DUF4176 - PFAM28P - GREMLIN Contacts

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DUF4176 - Domain of unknown function (DUF4176)

PFAM:	PF13780	Sequences: LLPIGSVVLLKGGTKKLMIIGRKQIDEGEGKIYDYSGCLYPEGNIGPEQTYLFNHEDIEEVVFEGYQDEEEEEF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	74 (73)
Sequences:	1690 (1435)
Seq/√Len:	167.9
META:	0.77

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
22_R	71_E	4.155	1.00
64_E	67_Q	3.420	1.00
15_K	42_E	2.997	1.00
16_K	68_D	2.983	1.00
21_G	36_S	2.404	1.00
37_G	53_F	2.318	1.00
11_K	59_E	1.953	1.00
20_I	44_N	1.933	1.00
16_K	62_V	1.923	1.00
9_L	60_E	1.850	1.00
26_D	33_Y	1.709	1.00
67_Q	72_E	1.677	1.00
69_E	72_E	1.675	1.00
9_L	59_E	1.600	1.00
46_G	49_Q	1.503	1.00
9_L	62_V	1.486	1.00
63_F	66_Y	1.479	1.00
9_L	16_K	1.412	1.00
26_D	29_E	1.399	1.00
17_L	51_Y	1.386	1.00
20_I	38_C	1.380	1.00
67_Q	71_E	1.362	1.00
10_L	13_G	1.294	1.00
18_M	38_C	1.270	1.00
33_Y	54_N	1.239	1.00
16_K	66_Y	1.221	1.00
6_S	64_E	1.182	1.00
2_L	6_S	1.178	1.00
16_K	70_E	1.161	1.00
4_I	18_M	1.119	1.00
20_I	36_S	1.052	0.99
20_I	50_T	1.042	0.99
13_G	17_L	1.029	0.99
40_Y	66_Y	1.019	0.99
34_D	54_N	0.998	0.99
33_Y	57_D	0.991	0.99
20_I	24_Q	0.977	0.99
25_I	30_G	0.975	0.99
25_I	32_I	0.935	0.99
24_Q	36_S	0.931	0.99
4_I	22_R	0.926	0.99
27_E	30_G	0.922	0.99
26_D	52_L	0.911	0.98
31_K	54_N	0.908	0.98
44_N	50_T	0.908	0.98
38_C	50_T	0.893	0.98
39_L	51_Y	0.886	0.98
21_G	24_Q	0.866	0.98
69_E	73_E	0.866	0.98
24_Q	52_L	0.846	0.97
21_G	70_E	0.842	0.97
36_S	50_T	0.825	0.97
19_I	37_G	0.822	0.97
20_I	49_Q	0.807	0.97
8_V	53_F	0.806	0.97
9_L	13_G	0.781	0.96
8_V	17_L	0.746	0.95
9_L	14_T	0.737	0.94
23_K	32_I	0.729	0.94
15_K	70_E	0.707	0.93
10_L	53_F	0.706	0.93
10_L	17_L	0.694	0.92
56_E	59_E	0.692	0.92
7_V	62_V	0.691	0.92
17_L	37_G	0.681	0.92
45_I	49_Q	0.661	0.90
42_E	45_I	0.656	0.90
27_E	32_I	0.652	0.90
19_I	53_F	0.647	0.90
21_G	34_D	0.646	0.89
11_K	33_Y	0.640	0.89
60_E	66_Y	0.639	0.89
26_D	32_I	0.638	0.89
4_I	21_G	0.636	0.89
23_K	49_Q	0.635	0.89
63_F	71_E	0.631	0.88
24_Q	44_N	0.630	0.88
28_G	31_K	0.628	0.88
36_S	44_N	0.627	0.88
64_E	72_E	0.623	0.88
11_K	29_E	0.599	0.86
22_R	52_L	0.597	0.85
42_E	70_E	0.596	0.85
61_V	72_E	0.593	0.85
34_D	55_H	0.593	0.85
44_N	49_Q	0.577	0.83
3_P	64_E	0.575	0.83
40_Y	58_I	0.570	0.83
2_L	5_G	0.570	0.83
62_V	66_Y	0.569	0.83
1_L	55_H	0.567	0.82
62_V	67_Q	0.566	0.82
12_G	42_E	0.563	0.82
20_I	23_K	0.557	0.81
62_V	68_D	0.555	0.81
6_S	18_M	0.552	0.81
6_S	63_F	0.551	0.81
10_L	51_Y	0.546	0.80
11_K	73_E	0.544	0.80
4_I	20_I	0.543	0.80
70_E	73_E	0.541	0.79
36_S	49_Q	0.536	0.79
4_I	14_T	0.532	0.78
26_D	31_K	0.532	0.78
38_C	44_N	0.530	0.78
25_I	49_Q	0.524	0.77
4_I	7_V	0.511	0.75
1_L	52_L	0.505	0.75
46_G	60_E	0.501	0.74
8_V	37_G	0.500	0.74

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
1t6aA	1	1	11	0.886	Contact Map
3tlaA	2	0.3378	6.5	0.897	Contact Map
4jvoA	2	0.3378	6.1	0.899	Contact Map
3g1jA	1	0.9054	4.7	0.904	Contact Map
4mp8A	2	0.3649	4.4	0.905	Contact Map
1qc6A	2	0.9324	4.1	0.906	Contact Map
1h7nA	5	0.4054	4	0.907	Contact Map
4anoA	1	0.8919	3.4	0.91	Contact Map
4annA	1	0.8784	3.3	0.911	Contact Map
2c1wA	1	0.5541	3.1	0.912	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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