2TM - PFAM28P - GREMLIN Contacts

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2TM - 2TM domain

PFAM:	PF13239	Sequences: ERAKKRVKKKKGFYIHLAVYVVVNAFLIVINLGYFWFLWPLLGWGIGLAFHALSVFGRNPFFGKDWEERKIEELME	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	76 (74)
Sequences:	13569 (9499)
Seq/√Len:	1104.3
META:	0.899

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
16_H	51_H	3.177	1.00
13_F	52_A	3.138	1.00
28_I	41_L	2.877	1.00
70_K	73_E	2.436	1.00
50_F	54_S	2.196	1.00
34_Y	39_W	2.067	1.00
24_N	41_L	2.053	1.00
31_N	37_F	1.830	1.00
35_F	38_L	1.734	1.00
23_V	27_L	1.617	1.00
20_Y	44_W	1.570	1.00
28_I	35_F	1.535	1.00
28_I	37_F	1.514	1.00
15_I	19_V	1.502	1.00
66_W	70_K	1.498	1.00
14_Y	56_F	1.425	1.00
10_K	74_L	1.406	1.00
67_E	70_K	1.398	1.00
27_L	40_P	1.386	1.00
20_Y	45_G	1.347	1.00
7_V	11_K	1.297	1.00
68_E	72_E	1.286	1.00
9_K	54_S	1.240	1.00
43_G	47_G	1.226	1.00
46_I	50_F	1.202	1.00
28_I	32_L	1.188	1.00
20_Y	24_N	1.181	1.00
6_R	10_K	1.174	1.00
8_K	12_G	1.166	1.00
51_H	55_V	1.144	1.00
23_V	44_W	1.143	1.00
16_H	44_W	1.136	1.00
32_L	35_F	1.123	1.00
31_N	35_F	1.106	1.00
17_L	48_L	1.101	1.00
53_L	58_R	1.079	1.00
31_N	38_L	1.070	1.00
24_N	44_W	1.054	1.00
70_K	74_L	1.037	1.00
66_W	69_R	1.033	1.00
4_K	8_K	1.004	1.00
34_Y	38_L	0.996	1.00
26_F	30_I	0.988	1.00
12_G	54_S	0.973	1.00
10_K	70_K	0.958	1.00
71_I	74_L	0.947	1.00
52_A	57_G	0.941	1.00
37_F	41_L	0.915	1.00
16_H	19_V	0.904	1.00
25_A	29_V	0.898	1.00
67_E	71_I	0.891	1.00
54_S	58_R	0.861	1.00
12_G	15_I	0.860	1.00
34_Y	37_F	0.860	1.00
53_L	57_G	0.846	1.00
68_E	71_I	0.836	1.00
13_F	55_V	0.830	1.00
44_W	47_G	0.823	1.00
40_P	43_G	0.805	1.00
12_G	51_H	0.795	1.00
6_R	9_K	0.793	1.00
52_A	56_F	0.787	1.00
20_Y	41_L	0.781	1.00
3_A	7_V	0.739	1.00
22_V	26_F	0.738	1.00
12_G	16_H	0.737	1.00
31_N	36_W	0.731	1.00
17_L	21_V	0.730	1.00
15_I	54_S	0.724	1.00
16_H	48_L	0.701	1.00
49_A	53_L	0.700	1.00
16_H	20_Y	0.695	1.00
39_W	43_G	0.693	1.00
65_D	69_R	0.679	1.00
51_H	54_S	0.679	1.00
13_F	56_F	0.674	1.00
10_K	52_A	0.672	1.00
38_L	42_L	0.670	1.00
33_G	36_W	0.666	1.00
28_I	38_L	0.665	1.00
13_F	17_L	0.664	1.00
44_W	51_H	0.662	1.00
33_G	37_F	0.654	1.00
21_V	25_A	0.650	1.00
7_V	71_I	0.647	1.00
44_W	48_L	0.642	1.00
8_K	11_K	0.640	1.00
59_N	63_G	0.633	1.00
11_K	15_I	0.612	1.00
12_G	47_G	0.612	1.00
5_K	9_K	0.605	1.00
49_A	52_A	0.600	1.00
11_K	67_E	0.598	1.00
31_N	34_Y	0.598	1.00
37_F	40_P	0.597	1.00
64_K	67_E	0.596	1.00
28_I	31_N	0.582	1.00
4_K	71_I	0.580	1.00
36_W	39_W	0.575	1.00
43_G	46_I	0.572	1.00
47_G	50_F	0.564	1.00
45_G	48_L	0.554	1.00
36_W	40_P	0.552	1.00
18_A	22_V	0.545	1.00
11_K	66_W	0.529	1.00
27_L	30_I	0.526	1.00
17_L	52_A	0.516	1.00
60_P	63_G	0.506	1.00
4_K	7_V	0.505	1.00
48_L	51_H	0.503	1.00
60_P	64_K	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
3ze3A	4	0.9868	8.9	0.865	Contact Map
4c5iC	1	0.1053	6.2	0.874	Contact Map
4c5eE	2	0.2368	5.4	0.878	Contact Map
3l1lA	2	0.8553	4.1	0.885	Contact Map
4bbjA	1	0.9868	3.8	0.887	Contact Map
1v54D	1	0.8816	3.5	0.888	Contact Map
2y69D	1	0.9211	3.3	0.89	Contact Map
2m8rA	1	0.4868	3.2	0.89	Contact Map
3mk7C	2	0.5526	3.1	0.892	Contact Map
3j08A	2	0.8553	2.9	0.894	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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