DUF2341 - PFAM28P - GREMLIN Contacts

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DUF2341 - Domain of unknown function (DUF2341)

PFAM:	PF10102	Sequences: DGSDIRFTDSDGTTLPYWIESWDSNTGTAVIWVKVPSISASSDTTIYMYYGNPSATSASNGTAVFDFFDDFSGTSLDTTKWTVN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	84 (73)
Sequences:	17772 (13817)
Seq/√Len:	1617.2
META:	0.979

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
61_G	68_F	2.754	1.00
2_G	22_W	2.604	1.00
16_P	34_K	2.562	1.00
19_I	31_I	2.544	1.00
2_G	24_S	2.542	1.00
8_T	49_Y	2.030	1.00
21_S	30_V	1.892	1.00
60_N	63_A	1.781	1.00
9_D	36_P	1.749	1.00
20_E	32_W	1.748	1.00
5_I	31_I	1.696	1.00
9_D	13_T	1.654	1.00
7_F	48_M	1.578	1.00
35_V	46_I	1.516	1.00
52_N	55_A	1.513	1.00
18_W	65_F	1.469	1.00
7_F	33_V	1.453	1.00
7_F	31_I	1.452	1.00
21_S	28_T	1.416	1.00
65_F	68_F	1.402	1.00
8_T	14_T	1.384	1.00
14_T	58_A	1.376	1.00
20_E	30_V	1.293	1.00
39_S	44_T	1.258	1.00
22_W	29_A	1.243	1.00
2_G	29_A	1.237	1.00
16_P	63_A	1.218	1.00
3_S	57_S	1.184	1.00
6_R	58_A	1.168	1.00
8_T	12_G	1.135	1.00
68_F	71_F	1.126	1.00
24_S	29_A	1.112	1.00
2_G	23_D	1.094	1.00
11_D	14_T	1.083	1.00
23_D	26_T	1.063	1.00
15_L	46_I	1.048	1.00
5_I	48_M	1.037	1.00
9_D	44_T	1.031	1.00
24_S	27_G	1.030	1.00
18_W	64_V	1.028	1.00
18_W	61_G	0.984	1.00
17_Y	58_A	0.968	1.00
67_F	71_F	0.955	1.00
70_D	73_G	0.939	1.00
61_G	65_F	0.915	1.00
39_S	42_S	0.906	1.00
24_S	28_T	0.871	1.00
7_F	17_Y	0.850	1.00
17_Y	57_S	0.839	1.00
32_W	65_F	0.832	1.00
6_R	55_A	0.827	1.00
16_P	60_N	0.824	1.00
3_S	59_S	0.816	1.00
61_G	64_V	0.812	1.00
65_F	71_F	0.804	1.00
12_G	49_Y	0.797	1.00
33_V	46_I	0.795	1.00
19_I	57_S	0.793	1.00
41_S	44_T	0.791	1.00
38_I	44_T	0.790	1.00
67_F	70_D	0.790	1.00
34_K	64_V	0.783	1.00
8_T	47_Y	0.774	1.00
3_S	55_A	0.770	1.00
66_D	69_D	0.766	1.00
26_T	29_A	0.758	1.00
3_S	19_I	0.758	1.00
9_D	14_T	0.757	1.00
65_F	70_D	0.752	1.00
15_L	36_P	0.747	1.00
40_A	43_D	0.732	1.00
6_R	14_T	0.727	1.00
23_D	28_T	0.720	1.00
37_S	40_A	0.718	1.00
10_S	45_T	0.715	1.00
15_L	33_V	0.702	1.00
22_W	31_I	0.698	1.00
14_T	17_Y	0.691	1.00
6_R	52_N	0.675	1.00
23_D	27_G	0.672	1.00
66_D	70_D	0.668	1.00
37_S	44_T	0.665	1.00
4_D	51_G	0.658	1.00
66_D	71_F	0.656	1.00
35_V	38_I	0.656	1.00
65_F	69_D	0.653	1.00
49_Y	52_N	0.652	1.00
23_D	29_A	0.652	1.00
9_D	15_L	0.634	1.00
69_D	72_S	0.622	1.00
67_F	73_G	0.610	1.00
7_F	46_I	0.610	1.00
42_S	45_T	0.606	1.00
38_I	41_S	0.602	1.00
18_W	32_W	0.594	1.00
6_R	17_Y	0.585	1.00
55_A	58_A	0.577	1.00
17_Y	33_V	0.573	1.00
19_I	23_D	0.569	1.00
10_S	13_T	0.566	1.00
40_A	44_T	0.560	1.00
12_G	47_Y	0.555	1.00
68_F	72_S	0.551	1.00
17_Y	59_S	0.528	1.00
49_Y	55_A	0.518	1.00
3_S	56_T	0.518	1.00
35_V	44_T	0.518	1.00
3_S	58_A	0.517	1.00
10_S	47_Y	0.514	1.00
9_D	12_G	0.500	1.00

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
2hykA	1	0.2619	23.6	0.866	Contact Map
3azyA	1	0.2857	20.8	0.869	Contact Map
3dgtA	1	0.3571	19.8	0.871	Contact Map
2vy0A	1	0.4048	16.9	0.875	Contact Map
1o7dC	1	0.5952	16.3	0.875	Contact Map
3juuA	1	0.4881	13.5	0.88	Contact Map
4ateA	1	0.369	12.3	0.882	Contact Map
1dypA	1	0.4048	10.9	0.885	Contact Map
1upsA	1	0.4167	8	0.892	Contact Map
4bpzA	1	0.3333	7.3	0.893	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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