SSB - ECOLI - GREMLIN Contacts

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SSB - Single-stranded DNA-binding protein

UniProt:	P0AGE0	Sequences: MASRGVNKVILVGNLGQDPEVRYMPNGGAVANITLATSESWRDKATGEMKEQTEWHRVVLFGKLAEVASEYLRKGSQVYIEGQLRTRKWTDQSGQDRYTTEVVVNVGGTMQMLGGRQGGGAPAGGNIGGGQPQGGWGQPQQPQGGNQFSGGAQSRPQQSAPAAPSNEPPMDFDDDIPF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10976
Length:	178 (158)
Sequences:	3167 (2418)
Seq/√Len:	192.3

ECOLI - SSB
BACSU - SSBA SSBB

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
90_T	96_D	3.565	1.00
77_Q	114_G	3.426	1.00
91_D	95_Q	3.157	1.00
23_Y	29_A	3.134	1.00
88_K	96_D	2.731	1.00
87_R	101_E	2.623	1.00
17_Q	34_T	2.597	1.00
34_T	57_R	2.565	1.00
58_V	104_V	2.551	1.00
6_V	10_I	2.454	1.00
60_L	68_A	2.430	1.00
87_R	99_T	2.373	1.00
16_G	55_W	2.359	1.00
21_V	31_A	2.314	1.00
24_M	30_V	2.246	1.00
43_D	50_K	2.203	1.00
72_L	78_V	2.198	1.00
33_I	60_L	2.154	1.00
14_N	77_Q	2.124	1.00
15_L	72_L	2.081	1.00
42_R	49_M	2.047	1.00
83_Q	105_N	2.008	1.00
52_Q	85_R	1.987	1.00
33_I	58_V	1.958	1.00
68_A	72_L	1.902	1.00
8_K	81_E	1.902	1.00
28_G	62_G	1.868	1.00
91_D	97_R	1.793	1.00
89_W	99_T	1.756	1.00
24_M	61_F	1.746	1.00
24_M	28_G	1.718	1.00
16_G	34_T	1.672	1.00
6_V	12_V	1.656	1.00
86_T	100_T	1.622	1.00
11_L	35_L	1.611	1.00
35_L	80_I	1.606	1.00
42_R	47_G	1.603	1.00
105_N	109_T	1.594	1.00
85_R	103_V	1.567	1.00
37_T	56_H	1.565	1.00
60_L	80_I	1.490	1.00
40_S	49_M	1.481	1.00
59_V	101_E	1.465	1.00
29_A	66_E	1.463	1.00
60_L	64_L	1.379	1.00
63_K	66_E	1.377	1.00
12_V	113_L	1.377	1.00
39_E	52_Q	1.335	1.00
17_Q	57_R	1.320	1.00
67_V	112_M	1.317	1.00
41_W	50_K	1.298	1.00
66_E	70_E	1.274	1.00
32_N	87_R	1.270	1.00
60_L	104_V	1.267	1.00
43_D	46_T	1.216	1.00
84_L	102_V	1.209	1.00
30_V	61_F	1.207	1.00
85_R	105_N	1.197	1.00
6_V	79_Y	1.184	1.00
68_A	78_V	1.184	1.00
9_V	84_L	1.143	1.00
21_V	69_S	1.132	1.00
17_Q	20_E	1.121	1.00
61_F	103_V	1.100	1.00
11_L	102_V	1.088	1.00
14_N	38_S	1.079	1.00
86_T	98_Y	1.077	1.00
19_P	31_A	1.066	1.00
56_H	100_T	1.060	1.00
167_E	170_M	1.031	1.00
59_V	87_R	1.027	1.00
57_R	99_T	1.014	1.00
104_V	110_M	1.005	1.00
25_P	28_G	0.999	1.00
29_A	69_S	0.970	0.99
166_N	169_P	0.952	0.99
67_V	71_Y	0.949	0.99
89_W	95_Q	0.945	0.99
32_N	59_V	0.930	0.99
39_E	83_Q	0.923	0.99
15_L	19_P	0.918	0.99
60_L	110_M	0.917	0.99
54_E	102_V	0.909	0.99
56_H	102_V	0.905	0.99
31_A	65_A	0.886	0.99
89_W	101_E	0.884	0.99
31_A	68_A	0.881	0.99
128_G	131_Q	0.878	0.99
76_S	114_G	0.869	0.99
23_Y	66_E	0.864	0.99
11_L	56_H	0.863	0.99
133_Q	136_W	0.854	0.98
29_A	65_A	0.854	0.98
83_Q	103_V	0.852	0.98
41_W	44_K	0.852	0.98
72_L	112_M	0.850	0.98
159_S	163_A	0.844	0.98
62_G	105_N	0.843	0.98
88_K	99_T	0.832	0.98
35_L	78_V	0.832	0.98
76_S	117_Q	0.826	0.98
158_Q	162_A	0.822	0.98
64_L	104_V	0.817	0.98
19_P	68_A	0.811	0.98
38_S	53_T	0.808	0.98
6_V	111_Q	0.806	0.98
23_Y	70_E	0.794	0.98
160_A	163_A	0.791	0.97
68_A	110_M	0.788	0.97
64_L	67_V	0.781	0.97
72_L	110_M	0.781	0.97
29_A	70_E	0.777	0.97
54_E	86_T	0.767	0.97
159_S	162_A	0.765	0.97
54_E	100_T	0.760	0.97
90_T	95_Q	0.760	0.97
33_I	104_V	0.759	0.97
18_D	73_R	0.756	0.97
89_W	92_Q	0.753	0.97
22_R	30_V	0.752	0.97
168_P	171_D	0.749	0.97
76_S	112_M	0.749	0.97
39_E	54_E	0.748	0.96
12_V	79_Y	0.746	0.96
164_P	167_E	0.740	0.96
64_L	110_M	0.735	0.96
118_G	122_P	0.734	0.96
73_R	76_S	0.725	0.96
134_G	137_G	0.722	0.96
63_K	70_E	0.721	0.96
46_T	50_K	0.720	0.96
38_S	51_E	0.717	0.96
141_Q	145_G	0.716	0.95
77_Q	111_Q	0.715	0.95
31_A	60_L	0.713	0.95
67_V	110_M	0.711	0.95
166_N	170_M	0.711	0.95
165_S	168_P	0.709	0.95
10_I	81_E	0.697	0.95
32_N	57_R	0.693	0.95
12_V	111_Q	0.679	0.94
42_R	48_E	0.679	0.94
59_V	103_V	0.672	0.94
77_Q	113_L	0.670	0.94
168_P	172_F	0.669	0.94
41_W	51_E	0.666	0.93
60_L	67_V	0.665	0.93
8_K	79_Y	0.665	0.93
167_E	171_D	0.661	0.93
143_Q	146_N	0.660	0.93
163_A	166_N	0.659	0.93
21_V	29_A	0.658	0.93
160_A	166_N	0.657	0.93
15_L	78_V	0.656	0.93
9_V	102_V	0.655	0.93
56_H	86_T	0.655	0.93
169_P	172_F	0.648	0.92
140_Q	144_G	0.647	0.92
44_K	47_G	0.646	0.92
122_P	125_G	0.639	0.92
131_Q	135_G	0.635	0.92
120_G	123_A	0.632	0.92
161_P	165_S	0.632	0.92
90_T	99_T	0.631	0.91
172_F	176_I	0.631	0.91
160_A	164_P	0.618	0.91
37_T	54_E	0.617	0.91
62_G	66_E	0.611	0.90
161_P	164_P	0.610	0.90
92_Q	95_Q	0.609	0.90
165_S	170_M	0.602	0.89
24_M	59_V	0.594	0.89
170_M	175_D	0.592	0.89
166_N	171_D	0.590	0.89
16_G	53_T	0.587	0.88
133_Q	139_P	0.586	0.88
62_G	77_Q	0.586	0.88
40_S	51_E	0.581	0.88
115_G	118_G	0.579	0.88
132_P	136_W	0.579	0.88
63_K	104_V	0.578	0.87
122_P	128_G	0.577	0.87
16_G	57_R	0.575	0.87
52_Q	83_Q	0.574	0.87
60_L	112_M	0.574	0.87
131_Q	136_W	0.572	0.87
21_V	65_A	0.571	0.87
71_Y	114_G	0.570	0.87
158_Q	161_P	0.570	0.87
136_W	140_Q	0.568	0.87
123_A	126_N	0.567	0.86
136_W	139_P	0.565	0.86
126_N	140_Q	0.563	0.86
173_D	176_I	0.562	0.86
76_S	116_R	0.560	0.86
129_G	136_W	0.558	0.86
129_G	138_Q	0.555	0.85
57_R	86_T	0.553	0.85
159_S	164_P	0.551	0.85
120_G	124_G	0.549	0.85
117_Q	121_A	0.549	0.85
137_G	142_P	0.549	0.85
137_G	141_Q	0.547	0.84
10_I	79_Y	0.546	0.84
62_G	65_A	0.545	0.84
129_G	132_P	0.543	0.84
89_W	96_D	0.541	0.84
67_V	70_E	0.540	0.84
141_Q	146_N	0.539	0.84
142_P	145_G	0.537	0.83
91_D	96_D	0.536	0.83
39_E	105_N	0.534	0.83
54_E	89_W	0.533	0.83
31_A	69_S	0.533	0.83
162_A	166_N	0.532	0.83
57_R	98_Y	0.532	0.83
83_Q	104_V	0.530	0.83
138_Q	144_G	0.530	0.83
50_K	83_Q	0.529	0.83
166_N	172_F	0.528	0.82
63_K	67_V	0.523	0.82
33_I	68_A	0.522	0.82
28_G	61_F	0.519	0.81
26_N	32_N	0.518	0.81
119_G	122_P	0.517	0.81
74_K	119_G	0.517	0.81
12_V	81_E	0.517	0.81
57_R	100_T	0.514	0.81
127_I	131_Q	0.514	0.81
162_A	165_S	0.514	0.81
41_W	49_M	0.513	0.81
124_G	127_I	0.509	0.80
116_R	120_G	0.506	0.80
128_G	134_G	0.505	0.80
130_G	146_N	0.502	0.79
126_N	129_G	0.502	0.79
140_Q	143_Q	0.500	0.79

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
4mz9A	4	0.6404	100	0.179	Contact Map
3pgzA	2	0.6292	100	0.247	Contact Map
1se8A	2	0.5787	100	0.278	Contact Map
3lgjA	2	0.5393	100	0.278	Contact Map
3afpA	3	0.6404	100	0.292	Contact Map
3tqyA	4	0.618	100	0.294	Contact Map
1z9fA	4	0.5	100	0.3	Contact Map
3eivA	3	0.6629	100	0.316	Contact Map
3ulpA	4	0.6404	100	0.342	Contact Map
2fxqA	2	0.5506	100	0.347	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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