pkaPS: prediction of protein kinase A phosphorylation sites with the simplified kinase-substrate binding model

Biology Direct

Table 4 Prediction of the clustered human proteome.

Cluster number	Total entries	Predicted S/T (%)	Predicted S/T	Predicted entries (%)	Predicted entries	Common domains/superfamily
171	21	39.7	52	100	21	High mobility group
88	32	36.2	141	100	32	Histone H2A
43	48	30.8	518	91.7	44	Splicing factor, predicted RNA-binding
84	34	29	249	100	34	TAFII28-like
109	27	27.3	81	100	27	Unknown
72	36	26.4	101	94.4	34	GAGE protein
131	24	24.7	80	87.5	21	Ribosomal protein L21e
123	25	22.8	146	100	25	Ribosomal protein L22
172	21	22.5	108	100	21	Histone H2B
33	59	21.6	390	98.3	58	Cyclophilin-like
94	30	21.1	111	93.3	28	Histones H3/H4
105	27	20.9	88	96.3	26	KRAB domain
7	136	20	1300	96.3	131	GTPase-activating protein
10	123	19.7	412	84.6	104	Unknown
115	26	19.6	126	100	26	60S ribosomal protein L6
154	22	18.7	94	100	22	HIV-1 Vpr-binding, High mobility group
79	35	17.5	206	91.4	32	Ras GTPase-activating protein
38	52	17.4	287	92.3	48	Septins
153	22	16.3	105	77.3	17	RNA-binding protein TIA-1/TIAR (RRM superfamily)
160	22	16.1	465	100	22	Uncharacterized conserved protein (KOG4791)

The table shows the 20 clusters with the best ratio between predicted and total S/T-sites. The column to the right displays a summary of the cluster with respect to the most common domains found using the CDD [85] and PFAM [86] databases (e-value cutoff of 0.01). Lower cluster numbers indicate clusters with more sequences included.

ISSN: 1745-6150