DUF3945 - PFAM28P - GREMLIN Contacts

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DUF3945 - Protein of unknown function (DUF3945)

PFAM:	PF13101	Sequences: EKIPSFVSIDKLTNELVALRADKIKIPDEIKGVKLTEEQKQDLREGKPVYLEGMTSKKG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	59 (57)
Sequences:	1243 (705)
Seq/√Len:	93.4
META:	0.87

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
29_E	34_K	3.548	1.00
42_D	47_K	3.355	1.00
28_D	40_K	3.284	1.00
41_Q	45_E	3.099	1.00
42_D	49_V	2.721	1.00
38_E	42_D	2.371	1.00
9_I	16_L	2.217	1.00
26_I	43_L	2.211	1.00
55_T	58_K	1.740	1.00
11_K	14_N	1.720	1.00
28_D	34_K	1.716	1.00
51_L	54_M	1.565	1.00
15_E	18_A	1.549	1.00
6_F	21_A	1.424	0.99
9_I	14_N	1.392	0.99
5_S	18_A	1.391	0.99
6_F	19_L	1.283	0.99
41_Q	44_R	1.268	0.99
37_E	40_K	1.229	0.98
36_T	39_Q	1.147	0.98
20_R	23_K	1.119	0.97
27_P	30_I	1.073	0.96
8_S	12_L	1.055	0.96
29_E	32_G	1.007	0.95
35_L	39_Q	1.005	0.95
20_R	50_Y	0.990	0.94
38_E	41_Q	0.972	0.94
37_E	41_Q	0.946	0.93
36_T	47_K	0.942	0.93
33_V	39_Q	0.904	0.91
8_S	15_E	0.898	0.91
8_S	32_G	0.895	0.90
16_L	43_L	0.893	0.90
9_I	21_A	0.866	0.89
33_V	53_G	0.844	0.88
10_D	35_L	0.811	0.86
52_E	56_S	0.801	0.85
30_I	51_L	0.756	0.81
10_D	15_E	0.749	0.81
15_E	20_R	0.749	0.81
23_K	26_I	0.729	0.79
4_P	7_V	0.707	0.77
31_K	43_L	0.706	0.77
30_I	35_L	0.697	0.76
43_L	49_V	0.686	0.75
44_R	48_P	0.685	0.75
7_V	44_R	0.683	0.74
4_P	10_D	0.682	0.74
4_P	11_K	0.680	0.74
53_G	57_K	0.678	0.74
25_K	39_Q	0.678	0.74
13_T	31_K	0.676	0.74
2_K	58_K	0.671	0.73
50_Y	53_G	0.660	0.72
30_I	58_K	0.646	0.70
25_K	40_K	0.627	0.68
4_P	8_S	0.616	0.67
35_L	54_M	0.611	0.66
52_E	58_K	0.608	0.66
33_V	54_M	0.590	0.63
25_K	44_R	0.587	0.63
24_I	30_I	0.583	0.62
13_T	30_I	0.579	0.62
10_D	24_I	0.570	0.61
33_V	49_V	0.569	0.60
53_G	56_S	0.568	0.60
36_T	41_Q	0.567	0.60
25_K	28_D	0.560	0.59
30_I	33_V	0.559	0.59
31_K	39_Q	0.557	0.59
39_Q	47_K	0.555	0.59
9_I	13_T	0.555	0.59
34_K	38_E	0.552	0.58
25_K	43_L	0.551	0.58
14_N	18_A	0.550	0.58
21_A	26_I	0.540	0.57
3_I	28_D	0.539	0.56
3_I	6_F	0.530	0.55
33_V	52_E	0.528	0.55
12_L	48_P	0.519	0.54
3_I	7_V	0.517	0.53
24_I	39_Q	0.516	0.53
37_E	45_E	0.513	0.53
28_D	41_Q	0.511	0.53
5_S	20_R	0.506	0.52
14_N	17_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
1jeyA	1	1	10.8	0.852	Contact Map
4i66A	2	0.9661	7.9	0.86	Contact Map
2vb2X	1	0.9831	6.6	0.865	Contact Map
2qcpX	1	0.9831	6.2	0.867	Contact Map
4mhrA	2	0.9492	6.1	0.868	Contact Map
2opwA	1	0.4576	5.7	0.869	Contact Map
1spuA	2	0.8644	5.5	0.87	Contact Map
2gksA	2	0.8136	5.4	0.871	Contact Map
2a1xA	1	0.5593	5.1	0.872	Contact Map
1jeyB	1	1	4.9	0.874	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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