IF2B - HALSA - GREMLIN Contacts

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IF2B - Translation initiation factor 2 subunit beta

UniProt:	Q9HQ97	Sequences: MDYEEQLDRAMDEKPDVTGSETRFEVPDPNVRKEGNVTVYENFQATLDALSRTQDHVLKFLQNEVGTSASIDESGRARLTGEFGQRRVSDTLDAYVETYVTCPECGLPDTNLETDGDTIQLHCEACGARSTV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	132 (118)
Sequences:	609 (361)
Seq/√Len:	33.2

HALSA - IF2B
SULSO - IF2B

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
56_H	95_Y	5.169	1.00
60_F	94_A	4.394	1.00
23_R	108_P	3.588	1.00
43_F	58_L	3.219	1.00
34_E	76_R	3.085	1.00
43_F	57_V	2.968	1.00
111_N	124_E	2.693	1.00
62_Q	69_A	2.457	1.00
112_L	121_L	2.253	0.99
29_P	89_S	2.025	0.98
27_P	49_A	1.970	0.98
90_D	99_Y	1.925	0.97
39_V	76_R	1.895	0.97
52_R	100_V	1.785	0.96
50_L	96_V	1.774	0.96
51_S	124_E	1.704	0.95
40_Y	46_T	1.690	0.94
52_R	110_T	1.681	0.94
114_T	117_D	1.680	0.94
27_P	45_A	1.658	0.94
32_R	39_V	1.652	0.94
101_T	108_P	1.607	0.93
66_G	99_Y	1.498	0.90
17_V	60_F	1.494	0.90
122_H	129_R	1.479	0.89
97_E	106_G	1.440	0.88
72_D	76_R	1.439	0.88
28_D	93_D	1.417	0.87
13_E	23_R	1.392	0.86
123_C	126_C	1.391	0.86
57_V	100_V	1.374	0.85
36_N	39_V	1.336	0.83
97_E	121_L	1.296	0.81
14_K	17_V	1.277	0.81
24_F	108_P	1.244	0.79
59_K	80_T	1.211	0.77
29_P	95_Y	1.204	0.76
43_F	71_I	1.179	0.75
29_P	46_T	1.160	0.74
96_V	101_T	1.155	0.73
93_D	101_T	1.146	0.73
68_S	80_T	1.139	0.72
74_S	112_L	1.137	0.72
106_G	122_H	1.129	0.72
63_N	67_T	1.129	0.72
118_T	128_A	1.103	0.70
56_H	67_T	1.089	0.69
87_R	90_D	1.081	0.68
47_L	79_L	1.036	0.65
40_Y	61_L	1.035	0.65
117_D	128_A	1.013	0.63
31_V	88_V	0.987	0.61
48_D	113_E	0.986	0.61
15_P	18_T	0.982	0.61
66_G	76_R	0.982	0.61
20_S	72_D	0.964	0.59
108_P	127_G	0.959	0.59
30_N	41_E	0.954	0.58
12_D	88_V	0.951	0.58
60_F	86_R	0.951	0.58
34_E	104_E	0.946	0.58
46_T	51_S	0.938	0.57
75_G	106_G	0.930	0.56
116_G	120_Q	0.919	0.56
61_L	88_V	0.918	0.55
47_L	57_V	0.910	0.55
16_D	48_D	0.910	0.55
90_D	94_A	0.907	0.55
21_E	107_L	0.902	0.54
82_E	117_D	0.895	0.54
43_F	114_T	0.895	0.54
19_G	22_T	0.894	0.53
47_L	58_L	0.888	0.53
24_F	96_V	0.881	0.52
27_P	125_A	0.879	0.52
16_D	19_G	0.876	0.52
69_A	114_T	0.867	0.51
74_S	79_L	0.858	0.50
77_A	107_L	0.853	0.50
51_S	111_N	0.848	0.50
40_Y	99_Y	0.837	0.49
44_Q	88_V	0.834	0.48
51_S	122_H	0.833	0.48
12_D	15_P	0.824	0.48
63_N	128_A	0.800	0.46
24_F	50_L	0.799	0.46
25_E	96_V	0.797	0.45
49_A	62_Q	0.786	0.44
66_G	78_R	0.783	0.44
32_R	41_E	0.781	0.44
71_I	79_L	0.779	0.44
31_V	85_Q	0.760	0.42
50_L	92_L	0.756	0.42
111_N	122_H	0.749	0.41
93_D	97_E	0.727	0.40
79_L	88_V	0.722	0.39
35_G	65_V	0.721	0.39
14_K	33_K	0.721	0.39
23_R	109_D	0.720	0.39
57_V	111_N	0.712	0.38
84_G	117_D	0.706	0.38
64_E	91_T	0.705	0.38
26_V	93_D	0.704	0.38
67_T	81_G	0.703	0.38
38_T	61_L	0.702	0.38
60_F	95_Y	0.697	0.37
90_D	117_D	0.687	0.36
35_G	108_P	0.686	0.36
104_E	117_D	0.684	0.36
47_L	80_T	0.683	0.36
108_P	125_A	0.682	0.36
85_Q	89_S	0.674	0.35
32_R	80_T	0.667	0.35
89_S	106_G	0.664	0.35
62_Q	79_L	0.663	0.35
21_E	95_Y	0.661	0.35
43_F	99_Y	0.656	0.34
43_F	103_P	0.653	0.34
61_L	101_T	0.651	0.34
59_K	71_I	0.650	0.34
65_V	86_R	0.646	0.33
89_S	122_H	0.645	0.33
99_Y	118_T	0.639	0.33
13_E	25_E	0.637	0.33
55_D	71_I	0.636	0.33
51_S	57_V	0.635	0.33
74_S	97_E	0.630	0.32
46_T	50_L	0.628	0.32
57_V	74_S	0.626	0.32
61_L	83_F	0.624	0.32
70_S	77_A	0.623	0.32
78_R	82_E	0.617	0.31
103_P	128_A	0.605	0.30
59_K	113_E	0.600	0.30
46_T	71_I	0.597	0.30
86_R	90_D	0.596	0.30
70_S	79_L	0.595	0.30
45_A	124_E	0.595	0.30
24_F	125_A	0.591	0.29
82_E	93_D	0.591	0.29
62_Q	80_T	0.585	0.29
33_K	61_L	0.584	0.29
15_P	66_G	0.583	0.29
15_P	69_A	0.582	0.29
49_A	60_F	0.579	0.29
50_L	107_L	0.578	0.29
72_D	78_R	0.575	0.28
40_Y	63_N	0.571	0.28
30_N	70_S	0.570	0.28
46_T	99_Y	0.569	0.28
13_E	75_G	0.568	0.28
33_K	82_E	0.568	0.28
86_R	118_T	0.562	0.27
95_Y	129_R	0.557	0.27
106_G	116_G	0.554	0.27
117_D	120_Q	0.554	0.27
77_A	95_Y	0.554	0.27
115_D	129_R	0.554	0.27
26_V	60_F	0.543	0.26
16_D	113_E	0.542	0.26
28_D	89_S	0.541	0.26
33_K	37_V	0.540	0.26
61_L	111_N	0.540	0.26
30_N	51_S	0.521	0.25
73_E	89_S	0.518	0.25
17_V	39_V	0.516	0.24
76_R	95_Y	0.516	0.24
44_Q	51_S	0.515	0.24
48_D	120_Q	0.514	0.24
106_G	121_L	0.514	0.24
45_A	89_S	0.512	0.24
68_S	125_A	0.512	0.24
44_Q	73_E	0.503	0.24
27_P	124_E	0.502	0.24
79_L	103_P	0.501	0.24
30_N	37_V	0.501	0.24
56_H	64_E	0.500	0.24

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
3cw2K	1	1	100	0.048	Contact Map
1neeA	1	0.9924	100	0.057	Contact Map
2d74B	1	0.9924	100	0.065	Contact Map
3j81l	1	0.1136	100	0.072	Contact Map
2g2kA	1	0.9394	100	0.169	Contact Map
2e9hA	1	0.9394	100	0.176	Contact Map
1k8bA	1	0.3939	99.8	0.628	Contact Map
1k81A	1	0.25	99	0.755	Contact Map
4bpeF	1	0.6061	76.7	0.913	Contact Map
3k1fM	1	0.3182	66.3	0.919	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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