DUF2780 - PFAM28P - GREMLIN Contacts

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DUF2780 - Protein of unknown function VcgC/VcgE (DUF2780)

PFAM:	PF11075	Sequences: LLTLAASPVFAFLDSLGDLAANAVSAAQGAAAAVGAAAAAAAAAAAKASPELVGALSKQLGVTPEQAAGGAGALFGLAKSRLSPDDFSQLAKAVPGMDSLLGAAPALSGSSGLSGLLGSAGGLGGSAGGLASLASAFSKLGLSPEMVGKFVPVLTQYVTKSGGQGVGSLLLGALS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	175 (157)
Sequences:	728 (538)
Seq/√Len:	42.9
META:	0.714

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
74_L	133_L	4.561	1.00
75_F	97_M	3.790	1.00
70_G	150_F	3.308	1.00
83_S	86_D	3.238	1.00
62_V	150_F	3.238	1.00
82_L	172_G	2.881	1.00
69_G	140_L	2.758	1.00
159_T	167_G	2.727	1.00
90_L	166_V	2.447	1.00
97_M	101_L	2.367	1.00
62_V	70_G	2.054	0.99
54_G	88_S	2.037	0.99
110_S	113_L	1.951	0.99
56_L	71_A	1.931	0.99
91_A	154_L	1.868	0.99
87_F	91_A	1.826	0.98
156_Q	159_T	1.777	0.98
131_A	134_A	1.766	0.98
77_L	133_L	1.749	0.98
74_L	136_A	1.679	0.97
62_V	67_A	1.675	0.97
32_A	35_G	1.659	0.97
89_Q	92_K	1.651	0.97
137_F	150_F	1.643	0.97
106_A	109_G	1.593	0.96
142_L	150_F	1.559	0.96
112_G	115_G	1.559	0.96
101_L	105_P	1.557	0.96
56_L	60_L	1.555	0.96
71_A	152_P	1.555	0.96
134_A	142_L	1.553	0.96
21_A	26_A	1.548	0.95
113_L	117_L	1.541	0.95
63_T	102_G	1.504	0.95
78_A	82_L	1.494	0.95
49_S	157_Y	1.467	0.94
21_A	24_V	1.464	0.94
44_A	47_K	1.448	0.94
71_A	75_F	1.437	0.93
73_A	111_S	1.429	0.93
69_G	137_F	1.388	0.92
77_L	81_R	1.386	0.92
114_S	117_L	1.383	0.92
110_S	118_G	1.354	0.91
146_M	157_Y	1.347	0.91
113_L	118_G	1.301	0.89
74_L	154_L	1.298	0.89
70_G	160_K	1.296	0.89
115_G	118_G	1.283	0.89
120_A	124_G	1.261	0.88
78_A	170_L	1.251	0.87
61_G	64_P	1.235	0.87
87_F	101_L	1.230	0.86
88_S	92_K	1.223	0.86
96_G	146_M	1.220	0.86
92_K	98_D	1.199	0.85
17_G	21_A	1.199	0.85
151_V	155_T	1.187	0.84
108_S	146_M	1.186	0.84
75_F	94_V	1.179	0.84
18_D	22_N	1.169	0.83
22_N	27_A	1.165	0.83
76_G	79_K	1.156	0.83
62_V	159_T	1.147	0.82
73_A	133_L	1.140	0.82
18_D	21_A	1.135	0.82
24_V	27_A	1.117	0.80
113_L	116_L	1.102	0.80
73_A	137_F	1.095	0.79
38_A	42_A	1.074	0.78
45_A	49_S	1.069	0.77
53_V	99_S	1.063	0.77
101_L	104_A	1.057	0.77
31_A	35_G	1.054	0.76
28_Q	31_A	1.047	0.76
24_V	28_Q	1.037	0.75
137_F	157_Y	1.035	0.75
70_G	137_F	1.024	0.74
96_G	144_P	1.016	0.74
69_G	150_F	1.001	0.73
112_G	118_G	0.993	0.72
158_V	173_A	0.990	0.72
127_A	147_V	0.987	0.72
146_M	150_F	0.981	0.71
25_S	29_G	0.977	0.71
43_A	51_E	0.972	0.70
79_K	87_F	0.969	0.70
70_G	143_S	0.953	0.69
97_M	103_A	0.952	0.69
51_E	54_G	0.946	0.68
86_D	89_Q	0.939	0.68
40_A	43_A	0.933	0.67
18_D	25_S	0.926	0.67
136_A	147_V	0.920	0.66
170_L	174_L	0.914	0.66
27_A	31_A	0.914	0.66
73_A	76_G	0.910	0.65
116_L	119_S	0.909	0.65
26_A	31_A	0.893	0.64
62_V	142_L	0.893	0.64
91_A	97_M	0.887	0.63
72_G	75_F	0.886	0.63
25_S	28_Q	0.873	0.62
82_L	86_D	0.869	0.62
24_V	30_A	0.858	0.61
42_A	45_A	0.855	0.60
71_A	94_V	0.853	0.60
128_G	158_V	0.839	0.59
90_L	149_K	0.837	0.59
162_G	166_V	0.836	0.59
133_L	145_E	0.833	0.58
49_S	57_S	0.832	0.58
38_A	41_A	0.825	0.58
56_L	150_F	0.818	0.57
77_L	80_S	0.815	0.57
67_A	135_S	0.809	0.56
32_A	40_A	0.808	0.56
95_P	157_Y	0.807	0.56
37_A	42_A	0.807	0.56
67_A	70_G	0.804	0.56
131_A	163_G	0.802	0.55
35_G	38_A	0.798	0.55
115_G	119_S	0.797	0.55
33_A	77_L	0.796	0.55
171_L	174_L	0.794	0.55
165_G	168_S	0.789	0.54
48_A	144_P	0.786	0.54
31_A	37_A	0.782	0.54
86_D	169_L	0.777	0.53
65_E	73_A	0.775	0.53
59_Q	86_D	0.765	0.52
41_A	84_P	0.761	0.52
130_L	144_P	0.758	0.51
57_S	68_A	0.758	0.51
68_A	103_A	0.748	0.50
76_G	89_Q	0.747	0.50
31_A	34_V	0.740	0.50
111_S	114_S	0.740	0.50
123_L	154_L	0.732	0.49
123_L	126_S	0.726	0.48
28_Q	32_A	0.724	0.48
51_E	84_P	0.724	0.48
18_D	23_A	0.717	0.47
86_D	98_D	0.715	0.47
88_S	107_L	0.713	0.47
110_S	114_S	0.712	0.47
124_G	148_G	0.710	0.47
29_G	34_V	0.708	0.47
82_L	99_S	0.706	0.46
137_F	153_V	0.704	0.46
135_S	147_V	0.704	0.46
49_S	72_G	0.699	0.46
124_G	138_S	0.698	0.46
52_L	70_G	0.693	0.45
28_Q	35_G	0.690	0.45
28_Q	130_L	0.690	0.45
90_L	164_Q	0.677	0.44
128_G	149_K	0.676	0.44
121_G	124_G	0.656	0.42
45_A	48_A	0.651	0.41
94_V	152_P	0.648	0.41
40_A	45_A	0.641	0.40
98_D	110_S	0.640	0.40
16_L	21_A	0.638	0.40
137_F	146_M	0.637	0.40
87_F	94_V	0.635	0.40
150_F	157_Y	0.634	0.40
155_T	159_T	0.634	0.40
81_R	153_V	0.629	0.39
107_L	138_S	0.628	0.39
56_L	149_K	0.624	0.39
41_A	108_S	0.624	0.39
92_K	99_S	0.622	0.39
75_F	91_A	0.619	0.38
36_A	41_A	0.618	0.38
161_S	164_Q	0.613	0.38
22_N	26_A	0.610	0.37
87_F	167_G	0.609	0.37
79_K	91_A	0.609	0.37
76_G	86_D	0.608	0.37
48_A	61_G	0.607	0.37
57_S	70_G	0.602	0.37
43_A	118_G	0.600	0.37
57_S	67_A	0.599	0.37
30_A	33_A	0.593	0.36
152_P	155_T	0.588	0.36
71_A	162_G	0.585	0.35
38_A	45_A	0.584	0.35
53_V	60_L	0.584	0.35
23_A	125_G	0.584	0.35
94_V	162_G	0.584	0.35
33_A	106_A	0.582	0.35
56_L	66_Q	0.581	0.35
106_A	139_K	0.575	0.34
97_M	105_P	0.562	0.33
48_A	59_Q	0.562	0.33
17_G	24_V	0.562	0.33
91_A	98_D	0.559	0.33
50_P	64_P	0.556	0.33
66_Q	69_G	0.555	0.33
116_L	120_A	0.555	0.33
28_Q	33_A	0.554	0.33
165_G	171_L	0.554	0.33
55_A	157_Y	0.549	0.32
118_G	157_Y	0.549	0.32
17_G	23_A	0.548	0.32
26_A	32_A	0.547	0.32
67_A	165_G	0.546	0.32
23_A	26_A	0.544	0.32
91_A	163_G	0.541	0.32
82_L	165_G	0.538	0.31
50_P	93_A	0.538	0.31
108_S	120_A	0.532	0.31
41_A	46_A	0.530	0.31
53_V	57_S	0.529	0.31
24_V	34_V	0.529	0.31
48_A	68_A	0.526	0.30
110_S	115_G	0.524	0.30
150_F	160_K	0.524	0.30
36_A	39_A	0.523	0.30
50_P	100_L	0.523	0.30
21_A	28_Q	0.522	0.30
53_V	116_L	0.520	0.30
84_P	111_S	0.518	0.30
62_V	137_F	0.516	0.30
155_T	167_G	0.516	0.30
65_E	68_A	0.515	0.29
152_P	173_A	0.514	0.29
35_G	42_A	0.513	0.29
37_A	40_A	0.513	0.29
63_T	135_S	0.507	0.29
90_L	93_A	0.506	0.29
80_S	133_L	0.503	0.29
74_L	78_A	0.502	0.28
60_L	140_L	0.500	0.28
30_A	41_A	0.500	0.28

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
1qgpA	1	0.2229	11.8	0.94	Contact Map
3ijwA	2	0.3371	5.8	0.947	Contact Map
4imiA	1	0.4171	5.3	0.948	Contact Map
2yskA	2	0.56	3.7	0.952	Contact Map
4hrrB	2	0.72	3.5	0.953	Contact Map
1jf3A	1	0.64	3.3	0.953	Contact Map
1gcvB	1	0.6629	3.1	0.954	Contact Map
3mvcA	1	0.6514	3.1	0.954	Contact Map
1ixsA	1	0.2686	2.9	0.955	Contact Map
3j21k	1	0	2.7	0.955	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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