Table 4

Selected protein kinase- phosphoprotein pairs showing functional correlations

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

TMD

    T
DQE

0.212

0.25

Ede1p

Endocytosis

CK1 group ******

Cellular morphogenesis, cytokinesis, endocytosis, DNA repair, cell growth, chromosome segregation, meiosis, mitosis, nuclear division

DGE

    S
V
    S
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

DFD

    S
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

ASA

    S
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

RTV

    S
AS
    S
GNG

0.082

0.85

Sec3p

Cytokinesis, cell polarity

Cdc15p

Cytokinesis, regulation of exit from mitosis

RTI

    S
GS
    S
AHH

0.232

0.15

Hsp26p

Chaperone, stress response

Mds1p

Proteolysis, response to stress, sporulation

EVS

    S
QE
    S
WGN

- *******

Nth1p

Trehalose hydrolysis, stress response

Yfl033cp

Regulation of meiosis, stress response

RRG

    S
EDD

0.082

0.85

Hxt2p

Hexose transport

Sha3p

Glucose transport, transcriptional regulation (Pol II promoter)

QQT

    S
IH
    S
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

RKG

    S
T
    S
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

RTS

    S
SM
    S
VGN

0.102

0.8

Mcm3p

DNA helicase, initiation of DNA replication

Sgv1p

Transcription

NSG

    S
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

KST

    S
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

DKE

    S
D
    S
D
    S
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)

VLT

    T
PKR

0

0.99

Abp1p

Actin binding (cell polarity)

Cdc28p

Cyclin-dependent protein kinase, regulation of mitosis and meiosis

PSK

    S
PAP

0.145

0.6

Abp1p

Actin binding (cell polarity)

Cdc28p

Cyclin-dependent protein kinase, regulation of mitosis and meiosis

PVK

    T
P
    S
PAP

0.125

0.75

Crn1p

Actin filament organization

Cdc28p

Cyclin-dependent protein kinase, regulation of mitosis and meiosis

APK

    S
P
    S
PLK

0.145

0.6

Pea2p

Actin filament organization, cell polarity, polar budding

Hog1p

Actin filament organization, osmoregulation, transcriptional regulation (Pol II promoter)

NTS

    S
PPI

0.102

0.8

Spc98p

Cytoskeleton component (microtubule nucleation, mitotic spindle assembly)

Ssk2p

MAPKKK, actin cytoskeleton organization and biogenesis, osmosensory signaling pathway

ERR

    S
MV
    S
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

RQS

    S
IYS

0.149

0.6

Shp1p

Glycogen metabolism, sporulation

Mds1p

Proteolysis, response to stress, sporulation

RKG

    S
T
    S
PEP

0.082

0.85

Ydl223cp

Cellular morphogenesis

CK1 group

Cellular morphogenesis, cytokinesis, endocytosis, DNA repair, cell growth, chromosome segregation, meiosis, mitosis, nuclear division

STH

    S
AEH

0.1

0.8

Ydl223cp

Cellular morphogenesis

Hsl1p

Cell cycle regulation (G2/M transition of mitotic cell cycle), cell morphogenesis checkpoint, septin checkpoint)

AEH

    T
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

EDE

    S
E
    S
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

EDE

    S
E
    S
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.

Brinkworth et al. BMC Bioinformatics 2006 7:47   doi:10.1186/1471-2105-7-47

Open Data