SSBB - BACSU - GREMLIN Contacts

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SSBB - Single-stranded DNA-binding protein B

UniProt:	C0SPB6	Sequences: MFNQVMLVGRLTKDPDLRYTSAGAAVAHVTLAVNRSFKNASGEIEADYVNCTLWRKTAENTALYCQKGSLVGVSGRIQTRSYENEEGVNVYVTEVLADTVRFMDPKPREKAAD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	113 (106)
Sequences:	4973 (2678)
Seq/√Len:	260.1

ECOLI - SSB
BACSU - SSBB SSBA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
84_N	88_V	2.608	1.00
19_Y	25_A	2.608	1.00
83_E	89_N	2.554	1.00
12_T	48_Y	2.359	1.00
51_C	97_A	2.307	1.00
80_R	94_E	2.263	1.00
24_A	55_R	2.198	1.00
81_S	89_N	2.170	1.00
80_R	92_V	2.103	1.00
4_Q	74_S	2.072	1.00
84_N	90_V	2.057	1.00
70_L	104_D	1.779	1.00
11_L	65_C	1.776	1.00
33_V	49_V	1.750	1.00
53_L	61_T	1.709	1.00
14_D	66_Q	1.695	1.00
29_V	51_C	1.675	1.00
20_T	54_W	1.640	1.00
10_R	70_L	1.610	1.00
82_Y	92_V	1.592	1.00
2_F	6_M	1.582	1.00
29_V	53_L	1.560	1.00
13_K	30_T	1.548	1.00
61_T	65_C	1.502	1.00
56_K	59_E	1.346	1.00
17_L	62_A	1.327	1.00
65_C	71_V	1.308	1.00
30_T	50_N	1.304	1.00
2_F	72_G	1.302	1.00
17_L	27_A	1.282	1.00
52_T	94_E	1.281	1.00
35_R	76_R	1.274	1.00
35_R	47_D	1.258	1.00
8_V	72_G	1.249	1.00
69_S	104_D	1.245	1.00
20_T	26_V	1.245	1.00
53_L	97_A	1.242	1.00
8_V	103_M	1.236	1.00
74_S	99_T	1.236	1.00
76_R	98_D	1.220	1.00
78_Q	96_L	1.201	1.00
34_N	44_I	1.178	1.00
7_L	31_L	1.174	1.00
79_T	93_T	1.172	1.00
25_A	59_E	1.129	1.00
83_E	87_G	1.127	1.00
97_A	100_V	1.122	1.00
10_R	34_N	1.106	1.00
50_N	92_V	1.102	1.00
45_E	78_Q	1.092	1.00
39_N	43_E	1.086	1.00
66_Q	69_S	1.070	1.00
60_N	102_F	1.068	1.00
35_R	45_E	1.055	1.00
12_T	30_T	1.038	1.00
15_P	61_T	1.038	1.00
15_P	27_A	1.029	1.00
47_D	79_T	1.024	1.00
61_T	100_V	1.021	1.00
49_V	95_V	1.019	1.00
7_L	95_V	1.016	1.00
76_R	96_L	0.998	1.00
64_Y	102_F	0.992	1.00
5_V	77_I	0.985	1.00
70_L	101_R	0.983	1.00
77_I	95_V	0.979	1.00
5_V	95_V	0.969	1.00
53_L	57_T	0.959	1.00
79_T	91_Y	0.950	1.00
11_L	15_P	0.917	1.00
18_R	26_V	0.915	1.00
60_N	100_V	0.914	1.00
26_V	54_W	0.914	1.00
34_N	46_A	0.891	1.00
2_F	101_R	0.890	1.00
2_F	8_V	0.880	1.00
57_T	60_N	0.874	1.00
18_R	28_H	0.872	1.00
38_K	42_G	0.856	1.00
31_L	71_V	0.855	1.00
20_T	24_A	0.855	1.00
13_K	50_N	0.835	0.99
25_A	62_A	0.824	0.99
69_S	102_F	0.816	0.99
50_N	91_Y	0.816	0.99
49_V	93_T	0.806	0.99
28_H	80_R	0.800	0.99
53_L	100_V	0.799	0.99
49_V	79_T	0.798	0.99
52_T	80_R	0.793	0.99
13_K	16_D	0.785	0.99
82_Y	91_Y	0.773	0.99
32_A	46_A	0.769	0.99
6_M	72_G	0.768	0.99
59_E	63_L	0.757	0.99
4_Q	98_D	0.752	0.99
82_Y	90_V	0.748	0.99
36_S	44_I	0.747	0.99
38_K	44_I	0.740	0.99
60_N	64_Y	0.739	0.99
56_K	60_N	0.725	0.98
37_F	44_I	0.724	0.98
24_A	54_W	0.715	0.98
17_L	25_A	0.715	0.98
70_L	103_M	0.708	0.98
40_A	43_E	0.699	0.98
61_T	71_V	0.698	0.98
28_H	50_N	0.695	0.98
14_D	67_K	0.689	0.98
20_T	23_G	0.688	0.98
57_T	100_V	0.687	0.98
39_N	44_I	0.681	0.98
72_G	103_M	0.679	0.98
47_D	78_Q	0.676	0.97
54_W	96_L	0.672	0.97
82_Y	85_E	0.667	0.97
27_A	62_A	0.664	0.97
39_N	45_E	0.662	0.97
33_V	47_D	0.656	0.97
28_H	52_T	0.651	0.97
65_C	102_F	0.649	0.97
6_M	74_S	0.640	0.96
7_L	33_V	0.639	0.96
19_Y	63_L	0.638	0.96
25_A	58_A	0.622	0.96
104_D	107_P	0.621	0.96
8_V	70_L	0.620	0.96
53_L	58_A	0.619	0.96
77_I	93_T	0.606	0.95
29_V	97_A	0.601	0.95
39_N	42_G	0.601	0.95
5_V	93_T	0.592	0.95
69_S	107_P	0.587	0.94
29_V	61_T	0.578	0.94
52_T	78_Q	0.577	0.94
37_F	45_E	0.576	0.94
35_R	98_D	0.570	0.93
37_F	42_G	0.564	0.93
82_Y	94_E	0.561	0.93
51_C	73_V	0.559	0.93
4_Q	99_T	0.554	0.92
16_D	28_H	0.550	0.92
65_C	69_S	0.549	0.92
27_A	61_T	0.547	0.92
85_E	88_V	0.545	0.92
28_H	94_E	0.539	0.91
59_E	62_A	0.528	0.91
57_T	97_A	0.528	0.91
7_L	49_V	0.525	0.90
81_S	91_Y	0.519	0.90
74_S	98_D	0.518	0.90
21_S	24_A	0.517	0.90
4_Q	72_G	0.513	0.89
2_F	70_L	0.512	0.89
31_L	73_V	0.511	0.89
70_L	105_P	0.506	0.89
52_T	96_L	0.504	0.88
34_N	45_E	0.503	0.88
32_A	48_Y	0.500	0.88

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
1z9fA	4	0.7611	100	0.136	Contact Map
3vdyA	3	0.8938	100	0.141	Contact Map
2vw9A	3	0.9381	100	0.146	Contact Map
3lgjA	2	0.7965	100	0.167	Contact Map
4mz9A	4	0.9292	100	0.168	Contact Map
1se8A	2	0.9027	100	0.17	Contact Map
3tqyA	4	0.9204	100	0.177	Contact Map
3ullA	3	0.8938	100	0.182	Contact Map
3pgzA	2	0.9204	100	0.185	Contact Map
3ulpA	4	0.9204	100	0.194	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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