DUF2469 - PFAM28P - GREMLIN Contacts

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DUF2469 - Protein of unknown function (DUF2469)

PFAM:	PF10611	Sequences: MSAEDLERYEAELELQLYREYRDVVPMFRYVVETERRFYLANEVDVQVRSEGGDVYFEVTLTDAWVWDMYRPARFVKSVRVLTFKDVNVEELPKKDLELP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	100 (96)
Sequences:	1495 (403)
Seq/√Len:	41.1
META:	0.902

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
24_V	27_M	4.102	1.00
6_L	11_A	3.665	1.00
43_E	62_T	3.024	1.00
8_R	13_L	2.607	1.00
19_R	23_D	2.474	1.00
47_Q	60_T	2.375	1.00
45_D	60_T	2.369	1.00
41_A	61_L	2.284	1.00
11_A	16_Q	2.060	0.99
46_V	59_V	2.003	0.99
9_Y	13_L	1.971	0.99
58_E	80_R	1.918	0.99
3_A	6_L	1.873	0.98
8_R	11_A	1.778	0.98
49_R	58_E	1.764	0.98
22_R	25_V	1.741	0.97
2_S	6_L	1.643	0.96
27_M	69_M	1.606	0.96
46_V	81_V	1.590	0.96
32_V	44_V	1.559	0.95
6_L	16_Q	1.480	0.94
13_L	16_Q	1.420	0.92
79_V	88_N	1.397	0.91
48_V	57_F	1.344	0.90
33_E	37_R	1.337	0.89
31_V	79_V	1.308	0.88
6_L	10_E	1.297	0.88
31_V	38_F	1.297	0.88
3_A	11_A	1.295	0.88
64_A	73_A	1.283	0.87
2_S	10_E	1.277	0.87
8_R	12_E	1.257	0.86
91_E	94_K	1.195	0.83
85_K	94_K	1.186	0.83
61_L	64_A	1.176	0.82
61_L	81_V	1.173	0.82
53_G	56_Y	1.170	0.82
5_D	8_R	1.161	0.82
29_R	76_V	1.141	0.80
18_Y	31_V	1.138	0.80
56_Y	77_K	1.125	0.79
3_A	8_R	1.115	0.79
46_V	54_D	1.094	0.77
57_F	73_A	1.092	0.77
77_K	93_P	1.088	0.77
62_T	78_S	1.084	0.77
2_S	11_A	1.081	0.77
70_Y	76_V	1.058	0.75
69_M	72_P	1.052	0.75
55_V	64_A	1.032	0.73
36_R	85_K	1.022	0.72
36_R	66_V	1.005	0.71
33_E	38_F	1.002	0.71
8_R	26_P	0.977	0.69
47_Q	51_E	0.976	0.69
18_Y	22_R	0.965	0.68
52_G	89_V	0.950	0.67
46_V	72_P	0.917	0.64
41_A	50_S	0.914	0.64
38_F	88_N	0.909	0.63
4_E	11_A	0.873	0.60
93_P	97_L	0.871	0.60
55_V	77_K	0.827	0.56
4_E	13_L	0.817	0.55
7_E	10_E	0.814	0.55
38_F	67_W	0.814	0.55
14_E	38_F	0.781	0.52
19_R	31_V	0.774	0.51
46_V	57_F	0.765	0.50
54_D	77_K	0.764	0.50
50_S	56_Y	0.755	0.49
70_Y	82_L	0.728	0.47
72_P	78_S	0.727	0.47
83_T	86_D	0.727	0.47
37_R	75_F	0.726	0.47
11_A	18_Y	0.719	0.46
50_S	55_V	0.718	0.46
45_D	48_V	0.709	0.45
77_K	95_K	0.708	0.45
49_R	55_V	0.700	0.44
54_D	61_L	0.698	0.44
50_S	53_G	0.694	0.44
12_E	28_F	0.691	0.43
56_Y	72_P	0.690	0.43
67_W	83_T	0.685	0.43
60_T	78_S	0.684	0.43
35_E	82_L	0.682	0.43
94_K	97_L	0.680	0.42
19_R	25_V	0.680	0.42
4_E	29_R	0.679	0.42
19_R	56_Y	0.678	0.42
56_Y	84_F	0.673	0.42
26_P	43_E	0.672	0.42
60_T	80_R	0.668	0.41
61_L	77_K	0.664	0.41
19_R	29_R	0.663	0.41
2_S	7_E	0.657	0.40
12_E	18_Y	0.655	0.40
62_T	81_V	0.655	0.40
73_A	83_T	0.654	0.40
85_K	93_P	0.651	0.40
23_D	54_D	0.650	0.40
2_S	5_D	0.643	0.39
82_L	85_K	0.643	0.39
31_V	67_W	0.633	0.38
3_A	7_E	0.630	0.38
18_Y	56_Y	0.629	0.38
15_L	18_Y	0.621	0.37
48_V	55_V	0.614	0.37
8_R	25_V	0.609	0.36
67_W	70_Y	0.607	0.36
51_E	55_V	0.607	0.36
33_E	75_F	0.604	0.36
76_V	82_L	0.600	0.35
13_L	17_L	0.600	0.35
21_Y	34_T	0.599	0.35
55_V	84_F	0.598	0.35
53_G	64_A	0.594	0.35
48_V	56_Y	0.591	0.35
12_E	16_Q	0.573	0.33
84_F	88_N	0.572	0.33
57_F	62_T	0.566	0.33
24_V	71_R	0.565	0.32
37_R	44_V	0.564	0.32
34_T	81_V	0.564	0.32
43_E	47_Q	0.537	0.30
32_V	84_F	0.536	0.30
49_R	56_Y	0.534	0.30
79_V	83_T	0.532	0.30
17_L	76_V	0.528	0.30
50_S	57_F	0.528	0.30
4_E	7_E	0.525	0.29
48_V	89_V	0.525	0.29
73_A	77_K	0.522	0.29
7_E	13_L	0.522	0.29
68_D	90_E	0.518	0.29
69_M	87_V	0.516	0.29
29_R	78_S	0.514	0.28
51_E	54_D	0.512	0.28
18_Y	54_D	0.506	0.28
33_E	71_R	0.505	0.28
52_G	55_V	0.501	0.28
18_Y	53_G	0.501	0.28
26_P	97_L	0.500	0.27

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
2e6oA	1	0.29	6.2	0.95	Contact Map
3hymA	1	0.16	5	0.952	Contact Map
4rbnA	3	0.86	4.5	0.953	Contact Map
2v7yA	1	0.29	4.1	0.954	Contact Map
4rtfD	1	0	4	0.954	Contact Map
1gvnA	2	0.29	3.7	0.955	Contact Map
2op6A	1	0.34	3.3	0.956	Contact Map
2hbpA	1	0.23	3.3	0.956	Contact Map
3dqgA	2	0.34	3.2	0.957	Contact Map
2jshA	1	0.13	2.9	0.957	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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