CLIPS-1D: analysis of multiple sequence alignments to deduce for residue-positions a role in catalysis, ligand-binding, or protein structure

Table 5 CLIPS-1D predictions for residue-positions in sIGPS (PDB-ID 1A53)

Residue	Position	p _CAT	p _LIG	p _STRUC	p _NOANN	p-value	Classification
							CS	LBS	STRUC
I	49	0.001	0.154	0.824	0.022	0.003			SC
E	51	0.806	0.075	0.114	0.005	0.020	CAT
K	53	0.835	0.065	0.088	0.012	0.004	CAT
K	55	0.051	0.544	0.197	0.208	0.011		SC
S	56	0.017	0.170	0.801	0.012	0.004			SC
L	60	0.002	0.128	0.829	0.041	0.019			IA
A	77	0.006	0.172	0.810	0.011	0.018			FC
I	82	0.002	0.259	0.667	0.073	0.011			SR
T	84	0.002	0.111	0.881	0.007	0.003			N
L	108	0.006	0.106	0.863	0.024	0.012			SR
K	110	0.866	0.078	0.046	0.011	0.002	CAT
F	112	0.146	0.053	0.788	0.014	0.020		STRUC	FC
Q	118	0.007	0.114	0.872	0.008	0.002			FC
A	122	0.001	0.066	0.882	0.051	0.010			FC
A	127	0.024	0.193	0.776	0.008	0.022			N
L	131	0.001	0.071	0.920	0.008	0.006		STRUC	SR
L	132	0.004	0.164	0.794	0.038	0.023			SR,FC
I	133	0.005	0.169	0.790	0.036	0.005			FC
L	137	0.007	0.151	0.813	0.029	0.020			SC,FC
L	157	0.001	0.105	0.886	0.008	0.010			SC,FC
E	159	0.899	0.048	0.050	0.003	0.005	CAT
D	165	0.189	0.071	0.699	0.040	0.007			N
I	179	0.001	0.819	0.068	0.112	0.021		SCE
N	180	0.098	0.770	0.116	0.016	0.016	LIG
S	181	0.011	0.774	0.134	0.081	0.019		SCE
L	184	0.009	0.157	0.818	0.016	0.020			IA
L	197	0.003	0.130	0.818	0.049	0.020			N
E	210	0.866	0.059	0.068	0.007	0.008		CAT
S	211	0.738	0.168	0.087	0.007	0.005	CAT
L	231	0.003	0.224	0.762	0.011	0.025		STRUC	SC
I	232	0.006	0.835	0.059	0.099	0.017		LIG

The first two columns give the residue and its position in sIGPS. The following four columns list the probabilities for the residue's membership with CAT_sites, LIG_sites, STRUC_sites, or NOANN_sites. The column labeled "p-value" lists the p-value for the class with max(p_CLASS). The columns "CS" and "LBS" indicate the classification of known catalytic and ligand-binding sites. The last column lists the annotation deduced for residues predicted as STRUC_sites. Meaning of labels: "CAT", "LIG", "STRUC", residues predicted as CAT_sites, LIG_sites, or STRUC_sites, respectively. "SC" element of a stabilization center pair in sIGPS, "SCE" ditto in eIGPS, "SR" stabilization residue in sIGPS; see [36]. "FC" element of the folding core; see [37]. "IA" interaction with substrate; see [38]. "N" no function assigned.

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