DUF4006 - PFAM28P - GREMLIN Contacts

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DUF4006 - Family of unknown function (DUF4006)

PFAM:	PF13179	Sequences: MNNTNRSVFGLHGITGMLIATVLLLSILAFLTVWAIGVQQANATNFYDIKDLNNIKMISTDNAKH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	65 (65)
Sequences:	690 (378)
Seq/√Len:	46.9
META:	0.897

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_A	33_V	3.387	1.00
30_F	34_W	3.266	1.00
17_M	21_T	3.016	1.00
8_V	14_I	2.715	1.00
14_I	18_L	2.570	1.00
7_S	10_G	2.470	1.00
42_N	45_N	2.406	1.00
51_D	54_N	2.344	1.00
34_W	38_V	2.219	1.00
59_S	62_N	2.107	1.00
61_D	64_K	1.844	0.99
20_A	23_L	1.796	0.99
18_L	22_V	1.778	0.99
14_I	17_M	1.752	0.98
33_V	37_G	1.603	0.97
11_L	15_T	1.522	0.96
26_S	30_F	1.403	0.94
42_N	46_F	1.385	0.94
18_L	21_T	1.354	0.93
32_T	36_I	1.326	0.92
42_N	48_D	1.281	0.91
9_F	14_I	1.251	0.90
49_I	52_L	1.250	0.90
23_L	27_I	1.244	0.89
25_L	29_A	1.216	0.88
55_I	58_I	1.206	0.88
60_T	63_A	1.203	0.88
28_L	32_T	1.083	0.81
50_K	54_N	0.992	0.75
38_V	42_N	0.960	0.73
42_N	52_L	0.920	0.70
38_V	41_A	0.902	0.68
49_I	55_I	0.883	0.67
14_I	21_T	0.882	0.66
7_S	15_T	0.873	0.66
58_I	61_D	0.834	0.62
51_D	60_T	0.825	0.61
58_I	62_N	0.818	0.61
24_L	28_L	0.805	0.59
29_A	34_W	0.804	0.59
52_L	55_I	0.794	0.58
22_V	25_L	0.789	0.58
5_N	10_G	0.787	0.58
22_V	26_S	0.779	0.57
53_N	58_I	0.754	0.54
35_A	40_Q	0.752	0.54
56_K	59_S	0.748	0.54
20_A	24_L	0.744	0.53
9_F	18_L	0.731	0.52
1_M	4_T	0.711	0.50
50_K	65_H	0.697	0.49
15_T	19_I	0.693	0.48
21_T	24_L	0.674	0.46
51_D	55_I	0.674	0.46
31_L	56_K	0.671	0.46
49_I	54_N	0.656	0.45
41_A	45_N	0.654	0.44
49_I	53_N	0.652	0.44
29_A	37_G	0.649	0.44
11_L	19_I	0.637	0.43
2_N	5_N	0.630	0.42
44_T	48_D	0.627	0.42
26_S	29_A	0.624	0.42
24_L	27_I	0.612	0.40
9_F	13_G	0.611	0.40
52_L	62_N	0.610	0.40
43_A	46_F	0.607	0.40
32_T	35_A	0.601	0.39
10_G	15_T	0.599	0.39
20_A	28_L	0.597	0.39
36_I	40_Q	0.596	0.39
30_F	49_I	0.594	0.39
55_I	65_H	0.583	0.38
48_D	54_N	0.581	0.37
22_V	37_G	0.575	0.37
5_N	8_V	0.571	0.37
48_D	55_I	0.571	0.37
37_G	41_A	0.570	0.36
3_N	6_R	0.568	0.36
13_G	16_G	0.564	0.36
1_M	6_R	0.562	0.36
59_S	64_K	0.554	0.35
9_F	39_Q	0.541	0.34
35_A	38_V	0.540	0.34
37_G	43_A	0.533	0.33
46_F	52_L	0.527	0.33
10_G	14_I	0.521	0.32
3_N	8_V	0.519	0.32
40_Q	43_A	0.517	0.32
11_L	14_I	0.516	0.32
30_F	35_A	0.510	0.31
28_L	31_L	0.508	0.31
2_N	7_S	0.507	0.31
23_L	32_T	0.505	0.31
1_M	50_K	0.504	0.31
56_K	65_H	0.503	0.31
50_K	53_N	0.501	0.30
33_V	36_I	0.500	0.30

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
2e84A	1	0.4308	34	0.874	Contact Map
1z1nX	1	0.3231	22.8	0.884	Contact Map
2x2zA	1	0.1077	8.3	0.905	Contact Map
2yewB	4	0.4769	6.3	0.91	Contact Map
2cvcA	1	0.3385	5.3	0.913	Contact Map
3j0fE	4	0.5077	4.3	0.917	Contact Map
2kluA	1	0.8308	4.3	0.917	Contact Map
4um9B	2	0	4	0.918	Contact Map
3s8fC	1	0.4769	3.7	0.92	Contact Map
1oahA	2	0.2	3.7	0.92	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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