DUF716 - PFAM28P - GREMLIN Contacts

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DUF716 - Family of unknown function (DUF716)

PFAM:	PF04819	Sequences: GLDRLLLALAFFVELLLFYFHSHDRSGLEGHYHSLLLLVIFLCALVTLLEVWLPDSFLLELLRSSLILLQGTWFWQIGFVLYPPSFIPKGCFLHLEEGGVKWDLEEDDHRAIMFVTLQFCWHLALVLVIVAGIYA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	135 (120)
Sequences:	825 (489)
Seq/√Len:	44.6
META:	0.109

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
50_E	63_R	3.931	1.00
21_H	33_H	3.730	1.00
72_T	122_H	3.636	1.00
11_F	67_I	3.237	1.00
43_C	66_L	3.093	1.00
25_R	29_E	2.868	1.00
18_F	40_I	2.858	1.00
11_F	47_T	2.477	1.00
76_Q	122_H	2.351	1.00
72_T	76_Q	2.279	1.00
18_F	74_F	2.213	1.00
46_V	62_L	2.158	1.00
5_L	10_A	2.090	0.99
14_E	70_Q	2.050	0.99
11_F	43_C	1.947	0.99
17_L	20_F	1.925	0.99
47_T	63_R	1.869	0.99
76_Q	80_V	1.866	0.99
44_A	115_V	1.828	0.99
84_P	121_W	1.826	0.99
109_H	113_M	1.788	0.98
70_Q	74_F	1.742	0.98
65_S	123_L	1.656	0.97
114_F	118_Q	1.652	0.97
15_L	40_I	1.621	0.97
14_E	74_F	1.510	0.95
35_L	119_F	1.460	0.94
62_L	129_I	1.456	0.94
36_L	74_F	1.383	0.93
69_L	126_V	1.360	0.92
22_S	30_G	1.325	0.91
55_D	58_L	1.299	0.90
12_F	44_A	1.290	0.90
22_S	25_R	1.287	0.90
50_E	60_E	1.231	0.87
80_V	122_H	1.216	0.87
27_G	30_G	1.204	0.86
49_L	131_A	1.169	0.85
41_F	45_L	1.154	0.84
101_K	104_L	1.132	0.83
21_H	74_F	1.120	0.82
17_L	21_H	1.110	0.81
46_V	66_L	1.099	0.81
12_F	16_L	1.096	0.81
55_D	131_A	1.085	0.80
103_D	107_D	1.081	0.80
25_R	33_H	1.066	0.79
46_V	59_L	1.059	0.78
60_E	63_R	1.035	0.77
43_C	70_Q	1.027	0.76
77_I	120_C	1.024	0.76
15_L	41_F	1.004	0.74
102_W	110_R	1.002	0.74
40_I	97_E	0.995	0.74
10_A	13_V	0.994	0.74
97_E	121_W	0.987	0.73
65_S	127_L	0.987	0.73
26_S	103_D	0.986	0.73
102_W	111_A	0.981	0.73
42_L	83_P	0.947	0.70
80_V	115_V	0.943	0.70
68_L	119_F	0.932	0.69
35_L	99_G	0.914	0.67
65_S	130_V	0.910	0.67
40_I	70_Q	0.904	0.66
11_F	26_S	0.896	0.66
66_L	77_I	0.888	0.65
129_I	133_I	0.877	0.64
33_H	84_P	0.869	0.63
9_L	15_L	0.858	0.62
10_A	70_Q	0.858	0.62
13_V	38_L	0.856	0.62
28_L	68_L	0.848	0.61
2_L	133_I	0.846	0.61
18_F	29_E	0.842	0.61
29_E	77_I	0.836	0.60
7_L	11_F	0.824	0.59
59_L	114_F	0.822	0.59
78_G	119_F	0.816	0.58
81_L	100_V	0.812	0.58
27_G	123_L	0.810	0.58
67_I	101_K	0.810	0.58
68_L	130_V	0.808	0.58
14_E	55_D	0.808	0.58
76_Q	118_Q	0.803	0.57
35_L	120_C	0.801	0.57
43_C	54_P	0.798	0.57
24_D	32_Y	0.797	0.57
19_Y	61_L	0.795	0.56
44_A	76_Q	0.790	0.56
69_L	127_L	0.770	0.54
9_L	134_Y	0.770	0.54
127_L	133_I	0.765	0.53
120_C	123_L	0.763	0.53
8_A	12_F	0.757	0.53
69_L	75_W	0.751	0.52
37_L	74_F	0.750	0.52
6_L	9_L	0.747	0.52
16_L	38_L	0.734	0.50
49_L	98_G	0.731	0.50
46_V	53_L	0.729	0.50
14_E	18_F	0.727	0.50
43_C	47_T	0.710	0.48
36_L	81_L	0.709	0.48
80_V	118_Q	0.706	0.48
71_G	78_G	0.703	0.47
32_Y	112_I	0.703	0.47
38_L	48_L	0.698	0.47
18_F	134_Y	0.695	0.47
7_L	62_L	0.693	0.47
43_C	53_L	0.680	0.45
41_F	65_S	0.678	0.45
80_V	102_W	0.677	0.45
27_G	100_V	0.676	0.45
2_L	6_L	0.672	0.44
55_D	119_F	0.671	0.44
50_E	76_Q	0.670	0.44
73_W	119_F	0.668	0.44
20_F	44_A	0.658	0.43
9_L	64_S	0.657	0.43
15_L	37_L	0.656	0.43
80_V	114_F	0.656	0.43
13_V	64_S	0.651	0.42
4_R	59_L	0.647	0.42
31_H	61_L	0.646	0.42
72_T	126_V	0.645	0.42
29_E	54_P	0.639	0.41
29_E	84_P	0.637	0.41
11_F	70_Q	0.635	0.41
102_W	117_L	0.632	0.41
103_D	122_H	0.628	0.40
6_L	104_L	0.626	0.40
32_Y	77_I	0.624	0.40
5_L	47_T	0.624	0.40
23_H	28_L	0.617	0.39
50_E	122_H	0.615	0.39
79_F	132_G	0.614	0.39
43_C	72_T	0.613	0.39
23_H	29_E	0.610	0.39
51_V	59_L	0.605	0.38
28_L	103_D	0.598	0.38
7_L	28_L	0.597	0.37
6_L	48_L	0.592	0.37
74_F	127_L	0.589	0.37
12_F	110_R	0.580	0.36
16_L	31_H	0.579	0.36
14_E	131_A	0.577	0.36
40_I	79_F	0.575	0.35
3_D	15_L	0.574	0.35
45_L	55_D	0.572	0.35
54_P	110_R	0.569	0.35
12_F	35_L	0.565	0.35
42_L	118_Q	0.561	0.34
58_L	61_L	0.560	0.34
18_F	61_L	0.554	0.34
71_G	79_F	0.553	0.34
17_L	33_H	0.552	0.33
29_E	75_W	0.547	0.33
71_G	81_L	0.544	0.33
45_L	120_C	0.543	0.33
62_L	114_F	0.542	0.33
20_F	36_L	0.540	0.32
14_E	36_L	0.540	0.32
49_L	52_W	0.539	0.32
14_E	20_F	0.538	0.32
42_L	123_L	0.538	0.32
74_F	81_L	0.533	0.32
2_L	134_Y	0.531	0.32
4_R	63_R	0.528	0.31
65_S	132_G	0.518	0.31
8_A	111_A	0.516	0.30
3_D	49_L	0.514	0.30
27_G	110_R	0.514	0.30
39_V	57_F	0.514	0.30
111_A	114_F	0.513	0.30
68_L	124_A	0.513	0.30
2_L	58_L	0.513	0.30
21_H	116_T	0.508	0.30
30_G	110_R	0.507	0.30
78_G	121_W	0.500	0.29

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
4grvA	1	0.9852	2.4	0.952	Contact Map
4o6yA	2	0.4148	2.1	0.954	Contact Map
2nr1A	1	0.1704	1.8	0.956	Contact Map
2mofA	1	0.2148	1.5	0.957	Contact Map
4xhjA	1	0.3556	1.1	0.96	Contact Map
4ogqE	1	0.1704	1	0.961	Contact Map
2k9pA	1	0.3037	0.8	0.964	Contact Map
2qjyA	2	0.7407	0.8	0.964	Contact Map
4zwjA	1	0.9333	0.8	0.965	Contact Map
1q90L	1	0.1704	0.8	0.965	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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