DUF2760 - PFAM28P - GREMLIN Contacts

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DUF2760 - Domain of unknown function (DUF2760)

PFAM:	PF10816	Sequences: PDGALQLLALLQREGRLVDFLMEDIAGYSDAQIGAAVRVVHEGCRKVLREHFTLEPVRDEEEGSRVTVPAGFDPAAIRLTGNVTGQPPFRGTLRHRGWRATKVKLPKLPEGQDARVIAPAEVE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	123 (122)
Sequences:	3407 (2110)
Seq/√Len:	191.0
META:	0.945

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
76_A	99_R	3.379	1.00
65_R	90_R	3.295	1.00
22_M	49_R	3.283	1.00
55_E	101_T	3.194	1.00
70_A	86_Q	2.974	1.00
45_R	49_R	2.795	1.00
73_D	76_A	2.688	1.00
39_V	42_E	2.652	1.00
15_G	44_C	2.631	1.00
67_T	90_R	2.609	1.00
20_F	41_H	2.577	1.00
61_E	64_S	2.573	1.00
53_T	102_K	2.494	1.00
17_L	21_L	2.370	1.00
53_T	101_T	2.177	1.00
58_R	77_I	2.153	1.00
10_L	51_H	1.859	1.00
52_F	103_V	1.827	1.00
58_R	66_V	1.820	1.00
54_L	117_I	1.748	1.00
37_V	40_V	1.714	1.00
60_E	64_S	1.667	1.00
29_S	32_Q	1.666	1.00
56_P	96_R	1.626	1.00
10_L	47_V	1.604	1.00
15_G	21_L	1.479	1.00
28_Y	32_Q	1.463	1.00
26_A	42_E	1.450	1.00
25_I	33_I	1.431	1.00
79_L	83_V	1.429	1.00
39_V	43_G	1.424	1.00
14_E	46_K	1.420	1.00
85_G	89_F	1.418	1.00
6_Q	10_L	1.408	1.00
100_A	103_V	1.346	1.00
66_V	93_L	1.341	1.00
23_E	28_Y	1.299	1.00
57_V	99_R	1.287	1.00
55_E	59_D	1.283	1.00
24_D	27_G	1.237	1.00
18_V	22_M	1.221	1.00
53_T	104_K	1.203	1.00
3_G	6_Q	1.183	1.00
68_V	77_I	1.177	1.00
22_M	45_R	1.149	1.00
85_G	88_P	1.112	1.00
65_R	92_T	1.108	1.00
68_V	122_V	1.106	1.00
93_L	120_A	1.104	1.00
28_Y	36_A	1.081	1.00
108_L	114_A	1.063	1.00
18_V	21_L	1.050	1.00
68_V	79_L	1.048	1.00
58_R	93_L	1.021	1.00
55_E	99_R	1.012	1.00
29_S	33_I	1.009	1.00
78_R	121_E	1.006	1.00
7_L	18_V	1.004	1.00
47_V	52_F	0.996	0.99
4_A	7_L	0.994	0.99
79_L	87_P	0.989	0.99
42_E	46_K	0.987	0.99
6_Q	9_A	0.973	0.99
50_E	104_K	0.959	0.99
60_E	93_L	0.917	0.99
60_E	66_V	0.910	0.99
113_D	116_V	0.904	0.99
34_G	42_E	0.893	0.99
63_G	94_R	0.884	0.99
72_F	89_F	0.874	0.99
28_Y	37_V	0.873	0.99
73_D	116_V	0.846	0.98
5_L	100_A	0.844	0.98
25_I	41_H	0.833	0.98
46_K	49_R	0.828	0.98
99_R	115_R	0.822	0.98
40_V	43_G	0.821	0.98
23_E	50_E	0.820	0.98
68_V	74_P	0.816	0.98
28_Y	33_I	0.814	0.98
8_L	18_V	0.810	0.98
108_L	111_G	0.803	0.98
14_E	47_V	0.800	0.98
11_L	21_L	0.790	0.97
17_L	36_A	0.788	0.97
17_L	48_L	0.777	0.97
26_A	45_R	0.776	0.97
71_G	85_G	0.758	0.97
84_T	87_P	0.756	0.97
68_V	72_F	0.749	0.96
99_R	113_D	0.745	0.96
41_H	44_C	0.744	0.96
79_L	91_G	0.736	0.96
59_D	96_R	0.736	0.96
71_G	87_P	0.736	0.96
7_L	52_F	0.729	0.96
112_Q	115_R	0.710	0.95
18_V	48_L	0.703	0.95
78_R	92_T	0.700	0.95
25_I	39_V	0.696	0.95
6_Q	96_R	0.690	0.94
75_A	109_P	0.689	0.94
5_L	113_D	0.689	0.94
10_L	23_E	0.689	0.94
72_F	80_T	0.689	0.94
21_L	48_L	0.689	0.94
39_V	80_T	0.689	0.94
37_V	41_H	0.688	0.94
21_L	44_C	0.687	0.94
108_L	117_I	0.676	0.94
57_V	120_A	0.675	0.94
103_V	115_R	0.675	0.94
62_E	96_R	0.674	0.94
17_L	44_C	0.673	0.94
72_F	77_I	0.672	0.94
34_G	38_R	0.672	0.94
52_F	117_I	0.666	0.93
48_L	54_L	0.660	0.93
13_R	94_R	0.653	0.93
4_A	14_E	0.649	0.92
20_F	37_V	0.644	0.92
31_A	34_G	0.639	0.92
46_K	50_E	0.636	0.92
47_V	51_H	0.633	0.91
33_I	36_A	0.627	0.91
15_G	42_E	0.626	0.91
77_I	120_A	0.610	0.90
58_R	76_A	0.608	0.90
72_F	76_A	0.606	0.90
47_V	50_E	0.602	0.89
68_V	89_F	0.602	0.89
68_V	120_A	0.601	0.89
110_E	113_D	0.598	0.89
55_E	92_T	0.595	0.89
84_T	89_F	0.593	0.89
68_V	85_G	0.593	0.89
43_G	50_E	0.591	0.88
23_E	78_R	0.588	0.88
60_E	65_R	0.588	0.88
52_F	100_A	0.585	0.88
72_F	78_R	0.584	0.88
13_R	51_H	0.584	0.88
69_P	76_A	0.584	0.88
51_H	105_L	0.581	0.88
68_V	88_P	0.579	0.87
111_G	114_A	0.577	0.87
51_H	109_P	0.564	0.86
52_F	108_L	0.563	0.86
101_T	104_K	0.560	0.86
56_P	94_R	0.549	0.84
58_R	96_R	0.547	0.84
7_L	10_L	0.546	0.84
86_Q	107_K	0.545	0.84
94_R	123_E	0.544	0.84
40_V	44_C	0.542	0.84
49_R	53_T	0.542	0.84
30_D	34_G	0.539	0.83
15_G	47_V	0.538	0.83
72_F	79_L	0.537	0.83
32_Q	39_V	0.534	0.83
7_L	39_V	0.533	0.83
50_E	96_R	0.530	0.82
93_L	96_R	0.527	0.82
4_A	13_R	0.526	0.82
78_R	94_R	0.521	0.81
4_A	10_L	0.520	0.81
21_L	25_I	0.517	0.81
32_Q	37_V	0.516	0.81
24_D	29_S	0.515	0.81
18_V	54_L	0.511	0.80
10_L	94_R	0.511	0.80
8_L	11_L	0.509	0.80
62_E	67_T	0.508	0.80
32_Q	36_A	0.507	0.80
46_K	114_A	0.506	0.79
67_T	72_F	0.504	0.79
10_L	105_L	0.502	0.79
25_I	28_Y	0.502	0.79
106_P	118_A	0.502	0.79
10_L	13_R	0.501	0.79
73_D	113_D	0.501	0.79
43_G	78_R	0.500	0.79
83_V	91_G	0.500	0.79

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
2ckzA	1	0.3496	16.4	0.945	Contact Map
4aniA	2	0.8049	11.5	0.948	Contact Map
3a6mA	2	0.7886	11.1	0.949	Contact Map
2gkpA	1	0.3496	8.9	0.951	Contact Map
1wjtA	1	0.5285	8	0.952	Contact Map
4xbiA	1	0.8699	7.1	0.953	Contact Map
3g13A	2	0.5691	6.7	0.953	Contact Map
2hn1A	2	0.3984	5.9	0.955	Contact Map
3jqoA	7	0.4878	5.8	0.955	Contact Map
3bqwA	1	0.7236	5.6	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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