IF1 - BACSU - GREMLIN Contacts

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IF1 - Translation initiation factor IF-1

UniProt:	P20458	Sequences: MAKDDVIEVEGTIVETLPNAMFKVELENGHTVLAHVSGKIRMHFIRILPGDKVTVELSPYDLTRGRITYRYK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	72 (71)
Sequences:	1009 (375)
Seq/√Len:	44.5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
54_T	71_Y	3.226	1.00
25_E	29_G	2.936	1.00
12_T	25_E	2.897	1.00
14_V	25_E	2.851	1.00
16_T	49_P	2.604	1.00
40_I	69_Y	2.598	1.00
21_M	33_L	2.526	1.00
27_E	52_K	2.514	1.00
8_E	54_T	2.386	1.00
25_E	31_T	2.145	1.00
36_V	47_I	1.871	0.99
10_E	52_K	1.851	0.99
10_E	71_Y	1.812	0.98
23_K	31_T	1.603	0.97
36_V	44_F	1.558	0.96
32_V	55_V	1.345	0.92
12_T	52_K	1.320	0.91
10_E	27_E	1.313	0.90
9_V	57_L	1.300	0.90
10_E	54_T	1.292	0.90
13_I	47_I	1.272	0.89
44_F	47_I	1.250	0.88
17_L	23_K	1.237	0.88
30_H	62_L	1.184	0.85
32_V	65_G	1.152	0.84
40_I	43_H	1.110	0.81
42_M	69_Y	1.095	0.80
18_P	58_S	1.071	0.79
57_L	62_L	1.069	0.79
8_E	68_T	1.054	0.78
15_E	23_K	1.037	0.77
18_P	22_F	1.037	0.77
55_V	65_G	1.003	0.74
2_A	72_K	0.973	0.72
11_G	24_V	0.968	0.71
59_P	62_L	0.965	0.71
14_V	31_T	0.924	0.68
20_A	41_R	0.916	0.67
22_F	66_R	0.906	0.66
26_L	45_I	0.880	0.64
39_K	58_S	0.880	0.64
22_F	41_R	0.878	0.64
15_E	18_P	0.878	0.64
21_M	35_H	0.874	0.64
39_K	42_M	0.867	0.63
57_L	64_R	0.866	0.63
15_E	46_R	0.842	0.61
19_N	35_H	0.835	0.60
37_S	40_I	0.823	0.59
24_V	60_Y	0.804	0.57
18_P	33_L	0.793	0.56
21_M	36_V	0.787	0.55
68_T	71_Y	0.786	0.55
33_L	52_K	0.756	0.52
36_V	40_I	0.739	0.51
32_V	57_L	0.734	0.50
23_K	33_L	0.727	0.50
19_N	41_R	0.723	0.49
33_L	64_R	0.715	0.49
36_V	58_S	0.710	0.48
9_V	55_V	0.707	0.48
16_T	19_N	0.706	0.48
34_A	55_V	0.706	0.48
36_V	42_M	0.701	0.47
40_I	71_Y	0.684	0.46
7_I	62_L	0.680	0.45
28_N	37_S	0.677	0.45
14_V	63_T	0.637	0.41
37_S	47_I	0.636	0.41
61_D	64_R	0.630	0.40
8_E	40_I	0.627	0.40
15_E	48_L	0.624	0.40
35_H	45_I	0.616	0.39
28_N	63_T	0.614	0.39
19_N	33_L	0.614	0.39
24_V	34_A	0.612	0.39
16_T	44_F	0.602	0.38
50_G	54_T	0.601	0.38
50_G	71_Y	0.600	0.38
41_R	72_K	0.599	0.38
27_E	67_I	0.598	0.37
22_F	33_L	0.593	0.37
52_K	71_Y	0.591	0.37
30_H	63_T	0.588	0.37
8_E	56_E	0.568	0.35
10_E	14_V	0.566	0.35
12_T	39_K	0.566	0.35
48_L	68_T	0.564	0.34
4_D	35_H	0.552	0.33
36_V	41_R	0.546	0.33
2_A	64_R	0.544	0.33
18_P	46_R	0.543	0.33
33_L	36_V	0.537	0.32
13_I	24_V	0.536	0.32
23_K	72_K	0.535	0.32
3_K	48_L	0.530	0.32
42_M	72_K	0.528	0.31
28_N	58_S	0.518	0.31
28_N	62_L	0.514	0.30
24_V	66_R	0.510	0.30
56_E	66_R	0.510	0.30
11_G	61_D	0.509	0.30
47_I	57_L	0.506	0.30
35_H	64_R	0.505	0.29
57_L	65_G	0.505	0.29
7_I	59_P	0.500	0.29

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	0.9722	99.9	0.314	Contact Map
3wbkC	1	0	99.9	0.328	Contact Map
2oqkA	1	0.9722	99.9	0.331	Contact Map
3j80i	1	0.9861	99.9	0.334	Contact Map
4kzyn	1	0.9028	99.9	0.342	Contact Map
4mnoA	1	0.9583	99.9	0.345	Contact Map
1jt8A	1	0.9722	99.9	0.355	Contact Map
4ql5A	4	0.9444	99.9	0.372	Contact Map
1hr0W	1	0.9861	99.9	0.383	Contact Map
3i4oA	1	0.9306	99.9	0.389	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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