DUF202 - PFAM28P - GREMLIN Contacts

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DUF202 - Domain of unknown function (DUF202)

PFAM:	PF02656	Sequences: RTRLANERTFLAWIRTALALIAFGFAIARFFLPGGPSGLSRVLGLALILLGVLVLVLAAVRYRRVERR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	68 (66)
Sequences:	26947 (16899)
Seq/√Len:	2080.1
META:	0.874

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
59_A	63_R	2.582	1.00
60_V	64_R	2.384	1.00
61_R	65_V	2.265	1.00
56_V	60_V	1.914	1.00
19_A	23_F	1.798	1.00
17_A	55_L	1.744	1.00
6_N	10_F	1.739	1.00
12_A	15_R	1.722	1.00
45_L	49_L	1.703	1.00
35_G	38_G	1.663	1.00
7_E	13_W	1.605	1.00
29_R	32_L	1.602	1.00
26_A	29_R	1.483	1.00
62_Y	66_E	1.454	1.00
17_A	58_A	1.427	1.00
11_L	15_R	1.426	1.00
3_R	6_N	1.377	1.00
13_W	54_V	1.330	1.00
12_A	16_T	1.300	1.00
5_A	12_A	1.279	1.00
34_G	38_G	1.263	1.00
24_G	48_I	1.243	1.00
21_I	51_G	1.229	1.00
33_P	37_S	1.224	1.00
63_R	66_E	1.223	1.00
19_A	26_A	1.212	1.00
49_L	53_L	1.181	1.00
22_A	26_A	1.136	1.00
53_L	57_L	1.125	1.00
36_P	39_L	1.122	1.00
33_P	36_P	1.120	1.00
61_R	64_R	1.114	1.00
60_V	63_R	1.107	1.00
3_R	66_E	1.105	1.00
35_G	39_L	1.074	1.00
33_P	38_G	1.071	1.00
2_T	6_N	1.070	1.00
42_V	46_A	1.065	1.00
28_A	44_G	1.065	1.00
37_S	40_S	1.019	1.00
55_L	59_A	1.016	1.00
59_A	62_Y	1.012	1.00
23_F	26_A	0.984	1.00
57_L	61_R	0.983	1.00
41_R	45_L	0.970	1.00
17_A	51_G	0.934	1.00
10_F	14_I	0.926	1.00
28_A	41_R	0.917	1.00
14_I	23_F	0.916	1.00
6_N	62_Y	0.903	1.00
16_T	19_A	0.903	1.00
17_A	20_L	0.878	1.00
34_G	37_S	0.877	1.00
34_G	39_L	0.856	1.00
28_A	31_F	0.822	1.00
26_A	30_F	0.819	1.00
14_I	55_L	0.818	1.00
10_F	21_I	0.814	1.00
38_G	42_V	0.811	1.00
7_E	61_R	0.804	1.00
17_A	24_G	0.795	1.00
3_R	7_E	0.795	1.00
13_W	58_A	0.794	1.00
39_L	42_V	0.755	1.00
19_A	22_A	0.744	1.00
24_G	51_G	0.727	1.00
56_V	59_A	0.704	1.00
27_I	47_L	0.703	1.00
4_L	7_E	0.691	1.00
20_L	23_F	0.689	1.00
42_V	45_L	0.688	1.00
25_F	30_F	0.687	1.00
37_S	41_R	0.685	1.00
20_L	26_A	0.655	1.00
14_I	19_A	0.652	1.00
31_F	40_S	0.651	1.00
1_R	15_R	0.647	1.00
48_I	52_V	0.645	1.00
40_S	44_G	0.628	1.00
50_L	54_V	0.627	1.00
15_R	19_A	0.617	1.00
55_L	61_R	0.598	1.00
5_A	23_F	0.596	1.00
32_L	35_G	0.592	1.00
33_P	39_L	0.592	1.00
13_W	28_A	0.588	1.00
6_N	65_V	0.570	1.00
23_F	30_F	0.569	1.00
5_A	8_R	0.561	1.00
14_I	20_L	0.553	1.00
24_G	28_A	0.543	1.00
5_A	26_A	0.534	1.00
11_L	20_L	0.528	1.00
36_P	40_S	0.524	1.00
44_G	48_I	0.524	1.00
19_A	30_F	0.508	1.00
13_W	61_R	0.507	1.00
26_A	32_L	0.505	1.00
12_A	19_A	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
4ev6A	3	0.9559	13.9	0.828	Contact Map
4i0uA	4	0.9412	10.2	0.837	Contact Map
1zzaA	1	0.6324	9.4	0.84	Contact Map
4av3A	2	0.3971	5.5	0.856	Contact Map
4lxjA	1	0.7059	4.5	0.862	Contact Map
2l2tA	2	0.5588	4.1	0.865	Contact Map
2kluA	1	0.5147	3.8	0.866	Contact Map
2m20A	2	0.4706	3.1	0.873	Contact Map
2l9uA	2	0.5147	2.7	0.876	Contact Map
2kncA	1	0.6176	2.7	0.877	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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