Vwaint - PFAM28P - GREMLIN Contacts

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Vwaint - VWA / Hh protein intein-like

PFAM:	PF14624	Sequences: PLCKALLADLEGQVSEALSRRDWYEKWGRHYLLSLLRAHQLQQCNNFKDPGVQHYGGPLFKELRDRADQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	69 (64)
Sequences:	1132 (899)
Seq/√Len:	112.4
META:	0.739

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
39_H	55_Y	4.191	1.00
5_A	54_H	3.014	1.00
45_N	52_V	2.503	1.00
37_R	40_Q	2.444	1.00
37_R	41_L	2.368	1.00
21_R	25_E	2.284	1.00
20_R	23_W	2.169	1.00
39_H	51_G	2.123	1.00
13_Q	23_W	2.080	1.00
38_A	45_N	1.729	1.00
29_R	33_L	1.623	1.00
63_L	66_R	1.593	1.00
44_C	64_R	1.556	1.00
62_E	66_R	1.526	1.00
25_E	29_R	1.473	1.00
46_N	49_D	1.408	1.00
19_S	23_W	1.380	1.00
14_V	35_L	1.376	1.00
34_S	45_N	1.354	1.00
16_E	23_W	1.321	1.00
13_Q	16_E	1.313	1.00
11_E	58_P	1.128	0.99
35_L	39_H	1.113	0.98
30_H	33_L	1.107	0.98
12_G	16_E	1.100	0.98
58_P	62_E	1.096	0.98
46_N	52_V	1.084	0.98
18_L	32_L	1.047	0.98
57_G	60_F	1.047	0.98
17_A	45_N	1.039	0.97
63_L	67_A	1.019	0.97
51_G	55_Y	1.010	0.97
24_Y	32_L	1.004	0.97
34_S	44_C	0.968	0.96
58_P	61_K	0.960	0.96
27_W	46_N	0.937	0.95
42_Q	57_G	0.930	0.95
7_L	11_E	0.926	0.95
8_A	25_E	0.914	0.95
17_A	31_Y	0.894	0.94
38_A	52_V	0.886	0.94
61_K	65_D	0.874	0.93
13_Q	48_K	0.873	0.93
27_W	49_D	0.863	0.93
24_Y	29_R	0.822	0.91
4_K	10_L	0.763	0.87
27_W	47_F	0.760	0.87
58_P	66_R	0.746	0.86
24_Y	33_L	0.744	0.86
35_L	51_G	0.744	0.86
62_E	65_D	0.728	0.85
5_A	8_A	0.724	0.85
61_K	64_R	0.720	0.84
7_L	10_L	0.698	0.82
44_C	61_K	0.695	0.82
31_Y	35_L	0.694	0.82
23_W	48_K	0.692	0.82
12_G	42_Q	0.679	0.81
26_K	56_G	0.679	0.81
41_L	67_A	0.673	0.80
15_S	19_S	0.671	0.80
13_Q	17_A	0.670	0.80
56_G	61_K	0.669	0.80
4_K	7_L	0.659	0.79
59_L	62_E	0.659	0.79
24_Y	36_L	0.645	0.77
17_A	27_W	0.642	0.77
4_K	40_Q	0.641	0.77
18_L	41_L	0.638	0.76
59_L	63_L	0.626	0.75
36_L	40_Q	0.618	0.74
18_L	21_R	0.609	0.73
15_S	25_E	0.600	0.72
29_R	45_N	0.594	0.71
18_L	36_L	0.592	0.71
32_L	51_G	0.592	0.71
37_R	50_P	0.587	0.70
57_G	61_K	0.584	0.70
57_G	63_L	0.570	0.68
56_G	59_L	0.568	0.68
23_W	26_K	0.568	0.68
35_L	52_V	0.561	0.67
12_G	27_W	0.557	0.66
52_V	57_G	0.530	0.63
26_K	34_S	0.528	0.62
30_H	51_G	0.526	0.62
15_S	62_E	0.525	0.62
33_L	57_G	0.522	0.61
8_A	11_E	0.521	0.61
36_L	58_P	0.506	0.59
4_K	36_L	0.505	0.59
13_Q	45_N	0.505	0.59
27_W	48_K	0.503	0.59
17_A	32_L	0.501	0.58
4_K	25_E	0.501	0.58
25_E	37_R	0.500	0.58

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
1vw1A	5	1	27.1	0.857	Contact Map
2ixoA	1	0.9565	11	0.881	Contact Map
2ixnA	1	0.9275	9.5	0.884	Contact Map
1yvlA	3	0.8986	9.5	0.884	Contact Map
2ixmA	1	0.9565	9.3	0.885	Contact Map
2vsqA	1	0.971	8.7	0.886	Contact Map
1cp2A	2	0.4058	7.7	0.889	Contact Map
4ziaA	2	0.8986	6.9	0.891	Contact Map
3t5oA	1	0.9855	6.7	0.892	Contact Map
4e04A	2	0.3768	6.6	0.892	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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