DUF1736 - PFAM28P - GREMLIN Contacts

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DUF1736 - Domain of unknown function (DUF1736)

PFAM:	PF08409	Sequences: NFSLPEFSFVDNPLAGAPFWTTRLLTALYVLGRYLWLLLWPAPLSADYSYNQIPLVTSLSDPRALLSLALYLALV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	75 (66)
Sequences:	3089 (2409)
Seq/√Len:	296.6
META:	0.871

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
33_R	36_W	4.030	1.00
31_L	71_Y	2.693	1.00
33_R	37_L	2.682	1.00
64_A	67_S	2.577	1.00
29_Y	33_R	2.462	1.00
17_A	55_L	1.723	1.00
56_V	64_A	1.708	1.00
14_L	22_T	1.701	1.00
35_L	70_L	1.699	1.00
25_L	59_L	1.671	1.00
29_Y	56_V	1.661	1.00
19_F	22_T	1.638	1.00
51_N	54_P	1.619	1.00
23_R	27_A	1.555	1.00
45_S	52_Q	1.526	1.00
17_A	22_T	1.348	1.00
60_S	63_R	1.277	1.00
59_L	64_A	1.265	1.00
24_L	28_L	1.260	1.00
37_L	48_Y	1.258	1.00
65_L	69_A	1.224	1.00
29_Y	63_R	1.218	1.00
22_T	26_T	1.189	1.00
32_G	67_S	1.167	1.00
46_A	49_S	1.149	1.00
28_L	64_A	1.133	1.00
36_W	40_W	1.075	1.00
25_L	28_L	1.044	1.00
14_L	23_R	1.003	1.00
31_L	46_A	0.996	1.00
51_N	55_L	0.988	1.00
14_L	17_A	0.976	1.00
30_V	49_S	0.969	1.00
49_S	52_Q	0.967	1.00
10_V	46_A	0.953	1.00
14_L	27_A	0.948	1.00
13_P	55_L	0.946	1.00
18_P	22_T	0.941	1.00
17_A	57_T	0.931	1.00
11_D	47_D	0.930	1.00
11_D	52_Q	0.928	1.00
28_L	71_Y	0.926	1.00
13_P	18_P	0.904	1.00
25_L	64_A	0.899	1.00
14_L	55_L	0.892	1.00
22_T	55_L	0.889	1.00
18_P	21_T	0.881	1.00
38_L	52_Q	0.870	1.00
24_L	27_A	0.850	1.00
28_L	67_S	0.830	1.00
17_A	26_T	0.820	1.00
41_P	44_L	0.814	1.00
38_L	43_P	0.813	1.00
25_L	29_Y	0.809	1.00
28_L	32_G	0.807	1.00
13_P	52_Q	0.803	1.00
35_L	67_S	0.803	1.00
32_G	70_L	0.771	0.99
13_P	54_P	0.770	0.99
26_T	31_L	0.767	0.99
20_W	24_L	0.767	0.99
36_W	43_P	0.761	0.99
35_L	39_L	0.729	0.99
64_A	68_L	0.718	0.99
26_T	47_D	0.711	0.99
31_L	35_L	0.703	0.99
65_L	68_L	0.693	0.99
15_A	27_A	0.686	0.98
61_D	64_A	0.683	0.98
9_F	16_G	0.674	0.98
32_G	36_W	0.657	0.98
42_A	73_A	0.656	0.98
11_D	50_Y	0.647	0.98
27_A	30_V	0.639	0.98
27_A	34_Y	0.637	0.98
57_T	63_R	0.634	0.97
56_V	63_R	0.634	0.97
60_S	65_L	0.627	0.97
62_P	66_L	0.624	0.97
11_D	34_Y	0.611	0.97
34_Y	46_A	0.597	0.96
30_V	34_Y	0.596	0.96
33_R	53_I	0.580	0.96
67_S	71_Y	0.576	0.96
62_P	69_A	0.576	0.96
31_L	70_L	0.575	0.96
29_Y	64_A	0.568	0.95
46_A	52_Q	0.566	0.95
13_P	30_V	0.562	0.95
16_G	46_A	0.560	0.95
11_D	49_S	0.559	0.95
20_W	68_L	0.558	0.95
27_A	31_L	0.550	0.94
66_L	69_A	0.547	0.94
13_P	19_F	0.535	0.94
32_G	71_Y	0.528	0.93
44_L	53_I	0.522	0.93
60_S	73_A	0.510	0.92
11_D	16_G	0.500	0.91

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
2lf3A	1	0.36	6.7	0.891	Contact Map
1zzpA	1	0.3333	1.2	0.927	Contact Map
4ub6R	1	0.2	1.2	0.927	Contact Map
2bruC	1	0.48	1.1	0.927	Contact Map
4um9B	2	0	1.1	0.928	Contact Map
4pj0R	1	0.2	1	0.93	Contact Map
2mmuA	1	0.5333	0.9	0.931	Contact Map
2ohdA	5	0.2667	0.9	0.931	Contact Map
4i6mD	1	0	0.8	0.933	Contact Map
4httA	1	0.2533	0.8	0.934	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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