DUF3107 - PFAM28P - GREMLIN Contacts

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DUF3107 - Protein of unknown function (DUF3107)

PFAM:	PF11305	Sequences: VEVRIGVQNAPRELVVESDQSADEVEAAVEAALAGGGGVLWLTDEKGRRVLVPAAKIAYVEIGAPEARRVGFG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	73 (73)
Sequences:	5254 (3028)
Seq/√Len:	354.4
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
26_E	49_R	3.704	1.00
41_W	51_L	2.791	1.00
20_Q	24_E	2.438	1.00
27_A	31_A	2.385	1.00
41_W	49_R	2.341	1.00
8_Q	56_K	2.219	1.00
21_S	24_E	2.139	1.00
26_E	30_E	2.089	1.00
10_A	58_A	2.067	1.00
24_E	28_A	1.939	1.00
26_E	41_W	1.804	1.00
19_D	45_E	1.717	1.00
30_E	41_W	1.627	1.00
29_V	60_V	1.581	1.00
29_V	40_L	1.557	1.00
66_E	69_R	1.543	1.00
20_Q	28_A	1.443	1.00
35_G	38_G	1.443	1.00
39_V	51_L	1.441	1.00
28_A	31_A	1.419	1.00
16_V	50_V	1.375	1.00
37_G	55_A	1.350	1.00
48_R	61_E	1.301	1.00
7_V	53_P	1.298	1.00
9_N	55_A	1.288	1.00
30_E	34_A	1.287	1.00
24_E	27_A	1.242	1.00
25_V	42_L	1.219	1.00
31_A	35_G	1.181	1.00
17_E	45_E	1.172	1.00
31_A	34_A	1.167	1.00
27_A	30_E	1.156	1.00
9_N	56_K	1.153	1.00
31_A	36_G	1.140	1.00
23_D	27_A	1.113	1.00
23_D	26_E	1.054	1.00
13_E	59_Y	1.051	1.00
54_A	57_I	1.050	1.00
12_R	59_Y	1.025	1.00
20_Q	25_V	1.020	1.00
17_E	50_V	1.014	1.00
34_A	38_G	1.008	1.00
4_R	13_E	0.996	1.00
30_E	39_V	0.964	1.00
43_T	49_R	0.951	1.00
8_Q	58_A	0.940	1.00
49_R	70_V	0.902	1.00
2_E	15_V	0.876	1.00
32_A	40_L	0.869	1.00
22_A	26_E	0.857	1.00
26_E	62_I	0.829	1.00
40_L	57_I	0.828	1.00
32_A	54_A	0.797	1.00
31_A	38_G	0.767	1.00
65_P	68_R	0.747	1.00
14_L	54_A	0.745	1.00
26_E	70_V	0.739	1.00
6_G	59_Y	0.739	1.00
29_V	57_I	0.735	1.00
57_I	60_V	0.730	1.00
8_Q	11_P	0.727	0.99
25_V	28_A	0.709	0.99
2_E	63_G	0.706	0.99
64_A	70_V	0.694	0.99
36_G	55_A	0.689	0.99
64_A	68_R	0.689	0.99
4_R	56_K	0.688	0.99
5_I	52_V	0.687	0.99
34_A	37_G	0.675	0.99
7_V	52_V	0.660	0.99
11_P	19_D	0.637	0.99
23_D	49_R	0.628	0.99
48_R	64_A	0.624	0.98
5_I	57_I	0.621	0.98
22_A	25_V	0.620	0.98
33_L	54_A	0.616	0.98
44_D	48_R	0.616	0.98
18_S	45_E	0.615	0.98
50_V	73_G	0.614	0.98
46_K	66_E	0.609	0.98
18_S	42_L	0.607	0.98
53_P	58_A	0.605	0.98
22_A	49_R	0.600	0.98
12_R	68_R	0.599	0.98
68_R	73_G	0.597	0.98
40_L	52_V	0.594	0.98
44_D	62_I	0.586	0.98
66_E	70_V	0.577	0.97
7_V	10_A	0.563	0.97
61_E	68_R	0.560	0.97
9_N	58_A	0.559	0.97
28_A	40_L	0.557	0.97
9_N	64_A	0.556	0.97
33_L	39_V	0.554	0.97
21_S	65_P	0.550	0.97
22_A	65_P	0.547	0.97
18_S	21_S	0.547	0.97
16_V	63_G	0.541	0.96
50_V	53_P	0.537	0.96
10_A	56_K	0.536	0.96
4_R	15_V	0.534	0.96
2_E	17_E	0.534	0.96
29_V	62_I	0.522	0.95
7_V	58_A	0.518	0.95
3_V	7_V	0.512	0.95
45_E	70_V	0.510	0.95
20_Q	43_T	0.505	0.95
27_A	34_A	0.504	0.95
17_E	53_P	0.500	0.94
4_R	61_E	0.500	0.94

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
1t3oA	1	0.6301	19.9	0.879	Contact Map
1wfxA	3	0.7671	9.2	0.896	Contact Map
4wtvA	1	0.7945	9	0.896	Contact Map
1vpzA	2	0.3836	8.7	0.897	Contact Map
4lkbF	4	0.8082	7.1	0.901	Contact Map
2y9jY	3	0.8082	6.9	0.901	Contact Map
4yl8A	1	1	6.7	0.902	Contact Map
2i1jA	3	1	6.4	0.903	Contact Map
4w4mA	1	0.7671	6.3	0.903	Contact Map
2wgkA	2	0.9863	6.1	0.904	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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