DUF4099 - PFAM28P - GREMLIN Contacts

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DUF4099 - Protein of unknown function (DUF4099)

PFAM:	PF13351	Sequences: FDEEEIPWEQLEKLGLSREMLEKSGDLDALLNGRKTPLLPISIKLGGETIRTDARLSLRRDEDGKVVLAIHPIRKEPELDRP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	82 (80)
Sequences:	1249 (837)
Seq/√Len:	93.5
META:	0.861

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
5_E	60_R	3.333	1.00
30_L	36_T	3.237	1.00
26_D	37_P	3.140	1.00
61_D	65_K	3.121	1.00
9_E	12_E	3.077	1.00
57_S	71_H	2.720	1.00
60_R	66_V	2.169	1.00
2_D	5_E	2.155	1.00
7_P	10_Q	1.808	1.00
42_S	51_R	1.741	1.00
30_L	56_L	1.734	1.00
17_S	20_M	1.687	1.00
11_L	58_L	1.686	1.00
29_A	34_R	1.681	1.00
41_I	54_A	1.619	1.00
1_F	33_G	1.560	1.00
36_T	58_L	1.538	1.00
40_P	53_D	1.527	1.00
44_K	49_T	1.392	0.99
8_W	21_L	1.389	0.99
18_R	22_E	1.349	0.99
7_P	65_K	1.343	0.99
22_E	27_L	1.284	0.99
5_E	66_V	1.272	0.99
19_E	22_E	1.225	0.98
35_K	57_S	1.192	0.98
3_E	6_I	1.185	0.98
26_D	29_A	1.182	0.98
29_A	32_N	1.181	0.98
8_W	18_R	1.157	0.98
48_E	52_T	1.144	0.97
36_T	47_G	1.140	0.97
13_K	48_E	1.112	0.97
35_K	55_R	1.089	0.97
33_G	72_P	1.086	0.97
42_S	49_T	1.077	0.96
11_L	68_L	1.067	0.96
1_F	5_E	1.063	0.96
8_W	35_K	1.013	0.95
30_L	58_L	1.013	0.95
1_F	66_V	1.000	0.95
12_E	17_S	0.982	0.94
16_L	21_L	0.970	0.94
35_K	71_H	0.968	0.93
19_E	23_K	0.960	0.93
20_M	39_L	0.952	0.93
38_L	55_R	0.935	0.92
16_L	20_M	0.912	0.91
27_L	31_L	0.885	0.90
58_L	68_L	0.882	0.90
61_D	67_V	0.878	0.90
71_H	74_R	0.871	0.89
45_L	50_I	0.869	0.89
47_G	56_L	0.846	0.88
8_W	25_G	0.825	0.87
33_G	66_V	0.824	0.87
33_G	60_R	0.791	0.84
25_G	29_A	0.772	0.83
74_R	77_P	0.769	0.82
41_I	51_R	0.759	0.82
40_P	51_R	0.759	0.82
58_L	66_V	0.755	0.81
11_L	22_E	0.742	0.80
6_I	31_L	0.727	0.79
28_D	67_V	0.727	0.79
37_P	40_P	0.720	0.78
26_D	39_L	0.716	0.78
24_S	28_D	0.715	0.78
71_H	77_P	0.710	0.77
27_L	49_T	0.699	0.76
17_S	37_P	0.695	0.76
44_K	47_G	0.691	0.75
43_I	55_R	0.690	0.75
28_D	69_A	0.682	0.74
50_I	76_E	0.679	0.74
31_L	71_H	0.674	0.73
10_Q	16_L	0.668	0.73
1_F	60_R	0.665	0.72
41_I	52_T	0.664	0.72
57_S	64_G	0.657	0.72
20_M	40_P	0.655	0.71
29_A	33_G	0.650	0.71
39_L	78_E	0.644	0.70
39_L	43_I	0.641	0.70
53_D	57_S	0.639	0.69
14_L	33_G	0.634	0.69
5_E	36_T	0.634	0.69
11_L	79_L	0.627	0.68
56_L	68_L	0.617	0.67
68_L	71_H	0.614	0.66
43_I	52_T	0.613	0.66
13_K	49_T	0.613	0.66
10_Q	52_T	0.601	0.65
9_E	13_K	0.600	0.65
10_Q	68_L	0.592	0.64
43_I	51_R	0.591	0.63
13_K	69_A	0.586	0.63
28_D	48_E	0.586	0.63
21_L	24_S	0.585	0.63
64_G	71_H	0.576	0.61
14_L	55_R	0.574	0.61
25_G	62_E	0.574	0.61
14_L	70_I	0.561	0.59
50_I	68_L	0.547	0.58
9_E	42_S	0.536	0.56
9_E	50_I	0.535	0.56
63_D	67_V	0.530	0.55
35_K	38_L	0.527	0.55
52_T	55_R	0.527	0.55
67_V	72_P	0.525	0.55
30_L	68_L	0.521	0.54
15_G	36_T	0.519	0.54
6_I	34_R	0.514	0.53
69_A	72_P	0.513	0.53
8_W	22_E	0.508	0.52
24_S	64_G	0.507	0.52
51_R	59_R	0.506	0.52
10_Q	40_P	0.504	0.52
54_A	77_P	0.503	0.51
11_L	66_V	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
1khyA	1	0.3415	8.9	0.887	Contact Map
1t62A	2	0.9878	5.9	0.896	Contact Map
3rh7A	2	0.4024	5.8	0.896	Contact Map
2rr8A	1	0.3902	5.2	0.899	Contact Map
4irfA	1	0.3902	4.7	0.9	Contact Map
1x40A	1	0.5488	4.7	0.9	Contact Map
1q87A	1	0.8659	4.7	0.9	Contact Map
4ylfA	1	0.378	4.7	0.9	Contact Map
4bedB	3	1	4.5	0.902	Contact Map
4tp9L	1	0.0244	4.4	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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