DUF3128 - PFAM28P - GREMLIN Contacts

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DUF3128 - Protein of unknown function (DUF3128)

PFAM:	PF11326	Sequences: TMSCRQYFDEAFFCYSLGGQFHQYYRYGELDDCSQWWEDFKFCMRLKTKKPEEAREALREREAERKAERPSSEDVWELR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	79 (78)
Sequences:	575 (423)
Seq/√Len:	47.9
META:	0.301

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
56_E	60_E	4.131	1.00
4_C	43_C	3.476	1.00
16_S	19_G	2.678	1.00
62_E	65_R	2.547	1.00
20_Q	23_Q	2.281	1.00
35_Q	39_D	2.098	1.00
76_W	79_R	2.038	1.00
49_K	53_E	1.907	0.99
60_E	64_E	1.899	0.99
51_P	55_R	1.863	0.99
6_Q	10_E	1.840	0.99
66_K	69_R	1.607	0.97
7_Y	42_F	1.578	0.97
52_E	55_R	1.575	0.97
13_F	16_S	1.495	0.96
71_S	74_D	1.462	0.95
11_A	15_Y	1.447	0.95
70_P	78_L	1.446	0.95
22_H	36_W	1.346	0.93
50_K	53_E	1.338	0.93
10_E	36_W	1.319	0.92
7_Y	10_E	1.309	0.92
61_R	64_E	1.299	0.92
38_E	77_E	1.282	0.91
12_F	18_G	1.273	0.91
2_M	7_Y	1.259	0.90
62_E	66_K	1.252	0.90
11_A	41_K	1.235	0.89
50_K	57_A	1.210	0.88
64_E	68_E	1.186	0.87
54_A	58_L	1.144	0.85
38_E	60_E	1.107	0.84
69_R	74_D	1.099	0.83
3_S	24_Y	1.083	0.82
5_R	30_L	1.065	0.81
6_Q	9_D	1.057	0.81
5_R	9_D	1.046	0.80
44_M	47_K	1.017	0.78
7_Y	58_L	1.015	0.78
8_F	25_Y	1.013	0.78
14_C	33_C	1.013	0.78
15_Y	24_Y	1.007	0.77
49_K	52_E	0.959	0.74
17_L	32_D	0.952	0.73
70_P	74_D	0.949	0.73
11_A	37_W	0.939	0.72
19_G	31_D	0.930	0.71
20_Q	31_D	0.925	0.71
48_T	56_E	0.922	0.71
51_P	58_L	0.921	0.71
25_Y	31_D	0.921	0.71
40_F	61_R	0.912	0.70
39_D	62_E	0.895	0.68
17_L	52_E	0.884	0.67
21_F	43_C	0.860	0.65
4_C	14_C	0.853	0.65
52_E	64_E	0.850	0.64
41_K	45_R	0.833	0.63
27_Y	48_T	0.808	0.60
42_F	58_L	0.806	0.60
10_E	39_D	0.790	0.59
5_R	11_A	0.774	0.57
37_W	41_K	0.765	0.56
56_E	78_L	0.764	0.56
48_T	52_E	0.756	0.55
17_L	40_F	0.754	0.55
56_E	77_E	0.750	0.55
4_C	16_S	0.739	0.54
26_R	71_S	0.728	0.53
9_D	20_Q	0.727	0.52
23_Q	29_E	0.712	0.51
8_F	47_K	0.707	0.50
21_F	68_E	0.701	0.50
7_Y	54_A	0.697	0.49
31_D	35_Q	0.693	0.49
9_D	26_R	0.692	0.49
7_Y	62_E	0.688	0.49
17_L	68_E	0.687	0.48
6_Q	13_F	0.687	0.48
17_L	30_L	0.675	0.47
19_G	30_L	0.663	0.46
25_Y	76_W	0.662	0.46
38_E	61_R	0.651	0.45
60_E	63_A	0.649	0.45
5_R	52_E	0.631	0.43
59_R	69_R	0.630	0.43
21_F	29_E	0.623	0.42
19_G	29_E	0.622	0.42
39_D	61_R	0.604	0.40
70_P	73_E	0.599	0.40
34_S	44_M	0.595	0.39
34_S	77_E	0.593	0.39
69_R	73_E	0.592	0.39
49_K	56_E	0.578	0.38
71_S	78_L	0.570	0.37
29_E	62_E	0.567	0.37
12_F	60_E	0.564	0.36
2_M	42_F	0.562	0.36
2_M	39_D	0.558	0.36
65_R	69_R	0.549	0.35
3_S	77_E	0.548	0.35
27_Y	68_E	0.547	0.35
43_C	79_R	0.546	0.35
75_V	79_R	0.542	0.34
13_F	19_G	0.540	0.34
55_R	78_L	0.536	0.34
9_D	38_E	0.535	0.34
2_M	5_R	0.535	0.34
29_E	35_Q	0.529	0.33
25_Y	30_L	0.529	0.33
29_E	32_D	0.528	0.33
3_S	10_E	0.526	0.33
49_K	55_R	0.521	0.33
22_H	39_D	0.513	0.32
18_G	42_F	0.512	0.32
9_D	59_R	0.505	0.31
10_E	78_L	0.500	0.31

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
4xizM	1	0.8101	20.9	0.869	Contact Map
4xhrN	1	0.8228	9.2	0.888	Contact Map
2riqA	2	0.3038	2.1	0.919	Contact Map
4tpvA	2	0.519	1.9	0.92	Contact Map
4lirA	2	0.9114	1.8	0.921	Contact Map
3lb6A	1	0.3924	1.7	0.922	Contact Map
5aj3m	1	0.8481	1.7	0.922	Contact Map
1zhxA	1	0.9873	1.6	0.923	Contact Map
4b2zA	1	0.9747	1.6	0.924	Contact Map
2yg2A	1	0.4304	1.5	0.924	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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