SSBA - BACSU - GREMLIN Contacts

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SSBA - Single-stranded DNA-binding protein A

UniProt:	P37455	Sequences: MLNRVVLVGRLTKDPELRYTPNGAAVATFTLAVNRTFTNQSGEREADFINCVTWRRQAENVANFLKKGSLAGVDGRLQTRNYENQQGQRVFVTEVQAESVQFLEPKNGGGSGSGGYNEGNSGGGQYFGGGQNDNPFGGNQNNQRRNQGNSFNDDPFANDGKPIDISDDDLPF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	172 (131)
Sequences:	3342 (2236)
Seq/√Len:	195.4

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
83_E	89_R	3.458	1.00
19_Y	25_A	3.158	1.00
84_N	88_Q	2.990	1.00
70_L	104_E	2.943	1.00
51_C	97_A	2.622	1.00
80_R	94_E	2.551	1.00
81_N	89_R	2.501	1.00
80_R	92_V	2.345	1.00
12_T	48_F	2.271	1.00
53_T	61_V	2.253	1.00
13_K	30_T	2.242	1.00
2_L	6_V	2.201	1.00
30_T	50_N	2.161	1.00
10_R	70_L	2.147	1.00
84_N	90_V	2.115	1.00
29_F	53_T	2.101	1.00
11_L	65_L	2.082	1.00
24_A	55_R	2.059	1.00
76_R	98_E	1.957	1.00
17_L	27_A	1.951	1.00
4_R	74_D	1.948	1.00
20_T	54_W	1.946	1.00
20_T	26_V	1.931	1.00
65_L	71_A	1.924	1.00
61_V	65_L	1.897	1.00
29_F	51_C	1.875	1.00
45_E	78_Q	1.791	1.00
82_Y	92_V	1.765	1.00
56_R	59_E	1.616	1.00
20_T	24_A	1.611	1.00
2_L	8_V	1.553	1.00
78_Q	96_Q	1.504	1.00
7_L	31_L	1.501	1.00
25_A	59_E	1.476	1.00
31_L	73_V	1.455	1.00
33_V	49_I	1.429	1.00
8_V	103_L	1.428	1.00
79_T	93_T	1.403	1.00
53_T	97_A	1.389	1.00
17_L	62_A	1.356	1.00
28_T	80_R	1.337	1.00
52_V	94_E	1.314	1.00
12_T	30_T	1.308	1.00
35_R	45_E	1.298	1.00
53_T	57_Q	1.273	1.00
26_V	54_W	1.238	1.00
77_L	95_V	1.230	1.00
53_T	73_V	1.223	1.00
60_N	102_F	1.190	1.00
97_A	100_V	1.148	1.00
13_K	50_N	1.139	1.00
59_E	63_N	1.129	1.00
53_T	100_V	1.114	1.00
2_L	72_G	1.085	1.00
5_V	77_L	1.085	1.00
61_V	71_A	1.080	1.00
79_T	91_F	1.066	1.00
15_P	27_A	1.039	1.00
13_K	16_E	1.003	1.00
52_V	80_R	0.997	1.00
38_T	42_G	0.989	1.00
11_L	15_P	0.986	0.99
10_R	34_N	0.966	0.99
50_N	92_V	0.960	0.99
7_L	95_V	0.959	0.99
49_I	93_T	0.957	0.99
21_P	24_A	0.931	0.99
54_W	96_Q	0.918	0.99
69_S	104_E	0.917	0.99
66_K	69_S	0.907	0.99
14_D	66_K	0.887	0.99
8_V	72_G	0.884	0.99
49_I	95_V	0.878	0.99
81_N	92_V	0.878	0.99
34_N	46_A	0.873	0.99
118_E	121_S	0.852	0.99
19_Y	59_E	0.848	0.98
28_T	52_V	0.839	0.98
25_A	62_A	0.838	0.98
2_L	101_Q	0.837	0.98
34_N	44_R	0.837	0.98
60_N	100_V	0.831	0.98
70_L	101_Q	0.829	0.98
31_L	71_A	0.822	0.98
82_Y	94_E	0.819	0.98
39_N	42_G	0.818	0.98
78_Q	98_E	0.818	0.98
47_D	79_T	0.797	0.98
69_S	102_F	0.787	0.98
76_R	96_Q	0.786	0.98
18_R	26_V	0.779	0.97
57_Q	60_N	0.773	0.97
35_R	76_R	0.773	0.97
110_G	113_S	0.766	0.97
55_R	98_E	0.763	0.97
5_V	95_V	0.745	0.97
57_Q	97_A	0.728	0.96
61_V	100_V	0.728	0.96
37_F	42_G	0.728	0.96
19_Y	63_N	0.724	0.96
85_Q	88_Q	0.723	0.96
82_Y	88_Q	0.723	0.96
49_I	79_T	0.717	0.96
17_L	25_A	0.713	0.96
7_L	49_I	0.713	0.96
38_T	44_R	0.711	0.96
47_D	95_V	0.710	0.95
65_L	102_F	0.708	0.95
25_A	58_A	0.707	0.95
29_F	97_A	0.703	0.95
108_G	112_G	0.702	0.95
60_N	64_F	0.702	0.95
73_V	100_V	0.696	0.95
27_A	61_V	0.693	0.95
24_A	54_W	0.688	0.95
69_S	107_N	0.682	0.94
6_V	74_D	0.682	0.94
35_R	98_E	0.678	0.94
118_E	122_G	0.675	0.94
27_A	53_T	0.675	0.94
57_Q	100_V	0.674	0.94
83_E	92_V	0.665	0.94
50_N	91_F	0.663	0.94
38_T	41_S	0.653	0.93
123_G	126_Y	0.649	0.93
109_G	112_G	0.648	0.93
39_N	43_E	0.645	0.93
35_R	47_D	0.645	0.93
15_P	61_V	0.644	0.93
60_N	63_N	0.644	0.93
28_T	50_N	0.642	0.92
25_A	63_N	0.641	0.92
27_A	58_A	0.641	0.92
39_N	45_E	0.640	0.92
39_N	44_R	0.638	0.92
127_F	131_Q	0.636	0.92
47_D	82_Y	0.636	0.92
118_E	124_G	0.634	0.92
69_S	106_K	0.633	0.92
83_E	88_Q	0.624	0.91
125_Q	130_G	0.623	0.91
117_N	122_G	0.621	0.91
40_Q	43_E	0.620	0.91
104_E	107_N	0.611	0.90
33_V	47_D	0.611	0.90
36_T	44_R	0.611	0.90
70_L	103_L	0.609	0.90
53_T	60_N	0.608	0.90
121_S	124_G	0.601	0.90
116_Y	130_G	0.596	0.89
113_S	116_Y	0.595	0.89
124_G	127_F	0.593	0.89
47_D	93_T	0.591	0.89
119_G	122_G	0.589	0.89
82_Y	85_Q	0.586	0.89
56_R	60_N	0.579	0.88
74_D	99_S	0.576	0.88
17_L	58_A	0.570	0.87
37_F	40_Q	0.570	0.87
107_N	111_S	0.567	0.87
106_K	110_G	0.563	0.87
8_V	101_Q	0.563	0.87
127_F	130_G	0.560	0.86
126_Y	131_Q	0.560	0.86
6_V	72_G	0.559	0.86
121_S	125_Q	0.557	0.86
119_G	128_G	0.557	0.86
110_G	114_G	0.555	0.86
113_S	117_N	0.550	0.85
82_Y	89_R	0.549	0.85
119_G	127_F	0.548	0.85
77_L	92_V	0.547	0.85
112_G	115_G	0.547	0.85
119_G	132_N	0.546	0.85
107_N	112_G	0.546	0.85
60_N	103_L	0.546	0.85
108_G	111_S	0.545	0.85
117_N	121_S	0.545	0.85
125_Q	128_G	0.539	0.84
114_G	117_N	0.537	0.84
52_V	96_Q	0.531	0.83
76_R	97_A	0.528	0.83
129_G	132_N	0.520	0.82
119_G	130_G	0.520	0.82
11_L	71_A	0.517	0.82
116_Y	119_G	0.515	0.81
37_F	44_R	0.514	0.81
28_T	92_V	0.512	0.81
55_R	58_A	0.512	0.81
55_R	70_L	0.510	0.81
50_N	79_T	0.510	0.81
65_L	100_V	0.506	0.80
55_R	59_E	0.505	0.80
20_T	52_V	0.504	0.80
113_S	123_G	0.503	0.80
122_G	126_Y	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	0.6105	100	0.214	Contact Map
1se8A	2	0.5698	100	0.25	Contact Map
1z9fA	4	0.5	100	0.251	Contact Map
3pgzA	2	0.6047	100	0.262	Contact Map
3lgjA	2	0.5233	100	0.263	Contact Map
3afpA	3	0.6221	100	0.292	Contact Map
2vw9A	3	0.6163	100	0.294	Contact Map
3eivA	3	0.6395	100	0.296	Contact Map
2fxqA	2	0.5581	100	0.301	Contact Map
3tqyA	4	0.6047	100	0.301	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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