Protein kinases associated with the yeast phosphoproteome

Brinkworth, Ross I; Munn, Alan L; Kobe, Boštjan

doi:10.1186/1471-2105-7-47

BMC Bioinformatics

Table 4 Selected protein kinase- phosphoprotein pairs showing functional correlations

From: Protein kinases associated with the yeast phosphoproteome

Substrate protein	Function *	Predicted protein kinase	Function *	Phosphopeptide **	Scansite score ***	Estimated probability ****
Cdc47p	DNA replication	CK2 group *****	G1/S and G2/M transition of mitotic cell cycle, cell ion homeostasis, cell polarity, flocculation, regulation of transcription (Pol I and Pol III promoters), response to DNA damage, regulation of DNA replication	TMDT DQE	0.212	0.25
Ede1p	Endocytosis	CK1 group ******	Cellular morphogenesis, cytokinesis, endocytosis, DNA repair, cell growth, chromosome segregation, meiosis, mitosis, nuclear division	DGES VS SIQ	0.062	0.9
Ysc84p	Actin organization, endocytosis	CK1 group	Cellular morphogenesis, cytokinesis, endocytosis, DNA repair, cell growth, chromosome segregation, meiosis, mitosis, nuclear division	DFDS EDE	0.062	0.9
Pan1p	Endocytosis, cytokinesis, budding	CK1 group	Cellular morphogenesis, cytokinesis, endocytosis, DNA repair, cell growth, chromosome segregation, meiosis, mitosis, nuclear division	ASAS STS	0.1	0.8
Sec4p	Rab GTPase (cytokinesis, exocytosis, polar budding)	CK1 group	Cellular morphogenesis, cytokinesis, endocytosis, DNA repair, cell growth, chromosome segregation, meiosis, mitosis, nuclear division	RTVS ASS GNG	0.082	0.85
Sec3p	Cytokinesis, cell polarity	Cdc15p	Cytokinesis, regulation of exit from mitosis	RTIS GSS AHH	0.232	0.15
Hsp26p	Chaperone, stress response	Mds1p	Proteolysis, response to stress, sporulation	EVSS QES WGN	- *******
Nth1p	Trehalose hydrolysis, stress response	Yfl033cp	Regulation of meiosis, stress response	RRGS EDD	0.082	0.85
Hxt2p	Hexose transport	Sha3p	Glucose transport, transcriptional regulation (Pol II promoter)	QQTS IHS TPI	0.275	0.05
Shp1p	Glycogen metabolism, sporulation	Snf1p	AMP-activated protein kinase, cell adhesion, response to nitrogen starvation, filamentous growth, glucose metabolism, regulation of carbohydrate metabolism	RKGS TS PEP	0.145	0.6
Tps3p	Trehalose phosphatase (carbohydrate metabolism, stress response)	Snf1p	AMP-activated protein kinase, cell adhesion, response to nitrogen starvation, filamentous growth, glucose metabolism, regulation of carbohydrate metabolism	RTSS SMS VGN	0.102	0.8
Mcm3p	DNA helicase, initiation of DNA replication	Sgv1p	Transcription	NSGS PIK	0.082	0.85
Swi4p	Transcription factor (cell cycle)	CK2 group	G1/S and G2/M transition of mitotic cell cycle, cell ion homeostasis, cell polarity, flocculation, regulation of transcription (Pol I and Pol III promoters), response to DNA damage, regulation of DNA replication	KSTS ETS	0.168	0.5
Rpa190p	RNA polymerase subunit (transcription)	CK2 group	G1/S and G2/M transition of mitotic cell cycle, cell ion homeostasis, cell polarity, flocculation, regulation of transcription (Pol I and Pol III promoters), response to DNA damage, regulation of DNA replication	DKES DS DS EDE	0.104, 0.06, 0.02	0.8, 0.9, 0.99
Mob1p	Protein kinase regulation (cell cycle regulation)	Ume5p	Cyclin-dependent protein kinase, meiosis, regulation of transcription (Pol II promoter)	VLTT PKR	0	0.99
Abp1p	Actin binding (cell polarity)	Cdc28p	Cyclin-dependent protein kinase, regulation of mitosis and meiosis	PSKS PAP	0.145	0.6
Abp1p	Actin binding (cell polarity)	Cdc28p	Cyclin-dependent protein kinase, regulation of mitosis and meiosis	PVKT PS PAP	0.125	0.75
Crn1p	Actin filament organization	Cdc28p	Cyclin-dependent protein kinase, regulation of mitosis and meiosis	APKS PS PLK	0.145	0.6
Pea2p	Actin filament organization, cell polarity, polar budding	Hog1p	Actin filament organization, osmoregulation, transcriptional regulation (Pol II promoter)	NTSS PPI	0.102	0.8
Spc98p	Cytoskeleton component (microtubule nucleation, mitotic spindle assembly)	Ssk2p	MAPKKK, actin cytoskeleton organization and biogenesis, osmosensory signaling pathway	ERRS MVS SPN	0.121	0.75
Npr1p	Protein kinase (regulation of nitrogen utilization)	Snf1p	AMP-activated protein kinase, cell adhesion, response to nitrogen starvation, filamentous growth, glucose metabolism, regulation of carbohydrate metabolism	RQSS IYS	0.149	0.6
Shp1p	Glycogen metabolism, sporulation	Mds1p	Proteolysis, response to stress, sporulation	RKGS TS PEP	0.082	0.85
Ydl223cp	Cellular morphogenesis	CK1 group	Cellular morphogenesis, cytokinesis, endocytosis, DNA repair, cell growth, chromosome segregation, meiosis, mitosis, nuclear division	STHS AEH	0.1	0.8
Ydl223cp	Cellular morphogenesis	Hsl1p	Cell cycle regulation (G2/M transition of mitotic cell cycle), cell morphogenesis checkpoint, septin checkpoint)	AEHT PRH	0.127	0.75
Fpr4p	Peptidyl-prolyl cis-trans isomerase	CK1 group	Cellular morphogenesis, cytokinesis, endocytosis, DNA repair, cell growth, chromosome segregation, meiosis, mitosis, nuclear division	EDES ES EQE	0, 0.082	0.99, 0.85
Fpr4p	Peptidyl -prolyl cis-trans isomerase	CK2 group	G1/S and G2/M transition of mitotic cell cycle, cell ion homeostasis, cell polarity, flocculation, regulation of transcription (Pol I and Pol III promoters), response to DNA damage, regulation of DNA replication	EDES ES EQE	0.084, 0.149	0.85, 0.6

* Functional annotations based on RefSeq [68].
** The phosphorylated residues are underlined, and the residues not present in the phosphopeptide sequences [4] are shown in italic. When there is more than one phosphorylation site, the one discussed is shown in bold, unless the same protein kinase is predicted for all sites in the peptide.
*** Scansite [11] scores were calculated as described in the Methods Section. When the same protein kinase is predicted for more than one site in the peptide, the scores are given for the respective sites, starting at the N-terminus. If more than one protein kinase yields a similar score, all the possible kinases are listed.
**** Probabilities were calculated as described in the Methods section (Figure 1). When the same protein kinase is predicted for more than one site in the peptide, the values are given for the respective sites, starting at the N-terminus.
***** Protein kinases Cka1p, Cka2p or Cdc7p. The predicted specificties are too similar to be distinguished.
****** Protein kinases Yck1p, Yck2p, Yck3p or Hrr25p. The predicted specificities are identical.
******* Scansite score could not be measured because the phosphorylation site is too close to the C-terminus.

Back to article page

ISSN: 1471-2105

Contact us

General enquiries: journalsubmissions@springernature.com