GVPA1 - HALSA - GREMLIN Contacts

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GVPA1 - Gas vesicle structural protein 1

UniProt:	P08958	Sequences: MAQPDSSGLAEVLDRVLDKGVVVDVWARVSLVGIEILTVEARVVAASVDTFLHYAEEIAKIEQAELTAGAEAAPEA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	76 (63)
Sequences:	133 (38)
Seq/√Len:	4.7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
29_V	37_L	3.062	0.70
39_V	45_A	2.421	0.51
52_L	55_A	2.097	0.41
26_W	40_E	1.995	0.38
53_H	57_E	1.909	0.35
32_V	52_L	1.896	0.35
16_V	55_A	1.850	0.33
40_E	54_Y	1.795	0.32
10_A	19_K	1.611	0.27
11_E	48_V	1.505	0.25
16_V	52_L	1.490	0.24
54_Y	59_A	1.479	0.24
25_V	57_E	1.462	0.24
32_V	55_A	1.440	0.23
19_K	38_T	1.407	0.22
12_V	50_T	1.407	0.22
32_V	59_A	1.357	0.21
38_T	49_D	1.354	0.21
14_D	39_V	1.338	0.21
31_L	38_T	1.334	0.21
28_R	38_T	1.332	0.21
53_H	61_I	1.311	0.20
27_A	31_L	1.308	0.20
59_A	62_E	1.297	0.20
57_E	60_K	1.297	0.20
40_E	60_K	1.246	0.19
30_S	47_S	1.227	0.19
23_V	36_I	1.220	0.18
26_W	37_L	1.148	0.17
26_W	58_I	1.137	0.17
51_F	60_K	1.110	0.16
39_V	56_E	1.106	0.16
7_S	29_V	1.101	0.16
54_Y	60_K	1.088	0.16
7_S	28_R	1.061	0.16
8_G	21_V	1.059	0.16
11_E	21_V	1.032	0.15
53_H	60_K	0.978	0.14
43_V	67_T	0.972	0.14
36_I	49_D	0.925	0.14
40_E	62_E	0.917	0.13
11_E	15_R	0.906	0.13
25_V	43_V	0.875	0.13
15_R	54_Y	0.867	0.13
11_E	40_E	0.859	0.13
36_I	43_V	0.858	0.13
15_R	40_E	0.853	0.12
15_R	45_A	0.839	0.12
42_R	55_A	0.817	0.12
15_R	60_K	0.816	0.12
11_E	54_Y	0.810	0.12
49_D	53_H	0.784	0.12
51_F	57_E	0.781	0.12
15_R	25_V	0.777	0.11
6_S	43_V	0.769	0.11
18_D	64_A	0.759	0.11
42_R	52_L	0.748	0.11
14_D	52_L	0.746	0.11
38_T	47_S	0.741	0.11
11_E	49_D	0.736	0.11
29_V	36_I	0.727	0.11
16_V	32_V	0.715	0.11
8_G	37_L	0.710	0.11
54_Y	62_E	0.710	0.11
19_K	36_I	0.706	0.11
18_D	66_L	0.687	0.10
45_A	63_Q	0.675	0.10
27_A	47_S	0.668	0.10
13_L	16_V	0.667	0.10
52_L	58_I	0.654	0.10
16_V	42_R	0.648	0.10
5_D	11_E	0.645	0.10
52_L	59_A	0.642	0.10
54_Y	58_I	0.614	0.10
21_V	40_E	0.610	0.10
25_V	39_V	0.607	0.09
8_G	60_K	0.604	0.09
6_S	27_A	0.588	0.09
40_E	58_I	0.588	0.09
15_R	21_V	0.584	0.09
13_L	49_D	0.577	0.09
37_L	50_T	0.572	0.09
7_S	12_V	0.569	0.09
7_S	27_A	0.560	0.09
29_V	64_A	0.558	0.09
7_S	21_V	0.545	0.09
26_W	64_A	0.535	0.09
15_R	43_V	0.529	0.09
28_R	50_T	0.528	0.09
16_V	25_V	0.528	0.09
56_E	62_E	0.524	0.09
12_V	16_V	0.505	0.08
31_L	40_E	0.501	0.08
29_V	62_E	0.500	0.08

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
1vjoA	2	0.6974	15.5	0.915	Contact Map
2j3xA	1	0.9342	10.2	0.921	Contact Map
2qmxA	3	0.8289	10	0.922	Contact Map
4lubA	2	0.8158	8.4	0.924	Contact Map
3mwbA	3	0.8289	7.9	0.925	Contact Map
3e9kA	2	0.7105	7.9	0.925	Contact Map
3luyA	2	0.9868	7.5	0.926	Contact Map
2yrrA	2	0.7105	6.6	0.928	Contact Map
1eluA	2	0.7237	6.1	0.929	Contact Map
2aeuA	2	0.7632	5.7	0.93	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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