TRL - PFAM28P - GREMLIN Contacts

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TRL - TRL-like protein family

PFAM:	PF13146	Sequences: GLLYTDVKGPVAATSNAVGSKVGEACATSILGLVATGDASIEAAAKNGGITKISHVDYEVTNILGIYAKYTTIVYGE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	77 (75)
Sequences:	3751 (2842)
Seq/√Len:	328.1
META:	0.951

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_C	71_T	3.770	1.00
42_E	46_K	3.112	1.00
55_H	75_Y	2.932	1.00
27_A	39_A	2.906	1.00
45_A	53_I	2.031	1.00
24_E	71_T	1.953	1.00
38_D	43_A	1.901	1.00
52_K	77_E	1.765	1.00
28_T	69_K	1.709	1.00
9_G	58_Y	1.639	1.00
26_C	69_K	1.637	1.00
24_E	73_I	1.598	1.00
30_I	36_T	1.546	1.00
24_E	59_E	1.521	1.00
61_T	69_K	1.517	1.00
6_D	59_E	1.459	1.00
43_A	47_N	1.443	1.00
59_E	71_T	1.394	1.00
56_V	74_V	1.388	1.00
41_I	56_V	1.372	1.00
62_N	68_A	1.360	1.00
58_Y	70_Y	1.336	1.00
25_A	44_A	1.320	1.00
19_G	54_S	1.310	1.00
28_T	36_T	1.306	1.00
8_K	59_E	1.304	1.00
63_I	67_Y	1.276	1.00
60_V	68_A	1.255	1.00
15_S	18_V	1.231	1.00
23_G	44_A	1.215	1.00
60_V	70_Y	1.211	1.00
54_S	77_E	1.185	1.00
44_A	48_G	1.162	1.00
29_S	35_A	1.154	1.00
22_V	75_Y	1.119	1.00
28_T	67_Y	1.112	1.00
59_E	73_I	1.085	1.00
43_A	46_K	1.075	1.00
21_K	50_I	1.053	1.00
20_S	77_E	1.050	1.00
61_T	67_Y	1.030	1.00
22_V	73_I	0.986	1.00
21_K	51_T	0.940	1.00
29_S	68_A	0.916	1.00
14_T	18_V	0.910	1.00
11_V	58_Y	0.908	1.00
41_I	53_I	0.906	1.00
40_S	43_A	0.893	1.00
50_I	53_I	0.891	1.00
45_A	54_S	0.870	1.00
62_N	65_G	0.844	1.00
42_E	45_A	0.817	1.00
28_T	61_T	0.808	1.00
14_T	17_A	0.804	1.00
39_A	72_T	0.783	1.00
58_Y	72_T	0.773	1.00
6_D	61_T	0.770	1.00
6_D	36_T	0.758	1.00
9_G	60_V	0.758	1.00
54_S	75_Y	0.747	0.99
13_A	16_N	0.746	0.99
21_K	48_G	0.744	0.99
27_A	37_G	0.731	0.99
41_I	45_A	0.730	0.99
40_S	57_D	0.722	0.99
21_K	49_G	0.722	0.99
7_V	60_V	0.722	0.99
50_I	74_V	0.715	0.99
29_S	37_G	0.713	0.99
19_G	77_E	0.712	0.99
19_G	55_H	0.702	0.99
29_S	33_L	0.689	0.99
25_A	72_T	0.686	0.99
12_A	18_V	0.682	0.99
30_I	67_Y	0.679	0.99
10_P	13_A	0.679	0.99
53_I	74_V	0.677	0.99
65_G	68_A	0.675	0.99
39_A	70_Y	0.650	0.98
27_A	35_A	0.649	0.98
13_A	17_A	0.644	0.98
25_A	43_A	0.642	0.98
48_G	74_V	0.632	0.98
25_A	48_G	0.624	0.98
18_V	54_S	0.623	0.98
33_L	36_T	0.611	0.98
37_G	67_Y	0.608	0.98
45_A	52_K	0.605	0.98
23_G	47_N	0.604	0.98
45_A	48_G	0.602	0.97
17_A	52_K	0.600	0.97
35_A	39_A	0.599	0.97
12_A	15_S	0.592	0.97
8_K	73_I	0.585	0.97
25_A	47_N	0.567	0.96
49_G	53_I	0.567	0.96
40_S	72_T	0.565	0.96
32_G	68_A	0.563	0.96
10_P	15_S	0.554	0.96
6_D	69_K	0.552	0.96
63_I	69_K	0.549	0.96
30_I	34_V	0.547	0.96
8_K	40_S	0.537	0.95
50_I	54_S	0.524	0.94
44_A	74_V	0.515	0.94
5_T	62_N	0.514	0.94
12_A	17_A	0.510	0.94
36_T	61_T	0.504	0.93
48_G	53_I	0.504	0.93
11_V	16_N	0.503	0.93
35_A	63_I	0.503	0.93
46_K	51_T	0.500	0.93

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
2dfsA	2	0.7532	2.4	0.913	Contact Map
2v26A	1	0.7532	2.3	0.914	Contact Map
2xb0X	1	0.7792	2.3	0.914	Contact Map
1w7jA	2	0.7532	2	0.917	Contact Map
1g8xA	2	0.7532	2	0.917	Contact Map
1w9iA	1	0.7532	1.7	0.92	Contact Map
1m6bA	1	0.2078	1.6	0.921	Contact Map
4qbdA	1	0.7532	1.6	0.921	Contact Map
4akgA	2	0.987	1.6	0.921	Contact Map
1kk8A	1	0.7532	1.5	0.922	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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