VMA21 - PFAM28P - GREMLIN Contacts

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VMA21 - VMA21-like domain

PFAM:	PF09446	Sequences: SVIKKLLFFSLAMIVLPIGTYFLTKNYLFEGLFGLSSSDNTTYAGILAVVVVNVVLAAYIYVAF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	64 (63)
Sequences:	734 (559)
Seq/√Len:	70.5
META:	0.403

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
16_L	51_V	3.713	1.00
20_T	51_V	3.609	1.00
57_A	61_Y	3.324	1.00
20_T	47_L	3.029	1.00
10_S	13_M	2.220	1.00
46_I	50_V	2.114	1.00
5_K	62_V	2.033	1.00
61_Y	64_F	1.897	1.00
24_T	47_L	1.707	1.00
10_S	14_I	1.652	0.99
11_L	15_V	1.446	0.99
8_F	12_A	1.431	0.98
45_G	49_V	1.397	0.98
21_Y	25_K	1.368	0.98
42_T	46_I	1.345	0.98
24_T	44_A	1.295	0.97
6_L	10_S	1.270	0.97
9_F	62_V	1.255	0.97
24_T	28_L	1.237	0.96
9_F	58_A	1.234	0.96
4_K	23_L	1.199	0.95
9_F	13_M	1.190	0.95
50_V	53_N	1.189	0.95
46_I	49_V	1.183	0.95
2_V	5_K	1.158	0.95
4_K	44_A	1.113	0.93
36_S	54_V	1.066	0.92
57_A	62_V	1.047	0.91
12_A	50_V	1.023	0.90
60_I	64_F	1.011	0.89
30_E	51_V	0.999	0.89
44_A	60_I	0.994	0.89
5_K	59_Y	0.990	0.88
13_M	56_L	0.925	0.85
53_N	59_Y	0.916	0.84
34_G	37_S	0.913	0.84
6_L	60_I	0.889	0.82
14_I	56_L	0.887	0.82
8_F	57_A	0.870	0.81
7_L	19_G	0.866	0.81
33_F	36_S	0.862	0.80
42_T	56_L	0.861	0.80
10_S	59_Y	0.854	0.80
56_L	60_I	0.847	0.79
59_Y	63_A	0.836	0.78
5_K	9_F	0.827	0.78
8_F	49_V	0.812	0.76
21_Y	24_T	0.801	0.75
41_T	48_A	0.756	0.71
51_V	55_V	0.754	0.71
3_I	49_V	0.754	0.71
19_G	23_L	0.743	0.70
45_G	59_Y	0.708	0.66
14_I	49_V	0.705	0.66
45_G	48_A	0.702	0.65
11_L	61_Y	0.698	0.65
42_T	45_G	0.694	0.64
23_L	27_Y	0.689	0.64
9_F	59_Y	0.677	0.62
39_D	43_Y	0.674	0.62
26_N	35_L	0.639	0.58
15_V	19_G	0.633	0.57
25_K	42_T	0.631	0.57
11_L	19_G	0.630	0.57
6_L	55_V	0.622	0.56
44_A	58_A	0.622	0.56
53_N	56_L	0.620	0.56
52_V	55_V	0.615	0.55
11_L	60_I	0.612	0.55
28_L	43_Y	0.610	0.55
31_G	56_L	0.606	0.54
13_M	17_P	0.604	0.54
15_V	60_I	0.600	0.53
3_I	61_Y	0.596	0.53
25_K	44_A	0.595	0.53
10_S	55_V	0.594	0.53
42_T	49_V	0.594	0.53
30_E	36_S	0.590	0.52
29_F	47_L	0.586	0.52
37_S	40_N	0.583	0.51
14_I	64_F	0.582	0.51
26_N	50_V	0.571	0.50
40_N	54_V	0.556	0.48
54_V	58_A	0.555	0.48
4_K	8_F	0.552	0.48
17_P	48_A	0.549	0.47
40_N	53_N	0.543	0.46
10_S	18_I	0.542	0.46
12_A	64_F	0.535	0.45
23_L	30_E	0.528	0.45
22_F	53_N	0.524	0.44
22_F	25_K	0.518	0.43
27_Y	32_L	0.506	0.42
7_L	28_L	0.500	0.41

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
4httA	1	0.9531	1.8	0.891	Contact Map
4px7A	1	0.9531	1.7	0.891	Contact Map
1rz2A	1	0	1.7	0.892	Contact Map
4ev6A	3	0.875	1.5	0.894	Contact Map
1sdoA	2	0.3906	1.3	0.899	Contact Map
2k3cA	1	0.4844	1.2	0.901	Contact Map
3mk7C	2	0.4062	1.1	0.904	Contact Map
4i0uA	4	0.8594	1	0.906	Contact Map
2nwlA	3	0.9219	0.9	0.907	Contact Map
4b4aA	1	0.9844	0.9	0.908	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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