DUF5053 - PFAM28P - GREMLIN Contacts

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DUF5053 - Domain of unknown function (DUF5053)

PFAM:	PF16476	Sequences: KDILEIISWSYIAKTYFGKSRSWLYQRLNGNDVNGKPAKFTEEELETLNNALQDISKRI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	59 (58)
Sequences:	972 (622)
Seq/√Len:	81.6
META:	0.934

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
27_R	33_V	2.664	1.00
6_I	11_Y	2.591	1.00
16_Y	54_D	2.379	1.00
6_I	55_I	2.326	1.00
52_L	59_I	2.220	1.00
22_S	25_Y	2.111	1.00
24_L	28_L	2.074	1.00
42_E	46_E	1.976	1.00
53_Q	56_S	1.929	1.00
47_T	50_N	1.847	1.00
2_D	58_R	1.761	1.00
26_Q	29_N	1.695	1.00
53_Q	57_K	1.625	1.00
49_N	53_Q	1.529	0.99
6_I	15_T	1.456	0.99
46_E	49_N	1.449	0.99
50_N	53_Q	1.394	0.99
33_V	38_A	1.346	0.99
46_E	50_N	1.310	0.98
34_N	38_A	1.203	0.97
27_R	38_A	1.152	0.96
41_T	44_E	1.140	0.96
50_N	57_K	1.095	0.95
24_L	40_F	1.077	0.95
24_L	48_L	1.070	0.94
30_G	39_K	1.064	0.94
21_R	25_Y	1.063	0.94
21_R	24_L	1.026	0.93
12_I	51_A	1.024	0.93
10_S	21_R	0.968	0.91
25_Y	29_N	0.944	0.90
33_V	36_K	0.928	0.89
11_Y	15_T	0.925	0.89
43_E	46_E	0.921	0.89
34_N	37_P	0.915	0.88
45_L	49_N	0.885	0.87
26_Q	31_N	0.883	0.86
15_T	18_G	0.875	0.86
9_W	24_L	0.872	0.86
9_W	12_I	0.848	0.84
54_D	57_K	0.835	0.83
47_T	51_A	0.821	0.82
4_L	28_L	0.817	0.82
4_L	8_S	0.812	0.81
12_I	48_L	0.805	0.81
10_S	13_A	0.793	0.80
49_N	52_L	0.779	0.79
6_I	58_R	0.778	0.79
18_G	21_R	0.776	0.78
14_K	19_K	0.750	0.76
27_R	31_N	0.732	0.74
31_N	56_S	0.701	0.71
27_R	44_E	0.694	0.70
41_T	52_L	0.693	0.70
16_Y	19_K	0.690	0.70
42_E	45_L	0.688	0.70
9_W	25_Y	0.688	0.70
43_E	50_N	0.670	0.68
56_S	59_I	0.668	0.67
34_N	40_F	0.667	0.67
19_K	22_S	0.662	0.67
32_D	37_P	0.659	0.66
42_E	57_K	0.656	0.66
55_I	59_I	0.643	0.64
4_L	29_N	0.639	0.64
43_E	47_T	0.638	0.64
28_L	48_L	0.633	0.63
5_E	14_K	0.622	0.62
54_D	58_R	0.619	0.62
18_G	50_N	0.599	0.59
20_S	25_Y	0.592	0.58
49_N	56_S	0.590	0.58
20_S	51_A	0.588	0.58
10_S	14_K	0.586	0.57
12_I	24_L	0.569	0.55
39_K	48_L	0.552	0.53
10_S	15_T	0.546	0.52
42_E	55_I	0.540	0.51
2_D	9_W	0.530	0.50
3_I	8_S	0.530	0.50
26_Q	33_V	0.525	0.49
8_S	48_L	0.524	0.49
19_K	42_E	0.515	0.48
51_A	55_I	0.512	0.48
3_I	7_I	0.506	0.47
11_Y	24_L	0.504	0.47
34_N	58_R	0.500	0.46

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
4ecqA	1	0.9661	43	0.86	Contact Map
2aq4A	1	0.9831	32.4	0.869	Contact Map
3zg9B	1	0.9661	31.7	0.87	Contact Map
1zwwA	3	0.4068	30.9	0.87	Contact Map
1h8aC	1	1	28	0.873	Contact Map
4dezA	2	0.5932	25.7	0.875	Contact Map
4fczB	1	0.7458	24.5	0.876	Contact Map
2qguA	1	0.7288	24.2	0.877	Contact Map
3osgA	1	0.9831	23.1	0.878	Contact Map
2k9nA	1	1	20.8	0.881	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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