IF1A1 - HALSA - GREMLIN Contacts

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IF1A1 - Translation initiation factor 1A 1

UniProt:	Q9HN64	Sequences: MSDDGGGRKNLRMPEDDEVFAEVTDMLGANRVQVRCADGEERTARIPGRMQKRIWIREDDIVLVEPWDWQDDKADVTWRYEKSDADQLREEGHIE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	95 (89)
Sequences:	332 (175)
Seq/√Len:	18.5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
44_A	74_A	4.884	1.00
23_V	56_I	3.458	1.00
34_V	44_A	3.267	0.99
21_A	34_V	2.706	0.98
34_V	62_V	2.680	0.98
32_V	76_V	2.451	0.96
56_I	73_K	2.354	0.95
34_V	64_V	2.232	0.94
44_A	64_V	2.063	0.90
23_V	62_V	2.059	0.90
50_M	62_V	1.772	0.82
82_K	94_I	1.555	0.73
20_F	67_W	1.515	0.71
20_F	79_R	1.457	0.68
9_K	12_R	1.443	0.67
43_T	63_L	1.438	0.66
25_D	33_Q	1.430	0.66
43_T	70_Q	1.374	0.63
34_V	74_A	1.373	0.63
8_R	11_L	1.364	0.62
26_M	75_D	1.337	0.61
19_V	41_E	1.281	0.57
22_E	94_I	1.281	0.57
86_D	93_H	1.230	0.54
62_V	76_V	1.199	0.52
55_W	60_D	1.184	0.51
54_I	78_W	1.180	0.51
34_V	76_V	1.169	0.50
36_C	42_R	1.161	0.50
21_A	44_A	1.160	0.50
33_Q	41_E	1.156	0.50
23_V	74_A	1.146	0.49
50_M	54_I	1.141	0.49
13_M	91_E	1.126	0.48
63_L	84_D	1.115	0.47
61_I	85_A	1.100	0.46
63_L	90_E	1.091	0.46
19_V	37_A	1.064	0.44
23_V	73_K	1.058	0.43
44_A	51_Q	1.039	0.42
45_R	67_W	1.028	0.42
12_R	18_E	1.015	0.41
31_R	58_E	0.999	0.40
38_D	42_R	0.977	0.39
76_V	94_I	0.976	0.39
74_A	85_A	0.972	0.38
49_R	69_W	0.968	0.38
66_P	79_R	0.967	0.38
30_N	51_Q	0.959	0.38
20_F	93_H	0.958	0.37
30_N	71_D	0.957	0.37
23_V	32_V	0.956	0.37
9_K	63_L	0.948	0.37
31_R	68_D	0.945	0.37
38_D	80_Y	0.920	0.35
21_A	74_A	0.893	0.34
14_P	73_K	0.890	0.34
27_L	37_A	0.890	0.34
24_T	35_R	0.885	0.33
21_A	40_E	0.868	0.32
28_G	80_Y	0.858	0.32
13_M	17_D	0.856	0.32
84_D	88_L	0.854	0.32
50_M	69_W	0.853	0.32
11_L	20_F	0.850	0.31
48_G	55_W	0.837	0.31
57_R	79_R	0.835	0.31
47_P	67_W	0.830	0.30
34_V	49_R	0.819	0.30
30_N	86_D	0.816	0.30
20_F	86_D	0.809	0.29
50_M	63_L	0.768	0.27
70_Q	75_D	0.762	0.27
61_I	79_R	0.761	0.27
8_R	12_R	0.754	0.26
58_E	76_V	0.748	0.26
56_I	62_V	0.742	0.26
43_T	76_V	0.718	0.25
29_A	52_K	0.717	0.25
26_M	54_I	0.716	0.25
87_Q	90_E	0.705	0.24
39_G	47_P	0.702	0.24
56_I	74_A	0.702	0.24
50_M	77_T	0.702	0.24
53_R	79_R	0.700	0.24
32_V	46_I	0.688	0.23
40_E	71_D	0.686	0.23
16_D	85_A	0.686	0.23
27_L	43_T	0.684	0.23
18_E	83_S	0.681	0.23
10_N	87_Q	0.673	0.23
37_A	79_R	0.673	0.23
63_L	83_S	0.670	0.23
58_E	78_W	0.667	0.22
53_R	82_K	0.667	0.22
7_G	90_E	0.665	0.22
30_N	35_R	0.661	0.22
73_K	79_R	0.659	0.22
23_V	48_G	0.658	0.22
51_Q	82_K	0.656	0.22
36_C	53_R	0.654	0.22
29_A	47_P	0.649	0.22
7_G	12_R	0.646	0.22
7_G	44_A	0.630	0.21
64_V	74_A	0.626	0.21
13_M	16_D	0.625	0.21
87_Q	91_E	0.623	0.21
8_R	84_D	0.615	0.20
43_T	51_Q	0.610	0.20
54_I	84_D	0.607	0.20
89_R	94_I	0.603	0.20
13_M	19_V	0.601	0.20
35_R	56_I	0.591	0.19
14_P	64_V	0.589	0.19
52_K	55_W	0.583	0.19
33_Q	76_V	0.581	0.19
25_D	40_E	0.575	0.19
42_R	70_Q	0.552	0.18
41_E	79_R	0.552	0.18
14_P	26_M	0.549	0.18
15_E	65_E	0.549	0.18
30_N	33_Q	0.547	0.18
26_M	31_R	0.545	0.18
66_P	78_W	0.543	0.18
65_E	79_R	0.541	0.17
46_I	70_Q	0.540	0.17
31_R	78_W	0.536	0.17
47_P	65_E	0.529	0.17
19_V	67_W	0.527	0.17
65_E	68_D	0.516	0.17
46_I	55_W	0.510	0.16
45_R	68_D	0.503	0.16
46_I	76_V	0.500	0.16
27_L	31_R	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
4bpe0	1	0.9684	100	0.319	Contact Map
3j80i	1	0.9368	100	0.319	Contact Map
4kzyn	1	0.8316	100	0.32	Contact Map
3wbkC	1	0.0105	100	0.339	Contact Map
1jt8A	1	1	100	0.352	Contact Map
2oqkA	1	0.9368	99.9	0.357	Contact Map
4mnoA	1	0.9263	99.9	0.367	Contact Map
2dgyA	1	0.9789	99.9	0.383	Contact Map
4ql5A	4	0.7053	99.6	0.601	Contact Map
1ah9A	1	0.7368	99.6	0.601	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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