ATP_synt_H - PFAM28P - GREMLIN Contacts

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ATP_synt_H - ATP synthase subunit H

PFAM:	PF05493	Sequences: PLIIGTIIFAVLGIVAPFFVPKGPNRGLIRTLVILAAVCCWLMWACTYLAQMNPLIGPILSN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	62 (60)
Sequences:	941 (733)
Seq/√Len:	94.6
META:	0.561

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
48_Y	52_M	3.938	1.00
49_L	52_M	2.754	1.00
36_A	40_C	2.332	1.00
2_L	45_A	2.088	1.00
6_T	9_F	2.086	1.00
48_Y	53_N	1.861	1.00
17_P	34_I	1.777	1.00
9_F	12_L	1.748	1.00
33_V	37_A	1.737	1.00
13_G	37_A	1.732	1.00
43_M	47_T	1.660	1.00
28_L	32_L	1.645	1.00
6_T	10_A	1.544	1.00
8_I	12_L	1.529	1.00
13_G	17_P	1.467	1.00
28_L	39_C	1.436	1.00
13_G	34_I	1.363	0.99
31_T	35_L	1.363	0.99
7_I	11_V	1.351	0.99
27_G	30_R	1.330	0.99
3_I	7_I	1.269	0.99
11_V	15_V	1.245	0.99
5_G	9_F	1.236	0.99
32_L	36_A	1.196	0.98
9_F	13_G	1.144	0.98
2_L	52_M	1.088	0.97
34_I	38_V	1.087	0.97
2_L	37_A	1.062	0.96
37_A	41_W	1.055	0.96
16_A	20_V	1.022	0.95
42_L	46_C	1.009	0.95
2_L	5_G	0.957	0.93
28_L	35_L	0.955	0.93
33_V	40_C	0.947	0.93
32_L	35_L	0.919	0.92
47_T	56_I	0.914	0.92
6_T	13_G	0.900	0.91
25_N	28_L	0.898	0.91
17_P	30_R	0.883	0.90
6_T	41_W	0.876	0.90
50_A	56_I	0.870	0.90
45_A	49_L	0.859	0.89
4_I	8_I	0.856	0.89
16_A	19_F	0.807	0.86
11_V	16_A	0.790	0.84
11_V	20_V	0.782	0.84
25_N	30_R	0.764	0.82
29_I	47_T	0.754	0.82
54_P	58_P	0.751	0.81
16_A	43_M	0.738	0.80
35_L	38_V	0.738	0.80
29_I	50_A	0.736	0.80
43_M	46_C	0.733	0.80
10_A	14_I	0.727	0.79
38_V	42_L	0.712	0.78
43_M	49_L	0.707	0.77
4_I	24_P	0.699	0.76
26_R	30_R	0.697	0.76
30_R	34_I	0.668	0.73
29_I	56_I	0.667	0.73
46_C	50_A	0.654	0.72
51_Q	55_L	0.649	0.71
10_A	60_L	0.647	0.71
21_P	46_C	0.640	0.70
18_F	39_C	0.626	0.68
6_T	17_P	0.624	0.68
20_V	23_G	0.624	0.68
35_L	59_I	0.621	0.68
31_T	50_A	0.619	0.67
18_F	22_K	0.617	0.67
51_Q	54_P	0.607	0.66
16_A	33_V	0.607	0.66
7_I	14_I	0.602	0.65
18_F	23_G	0.601	0.65
8_I	15_V	0.595	0.64
32_L	39_C	0.593	0.64
47_T	59_I	0.588	0.64
26_R	49_L	0.585	0.63
41_W	45_A	0.569	0.61
32_L	47_T	0.565	0.60
15_V	21_P	0.563	0.60
15_V	19_F	0.557	0.59
5_G	14_I	0.554	0.59
24_P	27_G	0.547	0.58
27_G	35_L	0.546	0.58
30_R	37_A	0.521	0.54
49_L	55_L	0.516	0.54
9_F	15_V	0.511	0.53
41_W	52_M	0.501	0.52
21_P	60_L	0.500	0.51

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
4aw6A	2	1	7.7	0.879	Contact Map
4e6zA	1	0	5.5	0.886	Contact Map
2l2tA	2	0.4839	4.7	0.89	Contact Map
4il3A	1	1	3.9	0.894	Contact Map
1zcdA	1	0.9194	3.6	0.896	Contact Map
2ks1B	1	0.4677	3.3	0.898	Contact Map
2mfrA	1	0.5645	3.1	0.9	Contact Map
3qbgA	3	1	3	0.9	Contact Map
2mofA	1	0.5	2.9	0.901	Contact Map
2jwaA	2	0.4516	2.8	0.902	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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