GvpG - PFAM28P - GREMLIN Contacts

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GvpG - Gas vesicle protein G

PFAM:	PF05120	Sequences: LLTLPLAPVRGVRWVAEKIAEAAERELYDEAAIREELLELQMRLELGEISEEEFAEREAELLARLREIRERREEGAEEE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	79 (72)
Sequences:	5402 (2803)
Seq/√Len:	330.3
META:	0.915

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
43_R	48_E	2.917	1.00
40_L	57_R	2.744	1.00
50_S	53_E	2.741	1.00
18_K	21_E	2.570	1.00
20_A	24_E	2.402	1.00
44_L	54_F	2.375	1.00
22_A	25_R	2.206	1.00
44_L	51_E	1.986	1.00
57_R	60_E	1.963	1.00
42_M	46_L	1.951	1.00
33_I	61_L	1.941	1.00
39_E	43_R	1.769	1.00
4_L	7_A	1.766	1.00
40_L	54_F	1.732	1.00
12_V	16_A	1.652	1.00
36_E	57_R	1.531	1.00
41_Q	45_E	1.455	1.00
43_R	57_R	1.449	1.00
51_E	55_A	1.445	1.00
30_E	72_R	1.415	1.00
36_E	39_E	1.400	1.00
33_I	65_L	1.364	1.00
22_A	26_E	1.359	1.00
13_R	17_E	1.292	1.00
41_Q	54_F	1.269	1.00
24_E	28_Y	1.219	1.00
2_L	5_P	1.180	1.00
3_T	6_L	1.120	1.00
35_E	39_E	1.112	1.00
10_R	13_R	1.111	1.00
17_E	21_E	1.087	1.00
16_A	20_A	1.001	1.00
40_L	49_I	0.999	1.00
37_L	58_E	0.990	1.00
42_M	45_E	0.981	1.00
68_I	71_R	0.968	1.00
30_E	68_I	0.960	1.00
30_E	34_R	0.949	1.00
3_T	10_R	0.947	1.00
17_E	20_A	0.937	1.00
29_D	32_A	0.930	1.00
28_Y	68_I	0.928	1.00
20_A	23_A	0.923	1.00
62_L	66_R	0.922	1.00
13_R	16_A	0.905	1.00
32_A	36_E	0.900	1.00
2_L	6_L	0.885	1.00
36_E	64_R	0.883	1.00
21_E	25_R	0.875	1.00
56_E	60_E	0.873	1.00
3_T	7_A	0.873	1.00
59_A	63_A	0.870	1.00
6_L	10_R	0.814	1.00
2_L	7_A	0.779	1.00
63_A	67_E	0.773	1.00
14_W	18_K	0.771	1.00
11_G	14_W	0.741	0.99
12_V	15_V	0.741	0.99
67_E	71_R	0.740	0.99
38_L	41_Q	0.738	0.99
34_R	38_L	0.718	0.99
39_E	46_L	0.712	0.99
9_V	16_A	0.708	0.99
30_E	69_R	0.700	0.99
7_A	11_G	0.691	0.99
18_K	22_A	0.686	0.99
28_Y	71_R	0.678	0.99
44_L	58_E	0.667	0.99
15_V	19_I	0.660	0.99
53_E	56_E	0.658	0.99
28_Y	67_E	0.644	0.98
28_Y	33_I	0.643	0.98
63_A	66_R	0.639	0.98
31_A	35_E	0.638	0.98
7_A	14_W	0.629	0.98
33_I	64_R	0.616	0.98
69_R	73_E	0.616	0.98
54_F	58_E	0.613	0.98
65_L	69_R	0.610	0.98
41_Q	58_E	0.607	0.98
5_P	10_R	0.607	0.98
32_A	35_E	0.603	0.98
11_G	15_V	0.598	0.97
54_F	66_R	0.597	0.97
14_W	17_E	0.596	0.97
70_E	73_E	0.593	0.97
44_L	66_R	0.590	0.97
68_I	72_R	0.589	0.97
66_R	70_E	0.586	0.97
49_I	53_E	0.584	0.97
49_I	57_R	0.583	0.97
44_L	49_I	0.583	0.97
23_A	26_E	0.577	0.97
40_L	61_L	0.560	0.96
58_E	62_L	0.557	0.96
39_E	42_M	0.554	0.96
53_E	57_R	0.549	0.96
36_E	61_L	0.548	0.96
54_F	62_L	0.545	0.96
35_E	38_L	0.540	0.95
31_A	34_R	0.538	0.95
29_D	64_R	0.537	0.95
43_R	46_L	0.534	0.95
60_E	64_R	0.534	0.95
33_I	68_I	0.530	0.95
64_R	67_E	0.517	0.94
26_E	29_D	0.517	0.94
19_I	24_E	0.500	0.93

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
4wsbB	1	0.6203	72.1	0.786	Contact Map
4wrtB	1	0.5949	54.6	0.809	Contact Map
4kisA	2	1	31.9	0.834	Contact Map
3a1gA	1	0.7342	14.1	0.859	Contact Map
3sgiA	1	0.6962	7.8	0.875	Contact Map
4glxA	1	0.6456	7.5	0.875	Contact Map
4glwA	2	0.3797	6.4	0.879	Contact Map
4kqtA	1	1	6.1	0.88	Contact Map
4lh6A	1	0.7468	6.1	0.881	Contact Map
3jslA	2	0.6582	5.8	0.882	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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