IF3 - BACSU - GREMLIN Contacts

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IF3 - Translation initiation factor IF-3

UniProt:	P55872	Sequences: MISKDQLVNEGIRAREVRLIGQNGDQLGIKSRQEALEIAGRANLDLVLVAANAKPPVCRIMDYGKFRFEQQKKEKEARKNQKIINLKEVRLSPTIDEHDFNTKLRNAIKFLEKGDKVKASIRFKGRAITHKEIGQRVLDRFSEACAEVATVETKPKMDGRSMFLMLAPKNEKQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	173 (163)
Sequences:	2526 (1460)
Seq/√Len:	114.3

ECOLI - IF3
BACSU - IF3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
100_F	144_A	4.015	1.00
19_L	30_K	3.509	1.00
106_N	109_K	2.929	1.00
97_E	101_N	2.821	1.00
108_I	147_E	2.754	1.00
152_E	167_A	2.750	1.00
143_E	146_A	2.649	1.00
22_Q	42_A	2.568	1.00
149_A	166_L	2.553	1.00
108_I	112_E	2.216	1.00
37_E	41_R	2.198	1.00
21_G	25_D	2.157	1.00
136_R	139_D	2.149	1.00
34_E	37_E	2.124	1.00
108_I	148_V	2.093	1.00
48_L	58_C	2.035	1.00
21_G	42_A	2.025	1.00
31_S	34_E	2.019	1.00
98_H	101_N	2.017	1.00
107_A	141_F	1.979	1.00
130_H	133_I	1.968	1.00
135_Q	139_D	1.945	1.00
14_A	48_L	1.931	1.00
44_L	60_I	1.878	1.00
36_L	40_G	1.826	1.00
16_E	54_K	1.818	1.00
107_A	119_A	1.756	1.00
66_F	70_Q	1.740	1.00
111_L	149_A	1.667	1.00
38_I	42_A	1.666	1.00
17_V	58_C	1.665	1.00
38_I	60_I	1.635	1.00
18_R	26_Q	1.620	1.00
104_L	144_A	1.615	1.00
104_L	141_F	1.592	1.00
123_F	134_G	1.589	1.00
37_E	40_G	1.550	1.00
123_F	162_M	1.525	1.00
14_A	32_R	1.520	1.00
18_R	29_I	1.472	1.00
139_D	154_K	1.422	1.00
138_L	164_L	1.405	1.00
142_S	164_L	1.388	1.00
128_I	131_K	1.380	1.00
102_T	106_N	1.364	1.00
139_D	142_S	1.357	1.00
47_V	61_M	1.353	1.00
122_R	161_S	1.347	1.00
67_R	71_Q	1.330	1.00
107_A	117_V	1.329	1.00
101_N	104_L	1.314	1.00
10_E	40_G	1.311	1.00
38_I	41_R	1.300	1.00
151_V	164_L	1.298	1.00
21_G	27_L	1.288	0.99
150_T	169_K	1.267	0.99
17_V	32_R	1.267	0.99
100_F	140_R	1.241	0.99
119_A	141_F	1.240	0.99
140_R	144_A	1.240	0.99
27_L	30_K	1.240	0.99
109_K	113_K	1.201	0.99
70_Q	73_K	1.199	0.99
32_R	58_C	1.199	0.99
90_R	120_S	1.189	0.99
94_T	127_A	1.184	0.99
121_I	138_L	1.168	0.99
107_A	145_C	1.165	0.99
139_D	143_E	1.161	0.99
8_V	63_Y	1.133	0.99
85_N	115_D	1.109	0.98
48_L	56_P	1.101	0.98
112_E	148_V	1.099	0.98
89_V	107_A	1.082	0.98
135_Q	162_M	1.072	0.98
91_L	119_A	1.066	0.98
20_I	26_Q	1.066	0.98
100_F	104_L	1.064	0.98
90_R	122_R	1.060	0.98
121_I	131_K	1.060	0.98
68_F	72_K	1.042	0.98
105_R	108_I	1.032	0.97
9_N	45_D	1.029	0.97
22_Q	44_L	0.987	0.97
153_T	156_K	0.986	0.97
95_I	137_V	0.982	0.97
139_D	155_P	0.980	0.97
146_A	169_K	0.940	0.96
153_T	165_M	0.937	0.96
30_K	38_I	0.930	0.95
9_N	12_I	0.930	0.95
98_H	102_T	0.929	0.95
48_L	51_A	0.924	0.95
20_I	28_G	0.909	0.95
142_S	154_K	0.907	0.95
16_E	31_S	0.907	0.95
26_Q	29_I	0.902	0.95
116_K	165_M	0.869	0.93
133_I	136_R	0.868	0.93
67_R	73_K	0.860	0.93
145_C	149_A	0.857	0.93
92_S	122_R	0.855	0.93
124_K	127_A	0.853	0.93
17_V	35_A	0.841	0.92
51_A	55_P	0.837	0.92
111_L	145_C	0.830	0.92
30_K	34_E	0.830	0.92
34_E	38_I	0.830	0.92
33_Q	36_L	0.820	0.91
90_R	100_F	0.819	0.91
32_R	48_L	0.819	0.91
137_V	140_R	0.804	0.90
77_A	81_Q	0.804	0.90
33_Q	37_E	0.802	0.90
67_R	70_Q	0.798	0.90
49_V	54_K	0.792	0.90
91_L	121_I	0.781	0.89
146_A	149_A	0.780	0.89
96_D	114_G	0.778	0.89
39_A	45_D	0.778	0.89
136_R	140_R	0.775	0.89
72_K	75_K	0.773	0.89
157_M	161_S	0.770	0.88
109_K	117_V	0.770	0.88
46_L	58_C	0.769	0.88
138_L	160_R	0.766	0.88
142_S	151_V	0.761	0.88
117_V	145_C	0.759	0.88
121_I	137_V	0.758	0.88
65_K	68_F	0.751	0.87
142_S	146_A	0.741	0.86
157_M	162_M	0.739	0.86
104_L	108_I	0.739	0.86
14_A	17_V	0.737	0.86
16_E	29_I	0.734	0.86
49_V	57_V	0.731	0.86
142_S	166_L	0.723	0.85
128_I	160_R	0.722	0.85
21_G	28_G	0.719	0.85
95_I	153_T	0.713	0.84
20_I	24_G	0.712	0.84
21_G	26_Q	0.711	0.84
86_L	165_M	0.707	0.84
142_S	149_A	0.704	0.83
101_N	105_R	0.700	0.83
150_T	167_A	0.696	0.83
35_A	39_A	0.692	0.82
77_A	85_N	0.692	0.82
92_S	127_A	0.691	0.82
18_R	55_P	0.676	0.81
136_R	143_E	0.675	0.81
75_K	79_K	0.673	0.81
128_I	157_M	0.670	0.80
93_P	123_F	0.666	0.80
116_K	152_E	0.664	0.80
61_M	95_I	0.664	0.80
88_E	120_S	0.662	0.80
131_K	157_M	0.662	0.80
119_A	164_L	0.662	0.80
132_E	136_R	0.657	0.79
26_Q	61_M	0.656	0.79
74_E	78_R	0.655	0.79
93_P	120_S	0.652	0.79
152_E	165_M	0.649	0.78
92_S	124_K	0.648	0.78
32_R	38_I	0.644	0.78
73_K	76_E	0.643	0.78
96_D	161_S	0.632	0.76
91_L	137_V	0.627	0.76
69_E	73_K	0.626	0.76
82_K	158_D	0.625	0.76
129_T	133_I	0.625	0.76
27_L	38_I	0.623	0.75
22_Q	60_I	0.622	0.75
17_V	31_S	0.621	0.75
69_E	74_E	0.616	0.75
71_Q	82_K	0.614	0.74
135_Q	157_M	0.614	0.74
69_E	122_R	0.612	0.74
90_R	93_P	0.611	0.74
155_P	159_G	0.609	0.74
88_E	118_K	0.608	0.74
63_Y	68_F	0.605	0.73
71_Q	150_T	0.605	0.73
145_C	166_L	0.598	0.72
108_I	146_A	0.591	0.71
98_H	106_N	0.590	0.71
93_P	103_K	0.586	0.71
95_I	102_T	0.586	0.71
153_T	166_L	0.582	0.70
57_V	124_K	0.580	0.70
101_N	144_A	0.579	0.70
76_E	79_K	0.577	0.70
147_E	169_K	0.575	0.69
64_G	127_A	0.572	0.69
94_T	106_N	0.570	0.69
102_T	105_R	0.567	0.68
93_P	121_I	0.565	0.68
43_N	68_F	0.564	0.68
91_L	100_F	0.564	0.68
32_R	36_L	0.563	0.68
96_D	106_N	0.563	0.68
18_R	49_V	0.558	0.67
89_V	110_F	0.557	0.67
49_V	75_K	0.554	0.67
150_T	170_N	0.554	0.67
15_R	31_S	0.553	0.66
105_R	113_K	0.552	0.66
91_L	107_A	0.551	0.66
105_R	109_K	0.551	0.66
121_I	161_S	0.550	0.66
129_T	132_E	0.547	0.66
35_A	45_D	0.546	0.65
74_E	82_K	0.546	0.65
51_A	116_K	0.545	0.65
65_K	125_G	0.545	0.65
90_R	161_S	0.541	0.65
92_S	100_F	0.540	0.65
26_Q	49_V	0.539	0.64
87_K	99_D	0.536	0.64
124_K	155_P	0.536	0.64
103_K	134_G	0.534	0.64
135_Q	154_K	0.531	0.63
49_V	94_T	0.529	0.63
73_K	77_A	0.527	0.63
37_E	43_N	0.527	0.63
105_R	112_E	0.523	0.62
58_C	95_I	0.518	0.61
96_D	130_H	0.517	0.61
12_I	17_V	0.517	0.61
89_V	119_A	0.517	0.61
111_L	148_V	0.516	0.61
91_L	95_I	0.514	0.61
20_I	59_R	0.512	0.61
45_D	126_R	0.511	0.60
13_R	16_E	0.510	0.60
43_N	90_R	0.510	0.60
158_D	162_M	0.508	0.60
67_R	95_I	0.508	0.60
71_Q	74_E	0.506	0.60
132_E	165_M	0.505	0.60
94_T	133_I	0.504	0.59
112_E	147_E	0.503	0.59
29_I	32_R	0.500	0.59

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
2ifeA	1	0.5202	100	0.478	Contact Map
1tigA	1	0.5087	99.9	0.493	Contact Map
1tifA	1	0.4393	99.9	0.507	Contact Map
2crqA	1	0.5838	99.9	0.515	Contact Map
1i96V	1	0.4971	99.9	0.516	Contact Map
2m71A	1	0.5318	99.9	0.518	Contact Map
1pbjA	2	0.2254	38.2	0.933	Contact Map
2rihA	2	0.2717	26.8	0.938	Contact Map
3gbyA	2	0.2486	23.1	0.94	Contact Map
3kpbA	2	0.2312	23.1	0.94	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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