regulation of ribosomal protein genes and the cell wall/stress response; highly similar to Rsc30p	G[VQM]L[PTK]	30	IYG.L	Lck kinase phosphorylation site (peptide screen)					chromosome organization and biogenesis (sensu Eukaryota) (0.01)	Y	0.006	10
protein_40_YDR190C	2	RVB1:  Essential protein involved in transcription regulation; component of chromatin remodeling complexes; required for assembly and function of the INO80 complex; member of the RUVB-like protein family	[AFP]N.[PWI]K	30			Y				chromatin remodeling complex (0.01)		0.006	9
protein_40_YDR145W	2	TAF12:  Subunit (61/68 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation and in chromatin modification, similar to histone H2A	[EKC]D.[DSK]D	30	D.D	Ribose moiety of UDP and manganese binding site in glucuronyl transferase					transcription factor complex (1e-07)		0.006	10
protein_40_YDR099W	2	BMH2:  14-3-3 protein, minor isoform; controls proteome at post-transcriptional level, binds proteins and DNA, involved in regulation of many processes including exocytosis, vesicle transport, Ras/MAPK signaling, and rapamycin-sensitive signaling	[AHW][KHR].KN	30									0.005	10
protein_40_YDR064W	2	RPS13:  Protein component of the small (40S) ribosomal subunit; has similarity to E. coli S15 and rat S13 ribosomal proteins	K[GVA].K[VFA]	30							cytosolic ribosome (sensu Eukaryota) (1e-18)		0.006	10
protein_40_YDR012W	2	RPL4B:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl4Ap and has similarity to E. coli L4 and rat L4 ribosomal proteins	EA.[AVR][ETH]	30	IEAD	Protease Caspase 10	Y				cytosolic ribosome (sensu Eukaryota) (1e-06)		0.006	10
protein_40_YCR034W	2	FEN1:  Fatty acid elongase, involved in sphingolipid biosynthesis; acts on fatty acids of up to 24 carbons in length; mutations have regulatory effects on 1,3-beta-glucan synthase, vacuolar ATPase, and the secretory pathway	W.L[LFQ]	30	WDL	Binding motif for AP-2 and clathrin heavy chain ear					endoplasmic reticulum (0.001)		0.006	10
protein_40_YBR198C	2	TAF5:  Subunit (90 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation and in chromatin modification	[TGA]Q[QNY]Q	30	[ST]Q	ATM kinase phosphorylation site					transcription factor TFIID complex (1e-09)		0.005	7
protein_40_YBR106W	2	PHO88:  Probable membrane protein, involved in phosphate transport; pho88 pho86 double null mutant exhibits enhanced synthesis of repressible acid phosphatase at high inorganic phosphate concentrations	[EYG]Y..[KNV]Q	30	[EDY]Y	TC-PTP phosphatase substrate motif					basic amino acid transporter activity (0.001)		0.005	8
protein_40_YBR059C	2	AKL1:  Ser-Thr protein kinase, member (with Ark1p and Prk1p) of the Ark kinase family; involved in endocytosis and actin cytoskeleton organization	[SIA]E[DAG]E	30	[ST]E	G protein-coupled receptor kinase 1 substrate motif							0.006	9
protein_40_YBR009C	2	HHF1:  One of two identical histone H4 proteins (see also HHF2); core histone required for chromatin assembly and chromosome function; contributes to telomeric silencing; N-terminal domain involved in maintaining genomic integrity	L[QMR]Q	30	ARKGSLRQ	PKC alpha kinase substrate motif					DNA metabolism (1e-07)		0.006	10
protein_40_YBR009C	2	HHF1:  One of two identical histone H4 proteins (see also HHF2); core histone required for chromatin assembly and chromosome function; contributes to telomeric silencing; N-terminal domain involved in maintaining genomic integrity	Q[KVN]..[LTR]D	30									0.006	10
protein_40_YBL004W	2	UTP20:  Component of the small-subunit (SSU) processome, which is involved in the biogenesis of the 18S rRNA	A[QKS]..[KI]E	30							cytoplasm organization and biogenesis (1e-13)		0.006	10
protein_40_YAL032C	2	PRP45:  Protein required for pre-mRNA splicing; associates with the spliceosome and interacts with splicing factors Prp22p and Prp46p; orthologous to human transcriptional coactivator SKIP and can activate transcription of a reporter gene	[KWQ]N..R[LKS]	30							spliceosome (1e-08)	Y	0.006	9
protein_40_YAL032C	2	PRP45:  Protein required for pre-mRNA splicing; associates with the spliceosome and interacts with splicing factors Prp22p and Prp46p; orthologous to human transcriptional coactivator SKIP and can activate transcription of a reporter gene	I..L[TRD]	30			Y				nuclear mRNA splicing, via spliceosome (1e-11)	Y	0.006	10
protein_40_YAL032C	2	PRP45:  Protein required for pre-mRNA splicing; associates with the spliceosome and interacts with splicing factors Prp22p and Prp46p; orthologous to human transcriptional coactivator SKIP and can activate transcription of a reporter gene	Q.[VCH]N	30								Y	0.006	10
protein_40_YAL032C	2	PRP45:  Protein required for pre-mRNA splicing; associates with the spliceosome and interacts with splicing factors Prp22p and Prp46p; orthologous to human transcriptional coactivator SKIP and can activate transcription of a reporter gene	T[LTN]P	30	PLTLP	RAF1 kinase substrate motif					nuclear mRNA splicing, via spliceosome (1e-10)	Y	0.006	10
oshea_spindle_pole	2	oshea_spindle_pole	LE..[YLC][REI]	30							microtubule cytoskeleton (1e-19)		0.006	10
oshea_mitochondrion	2	oshea_mitochondrion	L[FIW]L	30									0.006	10
oshea_Golgi_or_Golgi_to_vacuole	2	oshea_Golgi_or_Golgi_to_vacuole	I.L[IEV]	30	YIDL	SH2 ligand for Syp (also tyr is phosphorylated by the insulin receptor)					Golgi apparatus (1e-42)	Y	0.006	10
oshea_bud	2	oshea_bud	[AWE][SVE]..PQ	30	HPQ	Biotin binding motif in streptavidin					bud (1e-04)		0.005	10
matsuyama_Spindle_or_SPB	2	matsuyama_Spindle_or_SPB	NSI[KHS][EGW]	30	RR.SI	PKA kinase phosphorylation site (peptide screen)					spindle (1e-10)		0.006	8
matsuyama_nuclear_envelope_or_dots	2	matsuyama_nuclear_envelope_or_dots	K[SMR][YEW]L	30	KR	CLV_PCSK_PC1ET2_1					spindle pole (1e-06)	Y	0.008	10
genetic_YPL055C	2	LGE1: Protein of unknown function; null mutant forms abnormally large cells, and homozygous diploid null mutant displays delayed premeiotic DNA synthesis and reduced efficiency of meiotic nuclear division	E..I[SNM]	30							DNA metabolism (1e-07)	Y	0.005	10
genetic_YPL055C	2	LGE1: Protein of unknown function; null mutant forms abnormally large cells, and homozygous diploid null mutant displays delayed premeiotic DNA synthesis and reduced efficiency of meiotic nuclear division	I..[LRQ]Q	30	[DE][DE][FL][FL][DE][LM][IL]...Q[GS].R[LM][DE][DE]QR	GoLoco motif, a G alpha binding motif					chromosome organization and biogenesis (sensu Eukaryota) (1e-11)	Y	0.006	10
genetic_YPL055C	2	LGE1: Protein of unknown function; null mutant forms abnormally large cells, and homozygous diploid null mutant displays delayed premeiotic DNA synthesis and reduced efficiency of meiotic nuclear division	L[SQH]T	30	IRRLSTRRR	Nek 2 kinase substrate motif					DNA metabolism (1e-09)	Y	0.005	8
genetic_YPL055C	2	LGE1: Protein of unknown function; null mutant forms abnormally large cells, and homozygous diploid null mutant displays delayed premeiotic DNA synthesis and reduced efficiency of meiotic nuclear division	P.[VLE]D	30	PYVD.[AT].F	Tak1 docking site in Tab1	Y				chromosome organization and biogenesis (sensu Eukaryota) (1e-04)		0.006	10
genetic_YPL055C	2	LGE1: Protein of unknown function; null mutant forms abnormally large cells, and homozygous diploid null mutant displays delayed premeiotic DNA synthesis and reduced efficiency of meiotic nuclear division	TP.[RYC][KYD]	30	[ST]P	LIG_WW_4							0.006	10
genetic_YNL153C	2	GIM3: Subunit of the heterohexameric cochaperone prefoldin complex which binds specifically to cytosolic chaperonin and transfers target proteins to it	[TYR]K.L[LES]Q	30	[ST]Q	ATM kinase phosphorylation site							0.005	9
genetic_YNL153C	2	GIM3: Subunit of the heterohexameric cochaperone prefoldin complex which binds specifically to cytosolic chaperonin and transfers target proteins to it	SN.[SWE]I[SIW]	30	N.[TS]	N-linked glycosylation site							0.005	10
genetic_YNL153C	2	GIM3: Subunit of the heterohexameric cochaperone prefoldin complex which binds specifically to cytosolic chaperonin and transfers target proteins to it	V[QPY]L[NAE]	30	P.V.L	Shadow-Chromo domain binding motif	Y				mitosis (0.01)		0.006	10
genetic_YLR262C	2	YPT6: GTPase, Ras-like GTP binding protein involved in the secretory pathway, required for fusion of endosome-derived vesicles with the late Golgi, maturation of the vacuolar carboxypeptidase Y; has similarity to the human GTPase, Rab6	P[LK].A[TIM]	30									0.006	10
genetic_YLR262C	2	YPT6: GTPase, Ras-like GTP binding protein involved in the secretory pathway, required for fusion of endosome-derived vesicles with the late Golgi, maturation of the vacuolar carboxypeptidase Y; has similarity to the human GTPase, Rab6	R[KDA]K	30	L..RR.KK	ERK docking motif in RSK stringent					chromosome organization and biogenesis (sensu Eukaryota) (1e-16)	Y	0.006	10
genetic_YLR200W	2	YKE2: Subunit of the heterohexameric Gim/prefoldin protein complex involved in the folding of alpha-tubulin, beta-tubulin, and actin	S[SKG]ID[GLH]	30	S[ST]	MDC1 BRCT domain binding motif					cytoskeleton-dependent intracellular transport (0.01)		0.005	10
genetic_YGL058W	2	RAD6: Ubiquitin-conjugating enzyme (E2), involved in postreplication repair (with Rad18p), sporulation, telomere silencing, and ubiquitin-mediated N-end rule protein degradation (with Ubr1p)	L..Q[LWE]	30							DNA metabolism (1e-10)		0.006	10
genetic_YER083C	2	GET2: Subunit of the GET complex; required for meiotic nuclear division and for the retrieval of HDEL proteins from the Golgi to the ER in an ERD2 dependent fashion; may be involved in cell wall function	E..[ASE]N	30							chromosome organization and biogenesis (sensu Eukaryota) (1e-15)	Y	0.006	10
genetic_YER083C	2	GET2: Subunit of the GET complex; required for meiotic nuclear division and for the retrieval of HDEL proteins from the Golgi to the ER in an ERD2 dependent fashion; may be involved in cell wall function	HL..[NGP][LMV]	30							chromosome organization and biogenesis (sensu Eukaryota) (0.001)		0.006	10
genetic_YDL020C	2	RPN4: Transcription factor that stimulates expression of proteasome genes; Rpn4p levels are in turn regulated by the 26S proteasome in a negative feedback control mechanism; RPN4 is transcriptionally regulated by various stress responses	R[DKS]K	30	L..RR.KK	ERK docking motif in RSK stringent					chromosome organization and biogenesis (sensu Eukaryota) (1e-11)		0.006	10
yeast-1166_GO-0005488	2	binding	P..P[SPK]	29	[RKY]..P..P	LIG_SH3_1		RRM_1	1.E-05	-2.5	nucleic acid binding (1e-74)		0.006	10
protein_40_YDR381W	2	YRA1:  Nuclear protein that binds to RNA and to Mex67p, required for export of poly(A)+ mRNA from the nucleus; member of the REF (RNA and export factor binding proteins) family; another family member, Yra2p, can substitute for Yra1p function	R[GVI]G	29	FRGGT	Phosphoinositide binding motif in ATG18 and ATG21		DEAD	1.E-02	-2.5	RNA metabolism (1e-04)	Y	0.005	10
protein_40_YPR016C	2	TIF6:  Constituent of 66S pre-ribosomal particles, has similarity to human translation initiation factor 6 (eIF6); may be involved in the biogenesis and or stability of 60S ribosomal subunits	Q..[AEK]E	29				Brix	1.E-04	-2.4	cytoplasm organization and biogenesis (1e-22)		0.005	10
protein_40_YDR324C	2	UTP4:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	E..E[EKV]	29	RE..E	Iron binding motif in ferritin L-chain and yeast Iron transport protein		WD40	1.E-04	-2.2	small nucleolar ribonucleoprotein complex (1e-39)		0.005	10
protein_40_YPL203W	2	TPK2:  cAMP-dependent protein kinase catalytic subunit; promotes vegetative growth in response to nutrients via the Ras-cAMP signaling pathway; inhibited by regulatory subunit Bcy1p in the absence of cAMP; partially redundant with Tpk1p and Tpk3p	P[QIV][QRN]Q	29				Pkinase	1.E-04	-1.9	protein kinase activity (0.01)		0.005	10
protein_40_YNL272C	2	SEC2:  Guanyl-nucleotide exchange factor for the small G-protein Sec4p, located on cytoplasmic vesicles; essential for post-Golgi vesicle transport	[TNS]Q[DEP]K	29	[ST]Q	ATM kinase phosphorylation site		Pkinase	1.E-12	-1.9	protein kinase activity (1e-12)		0.005	10
protein_40_YKR048C	2	NAP1:  Protein that interacts with mitotic cyclin Clb2p; required for the regulation of microtubule dynamics during mitosis; controls bud morphogenesis; involved in the transport of H2A and H2B histones to the nucleus; phosphorylated by CK2	K[ASQ].Q[SVM]	29				Pkinase	1.E-03	-1.8	protein kinase activity (0.001)	Y	0.006	9
protein_40_YER082C	2	UTP7:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	V..[TIN]K	29				WD40	1.E-02	-1.7	rRNA processing (1e-22)		0.005	9
protein_40_YDR099W	2	BMH2:  14-3-3 protein, minor isoform; controls proteome at post-transcriptional level, binds proteins and DNA, involved in regulation of many processes including exocytosis, vesicle transport, Ras/MAPK signaling, and rapamycin-sensitive signaling	AN.[QHT][LQR]	29	N.[TS]	N-linked glycosylation site		Pkinase	1.E-02	-1.5			0.005	9
yeast-649_GO-0003676	2	nucleic acid binding	S[DAN]S[APY]	29				PUF	1.E-03	-1.4	nucleic acid binding (1e-80)	Y	0.006	9
yeast-215_GO-0007010	2	cytoskeleton organization and biogenesis	P..P[NPT]	29	[RKY]..P..P	LIG_SH3_1		SH3_1	1.E-04	-1.4	cytoskeleton organization and biogenesis (1e-97)		0.006	9
yeast-1433_GO-0006139	2	nucleobase, nucleoside, nucleotide and nucleic acid metabolism	DA	29	DALDL	14-3-3 binding motif in ExoS		BRCT	1.E-03	-1.4	transcription (1e-15)	Y	0.006	10
protein_40_YKL009W	2	MRT4:  Protein involved in mRNA turnover and ribosome assembly, localizes to the nucleolus	E..E[DAN]	29	RE..E	Iron binding motif in ferritin L-chain and yeast Iron transport protein		Brix	1.E-03	-1.4	cytoplasm organization and biogenesis (1e-31)		0.005	10
protein_40_YDR388W	2	RVS167:  Actin-associated protein, subunit of a complex (Rvs161p-Rvs167p) involved in regulation of actin cytoskeleton, endocytosis, and viability following starvation or osmotic stress; homolog of mammalian amphiphysin	N.[LNQ]P	29				Pkinase	1.E-02	-1.4	cell cortex (0.01)		0.005	9
yeast-504_GO-0006350	2	transcription	HT.[EQS]K[PYF]	29				zf-C2H2	1.E-13	-1.2	transcription regulator activity (1e-12)		0.006	10
yeast-256_GO-0016462	2	pyrophosphatase activity	ER.[DKY][EGD]	29				ABC_tran	1.E-06	-1.1	pyrophosphatase activity (1e-40)		0.007	9
protein_40_YPL211W	2	NIP7:  Nucleolar protein required for 60S ribosome subunit biogenesis, constituent of 66S pre-ribosomal particles; physically interacts with Nop8p and the exosome subunit Rrp43p	KA..[EKF][LMD]	29				DEAD	1.E-03	-1.1	cytoplasm organization and biogenesis (1e-15)	Y	0.006	8
protein_40_YOR181W	2	LAS17:  Actin assembly factor, activates the Arp2/3 protein complex that nucleates branched actin filaments; localizes with the Arp2/3 complex to actin patches; homolog of the human Wiskott-Aldrich syndrome protein (WASP)	SA..[VAP][PQD]	29			Y	SH3_1	1.E-08	-1.1	actin cytoskeleton (1e-04)		0.006	10
protein_40_YOR181W	2	LAS17:  Actin assembly factor, activates the Arp2/3 protein complex that nucleates branched actin filaments; localizes with the Arp2/3 complex to actin patches; homolog of the human Wiskott-Aldrich syndrome protein (WASP)	AS..[VNP][GRA]	29				SH3_1	1.E-07	-1.1	bipolar bud site selection (1e-08)	Y	0.006	10
protein_40_YOR181W	2	LAS17:  Actin assembly factor, activates the Arp2/3 protein complex that nucleates branched actin filaments; localizes with the Arp2/3 complex to actin patches; homolog of the human Wiskott-Aldrich syndrome protein (WASP)	[DKP]QT[SER]	29	[KR].TQT	LIG_Dynein_DLC8_1		SH3_1	1.E-02	-1.1	actin cytoskeleton organization and biogenesis (1e-06)	Y	0.005	10
oshea_nucleus	2	oshea_nucleus	L[NVQ]N	29	HLVNK	Motif for targeting CD44 to basolateral membranes	Y	Zn_clus	1.E-04	-1.1	DNA metabolism (1e-38)		0.006	10
yeast-649_GO-0003676	2	nucleic acid binding	PLS[KYH][EKT]	29				RRM_1	1.E-02	-1	nucleic acid binding (1e-10)		0.006	9
yeast-460_GO-0006351	2	transcription, DNA-dependent	[TDE]G[EAR]KP	29	G[KR][KR]	Amidation after cleavage after Gly (must be in secretory pathway)		zf-C2H2	1.E-08	-1	transcription, DNA-dependent (1e-08)	Y	0.006	8
yeast-1939_GO-0003824	2	catalytic activity	N[NTQ].[NRS]S	29				Zn_clus	1.E-06	-1	transcription regulator activity (1e-15)		0.006	9
protein_40_YHL034C	2	SBP1:  Putative RNA binding protein; involved in translational repression and found in cytoplasmic P bodies; found associated with small nucleolar RNAs snR10 and snR11	A[AEG]K	29	WAQKW	Motif in Cet1 RNA triphosphosphatase for binding to RNA guanylyltransferase Ceg1		RRM_1	1.E-02	-1	ribonucleoprotein complex (1e-15)		0.005	9
yeast-335_GO-0016772	2	transferase activity, transferring phosphorus-containing groups	DK[YHD]	29	DKTGT[LIVM][TI]	ATPASE_E1_E2 PATTERN		Pkinase	1.E-19	-0.9	transferase activity, transferring phosphorus-containing groups (1e-10)		0.006	10
protein_40_YNL002C	2	RLP7:  Nucleolar protein with similarity to large ribosomal subunit L7 proteins; constituent of 66S pre-ribosomal particles; plays an essential role in processing of precursors to the large ribosomal subunit RNAs	NK[EYL]	29	NKLY	LIM3 domain in enigma binds to this site in Ret		Brix	1.E-02	-0.8	cytoplasm organization and biogenesis (1e-41)		0.005	9
oshea_bud_neck	2	oshea_bud_neck	[QEC]LE[ENL]	29	L..[LM]E	Sec24p		RhoGAP	1.E-02	-0.8	site of polarized growth (1e-27)	Y	0.006	10
yeast-256_GO-0016462	2	pyrophosphatase activity	[PGS]..VL	29				Helicase_C	1.E-12	-0.7	pyrophosphatase activity (1e-13)		0.006	10
protein_40_YOL004W	2	SIN3:  Component of the Sin3p-Rpd3p histone deacetylase complex, involved in transcriptional repression and activation of diverse processes, including mating-type switching and meiosis; involved in the maintenance of chromosomal integrity	E[ICA]..D[FAW]	29				SWIRM	1.E-02	-0.7		Y	0.004	8
protein_40_YGL105W	2	ARC1:  Protein that binds tRNA and methionyl- and glutamyl-tRNA synthetases (Mes1p and Gus1p), delivering tRNA to them, stimulating catalysis, and ensuring their localization to the cytoplasm; also binds quadruplex nucleic acids	K[VTA]..E[AHG]	29	[ST]..E	Casien kinase II consensus phosphorylation site	Y	Pkinase	1.E-05	-0.7	protein kinase activity (1e-05)	Y	0.006	10
yeast-216_GO-0006325	2	establishment and/or maintenance of chromatin architecture	P[ADQ]..[RKP]L	29				Myb_DNA-binding	1.E-03	-0.6	establishment and/or maintenance of chromatin architecture (1e-43)		0.006	10
yeast-216_GO-0006323	2	DNA packaging	P[ADQ]..[RKP]L	29				Myb_DNA-binding	1.E-03	-0.6	establishment and/or maintenance of chromatin architecture (1e-43)		0.006	10
protein_40_YOR181W	2	LAS17:  Actin assembly factor, activates the Arp2/3 protein complex that nucleates branched actin filaments; localizes with the Arp2/3 complex to actin patches; homolog of the human Wiskott-Aldrich syndrome protein (WASP)	[ATM]A..I[SDE]	29				SH3_1	1.E-02	-0.6	actin cytoskeleton (1e-04)		0.006	10
protein_40_YLL039C	2	UBI4:  Ubiquitin, becomes conjugated to proteins, marking them for selective degradation via the ubiquitin-26S proteasome system; essential for the cellular stress response; encoded as a polyubiquitin precursor comprised of 5 head-to-tail repeats	D.[PID]N	29	D.D	Ribose moiety of UDP and manganese binding site in glucuronyl transferase		F-box	1.E-03	-0.6	ubiquitin cycle (1e-10)		0.005	10
protein_40_YHR088W	2	RPF1:  Nucleolar protein involved in the assembly of the large ribosomal subunit; constituent of 66S pre-ribosomal particles; contains a sigma(70)-like motif, which is thought to bind RNA	K..K[ERV]	29	KR	CLV_PCSK_PC1ET2_1		IBN_N	1.E-02	-0.6	cytoplasm organization and biogenesis (1e-24)	Y	0.005	10
protein_40_YIL094C	2	LYS12:  Homo-isocitrate dehydrogenase, an NAD-linked mitochondrial enzyme required for the fourth step in the biosynthesis of lysine, in which homo-isocitrate is oxidatively decarboxylated to alpha-ketoadipate	V[VLI][QTV]V	29				IBN_N	1.E-03	-0.5	protein carrier activity (0.01)	Y	0.006	10
protein_40_YDR225W	2	HTA1:  One of two nearly identical (see also HTA2) histone H2A subtypes; core histone required for chromatin assembly and chromosome function; DNA damage-dependent phosphorylation by Mec1p facilitates DNA repair; acetylated by Nat4p	K[TPV].[TVQ]S	29				Histone	1.E-05	-0.5	nuclear nucleosome (1e-04)		0.006	9
protein_40_YDR225W	2	HTA1:  One of two nearly identical (see also HTA2) histone H2A subtypes; core histone required for chromatin assembly and chromosome function; DNA damage-dependent phosphorylation by Mec1p facilitates DNA repair; acetylated by Nat4p	R[AQE]V	29	[RK].V.F	PPI binding sites		Histone	1.E-04	-0.5	nuclear chromatin (1e-06)		0.006	10
yeast-468_GO-0051276	2	chromosome organization and biogenesis	N.[NTE]N	29	N.[TS]	N-linked glycosylation site		Bromodomain	1.E-05	-0.4	chromosome organization and biogenesis (1e-21)		0.006	9
yeast-457_GO-0007001	2	chromosome organization and biogenesis (sensu Eukaryota)	N.[NTE]N	29	N.[TS]	N-linked glycosylation site		Bromodomain	1.E-05	-0.4	chromosome organization and biogenesis (sensu Eukaryota) (1e-20)		0.006	9
protein_40_YPL217Cs	2	BMS1:  Essential conserved nucleolar GTP-binding protein required for synthesis of 40S ribosomal subunits and for processing of the 35S pre-rRNA at sites A0, A1, and A2; interacts with Rcl1p, has similarity to Tsr1p	DE[EIY]	29	SEDEE	CKII kinase phosphorylation site (peptide screen)		WD40	1.E-03	-0.4	rRNA processing (1e-30)		0.005	9
protein_40_YJR059W	2	PTK2:  Putative serine/threonine protein kinase involved in regulation of ion transport across plasma membrane; enhances spermine uptake	PK	29	K...VPK...V	Endothelin receptor motif required for endothelin stimulation		Pkinase	1.E-02	-0.4	phosphotransferase activity, alcohol group as acceptor (0.01)		0.006	10
yeast-207_GO-0006974	2	response to DNA damage stimulus	I..E[TFR]	29				BRCT	1.E-05	-0.2	response to DNA damage stimulus (1e-11)		0.006	9
protein_40_YDR060W	2	MAK21:  Constituent of 66S pre-ribosomal particles, required for large (60S) ribosomal subunit biogenesis; involved in nuclear export of pre-ribosomes; required for maintenance of dsRNA virus; homolog of human CAATT-binding protein	A.E[EKL]	29	A[EA]EEY[FV]F[LFMIV]F	FGFR kinase substrate motif	Y	Helicase_C	1.E-03	-0.2	cytoplasm organization and biogenesis (1e-26)		0.005	10
protein_40_YOL139C	2	CDC33:  Cytoplasmic mRNA cap binding protein; the eIF4E-cap complex is responsible for mediating cap-dependent mRNA translation via interactions with the translation initiation factor eIF4G (Tif4631p or Tif4632p)	[VEN]Q[NQM]I	29			Y	Pkinase	1.E-03	-0.1	protein kinase activity (0.01)		0.005	8
protein_40_YER165W	2	PAB1:  Poly(A) binding protein, part of the 3'-end RNA-processing complex, mediates interactions between the 5' cap structure and the 3' mRNA poly(A) tail, involved in control of poly(A) tail length, interacts with translation factor eIF-4G	K.[EGV]K	29	[VILMAFP]K.E	MOD_SUMO		RRM_1	1.E-02	-0.1	RNA metabolism (1e-14)		0.006	10
protein_40_YJL095W	2	BCK1:  Mitogen-activated protein (MAP) kinase kinase kinase acting in the protein kinase C signaling pathway, which controls cell integrity; upon activation by Pkc1p phosphorylates downstream kinases Mkk1p and Mkk2p	D..[EVC]D	29	C..D..C	40Fe/4-S cluster binding motif		Pkinase	1.E-02	0			0.005	10
yeast-661_GO-0050789	2	regulation of biological process	I..[LPV]K	29				Zn_clus	1.E-06	0.1	regulation of metabolism (1e-14)	Y	0.006	10
protein_40_YLR180W	2	SAM1:  S-adenosylmethionine synthetase, catalyzes transfer of the adenosyl group of ATP to the sulfur atom of methionine; one of two differentially regulated isozymes (Sam1p and Sam2p)	P.[FDQ]V	29	MC[LIV][GA][LIV]P.[QKR][LIV]	HUPF_HYPC PATTERN		GATase	1.E-02	0.1	amine metabolism (0.01)		0.006	10
protein_40_YJL010C	2	NOP9:  Essential component of pre-40S ribosomes that is required for early cleavages of 35S pre-rRNA and hence formation of 18S rRNA; binds RNA in vitro and contains multiple pumilio-like repeats	GR[LDY]	29	[AG]R	Protease matriptase protease site		WD40	1.E-04	0.1	nucleolus (1e-26)		0.006	9
yeast-470_GO-0006259	2	DNA metabolism	Q.[QPE]I	29			Y	BRCT	1.E-03	0.2	DNA metabolism (1e-11)		0.006	9
yeast-468_GO-0051276	2	chromosome organization and biogenesis	P[PRY]K	29	SPRK	CDK2 kinase phosphorylation site (peptide screen)		Bromodomain	1.E-02	0.2	chromosome organization and biogenesis (1e-11)	Y	0.006	10
yeast-215_GO-0005694	2	chromosome	E.[DQH]S	29	[LIVMA].EG[DN]SA.[STAG]	TOPOISOMERASE_II PATTERN		SMC_N	1.E-05	0.2	chromosome (1e-12)		0.006	10
protein_40_YKR001C	2	VPS1:  Dynamin-like GTPase required for vacuolar sorting; also involved in actin cytoskeleton organization, late Golgi-retention of some proteins, regulating peroxisome biogenesis	E[RN].A[TMP]	29			Y	Actin	1.E-02	0.2	DNA metabolism (1e-04)		0.004	9
protein_40_YJL081C	2	ARP4:  Nuclear actin-related protein involved in chromatin remodeling, component of chromatin-remodeling enzyme complexes	R[DHP].K[KRI]	29	KR	CLV_PCSK_PC1ET2_1		Histone	1.E-03	0.2	establishment and/or maintenance of chromatin architecture (1e-11)		0.005	10
protein_40_YDR388W	2	RVS167:  Actin-associated protein, subunit of a complex (Rvs161p-Rvs167p) involved in regulation of actin cytoskeleton, endocytosis, and viability following starvation or osmotic stress; homolog of mammalian amphiphysin	S.N[VTK]	29				HEAT	1.E-02	0.2	cell cortex (0.01)	Y	0.005	10
protein_40_YDR324C	2	UTP4:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	D..A[LVC]	29			Y	WD40	1.E-03	0.3	small nucleolar ribonucleoprotein complex (1e-26)		0.005	10
yeast-752_GO-0016787	2	hydrolase activity	[VDC]L[KVA]R	29	[KR]R	CLV_PCSK_KEX2_1		Helicase_C	1.E-04	0.4	pyrophosphatase activity (1e-21)	Y	0.006	10
protein_40_YDL148C	2	NOP14:  Nucleolar protein, forms a complex with Noc4p that mediates maturation and nuclear export of 40S ribosomal subunits; also present in the small subunit processome complex, which is required for processing of pre-18S rRNA	A.G[KNV]	29	RALAHGVRVL	Mitochondrial targetting motif in hepititis C core protein		S4	1.E-02	0.4	small nucleolar ribonucleoprotein complex (1e-27)		0.005	8
protein_40_YPL217Cs	2	BMS1:  Essential conserved nucleolar GTP-binding protein required for synthesis of 40S ribosomal subunits and for processing of the 35S pre-rRNA at sites A0, A1, and A2; interacts with Rcl1p, has similarity to Tsr1p	I..[LKS]A	29				WD40	1.E-05	0.5	small nucleolar ribonucleoprotein complex (1e-29)		0.005	9
yeast-513_GO-0005515	2	protein binding	NT[LEI]	29	TEY	MEK phosphorylation of MAPK activation sites - stringent		F-box	1.E-03	0.6	protein binding (1e-18)		0.006	10
yeast-424_GO-0006950	2	response to stress	D.[FGN]N	29	F.D.F	LIG_AP2alpha_1		BRCT	1.E-02	0.8	response to stress (1e-15)		0.006	10
yeast-217_GO-0007046	2	ribosome biogenesis	L[LGC]..[TGQ]D	29				WD40	1.E-05	0.8	ribosome biogenesis (1e-45)		0.006	9
protein_40_YMR047C	2	NUP116:  Subunit of the nuclear pore complex (NPC) that is localized to both sides of the pore; contains a repetitive GLFG motif that interacts with mRNA export factor Mex67p and with karyopherin Kap95p; homologous to Nup100p	Q[SQT]K	29	GQDQTKQQI	43_KD_POSTSYNAPTIC PATTERN	Y	IBN_N	1.E-03	0.8	nucleocytoplasmic transport (1e-19)		0.005	9
yeast-752_GO-0016787	2	hydrolase activity	E..A	29	[ED].D[ST]EG.A[LI]	Motif in sodium channel that binds ankIryn G		Ras	1.E-09	0.9	pyrophosphatase activity (1e-12)		0.006	9
protein_40_YLR222C	2	UTP13:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	I[TRY]S[LKV]	29	IY	cFGR and Csk kinase phosphorylation site (peptide screen)		WD40	1.E-06	0.9	small nucleolar ribonucleoprotein complex (1e-20)		0.006	10
protein_40_YMR128W	2	ECM16:  Essential DEAH-box ATP-dependent RNA helicase specific to the U3 snoRNP, predominantly nucleolar in distribution, required for 18S rRNA synthesis	K.L[ATK]	29	LLKIL	AP-2 binding motif in CXCR2 receptor		WD40	1.E-03	1	rRNA processing (1e-38)	Y	0.005	10
yeast-322_GO-0005654	2	nucleoplasm	K[QKS]E	29	[VILMAFP]K.E	MOD_SUMO	Y	Bromodomain	1.E-04	1.1	nucleoplasm (1e-17)		0.006	9
yeast-301_GO-0044451	2	nucleoplasm part	K[QKS]E	29	[VILMAFP]K.E	MOD_SUMO	Y	Bromodomain	1.E-04	1.1	nucleoplasm part (1e-16)		0.006	10
yeast-235_GO-0009653	2	morphogenesis	T..Q[EQI]	29				Ras	1.E-03	1.3	cellular morphogenesis (1e-10)		0.006	9
yeast-235_GO-0000902	2	cellular morphogenesis	T..Q[EQI]	29				Ras	1.E-03	1.3	cellular morphogenesis (1e-10)		0.006	9
protein_40_YGL120C	2	PRP43:  RNA helicase in the DEAH-box family, functions in both RNA polymerase I and polymerase II transcript metabolism, involved in release of the lariat-intron from the spliceosome	D[IKA]..V[ETM]	29				Brix	1.E-03	1.3	nucleolus (1e-10)		0.006	10
protein_40_YPL235W	2	RVB2:  Essential protein involved in transcription regulation; component of chromatin remodeling complexes; required for assembly and function of the INO80 complex; member of the RUVB-like protein family	D.[ERA]V	29	SD.E	Casein kinase II substrate motif		Actin	1.E-04	1.4	chromatin remodeling complex (1e-05)		0.006	10
protein_40_YKR048C	2	NAP1:  Protein that interacts with mitotic cyclin Clb2p; required for the regulation of microtubule dynamics during mitosis; controls bud morphogenesis; involved in the transport of H2A and H2B histones to the nucleus; phosphorylated by CK2	[PVA]R..Q[LTK]	29	[AG]R	Protease matriptase protease site		Histone	1.E-10	1.4	nuclear chromatin (1e-07)		0.006	10
yeast-235_GO-0009653	2	morphogenesis	[TPM]A[GSN]Q	29	[ST]Q	ATM kinase phosphorylation site		Ras	1.E-06	1.5	cellular morphogenesis (1e-33)		0.007	10
yeast-216_GO-0006325	2	establishment and/or maintenance of chromatin architecture	[VKI]LEY[LGC]	29	Y[VLTFIC]	LIG_SH2_STAT5		Histone	1.E-04	1.5	establishment and/or maintenance of chromatin architecture (1e-12)		0.005	9
yeast-216_GO-0006323	2	DNA packaging	[VKI]LEY[LGC]	29	Y[VLTFIC]	LIG_SH2_STAT5		Histone	1.E-04	1.5	establishment and/or maintenance of chromatin architecture (1e-12)		0.005	9
protein_40_YDR224C	2	HTB1:  One of two nearly identical (see HTB2) histone H2B subtypes required for chromatin assembly and chromosome function; Rad6p-Bre1p-Lge1p mediated ubiquitination regulates transcriptional activation, meiotic DSB formation and H3 methylation	[LD]Q[LTE]A	29				Histone	1.E-02	1.5	nuclear chromatin (1e-04)	Y	0.005	10
protein_40_YDL153C	2	SAS10:  Component of the small (ribosomal) subunit (SSU) processosome required for pre-18S rRNa processing; essential nucleolar protein that, when overproduced, disrupts silencing	TRWYR	29				Pkinase	1.E-02	1.5	protein amino acid phosphorylation (0.01)	Y	0.003	7
yeast-235_GO-0000902	2	cellular morphogenesis	[TPM]A[GSN]Q	29	[ST]Q	ATM kinase phosphorylation site		Ras	1.E-06	1.6	cellular morphogenesis (1e-33)		0.007	10
yeast-1340_GO-0044267	2	cellular protein metabolism	[GLK]P..TP[YLC]	29	[ST]P	LIG_WW_4		UQ_con	1.E-11	1.6	ubiquitin conjugating enzyme activity (1e-11)		0.006	10
protein_40_YMR229C	2	RRP5:  Protein required for the synthesis of both 18S and 5.8S rRNA; C-terminal region is crucial for the formation of 18S rRNA and N-terminal region is required for the 5.8S rRNA; component of small ribosomal subunit (SSU) processosome	R..A	29	R..[PA]DG	LIG_TNKBM	Y	Pkinase	1.E-07	1.7	nucleolus (1e-39)	Y	0.005	10
protein_40_YDR225W	2	HTA1:  One of two nearly identical (see also HTA2) histone H2A subtypes; core histone required for chromatin assembly and chromosome function; DNA damage-dependent phosphorylation by Mec1p facilitates DNA repair; acetylated by Nat4p	D.[GF]L	29	F.D.F	LIG_AP2alpha_1		IBN_N	1.E-02	1.7	protein carrier activity (1e-04)		0.005	10
protein_40_YBR106W	2	PHO88:  Probable membrane protein, involved in phosphate transport; pho88 pho86 double null mutant exhibits enhanced synthesis of repressible acid phosphatase at high inorganic phosphate concentrations	M[NFV].[YVM]L	29			Y	DUP	1.E-04	1.8		Y	0.005	10
protein_40_YML010W	2	SPT5:  Protein that forms a complex with Spt4p and mediates both activation and inhibition of transcription elongation; Spt4p-Spt5p complex also plays a role in pre-mRNA processing	Q..[NEG]V	29				DEAD	1.E-03	2	nuclear lumen (1e-12)	Y	0.005	10
yeast-205_GO-0005856	2	cytoskeleton	SS[REF]S[HID]	29	S[ST]	MDC1 BRCT domain binding motif		Kinesin	1.E-07	2.1	cytoskeletal part (1e-18)		0.006	10
yeast-921_GO-0006810	2	transport	L[YFG]V	29	LLG	Beta2-Integrin binding motif		MFS_1	1.E-04	2.2	intracellular transport (1e-78)		0.006	9
matsuyama_Spindle_or_SPB	2	matsuyama_Spindle_or_SPB	I[HLT]..[LNR]K	29				Pkinase	1.E-03	2.3	spindle (1e-43)		0.007	10
protein_40_YFR010W	2	UBP6:  Ubiquitin-specific protease situated in the base subcomplex of the 26S proteasome, releases free ubiquitin from branched polyubiquitin chains; deletion causes hypersensitivity to cycloheximide and other toxic compounds	[RDW]D.K[PEQ]	29				Pkinase	1.E-03	2.4	protein kinase activity (1e-04)	Y	0.006	8
protein_40_YNL272C	2	SEC2:  Guanyl-nucleotide exchange factor for the small G-protein Sec4p, located on cytoplasmic vesicles; essential for post-Golgi vesicle transport	M.Y[CM]	29	YM	SH2 ligand for Vav1 (group II) (phospho-peptide)		Pkinase	1.E-07	2.6	protein kinase activity (1e-06)	Y	0.003	9
yeast-631_GO-0050794	2	regulation of cellular process	RA[AKN][QPT]	29				bZIP_1	1.E-04	2.7	regulation of metabolism (1e-20)		0.006	10
protein_40_YLL008W	2	DRS1:  Nucleolar DEAD-box protein required for ribosome assembly and function, including synthesis of 60S ribosomal subunits; constituent of 66S pre-ribosomal particles	VA[IAF][KRM]	29	DVAD	Protease Caspase 2 -stringent		Pkinase	1.E-07	2.9	protein kinase activity (1e-07)		0.006	10
protein_40_YLR429W	2	CRN1:  Coronin, cortical actin cytoskeletal component that associates with the Arp2p/Arp3p complex to regulate its activity; plays a role in regulation of actin patch assembly	AP[EKN]	29	APAP	Motif for hydroxylation of Pro residues, which can further be modified with arabinogalactan		Pkinase	1.E-04	3	protein serine/threonine kinase activity (1e-04)		0.005	10
protein_40_YGR128C	2	UTP8:  Nucleolar protein required for export of tRNAs from the nucleus; also copurifies with the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	D..[EVD]K	29				WD40	1.E-06	3	processing of 20S pre-rRNA (1e-31)	Y	0.005	9
protein_40_YDR449C	2	UTP6:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	[AYV]T..[YMR]D	29	T..RDP.[FY][FYW]	HEMOCYANIN_2 PATTERN		WD40	1.E-03	3	snoRNA binding (1e-13)	Y	0.004	9
yeast-593_GO-0031981	2	nuclear lumen	TP..[VLH][LMF]D	29	[ST]P	LIG_WW_4		DEAD	1.E-06	3.2	nuclear lumen (1e-07)		0.006	8
protein_40_YLL008W	2	DRS1:  Nucleolar DEAD-box protein required for ribosome assembly and function, including synthesis of 60S ribosomal subunits; constituent of 66S pre-ribosomal particles	D.K[PKE]	29				Pkinase	1.E-11	3.3	cytoplasm organization and biogenesis (1e-20)		0.005	8
protein_40_YGL111W	2	NSA1:  Constituent of 66S pre-ribosomal particles, involved in 60S ribosomal subunit biogenesis	[REQ][EQW]LA	29	[KRHQSA][DENQ]EL	ER_TARGET PATTERN	Y	DEAD	1.E-03	3.3	cytoplasm organization and biogenesis (1e-12)	Y	0.006	10
protein_40_YAR019C	2	CDC15:  Protein kinase of the Mitotic Exit Network that is localized to the spindle pole bodies at late anaphase; promotes mitotic exit by directly switching on the kinase activity of Dbf2p	Y[LMH]H	29				Pkinase	1.E-19	3.3	protein kinase activity (1e-19)	Y	0.006	10
protein_40_YNL186W	2	UBP10:  Ubiquitin-specific protease that deubiquitinates ubiquitin-protein moieties; may regulate silencing by acting on Sir4p; involved in posttranscriptionally regulating Gap1p and possibly other transporters; primarily located in the nucleus	[IFV].HR	29			Y	Pkinase	1.E-22	3.5	protein kinase activity (1e-19)	Y	0.006	9
protein_40_YNL175C	2	NOP13:  Protein of unknown function, localizes to the nucleolus and nucleoplasm; contains an RNA recognition motif (RRM) and has similarity to Nop12p, which is required for processing of pre-18S rRNA	[LM]L.SA[TI]	29			Y	DEAD	1.E-06	3.5	RNA helicase activity (1e-05)		0.004	7
yeast-593_GO-0031981	2	nuclear lumen	TD.[SAP][KFA]R	29	[KR]R	CLV_PCSK_KEX2_1		Helicase_C	1.E-03	3.6	nuclear lumen (1e-08)		0.006	9
protein_40_YMR290C	2	HAS1:  ATP-dependent RNA helicase; localizes to both the nuclear periphery and nucleolus; highly enriched in nuclear pore complex fractions; constituent of 66S pre-ribosomal particles	R[ECF][LQT]A	29				DEAD	1.E-03	3.6	cytoplasm organization and biogenesis (1e-11)		0.006	10
matsuyama_periphery	2	matsuyama_periphery	G..[HLY]R	29	FQ...RG...R..[FY]	Myosin light chain binding motifs Type IA - Ca independent Smooth muscle		Pkinase	1.E-07	3.9	cell septum (1e-46)	Y	0.007	10
yeast-548_GO-0051641	2	cellular localization	KL[IVF]T	29				IBN_N	1.E-02	4	intracellular transport (1e-42)		0.006	10
protein_40_YGL245W	2	GUS1:  Glutamyl-tRNA synthetase (GluRS), forms a complex with methionyl-tRNA synthetase (Mes1p) and Arc1p; complex formation increases the catalytic efficiency of both tRNA synthetases and ensures their correct localization to the cytoplasm	[MRA]AP[ETR]	29	P[TS]AP	LIG_PTAP		Pkinase	1.E-12	4.3	protein kinase activity (1e-13)	Y	0.005	9
yeast-544_GO-0016070	2	RNA metabolism	DEA[DNP][RKQ]	29	[LIVMF][LIVMF]DEAD[RKEN].[LIVMFYGSTN]	DEAD_ATP_HELICASE PATTERN		DEAD	1.E-13	4.5	RNA helicase activity (1e-12)		0.006	8
protein_40_YKL172W	2	EBP2:  Essential protein required for the maturation of 25S rRNA and 60S ribosomal subunit assembly, localizes to the nucleolus; constituent of 66S pre-ribosomal particles	V[GKS]R[TRL]	29	[KR]R	CLV_PCSK_KEX2_1	Y	Helicase_C	1.E-02	4.5	cytoplasm organization and biogenesis (1e-11)		0.006	10
yeast-1464_GO-0019538	2	protein metabolism	[HDG]R..[KQ]P	29	R..K	SH3 binding motif for GADS SH3 recognizing slp-76 motif (nonconventional)	Y	Pkinase	1.E-28	5.4	protein amino acid phosphorylation (1e-32)		0.006	9
protein_40_YMR049C	2	ERB1:  Protein required for maturation of the 25S and 5.8S ribosomal RNAs; constituent of 66S pre-ribosomal particles; homologous to mammalian Bop1	[HGE]R.G[RCQ]	29	RGG	Alternative integrin binding site in FMDV virus		Helicase_C	1.E-04	6	ATP-dependent RNA helicase activity (1e-06)		0.006	10
yeast-661_GO-0050789	2	regulation of biological process	R.[HNT]T	29	R.[ST]	PKA consensus phosphorylation site		zf-C2H2	1.E-07	6.7	regulation of metabolism (1e-79)	Y	0.006	10
yeast-939_GO-0051234	2	establishment of localization	[LKQ]V..[ED]N	29							establishment of cellular localization (1e-28)		0.006	10
yeast-792_GO-0006412	2	protein biosynthesis	S.D[GNM]	29	S.D	CAMKII phosphorylation site							0.006	10
yeast-661_GO-0050789	2	regulation of biological process	[FTC]T..[TND]K	29	T..D	FHA1 binding motif, Thr must be phosphorylated, binding motif of proteins binding to Chk2					regulation of metabolism (1e-27)	Y	0.006	10
yeast-649_GO-0003676	2	nucleic acid binding	G[QPV][KHQ]R	29	[KR]R	CLV_PCSK_KEX2_1					nucleic acid binding (1e-28)		0.006	10
yeast-521_GO-0051649	2	establishment of cellular localization	E[SIV]..[DTM]A	29			Y				establishment of cellular localization (1e-48)		0.006	10
yeast-513_GO-0005515	2	protein binding	GS..[PQW][FQM]	29							protein binding (1e-29)	Y	0.006	10
yeast-512_GO-0046907	2	intracellular transport	[IMW]EL[LEC]	29							intracellular transport (1e-60)		0.006	10
yeast-470_GO-0006259	2	DNA metabolism	R[QKA]Q	29	KRKQISVR	Phosphorylase kinase substrate motif	Y				DNA metabolism (1e-11)	Y	0.006	10
yeast-468_GO-0051276	2	chromosome organization and biogenesis	L[LKT]..[QHM]Q	29							chromosome organization and biogenesis (sensu Eukaryota) (1e-45)		0.006	10
yeast-468_GO-0051276	2	chromosome organization and biogenesis	Q[KNQ]L[LEQ]	29							chromosome organization and biogenesis (1e-86)		0.006	10
yeast-437_GO-0044429	2	mitochondrial part	I..[KTP]S	29									0.006	10
yeast-410_GO-0007049	2	cell cycle	LI..[EFD][SEA]L	29							cell cycle (1e-19)		0.007	10
yeast-379_GO-0031975	2	envelope	E.E[LDC]	29	Y.E.E	Src phosphorylation site							0.006	10
yeast-379_GO-0031967	2	organelle envelope	E.E[LDC]	29	Y.E.E	Src phosphorylation site							0.006	10
yeast-371_GO-0009056	2	catabolism	[AQT]G..[TEA]A	29							catabolism (1e-50)		0.006	9
yeast-336_GO-0005783	2	endoplasmic reticulum	VA[LIF]	29							endoplasmic reticulum (1e-14)		0.006	10
yeast-320_GO-0006355	2	regulation of transcription, DNA-dependent	[DNH]G.[EMV]K	29							regulation of transcription, DNA-dependent (1e-42)		0.006	10
yeast-284_GO-0005740	2	mitochondrial envelope	F.I[LRN]	29									0.006	10
yeast-274_GO-0005840	2	ribosome	[EKV][AVE]AKK	29							ribosome (1e-22)		0.007	10
yeast-262_GO-0031224	2	intrinsic to membrane	F[GEQ].S[AM]	29							integral to membrane (1e-26)		0.007	10
yeast-262_GO-0031224	2	intrinsic to membrane	V.A[VYF]	29							intrinsic to membrane (1e-09)	Y	0.006	9
yeast-255_GO-0042254	2	ribosome biogenesis and assembly	R..A[RQL]	29							cytoplasm organization and biogenesis (1e-11)	Y	0.006	9
yeast-255_GO-0007028	2	cytoplasm organization and biogenesis	R..A[RQL]	29							cytoplasm organization and biogenesis (1e-11)	Y	0.006	9
yeast-251_GO-0005886	2	plasma membrane	[SYW]T..V[TYI]	29			Y				plasma membrane (1e-34)		0.006	10
yeast-251_GO-0005886	2	plasma membrane	Y[GYN]G	29	GGQ	N-methylation motif in E. coli, Gln residue in methylated, mimics CCA motif at the end of tRNA molecule					plasma membrane (1e-73)		0.006	10
yeast-248_GO-0043285	2	biopolymer catabolism	AL.[AG][YTW]S	29							biopolymer catabolism (1e-07)		0.004	7
yeast-248_GO-0031966	2	mitochondrial membrane	K.[KTI]K	29	P.[ST]PKK.KK	Cdc2 like protein kinase substrate motif							0.006	10
yeast-238_GO-0017111	2	nucleoside-triphosphatase activity	I.G[PNR]	29	GP	Protease TTP cleavage site	Y				nucleoside-triphosphatase activity (1e-95)		0.006	10
yeast-222_GO-0009308	2	amine metabolism	A[LKF]..[MCY]G	29							amine metabolism (1e-27)		0.007	10
yeast-222_GO-0009308	2	amine metabolism	A[VRL]..[EYD]T	29							amine metabolism (1e-40)		0.006	10
yeast-219_GO-0046903	2	secretion	[ESC]N.IK[SLD]	29							secretory pathway (1e-12)	Y	0.005	8
yeast-215_GO-0007010	2	cytoskeleton organization and biogenesis	[LVC]E..Q[AM]	29			Y				cytoskeleton organization and biogenesis (1e-21)		0.007	10
yeast-215_GO-0007010	2	cytoskeleton organization and biogenesis	[PNL]T[NEL]I	29	PTL	Motif in Fos for proteosome degredation					cytoskeleton organization and biogenesis (1e-55)		0.006	10
yeast-215_GO-0007010	2	cytoskeleton organization and biogenesis	S..[IRM]N	29							cytoskeleton organization and biogenesis (1e-12)	Y	0.006	9
yeast-203_GO-0005975	2	carbohydrate metabolism	D..[NVL]S	29							carbohydrate metabolism (1e-14)		0.006	10
yeast-1547_GO-0043283	2	biopolymer metabolism	Y[IVT]..Y[LDQ]	29	Y[VLTFIC]	LIG_SH2_STAT5					DNA metabolism (0.001)		0.006	10
protein_40_YPR120C	2	CLB5:  B-type cyclin involved in DNA replication during S phase; activates Cdc28p to promote initiation of DNA synthesis; functions in formation of mitotic spindles along with Clb3p and Clb4p; most abundant during late G1 phase	L.[SRP]P	29	[ST]P	LIG_WW_4	Y					Y	0.005	10
protein_40_YPR120C	2	CLB5:  B-type cyclin involved in DNA replication during S phase; activates Cdc28p to promote initiation of DNA synthesis; functions in formation of mitotic spindles along with Clb3p and Clb4p; most abundant during late G1 phase	R.L[KSC]	29	R.L	Cyclin A motif that binds cdk2 complexes						Y	0.005	9
protein_40_YPR119W	2	CLB2:  B-type cyclin involved in cell cycle progression; activates Cdc28p to promote the transition from G2 to M phase; accumulates during G2 and M, then targeted via a destruction box motif for ubiquitin-mediated degradation by the proteasome	[YMH]G..N[NDS]	29			Y					Y	0.006	10
protein_40_YPR034W	2	ARP7:  Component of both the SWI/SNF and RSC chromatin remodeling complexes; actin-related protein involved in transcriptional regulation	[QGC]N.L[IPV]	29							chromatin remodeling complex (1e-10)		0.005	9
protein_40_YPR034W	2	ARP7:  Component of both the SWI/SNF and RSC chromatin remodeling complexes; actin-related protein involved in transcriptional regulation	[RF]TF[TDR]	29							SWI/SNF complex (0.01)		0.004	9
protein_40_YPL240C	2	HSP82:  Hsp90 chaperone required for pheromone signaling and negative regulation of Hsf1p; docks with Tom70p for mitochondrial preprotein delivery; promotes telomerase DNA binding and nucleotide addition; interacts with Cns1p, Cpr6p, Cpr7p, Sti1p	F[NIL]S[SDK]	29	S[ST]	MDC1 BRCT domain binding motif						Y	0.005	10
protein_40_YPL240C	2	HSP82:  Hsp90 chaperone required for pheromone signaling and negative regulation of Hsf1p; docks with Tom70p for mitochondrial preprotein delivery; promotes telomerase DNA binding and nucleotide addition; interacts with Cns1p, Cpr6p, Cpr7p, Sti1p	LL.D[VGQ][VFQ]	29	LLG	Beta2-Integrin binding motif							0.005	10
protein_40_YPL240C	2	HSP82:  Hsp90 chaperone required for pheromone signaling and negative regulation of Hsf1p; docks with Tom70p for mitochondrial preprotein delivery; promotes telomerase DNA binding and nucleotide addition; interacts with Cns1p, Cpr6p, Cpr7p, Sti1p	T...Y	29									0.006	10
protein_40_YPL204W	2	HRR25:  Protein kinase involved in regulating diverse events including vesicular trafficking, DNA repair, and chromosome segregation; binds the CTD of RNA pol II; homolog of mammalian casein kinase 1delta (CK1delta)	K.G[KMR]	29							ribosome biogenesis (0.01)		0.005	8
protein_40_YPL153C	2	RAD53:  Protein kinase, required for cell-cycle arrest in response to DNA damage; activated by trans autophosphorylation when interacting with hyperphosphorylated Rad9p; also interacts with ARS1 and plays a role in initiation of DNA replication	[DAE]K..I[TNK]	29								Y	0.006	10
protein_40_YPL151C	2	PRP46:  Splicing factor that is found in the Cef1p subcomplex of the spliceosome	TE[VY][LGR]	29	TEY	MEK phosphorylation of MAPK activation sites - stringent					nuclear mRNA splicing, via spliceosome (1e-08)		0.005	10
protein_40_YPL043W	2	NOP4:  Nucleolar protein, essential for processing and maturation of 27S pre-rRNA and large ribosomal subunit biogenesis; constituent of 66S pre-ribosomal particles; contains four RNA recognition motifs (RRMs)	[FGA]R.I[SPM]	29	[AG]R	Protease matriptase protease site					rRNA metabolism (1e-10)		0.005	8
protein_40_YPL043W	2	NOP4:  Nucleolar protein, essential for processing and maturation of 27S pre-rRNA and large ribosomal subunit biogenesis; constituent of 66S pre-ribosomal particles; contains four RNA recognition motifs (RRMs)	D.E[EHI]	29	SD.E	Casein kinase II substrate motif					nucleolus (1e-28)		0.006	10
protein_40_YPL012W	2	RRP12:  Protein required for export of the ribosomal subunits; associates with the RNA components of the pre-ribosomes; contains HEAT-repeats	R..[KRD]T	29	R..K	SH3 binding motif for GADS SH3 recognizing slp-76 motif (nonconventional)					nucleolus (1e-24)	Y	0.005	10
protein_40_YOR326W	2	MYO2:  One of two type V myosin motors (along with MYO4) involved in actin-based transport of cargos; required for the polarized delivery of secretory vesicles, the vacuole, late Golgi elements, peroxisomes, and the mitotic spindle	L[AMH][TGD]V	29									0.005	9
protein_40_YOR310C	2	NOP58:  Protein involved in pre-rRNA processing, 18S rRNA synthesis, and snoRNA synthesis; component of the small subunit processome complex, which is required for processing of pre-18S rRNA	R[AVS]Q[LKF]	29	[ST]Q	ATM kinase phosphorylation site					ribosome biogenesis (1e-10)		0.006	10
protein_40_YOR272W	2	YTM1:  Constituent of 66S pre-ribosomal particles, required for maturation of the large ribosomal subunit	VG..[EIG][NTH]	29							cytoplasm organization and biogenesis (1e-09)		0.005	9
protein_40_YOR206W	2	NOC2:  Protein that forms a nucleolar complex with Mak21p that binds to 90S and 66S pre-ribosomes, as well as a nuclear complex with Noc3p that binds to 66S pre-ribosomes; both complexes mediate intranuclear transport of ribosomal precursors	E[AED].V[PKS]	29	EEEYV	PDGF receptor kinase phosphorylation site (peptide screen)	Y				nucleolus (1e-13)	Y	0.006	10
protein_40_YOR174W	2	MED4:  Subunit of the RNA polymerase II mediator complex; associates with core polymerase subunits to form the RNA polymerase II holoenzyme; essential for transcriptional regulation	NG[SNI][SNA]	29							general RNA polymerase II transcription factor activity (1e-15)		0.006	9
protein_40_YOR133W	2	EFT1:  Elongation factor 2 (EF-2), also encoded by EFT2; catalyzes ribosomal translocation during protein synthesis; contains diphthamide, the unique posttranslationally modified histidine residue specifically ADP-ribosylated by diphtheria toxin	T[VSD].V[ELF]	29									0.006	10
protein_40_YOR133W	2	EFT1:  Elongation factor 2 (EF-2), also encoded by EFT2; catalyzes ribosomal translocation during protein synthesis; contains diphthamide, the unique posttranslationally modified histidine residue specifically ADP-ribosylated by diphtheria toxin	TV[AGE]	29	YTV	14-3-3 domain binding motif					translation elongation factor activity (0.001)		0.005	10
protein_40_YOL139C	2	CDC33:  Cytoplasmic mRNA cap binding protein; the eIF4E-cap complex is responsible for mediating cap-dependent mRNA translation via interactions with the translation initiation factor eIF4G (Tif4631p or Tif4632p)	T[VQK]..I[LAH]	29			Y						0.006	10
protein_40_YOL133W	2	HRT1:  RING finger containing subunit of Skp1-Cullin-F-box ubiquitin protein ligases (SCF); required for Gic2p, Far1p, Sic1p and Cln2p degradation; may tether Cdc34p (a ubiquitin conjugating enzyme or E2) and Cdc53p (a cullin) subunits of SCF	[DEG]E.F[STD]	29	EEEYF	EGFR kinase phosphorylation site (peptide screen)					catabolism (0.001)	Y	0.006	8
protein_40_YOL086C	2	ADH1:  Alcohol dehydrogenase, fermentative isozyme active as homo- or heterotetramers; required for the reduction of acetaldehyde to ethanol, the last step in the glycolytic pathway	K[QVH].N[VWT]	29								Y	0.004	7
protein_40_YOL086C	2	ADH1:  Alcohol dehydrogenase, fermentative isozyme active as homo- or heterotetramers; required for the reduction of acetaldehyde to ethanol, the last step in the glycolytic pathway	P[ETF][VRD]K	29	P[ST]	DNA dependent Protein kinase substrate motif	Y						0.005	8
protein_40_YOL069W	2	NUF2:  Component of the evolutionarily conserved kinetochore-associated Ndc80 complex (Ndc80p-Nuf2p-Spc24p-Spc25p); involved in chromosome segregation, spindle checkpoint activity and kinetochore clustering	[VKP]DS[TEG]	29	[DE]S[DE].[DE]	Casein Kinase II substrate motif							0.005	10
protein_40_YOL069W	2	NUF2:  Component of the evolutionarily conserved kinetochore-associated Ndc80 complex (Ndc80p-Nuf2p-Spc24p-Spc25p); involved in chromosome segregation, spindle checkpoint activity and kinetochore clustering	RR..[EST][ETG]	29	R..[ST]	CamKII consensus phosphorylation site					microtubule cytoskeleton (0.001)		0.006	10
protein_40_YOL013C	2	HRD1:  Ubiquitin-protein ligase required for endoplasmic reticulum-associated degradation (ERAD) of misfolded proteins; genetically linked to the unfolded protein response (UPR); regulated through association with Hrd3p; contains an H2 ring finger	A[NDR].I[ADF]	29									0.005	9
protein_40_YNL308C	2	KRI1:  Essential nucleolar protein required for 40S ribosome biogenesis; physically and functionally interacts with Krr1p	A.R[IDP]	29			Y				rRNA processing (1e-09)		0.006	9
protein_40_YNL307C	2	MCK1:  Protein serine/threonine/tyrosine (dual-specificity) kinase involved in control of chromosome segregation and in regulating entry into meiosis; related to mammalian glycogen synthase kinases of the GSK-3 family	E..V	29									0.005	10
protein_40_YNL307C	2	MCK1:  Protein serine/threonine/tyrosine (dual-specificity) kinase involved in control of chromosome segregation and in regulating entry into meiosis; related to mammalian glycogen synthase kinases of the GSK-3 family	P.[IAS]A	29									0.005	10
protein_40_YNL307C	2	MCK1:  Protein serine/threonine/tyrosine (dual-specificity) kinase involved in control of chromosome segregation and in regulating entry into meiosis; related to mammalian glycogen synthase kinases of the GSK-3 family	S.E[ESY]	29	LSQE	ATM kinase substrate motif						Y	0.006	10
protein_40_YNL289W	2	PCL1:  Pho85 cyclin of the Pcl1,2-like subfamily, involved in entry into the mitotic cell cycle and regulation of morphogenesis, localizes to sites of polarized cell growth	S..T[SNP]	29	S..[ST]	Casein Kinase I consensus phosphorylation site (N-term Ser must first be phosphorylated)							0.006	10
protein_40_YNL154C	2	YCK2:  Palmitoylated, plasma membrane-bound casein kinase I isoform; shares redundant functions with Yck1p in morphogenesis, proper septin assembly, endocytic trafficking; provides an essential function overlapping with that of Yck1p	GL..[DTV][RDE]	29			Y				cytokinesis (0.01)		0.005	10
protein_40_YNL154C	2	YCK2:  Palmitoylated, plasma membrane-bound casein kinase I isoform; shares redundant functions with Yck1p in morphogenesis, proper septin assembly, endocytic trafficking; provides an essential function overlapping with that of Yck1p	Q[DIG]..P[SIY]	29	P[ST]	DNA dependent Protein kinase substrate motif						Y	0.006	10
protein_40_YNL132W	2	KRE33:  Essential protein of unknown function; heterozygous mutant shows haploinsufficiency in K1 killer toxin resistance	V[RQF]V	29	RALAHGVRVL	Mitochondrial targetting motif in hepititis C core protein					cytoplasm organization and biogenesis (1e-17)		0.005	9
protein_40_YNL118C	2	DCP2:  Catalytic subunit of the Dcp1p-Dcp2p decapping enzyme complex, which removes the 5' cap structure from mRNAs prior to their degradation; member of the Nudix hydrolase family	K[SAW].[TDA]F	29								Y	0.005	8
protein_40_YNL118C	2	DCP2:  Catalytic subunit of the Dcp1p-Dcp2p decapping enzyme complex, which removes the 5' cap structure from mRNAs prior to their degradation; member of the Nudix hydrolase family	R[AKW]..L[LK]	29			Y					Y	0.006	10
protein_40_YNL055C	2	POR1:  Mitochondrial porin (voltage-dependent anion channel), outer membrane protein required for the maintenance of mitochondrial osmotic stability and mitochondrial membrane permeability; phosphorylated	RV[GHE][GQI]	29	VEID	Protease Caspase 6 -stringent							0.004	9
protein_40_YNL031C	2	HHT2:  One of two identical histone H3 proteins (see also HHT1); core histone required for chromatin assembly, involved in heterochromatin-mediated telomeric and HM silencing; regulated by acetylation, methylation, and mitotic phosphorylation	DE[DTW][GIR]	29	YDE[PDV]	SH2 ligand for Nck1 and Nck2 (Tyr must be phosphorylated)					transcription, DNA-dependent (1e-04)		0.006	9
protein_40_YMR304W	2	UBP15:  Ubiquitin-specific protease that may play a role in ubiquitin precursor processing	[LKM]Q[RVQ]E	29			Y				establishment and/or maintenance of cell polarity (sensu Fungi) (0.01)		0.005	9
protein_40_YMR290C	2	HAS1:  ATP-dependent RNA helicase; localizes to both the nuclear periphery and nucleolus; highly enriched in nuclear pore complex fractions; constituent of 66S pre-ribosomal particles	A.R	29	[RK].PNS[AR].R	RIBOSOMAL_S12 PATTERN					cytoplasm organization and biogenesis (1e-40)		0.005	10
protein_40_YMR288W	2	HSH155:  U2-snRNP associated splicing factor that forms extensive associations with the branch site-3' splice site-3' exon region upon prespliceosome formation; similarity to the mammalian U2 snRNP-associated splicing factor SAP155	K..[KQ]V	29	K...VPK...V	Endothelin receptor motif required for endothelin stimulation					nuclear mRNA splicing, via spliceosome (1e-38)		0.006	10
protein_40_YMR236W	2	TAF9:  Subunit (17 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation and in chromatin modification, similar to histone H3	G[ELA][DYW]D	29	[WFY]G[PDE][WFYLM]	gamma-adaptin ear binding motif					transcription factor complex (1e-11)	Y	0.005	9
protein_40_YMR229C	2	RRP5:  Protein required for the synthesis of both 18S and 5.8S rRNA; C-terminal region is crucial for the formation of 18S rRNA and N-terminal region is required for the 5.8S rRNA; component of small ribosomal subunit (SSU) processosome	[GPH]R[KHR]V	29	[AG]R	Protease matriptase protease site					nucleolus (0.001)		0.006	10
protein_40_YMR142C	2	RPL13B:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl13Ap; not essential for viability; has similarity to rat L13 ribosomal protein	K[IVT]R[AG]	29							cytosolic ribosome (sensu Eukaryota) (1e-09)		0.004	8
protein_40_YMR047C	2	NUP116:  Subunit of the nuclear pore complex (NPC) that is localized to both sides of the pore; contains a repetitive GLFG motif that interacts with mRNA export factor Mex67p and with karyopherin Kap95p; homologous to Nup100p	Q.[KQC]P	29							nuclear pore (1e-19)	Y	0.006	10
protein_40_YMR012W	2	CLU1:  eIF3 component of unknown function; deletion causes defects in mitochondrial organization but not in growth or translation initiation, can rescue cytokinesis and mitochondrial organization defects of the Dictyostelium cluA- mutant	[GTY]V..T[FHM]	29									0.005	8
protein_40_YMR001C	2	CDC5:  Polo-like kinase with similarity to Xenopus Plx1 and S. pombe Plo1p; found at bud neck, nucleus and SPBs; has multiple functions in mitosis and cytokinesis through phosphorylation of substrates; may be a Cdc28p substrate	N[KLV][DAN]G	29							microtubule cytoskeleton organization and biogenesis (0.01)		0.006	10
protein_40_YMR001C	2	CDC5:  Polo-like kinase with similarity to Xenopus Plx1 and S. pombe Plo1p; found at bud neck, nucleus and SPBs; has multiple functions in mitosis and cytokinesis through phosphorylation of substrates; may be a Cdc28p substrate	V[IKH].K[QAK]	29							M phase (1e-04)		0.005	10
protein_40_YML069W	2	POB3:  Subunit of the heterodimeric FACT complex (Spt16p-Pob3p), which facilitates RNA Pol II transcription elongation through nucleosomes by destabilizing and then reassembling nucleosome structure; interacts with DNA polymerase alpha (Pol1p)	[DYW]E.E[DAN]	29	YE	TPK-IIB/P38Syk kinase phosphorylation site (peptide screen)					RNA elongation from RNA polymerase II promoter (1e-10)		0.006	10
protein_40_YLR448W	2	RPL6B:  Protein component of the large (60S) ribosomal subunit, has similarity to Rpl6Ap and to rat L6 ribosomal protein; binds to 5.8S rRNA	A[PAG]K[IGR]	29	KR	CLV_PCSK_PC1ET2_1					cytosolic ribosome (sensu Eukaryota) (1e-14)	Y	0.006	10
protein_40_YLR372W	2	SUR4:  Elongase, involved in fatty acid and sphingolipid biosynthesis; synthesizes very long chain 20-26-carbon fatty acids from C18-CoA primers; involved in regulation of sphingolipid biosynthesis	T[LWF]..[AGR]V	29									0.006	10
protein_40_YLR287C-A	2	RPS30A:  Protein component of the small (40S) ribosomal subunit; nearly identical to Rps30Bp and has similarity to rat S30 ribosomal protein	A[RGA].[KPY]A	29							cytosolic ribosome (sensu Eukaryota) (1e-21)		0.006	10
protein_40_YLR222C	2	UTP13:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	L[TKN]G[QG]	29	LFG	Protease Papain substrate, a prototype cysteine proteinase	Y				small nucleolar ribonucleoprotein complex (1e-11)	Y	0.005	9
protein_40_YLR186W	2	EMG1:  Protein required for the maturation of the 18S rRNA and for 40S ribosome production; associated with spindle/microtubules; nuclear localization depends on physical interaction with Nop14p; may bind snoRNAs	[ADT][FKN].KF	29							rRNA processing (1e-12)	Y	0.005	9
protein_40_YLR180W	2	SAM1:  S-adenosylmethionine synthetase, catalyzes transfer of the adenosyl group of ATP to the sulfur atom of methionine; one of two differentially regulated isozymes (Sam1p and Sam2p)	D.R[DRV]	29							carboxylic acid metabolism (0.01)	Y	0.005	9
protein_40_YLR180W	2	SAM1:  S-adenosylmethionine synthetase, catalyzes transfer of the adenosyl group of ATP to the sulfur atom of methionine; one of two differentially regulated isozymes (Sam1p and Sam2p)	NL.[LP][RS]K	29								Y	0.003	8
protein_40_YLR166C	2	SEC10:  Essential 100kDa subunit of the exocyst complex (Sec3p, Sec5p, Sec6p, Sec8p, Sec10p, Sec15p, Exo70p, and Exo84p), which has the essential function of mediating polarized targeting of secretory vesicles to active sites of exocytosis	E[KEA]A[EKT]	29							exocyst (1e-04)		0.006	10
protein_40_YLR129W	2	DIP2:  Nucleolar protein, specifically associated with the U3 snoRNA, part of the large ribonucleoprotein complex known as the small subunit (SSU) processome, required for 18S rRNA biogenesis, part of the active pre-rRNA processing complex	[KPF]D..[TGA]K	29	D..G	motif that binds phosphate in GDP and GTP binding proteins					rRNA processing (1e-18)	Y	0.006	9
protein_40_YLR129W	2	DIP2:  Nucleolar protein, specifically associated with the U3 snoRNA, part of the large ribonucleoprotein complex known as the small subunit (SSU) processome, required for 18S rRNA biogenesis, part of the active pre-rRNA processing complex	K[QVA]..L[IQG]	29							rRNA processing (1e-21)	Y	0.006	10
protein_40_YLR106C	2	MDN1:  Huge dynein-related AAA-type ATPase (midasin), forms extended pre-60S particle with the Rix1 complex (Rix1p-Ipi1p-Ipi3p), may mediate ATP-dependent remodeling of 60S subunits and subsequent export from nucleoplasm to cytoplasm	AG.[NSV][TAW]	29			Y						0.005	9
protein_40_YLR096W	2	KIN2:  Serine/threonine protein kinase involved in regulation of exocytosis; localizes to the cytoplasmic face of the plasma membrane; closely related to Kin1p	[SDR][TDW].SL	29									0.006	10
protein_40_YLR074C	2	BUD20:  Protein involved in bud-site selection; diploid mutants display a random budding pattern instead of the wild-type bipolar pattern	A[VW][TRV]K	29								Y	0.005	9
protein_40_YLR074C	2	BUD20:  Protein involved in bud-site selection; diploid mutants display a random budding pattern instead of the wild-type bipolar pattern	R[AEN][APQ]R	29	[AG]R	Protease matriptase protease site	Y				ribosomal large subunit biogenesis (0.001)		0.005	9
protein_40_YLL045C	2	RPL8B:  Ribosomal protein L4 of the large (60S) ribosomal subunit, nearly identical to Rpl8Ap and has similarity to rat L7a ribosomal protein; mutation results in decreased amounts of free 60S subunits	A..V[AED]	29							cytosolic ribosome (sensu Eukaryota) (1e-21)		0.005	9
protein_40_YKR026C	2	GCN3:  Alpha subunit of the translation initiation factor eIF2B, the guanine-nucleotide exchange factor for eIF2; activity subsequently regulated by phosphorylated eIF2; first identified as a positive regulator of GCN4 expression	G[SAH][NKY]V	29							eukaryotic translation initiation factor 2B complex (0.001)		0.005	10
protein_40_YKL203C	2	TOR2:  PIK-related protein kinase and rapamycin target; subunit of TORC1, a complex that regulates growth in response to nutrients and TORC2, a complex that regulates cell-cycle dependent polarization of the actin cytoskeleton; involved in meiosis	G[IMA]..[LMD]S	29							plasma membrane (1e-06)	Y	0.006	10
protein_40_YKL203C	2	TOR2:  PIK-related protein kinase and rapamycin target; subunit of TORC1, a complex that regulates growth in response to nutrients and TORC2, a complex that regulates cell-cycle dependent polarization of the actin cytoskeleton; involved in meiosis	I.[LMR]I	29							plasma membrane (1e-17)	Y	0.006	9
protein_40_YKL172W	2	EBP2:  Essential protein required for the maturation of 25S rRNA and 60S ribosomal subunit assembly, localizes to the nucleolus; constituent of 66S pre-ribosomal particles	EE[ERV][EG]	29	YEE[IV]	SH2 ligand group 1A, Src FGR SH2 domain (needs to be Tyr phosphorylated)					cytoplasm organization and biogenesis (1e-20)	Y	0.006	10
protein_40_YKL104C	2	GFA1:  Glutamine-fructose-6-phosphate amidotransferase, catalyzes the formation of glucosamine-6-P and glutamate from fructose-6-P and glutamine in the first step of chitin biosynthesis	D..L[RAQ]	29			Y				INO80 complex (0.001)	Y	0.005	8
protein_40_YKL065C	2	YET1:  Endoplasmic reticulum transmembrane protein; may interact with ribosomes, based on co-purification experiments; homolog of human BAP31 protein	[GWM]L..L[IPC]	29	[LV][DE].[LM][LM]..L	LIG_PXL					cation transporter activity (0.01)		0.005	9
protein_40_YJR123W	2	RPS5:  Protein component of the small (40S) ribosomal subunit, the least basic of the non-acidic ribosomal proteins; phosphorylated in vivo; essential for viability; has similarity to E. coli S7 and rat S5 ribosomal proteins	AG[KRH][GFC]	29							cytosolic ribosome (sensu Eukaryota) (1e-04)		0.005	10
protein_40_YJR059W	2	PTK2:  Putative serine/threonine protein kinase involved in regulation of ion transport across plasma membrane; enhances spermine uptake	A..[HET]S	29	[VA]P[IL]A..E[SD]D	Ankryn G binding motif in voltage gated sodium channels							0.005	10
protein_40_YJL190C	2	RPS22A:  Protein component of the small (40S) ribosomal subunit; nearly identical to Rps22Bp and has similarity to E. coli S8 and rat S15a ribosomal proteins	K[KRP]A	29	KR	CLV_PCSK_PC1ET2_1					cytosolic part (1e-23)		0.005	8
protein_40_YJL109C	2	UTP10:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	[RFY]VD[IPC]	29							nucleolus (1e-08)		0.005	9
protein_40_YJL095W	2	BCK1:  Mitogen-activated protein (MAP) kinase kinase kinase acting in the protein kinase C signaling pathway, which controls cell integrity; upon activation by Pkc1p phosphorylates downstream kinases Mkk1p and Mkk2p	A[AMI]E[VYL]	29	AEVD	Protease Caspase 10	Y						0.006	9
protein_40_YJL092W	2	SRS2:  DNA helicase and DNA-dependent ATPase involved in DNA repair, needed for proper timing of commitment to meiotic recombination and transition from Meiosis I to II; affects genome stability by suppressing unscheduled homologous recombination	[SER]I.[VNW]E	29			Y						0.006	10
protein_40_YJL074C	2	SMC3:  Subunit of the multiprotein cohesin complex required for sister chromatid cohesion in mitotic cells; also required, with Rec8p, for cohesion and recombination during meiosis; phylogenetically conserved SMC chromosomal ATPase family member	V[DCK].A[LTY]	29									0.005	10
protein_40_YIL144W	2	TID3:  Component of the evolutionarily conserved kinetochore-associated Ndc80 complex (Ndc80p-Nuf2p-Spc24p-Spc25p); conserved coiled-coil protein involved in chromosome segregation, spindle checkpoint activity, kinetochore assembly and clustering	Q[LQE]..[LYA]E	29	YE	TPK-IIB/P38Syk kinase phosphorylation site (peptide screen)					microtubule cytoskeleton organization and biogenesis (1e-05)		0.006	10
protein_40_YIL133C	2	RPL16A:  N-terminally acetylated protein component of the large (60S) ribosomal subunit, binds to 5.8 S rRNA; has similarity to Rpl16Bp, E. coli L13 and rat L13a ribosomal proteins; transcriptionally regulated by Rap1p	[AHK][GV]..RG	29							cytoplasm organization and biogenesis (1e-05)		0.005	9
protein_40_YIL075C	2	RPN2:  Subunit of the 26S proteasome, substrate of the N-acetyltransferase Nat1p	A[TKQ].[VAM]D	29							proteasome complex (sensu Eukaryota) (1e-04)		0.005	9
protein_40_YIL061C	2	SNP1:  Component of U1 snRNP required for mRNA splicing via spliceosome; may interact with poly(A) polymerase to regulate polyadenylation; homolog of human U1 70K protein	RL[EMW][KVI]	29	LEVD	Protease Caspase 4-stringent					mRNA metabolism (0.001)		0.006	10
protein_40_YIL061C	2	SNP1:  Component of U1 snRNP required for mRNA splicing via spliceosome; may interact with poly(A) polymerase to regulate polyadenylation; homolog of human U1 70K protein	Y.[RDC]E	29	FRY.CEG	REL_1 PATTERN					small nuclear ribonucleoprotein complex (1e-07)		0.005	8
protein_40_YHR203C	2	RPS4B:  Protein component of the small (40S) ribosomal subunit; identical to Rps4Ap and has similarity to rat S4 ribosomal protein	R..[VA]R	29	[AG]R	Protease matriptase protease site					cytosolic ribosome (sensu Eukaryota) (1e-18)		0.006	9
protein_40_YHR197W	2	RIX1:  Essential component of the Rix1 complex (Rix1p, Ipi1p, Ipi3p) that is required for processing of ITS2 sequences from 35S pre-rRNA; Rix1 complex associates with Mdn1p in pre-60S ribosomal particles	[VKP]K..[SKA]K	29	K..[ST]	PKA kinase substrate motif	Y				cytoplasm organization and biogenesis (1e-22)		0.006	8
protein_40_YHR196W	2	UTP9:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	[QYG]G.K[ILG]	29							rRNA processing (1e-14)	Y	0.006	10
protein_40_YHR196W	2	UTP9:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	K[LEC]D	29	[NT]K.D	Motif for binding guanine nucleotides					nucleolus (1e-29)	Y	0.005	10
protein_40_YHR082C	2	KSP1:  Nonessential putative serine/threonine protein kinase of unknown cellular role; overproduction causes allele-specific suppression of the prp20-10 mutation	VT.[NDW][DFS]	29									0.005	10
protein_40_YHR079C	2	IRE1:  Serine-threonine kinase and endoribonuclease; transmembrane protein that mediates the unfolded protein response (UPR) by regulating Hac1p synthesis through HAC1 mRNA splicing; Kar2p binds inactive Ire1p and releases from it upon ER stress	S..R[GHP]	29	R..[ST]..R	CLK1 kinase substrate motif						Y	0.006	10
protein_40_YHR064C	2	SSZ1:  Hsp70 protein that interacts with Zuo1p (a DnaJ homolog) to form a ribosome-associated complex that binds the ribosome via the Zuo1p subunit; also involved in pleiotropic drug resistance via sequential activation of PDR1 and PDR5; binds ATP	D[NAY]..[VR]T	29									0.005	9
protein_40_YHR030C	2	SLT2:  Serine/threonine MAP kinase involved in regulating the maintenance of cell wall integrity and progression through the cell cycle; regulated by the PKC1-mediated signaling pathway	ST[DTM][DIK]	29	S[ST]	MDC1 BRCT domain binding motif					signal transduction (0.001)		0.006	10
protein_40_YHL034C	2	SBP1:  Putative RNA binding protein; involved in translational repression and found in cytoplasmic P bodies; found associated with small nucleolar RNAs snR10 and snR11	[RDP][VKE]AA	29							ribonucleoprotein complex (1e-07)		0.006	10
protein_40_YGR274C	2	TAF1:  TFIID subunit (145 kDa), involved in RNA polymerase II transcription initiation, has histone acetyltransferase activity, involved in promoter binding and G1/S progression	E[KQP]D[EDF]	29	IEPD	Protease Granzyme B					transcription factor complex (1e-07)		0.006	10
protein_40_YGR218W	2	CRM1:  Major karyopherin, involved in export of proteins, RNAs, and ribosomal subunits from the nucleus	[KAT]V.[AVI]K	29								Y	0.006	10
protein_40_YGR218W	2	CRM1:  Major karyopherin, involved in export of proteins, RNAs, and ribosomal subunits from the nucleus	Q..[QGV]E	29								Y	0.005	10
protein_40_YGR128C	2	UTP8:  Nucleolar protein required for export of tRNAs from the nucleus; also copurifies with the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	V[GT].[SR]TR	29								Y	0.003	7
protein_40_YGR090W	2	UTP22:  Possible U3 snoRNP protein involved in maturation of pre-18S rRNA, based on computational analysis of large-scale protein-protein interaction data	R[PGH]G[RDH]	29	GGRGG	Arginine methyl transferease substrate motif (PRMT1)					35S primary transcript processing (1e-04)	Y	0.005	10
protein_40_YGR085C	2	RPL11B:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl11Ap; involved in ribosomal assembly; depletion causes degradation of proteins and RNA of the 60S subunit; has similarity to E. coli L5 and rat L11	AA..[ARC][EHA]	29							cytosolic ribosome (sensu Eukaryota) (1e-27)		0.006	8
protein_40_YGR040W	2	KSS1:  Mitogen-activated protein kinase (MAPK) involved in signal transduction pathways that control filamentous growth and pheromone response; the KSS1 gene is nonfunctional in S288C strains and functional in W303 strains	AN[STR]	29			Y				cell growth (0.01)	Y	0.005	10
protein_40_YGR040W	2	KSS1:  Mitogen-activated protein kinase (MAPK) involved in signal transduction pathways that control filamentous growth and pheromone response; the KSS1 gene is nonfunctional in S288C strains and functional in W303 strains	K[KGP]..L[SDE]	29								Y	0.005	9
protein_40_YGL195W	2	GCN1:  Positive regulator of the Gcn2p kinase activity, forms a complex with Gcn20p; proposed to stimulate Gcn2p activation by an uncharged tRNA	G[LVC]..[NKY]V	29									0.005	10
protein_40_YGL180W	2	ATG1:  Protein serine/threonine kinase, required for vesicle formation during autophagy and the cytoplasm-to-vacuole targeting (Cvt) pathway; structurally required for pre-autophagosome formation; forms a complex with Atg13p and Atg17p	D.P	29	DLPPP	EVH1 binding motif							0.005	10
protein_40_YGL179C	2	TOS3:  Protein kinase, related to and functionally redundant with Elm1p and Sak1p for the phosphorylation and activation of Snf1p; functionally orthologous to LKB1, a mammalian kinase associated with Peutz-Jeghers cancer-susceptibility syndrome	[SRH]DQ[NQR]	29									0.005	10
protein_40_YGL173C	2	KEM1:  Evolutionarily-conserved 5'-3' exonuclease component of cytoplasmic processing (P) bodies involved in mRNA decay; plays a role in microtubule-mediated processes, filamentous growth, ribosomal RNA maturation, and telomere maintenance	[ET]S.[SG]LT	29									0.003	7
protein_40_YGL137W	2	SEC27:  Essential beta'-coat protein of the COPI coatomer, involved in ER-to-Golgi and Golgi-to-ER transport; contains WD40 domains that mediate cargo selective interactions; 45% sequence identity to mammalian beta'-COP	A[EG]A[QFE]	29	CL[LV]A.A[LVF]A	CASEIN_ALPHA_BETA PATTERN	Y				double-strand break repair via break-induced replication (0.001)		0.005	9
protein_40_YGL120C	2	PRP43:  RNA helicase in the DEAH-box family, functions in both RNA polymerase I and polymerase II transcript metabolism, involved in release of the lariat-intron from the spliceosome	LLE[DKA][DQY]	29							ribosome biogenesis (0.01)		0.005	8
protein_40_YGL111W	2	NSA1:  Constituent of 66S pre-ribosomal particles, involved in 60S ribosomal subunit biogenesis	Q[DEF]K[QPE]	29	FKPY	TLA binding motif in Brinker transcription factor for binding TLA domain in Groucho					cytoplasm organization and biogenesis (1e-11)		0.005	7
protein_40_YGL076C	2	RPL7A:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl7Bp and has similarity to E. coli L30 and rat L7 ribosomal proteins; contains a conserved C-terminal Nucleic acid Binding Domain (NDB2)	E[DGA]..E[ISA]D	29	E[ST]D	Ankyrin G binding motif in KNCQ2 and KNCQ3 potaqssium channels							0.003	7
protein_40_YGL076C	2	RPL7A:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl7Bp and has similarity to E. coli L30 and rat L7 ribosomal proteins; contains a conserved C-terminal Nucleic acid Binding Domain (NDB2)	R..R[AKC]	29	R.[RK]R	CLV_PCSK_FUR_1					cytosolic ribosome (sensu Eukaryota) (1e-17)		0.005	10
protein_40_YFR037C	2	RSC8:  Component of the RSC chromatin remodeling complex; essential for viability and mitotic growth; homolog of SWI/SNF subunit Swi3p, but unlike Swi3p, does not activate transcription of reporters	E..[KTS]R	29	[KR]R	CLV_PCSK_KEX2_1					nucleoplasm part (1e-14)		0.005	10
protein_40_YFR037C	2	RSC8:  Component of the RSC chromatin remodeling complex; essential for viability and mitotic growth; homolog of SWI/SNF subunit Swi3p, but unlike Swi3p, does not activate transcription of reporters	K[RPM]..G[LNQ]	29	KR	CLV_PCSK_PC1ET2_1					RSC complex (1e-04)		0.005	9
protein_40_YFL037W	2	TUB2:  Beta-tubulin; associates with alpha-tubulin (Tub1p and Tub3p) to form tubulin dimer, which polymerizes to form microtubules	[IQM]N..[IQT]Q	29	[ST]Q	ATM kinase phosphorylation site							0.005	10
protein_40_YFL037W	2	TUB2:  Beta-tubulin; associates with alpha-tubulin (Tub1p and Tub3p) to form tubulin dimer, which polymerizes to form microtubules	[RQA][ACG]..NK	29	G[SA]LNK	GDP-mannose binding motif in transporter	Y					Y	0.004	8
protein_40_YER133W	2	GLC7:  Catalytic subunit of type 1 serine/threonine protein phosphatase, involved in many processes including glycogen metabolism, sporulation, and mitosis; interacts with multiple regulatory subunits; predominantly isolated with Sds22p	[TAW]A..[NRD]A	29	LK[EAD]AE.RA[ET]	TROPOMYOSIN PATTERN						Y	0.006	10
protein_40_YER082C	2	UTP7:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	[SQL]D[DI]E	29	S[LW]LD[DE]EL[LM]	TRG_LysEnd_GGAAcLL_2					snoRNA binding (1e-12)	Y	0.006	10
protein_40_YER036C	2	ARB1:  ATPase of the ATP-binding cassette (ABC) family involved in 40S and 60S ribosome biogenesis, has similarity to Gcn20p; shuttles from nucleus to cytoplasm, physically interacts with Tif6p, Lsg1p	E[KPF]K[ER]	29	KR	CLV_PCSK_PC1ET2_1					translation (0.001)		0.006	10
protein_40_YER018C	2	SPC25:  Component of the evolutionarily conserved kinetochore-associated Ndc80 complex (Ndc80p-Nuf2p-Spc24p-Spc25p); involved in chromosome segregation, spindle checkpoint activity and kinetochore clustering	D[DNF].H[SNQ]	29			Y				microtubule associated complex (0.001)		0.005	10
protein_40_YER006W	2	NUG1:  GTPase that associates with nuclear 60S pre-ribosomes, required for export of 60S ribosomal subunits from the nucleus	R..V[KPR]	29							cytoplasm organization and biogenesis (1e-17)		0.005	10
protein_40_YDR510W	2	SMT3:  Ubiquitin-like protein of the SUMO family, conjugated to lysine residues of target proteins; regulates chromatid cohesion, chromosome segregation, APC-mediated proteolysis, DNA replication and septin ring dynamics	T[TKE]T	29	AGYGST.T	ICE_NUCLEATION PATTERN	Y					Y	0.005	10
protein_40_YDR471W	2	RPL27B:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl27Ap and has similarity to rat L27 ribosomal protein	A[RG]K[AGV]	29							cytosolic ribosome (sensu Eukaryota) (1e-17)		0.006	10
protein_40_YDR418W	2	RPL12B:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl12Ap; rpl12a rpl12b double mutant exhibits slow growth and slow translation; has similarity to E. coli L11 and rat L12 ribosomal proteins	L..I[LTF]	29									0.005	10
protein_40_YDR414C	2	ERD1:  Predicted membrane protein required for the retention of lumenal endoplasmic reticulum proteins; mutants secrete the endogenous ER protein, BiP (Kar2p)	II.[TYL][ICT]	29									0.006	9
protein_40_YDR388W	2	RVS167:  Actin-associated protein, subunit of a complex (Rvs161p-Rvs167p) involved in regulation of actin cytoskeleton, endocytosis, and viability following starvation or osmotic stress; homolog of mammalian amphiphysin	M[IPY]D	29	DMQD	Protease Caspase 3 -stringent							0.005	10
protein_40_YDR381W	2	YRA1:  Nuclear protein that binds to RNA and to Mex67p, required for export of poly(A)+ mRNA from the nucleus; member of the REF (RNA and export factor binding proteins) family; another family member, Yra2p, can substitute for Yra1p function	DI..[NVL][FRS]	29			Y				nuclear lumen (0.001)	Y	0.005	9
protein_40_YDR381W	2	YRA1:  Nuclear protein that binds to RNA and to Mex67p, required for export of poly(A)+ mRNA from the nucleus; member of the REF (RNA and export factor binding proteins) family; another family member, Yra2p, can substitute for Yra1p function	PS.[YKE][ALK]	29	P[ST]	DNA dependent Protein kinase substrate motif							0.005	9
protein_40_YDR365C	2	ESF1:  Nucleolar protein involved in pre-rRNA processing; depletion causes severely decreased 18S rRNA levels	[DTP]K.[GTN]R	29	[AG]R	Protease matriptase protease site					nucleolus (1e-05)		0.006	10
protein_40_YDR356W	2	SPC110:  Inner plaque spindle pole body (SPB) component, ortholog of human kendrin; involved in connecting nuclear microtubules to SPB; interacts with Tub4p-complex and calmodulin; phosphorylated by Mps1p in cell cycle-dependent manner	L[KEW].[ATM]N	29							spindle pole body (1e-17)		0.006	9
protein_40_YDR324C	2	UTP4:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	I..[APT]R	29	[AG]R	Protease matriptase protease site	Y				nucleolus (1e-24)	Y	0.006	10
protein_40_YDR303C	2	RSC3:  Component of the RSC chromatin remodeling complex; essential gene required for maintenance of proper ploidy and regulation of ribosomal protein genes and the cell wall/stress response; highly similar to Rsc30p	IN..[IFV][VYC]	29							RSC complex (1e-07)	Y	0.004	7
protein_40_YDR174W	2	HMO1:  Chromatin associated high mobility group (HMG) family member involved in genome maintenance; rDNA-binding component of the Pol I transcription system; associates with a 5'-3' DNA helicase and Fpr1p, a prolyl isomerase	E.[KIC]E	29	EEEIYEEIE	cFPS/FES kinase phosphorylation site					nuclear lumen (0.001)		0.005	9
protein_40_YDR145W	2	TAF12:  Subunit (61/68 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation and in chromatin modification, similar to histone H2A	[QDS]AD[ESC]	29	DVAD	Protease Caspase 2 -stringent					SLIK (SAGA-like) complex (1e-06)		0.006	10
protein_40_YDR145W	2	TAF12:  Subunit (61/68 kDa) of TFIID and SAGA complexes, involved in RNA polymerase II transcription initiation and in chromatin modification, similar to histone H2A	N.T[NAQ]	29	N.[TS]	N-linked glycosylation site					transcription factor complex (1e-14)		0.006	9
protein_40_YDR064W	2	RPS13:  Protein component of the small (40S) ribosomal subunit; has similarity to E. coli S15 and rat S13 ribosomal proteins	SS[SFY]	29	S[ST]	MDC1 BRCT domain binding motif							0.005	10
protein_40_YDR060W	2	MAK21:  Constituent of 66S pre-ribosomal particles, required for large (60S) ribosomal subunit biogenesis; involved in nuclear export of pre-ribosomes; required for maintenance of dsRNA virus; homolog of human CAATT-binding protein	[VRT]VR[AVG]	29							cytosolic ribosome (sensu Eukaryota) (1e-08)		0.006	10
protein_40_YDL213C	2	NOP6:  Putative RNA-binding protein implicated in ribosome biogenesis; contains an RNA recognition motif (RRM) and has similarity to hydrophilins; NOP6 may be a fungal-specific gene as no homologs have been yet identified in higher eukaryotes	QK.[KRL][ICH]	29	WAQKW	Motif in Cet1 RNA triphosphosphatase for binding to RNA guanylyltransferase Ceg1					nucleolus (1e-07)		0.006	9
protein_40_YDL153C	2	SAS10:  Component of the small (ribosomal) subunit (SSU) processosome required for pre-18S rRNa processing; essential nucleolar protein that, when overproduced, disrupts silencing	M[SR]..SSL	29	RSSLHL	Motif in beta-arrestin 2 for interaction with Jnk3							0.004	8
protein_40_YDL097C	2	RPN6:  Essential, non-ATPase regulatory subunit of the 26S proteasome lid required for the assembly and activity of the 26S proteasome; the human homolog (S9 protein) partially rescues Rpn6p depletion	[LYC][LYA]DK	29							proteasome regulatory particle (sensu Eukaryota) (0.001)		0.006	10
protein_40_YDL047W	2	SIT4:  Type 2A-related serine-threonine phosphatase that functions in the G1/S transition of the mitotic cycle; cytoplasmic and nuclear protein that modulates functions mediated by Pkc1p including cell wall and actin cytoskeleton organization	H[LPR]N[SNV]	29							phosphotransferase activity, alcohol group as acceptor (0.01)		0.004	8
protein_40_YDL013W	2	SLX5:  Subunit of the Slx5-Slx8 substrate-specific ubiquitin ligase complex; stimulated by prior attachment of SUMO to the substrate	[NYK]Q..Q[QDN]	29									0.005	9
protein_40_YCR086W	2	CSM1:  Nucleolar protein that forms a complex with Lrs4p which binds Mam1p at kinetochores during meiosis I to mediate accurate chromosome segregation, may be involved in premeiotic DNA replication; possible role in telomere maintenance	F[DKM].N[SEQ]	29									0.005	7
protein_40_YCR031C	2	RPS14A:  Ribosomal protein 59 of the small subunit, required for ribosome assembly and 20S pre-rRNA processing; mutations confer cryptopleurine resistance; nearly identical to Rps14Bp and similar to E. coli S11 and rat S14 ribosomal proteins	[KRH]RA[RAQ]	29	[KR]R	CLV_PCSK_KEX2_1					cytosolic ribosome (sensu Eukaryota) (1e-15)		0.006	10
protein_40_YCL059C	2	KRR1:  Essential nucleolar protein required for the synthesis of 18S rRNA and for the assembly of 40S ribosomal subunit	[VTA]E..E[EPD]	29							nucleolus (1e-14)		0.006	10
protein_40_YBR247C	2	ENP1:  Protein associated with U3 and U14 snoRNAs, required for pre-rRNA processing and 40S ribosomal subunit synthesis; localized in the nucleus and concentrated in the nucleolus	[KCA]ED[DER]	29	EDAIY	Abl kinase substrate motif					nucleolus (1e-15)		0.006	10
protein_40_YBR217W	2	ATG12:  Ubiquitin-like modifier, conjugated via an isopeptide bond to a lysine residue of Atg5p by the E1 enzyme, Atg7p, and the E2 enzyme, Atg10p, a step that is essential for autophagy	G.[TQE]A	29									0.006	10
protein_40_YBR217W	2	ATG12:  Ubiquitin-like modifier, conjugated via an isopeptide bond to a lysine residue of Atg5p by the E1 enzyme, Atg7p, and the E2 enzyme, Atg10p, a step that is essential for autophagy	K[VAF]I	29	D.G.T..K.I	Pyrophosphate binding motif, active site for S-Adenosylmethionine (AdoMet) synthetase	Y				amine metabolism (0.01)		0.005	9
protein_40_YBR191W	2	RPL21A:  Protein component of the large (60S) ribosomal subunit, nearly identical to Rpl21Bp and has similarity to rat L21 ribosomal protein	[ALT][RGH].KA	29							cytosolic ribosome (sensu Eukaryota) (1e-12)		0.005	9
protein_40_YBR079C	2	RPG1:  Subunit of the core complex of translation initiation factor 3(eIF3), essential for translation; part of a subcomplex (Prt1p-Rpg1p-Nip1p) that stimulates binding of mRNA and tRNA(i)Met to ribosomes	V[ACH]K[SP]	29	HLVNK	Motif for targeting CD44 to basolateral membranes					eukaryotic 43S preinitiation complex (1e-04)		0.004	8
protein_40_YBR055C	2	PRP6:  Splicing factor, component of the U4/U6-U5 snRNP complex	A[AMK]..[VDH]A	29							nuclear mRNA splicing, via spliceosome (0.01)		0.006	10
protein_40_YBR048W	2	RPS11B:  Protein component of the small (40S) ribosomal subunit; identical to Rps11Ap and has similarity to E. coli S17 and rat S11 ribosomal proteins	KK[AV]	29	RKK.[ST]	ZIP kinase phosphorylation motif					ribonucleoprotein complex (1e-26)		0.005	10
protein_40_YBR010W	2	HHT1:  One of two identical histone H3 proteins (see also HHT2); core histone required for chromatin assembly, involved in heterochromatin-mediated telomeric and HM silencing; regulated by acetylation, methylation, and mitotic phosphorylation	GS..[KEH][AEH]	29	S..[ED]	Casein kinase II substrate motif					establishment and/or maintenance of chromatin architecture (1e-10)	Y	0.006	9
protein_40_YAL035W	2	FUN12:  GTPase, required for general translation initiation by promoting Met-tRNAiMet binding to ribosomes and ribosomal subunit joining; homolog of bacterial IF2	V[KT].[DFW]G	29							translation (0.001)		0.004	9
protein_40_YAL032C	2	PRP45:  Protein required for pre-mRNA splicing; associates with the spliceosome and interacts with splicing factors Prp22p and Prp46p; orthologous to human transcriptional coactivator SKIP and can activate transcription of a reporter gene	[ACQ]A..[VHI]A	29							nuclear mRNA splicing, via spliceosome (0.001)	Y	0.005	9
protein_40_YAL032C	2	PRP45:  Protein required for pre-mRNA splicing; associates with the spliceosome and interacts with splicing factors Prp22p and Prp46p; orthologous to human transcriptional coactivator SKIP and can activate transcription of a reporter gene	K..[WHV]D	29							mRNA processing (1e-04)		0.005	10
oshea_spindle_pole	2	oshea_spindle_pole	Q[IHM]D[KLH]	29	Q[MLVI]DG..[DE]	CLV_TASPASE1					microtubule cytoskeleton (1e-15)		0.005	9
oshea_mitochondrion	2	oshea_mitochondrion	ML[RGK]	29	LRT	LKB1 Kinase substrate motif	Y				mitochondrial part (1e-29)	Y	0.006	10
oshea_ER	2	oshea_ER	[ERC]..RT	29									0.006	10
oshea_endosome	2	oshea_endosome	L[NSA][PFH]E	29			Y				endosome (1e-17)		0.006	10
oshea_bud	2	oshea_bud	[LKR]N..[NHY]G	29	N..Y	FRIP PTB domain binding motif					bud (1e-10)		0.006	10
matsuyama_Spindle_or_SPB	2	matsuyama_Spindle_or_SPB	S.[QLD]T	29	[KR]STQT	Light chain 8 of dynein binding motif					spindle (1e-13)		0.007	9
matsuyama_Nucleus	2	matsuyama_Nucleus	A.[VAY]A	29	A.AA.VP....VP........P	PLU-1 transcription factor binding motif in BF-1 and PAX9					carboxylic acid metabolism (1e-07)		0.007	10
matsuyama_ER	2	matsuyama_ER	G..I[GFT]	29	D[DE].G..[VI][TS]	DNA polymerase interaction motif in Cdc27	Y				endoplasmic reticulum part (1e-13)	Y	0.007	10
matsuyama_Cytosol	2	matsuyama_Cytosol	[KNY]L[RCM]G	29	LFG	Protease Papain substrate, a prototype cysteine proteinase						Y	0.007	10
matsuyama_Cytoplasmic_dots	2	matsuyama_Cytoplasmic_dots	[SMN]R..Q[NVL]	29									0.007	10
matsuyama_Cytoplasmic_dots	2	matsuyama_Cytoplasmic_dots	[TLG]L..I[IND]	29							Golgi apparatus (0.001)		0.007	10
genetic_YPL055C	2	LGE1: Protein of unknown function; null mutant forms abnormally large cells, and homozygous diploid null mutant displays delayed premeiotic DNA synthesis and reduced efficiency of meiotic nuclear division	DS.I[SLM][SKL]	29							regulation of gene expression, epigenetic (0.01)		0.006	9
genetic_YPL055C	2	LGE1: Protein of unknown function; null mutant forms abnormally large cells, and homozygous diploid null mutant displays delayed premeiotic DNA synthesis and reduced efficiency of meiotic nuclear division	Q..[SDN]T	29	P.Q..D	LIG_TRAF2_2					chromosome organization and biogenesis (sensu Eukaryota) (1e-07)		0.005	10
genetic_YPL055C	2	LGE1: Protein of unknown function; null mutant forms abnormally large cells, and homozygous diploid null mutant displays delayed premeiotic DNA synthesis and reduced efficiency of meiotic nuclear division	S[INQ]K	29	RRK.S.KR	PKCgamma kinase phosphorylation site (peptide screen)					DNA metabolism (1e-12)	Y	0.005	9
genetic_YNL153C	2	GIM3: Subunit of the heterohexameric cochaperone prefoldin complex which binds specifically to cytosolic chaperonin and transfers target proteins to it	[SLH]A.[KAV]P	29	APAP	Motif for hydroxylation of Pro residues, which can further be modified with arabinogalactan					cell cycle (1e-05)		0.005	10
genetic_YLR262C	2	YPT6: GTPase, Ras-like GTP binding protein involved in the secretory pathway, required for fusion of endosome-derived vesicles with the late Golgi, maturation of the vacuolar carboxypeptidase Y; has similarity to the human GTPase, Rab6	L..T[SVG]	29	LP.TG	C-terminal sorting signal which targets surface proteins of Staphylococcus aureus to the cell wall peptidoglycan; Sortase cleaves between Thr and Gly and C-termini is used for crosslinking in cell wall	Y				vesicle-mediated transport (1e-10)	Y	0.005	9
genetic_YLR039C	2	RIC1: Protein involved in retrograde transport to the cis-Golgi network; forms heterodimer with Rgp1p that acts as a GTP exchange factor for Ypt6p; involved in transcription of rRNA and ribosomal protein genes	L..L[TRD]	29							vesicle-mediated transport (1e-15)		0.006	10
genetic_YLR039C	2	RIC1: Protein involved in retrograde transport to the cis-Golgi network; forms heterodimer with Rgp1p that acts as a GTP exchange factor for Ypt6p; involved in transcription of rRNA and ribosomal protein genes	S[QDS].L[KET]	29	S[ST]	MDC1 BRCT domain binding motif	Y				vesicle-mediated transport (1e-08)		0.005	10
genetic_YGL058W	2	RAD6: Ubiquitin-conjugating enzyme (E2), involved in postreplication repair (with Rad18p), sporulation, telomere silencing, and ubiquitin-mediated N-end rule protein degradation (with Ubr1p)	Q..K[NRT]	29	KR	CLV_PCSK_PC1ET2_1					DNA metabolism (1e-11)	Y	0.005	10
genetic_YGL020C	2	GET1: Subunit of the GET complex; required for the retrieval of HDEL proteins from the Golgi to the ER in an ERD2 dependent fashion and for normal mitochondrial morphology and inheritance	I..L[QYI]	29							endoplasmic reticulum (1e-09)		0.005	9
genetic_YEL003W	2	GIM4: Subunit of the heterohexameric cochaperone prefoldin complex which binds specifically to cytosolic chaperonin and transfers target proteins to it	D..[LNQ]S	29							cell cycle (1e-05)		0.005	10
genetic_YEL003W	2	GIM4: Subunit of the heterohexameric cochaperone prefoldin complex which binds specifically to cytosolic chaperonin and transfers target proteins to it	DDL[NTM][EFP]	29			Y						0.005	10
genetic_YDL020C	2	RPN4: Transcription factor that stimulates expression of proteasome genes; Rpn4p levels are in turn regulated by the 26S proteasome in a negative feedback control mechanism; RPN4 is transcriptionally regulated by various stress responses	S[NTK]N	29	S[ST]	MDC1 BRCT domain binding motif					chromosome organization and biogenesis (sensu Eukaryota) (1e-21)		0.005	10
ucsf_loc_k_means_G6	6	Sub-cellular localization, 6 clusters	V.[ILV]I	29				MFS_1	1.E-03	-0.6	endoplasmic reticulum (1e-23)	Y	0.018	10
protein_40_YGL105W	2	ARC1:  Protein that binds tRNA and methionyl- and glutamyl-tRNA synthetases (Mes1p and Gus1p), delivering tRNA to them, stimulating catalysis, and ensuring their localization to the cytoplasm; also binds quadruplex nucleic acids	S[DQP]S	28	R.S.S.P	14-3-3 binding motifs, Ser must be phosphorylated		Pkinase	1.E-14	-3.9	protein kinase activity (1e-13)		0.005	10
protein_40_YDL153C	2	SAS10:  Component of the small (ribosomal) subunit (SSU) processosome required for pre-18S rRNa processing; essential nucleolar protein that, when overproduced, disrupts silencing	S[MQN][DLK]S	28	SQ	ATM kinase substrate motif		Pkinase	1.E-18	-2.9	protein kinase activity (1e-16)	Y	0.006	10
protein_40_YBR010W	2	HHT1:  One of two identical histone H3 proteins (see also HHT2); core histone required for chromatin assembly, involved in heterochromatin-mediated telomeric and HM silencing; regulated by acetylation, methylation, and mitotic phosphorylation	KP..[KFV][KHA]	28	KP..[QK]	LIG_SH3_4		Histone	1.E-02	-2.8	establishment and/or maintenance of chromatin architecture (1e-07)		0.006	9
protein_40_YPL004C	2	LSP1:  Primary component of eisosomes, which are large immobile patch structures at the cell cortex associated with endocytosis, along with Pil1p and Sur7p; null mutants show activation of Pkc1p/Ypk1p stress resistance pathways	P[PKE]P	28	QHR.P[PL]PP[GS]H[RH]	Motif recognized by GYF domains	Y	Pkinase	1.E-02	-2.3	phosphotransferase activity, alcohol group as acceptor (0.01)	Y	0.005	10
protein_40_YMR304W	2	UBP15:  Ubiquitin-specific protease that may play a role in ubiquitin precursor processing	A.[TSL]S	28				Pkinase	1.E-03	-2.1	protein kinase activity (0.001)		0.005	10
protein_40_YPR144C	2	NOC4:  Nucleolar protein, forms a complex with Nop14p that mediates maturation and nuclear export of 40S ribosomal subunits	ES[SNA]	28	S[ST]	MDC1 BRCT domain binding motif		WD40	1.E-04	-1.5	nucleolus (1e-29)		0.005	8
yeast-649_GO-0003676	2	nucleic acid binding	D.[AEL]V	28	SD.E	Casein kinase II substrate motif		RRM_1	1.E-08	-1.4	nucleic acid binding (1e-18)		0.006	10
yeast-648_GO-0050791	2	regulation of physiological process	E[KVQ]P	28	VP	Interleukin converting enzyme protease		zf-C2H2	1.E-04	-1.4	regulation of metabolism (1e-09)	Y	0.006	10
yeast-207_GO-0006974	2	response to DNA damage stimulus	E..[DLM]L	28				BRCT	1.E-04	-1.4	response to DNA damage stimulus (1e-15)		0.006	10
protein_40_YMR093W	2	UTP15:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	A.[RKD]L	28	DALDL	14-3-3 binding motif in ExoS		WD40	1.E-06	-1.4	rRNA processing (1e-33)	Y	0.005	9
protein_40_YIL019W	2	FAF1:  Protein required for pre-rRNA processing and 40S ribosomal subunit assembly	[QGP]G[LNA]K	28	GAKRH	HISTONE_H4 PATTERN		WD40	1.E-04	-1.3	nucleolus (1e-16)		0.005	9
protein_40_YHR052W	2	CIC1:  Essential protein that interacts with proteasome components and has a potential role in proteasome substrate specificity; also copurifies with 66S pre-ribosomal particles	[REK]G..[IKA]P	28				DEAD	1.E-04	-1.3	ribosome biogenesis (1e-15)		0.006	10
protein_40_YGR128C	2	UTP8:  Nucleolar protein required for export of tRNAs from the nucleus; also copurifies with the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	[LTH]L.[AHW]S	28				WD40	1.E-04	-1.3	rRNA processing (1e-19)		0.005	9
oshea_nucleus	2	oshea_nucleus	I..[AKE]R	28	[KR]R	CLV_PCSK_KEX2_1		Helicase_C	1.E-03	-1.3	DNA metabolism (1e-24)		0.006	10
yeast-1036_GO-0005739	2	mitochondrion	A.[ALG]K	28				Helicase_C	1.E-02	-1.2	mitochondrial part (1e-66)		0.006	9
yeast-1721_GO-0016043	2	cell organization and biogenesis	P[PDY]K	28	P..P.K	SH3 binding motif for Crk, general		Helicase_C	1.E-02	-1.1	chromosome organization and biogenesis (1e-28)	Y	0.006	10
protein_40_YJL010C	2	NOP9:  Essential component of pre-40S ribosomes that is required for early cleavages of 35S pre-rRNA and hence formation of 18S rRNA; binds RNA in vitro and contains multiple pumilio-like repeats	N[EVM]..D[DQT]	28				WD40	1.E-02	-1.1	nucleolus (1e-15)	Y	0.005	10
oshea_cell_periphery	2	oshea_cell_periphery	V[GAV]L	28	P[MVLIRWY]V[MVLIAS][LM]	LIG_HP1_1		MFS_1	1.E-03	-1.1	plasma membrane (1e-24)		0.005	9
yeast-207_GO-0006974	2	response to DNA damage stimulus	L.[DQN]I	28				BRCT	1.E-06	-1	response to DNA damage stimulus (1e-16)		0.006	9
yeast-1216_GO-0009058	2	biosynthesis	I..N[LSN]	28				HEAT	1.E-02	-1	cell cycle (1e-09)		0.006	9
matsuyama_nucleolus	2	matsuyama_nucleolus	[TKS][PG]GR	28	GGRGG	Arginine methyl transferease substrate motif (PRMT1)		Helicase_C	1.E-09	-1	nucleolus (1e-20)		0.007	10
yeast-436_GO-0031323	2	regulation of cellular metabolism	TA[APQ]	28	P[TS]AP	LIG_PTAP		Zn_clus	1.E-06	-0.9	regulation of cellular metabolism (1e-14)		0.006	9
yeast-335_GO-0016772	2	transferase activity, transferring phosphorus-containing groups	[NDP]Q[PHC]Y	28				HATPase_c	1.E-03	-0.9	transferase activity, transferring phosphorus-containing groups (1e-14)		0.006	9
yeast-256_GO-0016462	2	pyrophosphatase activity	T[LYK].[NFH]T	28				Helicase_C	1.E-06	-0.9	pyrophosphatase activity (1e-37)		0.006	9
protein_40_YPL131W	2	RPL5:  Protein component of the large (60S) ribosomal subunit with similarity to E. coli L18 and rat L5 ribosomal proteins; binds 5S rRNA and is required for 60S subunit assembly	DS[DNEQ][DKA]E	28	S[DE][DE]E	BARD1 BRCT domain binding motif		DEAD	1.E-02	-0.9	ribosome assembly (1e-05)		0.004	8
protein_40_YOL133W	2	HRT1:  RING finger containing subunit of Skp1-Cullin-F-box ubiquitin protein ligases (SCF); required for Gic2p, Far1p, Sic1p and Cln2p degradation; may tether Cdc34p (a ubiquitin conjugating enzyme or E2) and Cdc53p (a cullin) subunits of SCF	P.L[KVR]	28	P.L	Motif in C-Fos for protein instability		F-box	1.E-07	-0.9	ubiquitin ligase complex (1e-10)	Y	0.006	10
protein_40_YLR293C	2	GSP1:  GTP binding protein (mammalian Ranp homolog) involved in the maintenance of nuclear organization, RNA processing and transport; regulated by Prp20p, Rna1p, Yrb1p, Yrb2p, Yrp4p, Yrb30p, Cse1p and Kap95p; yeast Gsp2p homolog	E..[KQP]A	28				IBN_N	1.E-09	-0.9	nucleocytoplasmic transport (1e-14)		0.005	9
protein_40_YML085C	2	TUB1:  Alpha-tubulin; associates with beta-tubulin (Tub2p) to form tubulin dimer, which polymerizes to form microtubules	L[YKQ]..I[ERY]	28	IY	cFGR and Csk kinase phosphorylation site (peptide screen)		HEAT	1.E-03	-0.8	protein carrier activity (0.01)		0.006	10
protein_40_YML007W	2	YAP1:  Basic leucine zipper (bZIP) transcription factor required for oxidative stress tolerance; activated by H2O2 through the multistep formation of disulfide bonds and transit from the cytoplasm to the nucleus; mediates resistance to cadmium	A[ADN].A[DNK]	28				HEAT	1.E-02	-0.8	nucleoplasm part (1e-08)	Y	0.006	10
yeast-630_GO-0051244	2	regulation of cellular physiological process	I.E	28	D..IYE	Lyn kinase phosphorylation site (peptide screen)		Zn_clus	1.E-06	-0.7	regulation of cellular metabolism (10)	Y	0.006	10
protein_40_YGL105W	2	ARC1:  Protein that binds tRNA and methionyl- and glutamyl-tRNA synthetases (Mes1p and Gus1p), delivering tRNA to them, stimulating catalysis, and ensuring their localization to the cytoplasm; also binds quadruplex nucleic acids	[SRH]K.K[ST]	28				Pkinase	1.E-07	-0.7	protein kinase activity (1e-08)		0.006	10
protein_40_YER102W	2	RPS8B:  Protein component of the small (40S) ribosomal subunit; identical to Rps8Ap and has similarity to rat S8 ribosomal protein	R[EVL][LTA]A	28	C[SA]DSR[LIVM].[AP]	PROK_CO2_ANHYDRASE_1 PATTERN		Helicase_C	1.E-02	-0.7	ribonucleoprotein complex (1e-10)		0.006	9
yeast-631_GO-0050794	2	regulation of cellular process	I.E	28	D..IYE	Lyn kinase phosphorylation site (peptide screen)		Zn_clus	1.E-06	-0.6	regulation of cellular metabolism (10)	Y	0.006	10
protein_40_YOL139C	2	CDC33:  Cytoplasmic mRNA cap binding protein; the eIF4E-cap complex is responsible for mediating cap-dependent mRNA translation via interactions with the translation initiation factor eIF4G (Tif4631p or Tif4632p)	N.[KDR]R	28	[KR]R	CLV_PCSK_KEX2_1		Pkinase	1.E-03	-0.6	protein kinase activity (0.01)		0.005	10
protein_40_YMR229C	2	RRP5:  Protein required for the synthesis of both 18S and 5.8S rRNA; C-terminal region is crucial for the formation of 18S rRNA and N-terminal region is required for the 5.8S rRNA; component of small ribosomal subunit (SSU) processosome	[FRI][GRE].AR	28	[AG]R	Protease matriptase protease site		Helicase_C	1.E-02	-0.6	nucleolus (1e-09)	Y	0.005	10
protein_40_YER082C	2	UTP7:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	A[IVL].L[LPE]	28	DALDL	14-3-3 binding motif in ExoS	Y	WD40	1.E-02	-0.6	nucleolus (1e-16)	Y	0.006	10
yeast-468_GO-0051276	2	chromosome organization and biogenesis	SK[KNC][IRE]	28				HEAT	1.E-02	-0.5	chromosome organization and biogenesis (1e-81)		0.006	10
yeast-213_GO-0009719	2	response to endogenous stimulus	L[SRL]Q	28	ARKGSLRQ	PKC alpha kinase substrate motif	Y	BRCT	1.E-05	-0.5	response to endogenous stimulus (1e-15)		0.006	9
protein_40_YIL094C	2	LYS12:  Homo-isocitrate dehydrogenase, an NAD-linked mitochondrial enzyme required for the fourth step in the biosynthesis of lysine, in which homo-isocitrate is oxidatively decarboxylated to alpha-ketoadipate	IA.[KAL][NAT]	28				IBN_N	1.E-03	-0.5	protein carrier activity (0.01)	Y	0.006	10
protein_40_YHR052W	2	CIC1:  Essential protein that interacts with proteasome components and has a potential role in proteasome substrate specificity; also copurifies with 66S pre-ribosomal particles	[DEN]V.A[RKW]	28				DEAD	1.E-04	-0.5	cytoplasm organization and biogenesis (1e-07)		0.005	9
protein_40_YPR144C	2	NOC4:  Nucleolar protein, forms a complex with Nop14p that mediates maturation and nuclear export of 40S ribosomal subunits	DL[VEL]	28	WDL	Binding motif for AP-2 and clathrin heavy chain ear		WD40	1.E-02	-0.3	small nucleolar ribonucleoprotein complex (1e-34)	Y	0.005	9
protein_40_YDR328C	2	SKP1:  Evolutionarily conserved kinetochore protein that is part of multiple protein complexes, including the SCF ubiquitin ligase complex, the CBF3 complex that binds centromeric DNA, and the RAVE complex that regulates assembly of the V-ATPase	KK[DLI]	28	KKKLPATGDYMNMSPVGD	Insulin receptor kinase substrate motif		F-box	1.E-17	-0.3	ubiquitin ligase complex (1e-15)		0.005	10
protein_40_YDR224C	2	HTB1:  One of two nearly identical (see HTB2) histone H2B subtypes required for chromatin assembly and chromosome function; Rad6p-Bre1p-Lge1p mediated ubiquitination regulates transcriptional activation, meiotic DSB formation and H3 methylation	G..A[KPN]	28	GR.A	Protease tPA proteolytic site		Histone	1.E-06	-0.3	DNA metabolism (1e-05)	Y	0.005	10
protein_40_YLR222C	2	UTP13:  Nucleolar protein, component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA	K..K[RLC]	28	KR	CLV_PCSK_PC1ET2_1		WD40	1.E-08