IF1A2 - HALSA - GREMLIN Contacts

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IF1A2 - Translation initiation factor 1A 2

UniProt:	Q9HP87	Sequences: MSDESGRRNLRMPNDDEVFAVVKRHDGGNHVTLQCEDGKERMGRIPGRMKYRTWINEGDVVLAEPWDWQDEKANVEWRYSDQDADQLREEGHIE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	94 (88)
Sequences:	328 (166)
Seq/√Len:	17.7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
43_G	73_A	4.855	1.00
33_L	43_G	3.184	0.99
22_V	55_I	3.090	0.99
20_A	33_L	2.517	0.96
33_L	61_V	2.313	0.94
33_L	63_A	2.207	0.92
55_I	72_K	2.151	0.91
31_V	75_V	2.018	0.88
54_W	59_D	1.946	0.86
22_V	61_V	1.876	0.84
43_G	63_A	1.865	0.84
49_M	61_V	1.741	0.79
81_D	93_I	1.722	0.79
42_M	62_L	1.594	0.73
35_C	41_R	1.569	0.72
8_R	11_R	1.512	0.69
21_V	93_I	1.496	0.68
24_R	32_T	1.441	0.65
49_M	53_T	1.439	0.65
19_F	78_R	1.400	0.63
42_M	75_V	1.371	0.61
62_L	83_D	1.356	0.60
7_R	10_L	1.350	0.60
33_L	73_A	1.333	0.59
12_M	90_E	1.306	0.57
25_H	74_N	1.288	0.56
19_F	66_W	1.261	0.54
33_L	75_V	1.246	0.53
18_V	40_E	1.229	0.52
47_G	54_W	1.206	0.51
53_T	77_W	1.156	0.48
32_T	40_E	1.143	0.47
30_H	57_E	1.139	0.47
18_V	36_E	1.124	0.46
20_A	43_G	1.124	0.46
61_V	75_V	1.119	0.46
42_M	69_Q	1.089	0.44
37_D	41_R	1.052	0.42
6_G	43_G	1.049	0.41
60_V	84_A	1.043	0.41
73_A	84_A	1.031	0.40
23_K	34_Q	1.026	0.40
62_L	89_E	1.025	0.40
85_D	92_H	1.023	0.40
22_V	73_A	1.015	0.39
22_V	31_V	1.014	0.39
44_R	66_W	0.984	0.38
48_R	68_W	0.982	0.38
37_D	79_Y	0.976	0.37
17_E	82_Q	0.953	0.36
13_P	72_K	0.939	0.35
42_M	50_K	0.906	0.33
33_L	48_R	0.888	0.32
52_R	81_D	0.880	0.32
45_I	54_W	0.870	0.31
49_M	62_L	0.866	0.31
26_D	36_E	0.862	0.31
29_N	50_K	0.855	0.31
22_V	72_K	0.854	0.31
29_N	70_D	0.853	0.31
20_A	73_A	0.850	0.30
8_R	62_L	0.846	0.30
27_G	79_Y	0.837	0.30
52_R	78_R	0.831	0.29
62_L	82_Q	0.806	0.28
86_Q	89_E	0.806	0.28
9_N	86_Q	0.801	0.28
29_N	85_D	0.799	0.28
43_G	50_K	0.792	0.27
69_Q	74_N	0.779	0.27
20_A	39_K	0.779	0.27
36_E	78_R	0.766	0.26
46_P	66_W	0.764	0.26
10_L	19_F	0.756	0.26
28_G	51_Y	0.752	0.26
6_G	89_E	0.747	0.25
19_F	92_H	0.745	0.25
39_K	70_D	0.743	0.25
7_R	11_R	0.742	0.25
39_K	48_R	0.741	0.25
63_A	73_A	0.741	0.25
49_M	68_W	0.728	0.24
19_F	85_D	0.716	0.24
31_V	45_I	0.713	0.24
49_M	76_E	0.707	0.24
76_E	89_E	0.704	0.23
29_N	34_Q	0.704	0.23
38_G	46_P	0.697	0.23
65_P	78_R	0.687	0.23
30_H	77_W	0.673	0.22
64_E	78_R	0.670	0.22
11_R	17_E	0.669	0.22
43_G	62_L	0.668	0.22
6_G	11_R	0.653	0.21
57_E	75_V	0.649	0.21
8_R	12_M	0.642	0.21
15_D	84_A	0.638	0.21
28_G	46_P	0.637	0.21
14_N	64_E	0.632	0.20
21_V	30_H	0.631	0.20
22_V	45_I	0.630	0.20
25_H	53_T	0.628	0.20
12_M	16_D	0.624	0.20
24_R	39_K	0.619	0.20
56_N	78_R	0.618	0.20
26_D	42_M	0.612	0.20
58_G	77_W	0.610	0.20
47_G	53_T	0.608	0.19
44_R	67_D	0.590	0.19
12_M	18_V	0.586	0.19
12_M	15_D	0.586	0.19
57_E	77_W	0.579	0.18
19_F	40_E	0.576	0.18
65_P	77_W	0.570	0.18
72_K	78_R	0.565	0.18
60_V	78_R	0.564	0.18
29_N	72_K	0.562	0.18
15_D	64_E	0.556	0.18
88_R	92_H	0.555	0.18
14_N	76_E	0.550	0.17
44_R	56_N	0.544	0.17
35_C	52_R	0.534	0.17
13_P	25_H	0.533	0.17
40_E	49_M	0.532	0.17
8_R	83_D	0.526	0.17
18_V	66_W	0.524	0.16
25_H	30_H	0.523	0.16
7_R	12_M	0.518	0.16
34_Q	55_I	0.510	0.16
64_E	82_Q	0.505	0.16
13_P	63_A	0.502	0.16
55_I	61_V	0.500	0.16

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
4kzyn	1	0.8404	100	0.324	Contact Map
3j80i	1	0.9468	100	0.325	Contact Map
4bpe0	1	0.9787	100	0.328	Contact Map
3wbkC	1	0.0106	100	0.344	Contact Map
2oqkA	1	0.9468	99.9	0.358	Contact Map
1jt8A	1	1	99.9	0.366	Contact Map
4mnoA	1	0.9362	99.9	0.371	Contact Map
2dgyA	1	0.9894	99.9	0.383	Contact Map
4ql5A	4	0.7128	99.6	0.602	Contact Map
1ah9A	1	0.7447	99.6	0.603	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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