EFP - ECOLI - GREMLIN Contacts

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EFP - Elongation factor P

UniProt:	P0A6N4	Sequences: MATYYSNDFRAGLKIMLDGEPYAVEASEFVKPGKGQAFARVKLRRLLTGTRVEKTFKSTDSAEGADVVDMNLTYLYNDGEFWHFMNNETFEQLSADAKAIGDNAKWLLDQAECIVTLWNGQPISVTPPNFVELEIVDTDPGLKGDTAGTGGKPATLSTGAVVKVPLFVQIGEVIKVDTRSGEYVSRVK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12099
Length:	188 (183)
Sequences:	2794 (1329)
Seq/√Len:	98.2

ECOLI - EFP EFPL
BACSU - EFP

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
134_E	173_V	3.729	1.00
71_N	112_E	2.896	1.00
70_M	86_N	2.755	1.00
20_E	45_R	2.588	1.00
30_V	38_F	2.486	1.00
106_W	181_G	2.480	1.00
155_T	161_V	2.472	1.00
138_T	154_A	2.436	1.00
75_L	92_Q	2.403	1.00
47_L	121_Q	2.395	1.00
169_Q	172_E	2.348	1.00
162_V	174_I	2.339	1.00
134_E	157_S	2.311	1.00
175_K	185_S	2.243	1.00
105_K	160_A	2.178	1.00
132_E	173_V	2.172	1.00
135_I	174_I	2.160	1.00
16_M	63_E	2.148	1.00
136_V	155_T	2.084	1.00
137_D	170_I	1.965	1.00
83_H	94_S	1.937	1.00
6_S	59_T	1.925	1.00
132_E	175_K	1.885	1.00
154_A	164_V	1.882	1.00
134_E	170_I	1.879	1.00
133_L	156_L	1.864	1.00
81_F	94_S	1.846	1.00
71_N	114_I	1.789	1.00
73_T	87_N	1.770	1.00
134_E	171_G	1.747	1.00
108_L	157_S	1.713	1.00
18_D	54_K	1.706	1.00
72_L	115_V	1.686	1.00
17_L	54_K	1.663	1.00
87_N	112_E	1.649	1.00
137_D	155_T	1.641	1.00
73_T	112_E	1.637	1.00
77_N	97_A	1.633	1.00
115_V	122_P	1.606	1.00
16_M	119_N	1.565	1.00
74_Y	77_N	1.556	1.00
30_V	34_K	1.499	1.00
9_F	24_V	1.491	1.00
135_I	168_V	1.483	1.00
167_F	183_Y	1.477	1.00
57_K	60_D	1.474	1.00
77_N	80_E	1.471	1.00
136_V	156_L	1.469	1.00
72_L	93_L	1.466	1.00
106_W	160_A	1.386	0.99
150_G	166_L	1.378	0.99
78_D	81_F	1.371	0.99
133_L	157_S	1.336	0.99
130_F	184_V	1.333	0.99
143_K	146_T	1.331	0.99
15_I	62_A	1.313	0.99
96_D	99_A	1.301	0.99
78_D	94_S	1.283	0.99
45_R	48_T	1.272	0.99
41_V	56_F	1.253	0.99
32_P	38_F	1.246	0.99
108_L	111_A	1.243	0.99
9_F	62_A	1.242	0.99
76_Y	83_H	1.241	0.99
85_M	92_Q	1.235	0.99
97_A	104_A	1.234	0.99
129_N	179_R	1.226	0.99
15_I	43_L	1.193	0.98
34_K	38_F	1.186	0.98
156_L	176_V	1.176	0.98
82_W	104_A	1.175	0.98
168_V	172_E	1.173	0.98
133_L	158_T	1.157	0.98
141_G	166_L	1.149	0.98
156_L	174_I	1.147	0.98
105_K	181_G	1.129	0.98
130_F	175_K	1.110	0.97
136_V	157_S	1.090	0.97
84_F	100_I	1.087	0.97
11_A	26_A	1.076	0.97
16_M	118_W	1.074	0.97
135_I	170_I	1.066	0.97
22_Y	52_V	1.063	0.97
21_P	118_W	1.060	0.97
132_E	187_V	1.060	0.97
81_F	96_D	1.043	0.96
6_S	24_V	1.035	0.96
77_N	82_W	1.034	0.96
135_I	154_A	1.033	0.96
27_S	39_A	1.020	0.96
20_E	47_L	1.013	0.96
6_S	58_S	1.002	0.95
17_L	56_F	1.000	0.95
14_K	21_P	0.998	0.95
130_F	177_D	0.992	0.95
108_L	173_V	0.986	0.95
40_R	55_T	0.982	0.95
32_P	35_G	0.979	0.95
117_L	122_P	0.974	0.94
175_K	184_V	0.969	0.94
25_E	44_R	0.966	0.94
162_V	176_V	0.962	0.94
138_T	153_P	0.959	0.94
84_F	125_V	0.949	0.94
167_F	172_E	0.945	0.94
21_P	65_A	0.943	0.93
69_D	126_T	0.942	0.93
42_K	53_E	0.936	0.93
101_G	104_A	0.935	0.93
73_T	110_Q	0.933	0.93
156_L	160_A	0.925	0.93
177_D	180_S	0.909	0.92
29_F	39_A	0.897	0.92
151_G	163_K	0.894	0.92
6_S	9_F	0.893	0.91
77_N	83_H	0.888	0.91
145_D	166_L	0.886	0.91
45_R	50_T	0.882	0.91
82_W	97_A	0.878	0.91
11_A	27_S	0.870	0.90
70_M	117_L	0.868	0.90
80_E	97_A	0.866	0.90
30_V	40_R	0.861	0.90
21_P	66_D	0.859	0.90
14_K	69_D	0.841	0.89
175_K	187_V	0.835	0.88
9_F	13_L	0.832	0.88
14_K	65_A	0.831	0.88
39_A	58_S	0.822	0.88
82_W	100_I	0.820	0.88
107_L	111_A	0.816	0.87
100_I	125_V	0.816	0.87
95_A	99_A	0.816	0.87
16_M	65_A	0.809	0.87
7_N	24_V	0.809	0.87
33_G	37_A	0.805	0.87
138_T	142_L	0.804	0.87
145_D	150_G	0.803	0.86
142_L	145_D	0.802	0.86
21_P	46_L	0.795	0.86
16_M	19_G	0.788	0.85
99_A	121_Q	0.786	0.85
21_P	47_L	0.786	0.85
151_G	161_V	0.776	0.85
165_P	183_Y	0.769	0.84
93_L	117_L	0.764	0.84
78_D	83_H	0.762	0.83
156_L	161_V	0.759	0.83
9_F	41_V	0.758	0.83
95_A	122_P	0.755	0.83
142_L	166_L	0.754	0.83
69_D	116_T	0.753	0.83
153_P	163_K	0.753	0.83
103_N	124_S	0.750	0.83
84_F	95_A	0.747	0.82
138_T	170_I	0.746	0.82
143_K	147_A	0.745	0.82
31_K	34_K	0.744	0.82
32_P	37_A	0.742	0.82
22_Y	43_L	0.738	0.82
77_N	104_A	0.738	0.82
30_V	35_G	0.735	0.81
137_D	161_V	0.732	0.81
172_E	186_R	0.726	0.80
72_L	113_C	0.724	0.80
86_N	89_T	0.724	0.80
68_V	120_G	0.722	0.80
40_R	53_E	0.721	0.80
130_F	187_V	0.717	0.80
5_Y	8_D	0.710	0.79
26_A	42_K	0.710	0.79
100_I	103_N	0.708	0.79
35_G	40_R	0.706	0.79
65_A	118_W	0.703	0.78
15_I	24_V	0.695	0.77
136_V	158_T	0.690	0.77
117_L	120_G	0.689	0.77
7_N	11_A	0.687	0.77
27_S	41_V	0.686	0.77
13_L	24_V	0.685	0.76
141_G	154_A	0.679	0.76
138_T	164_V	0.674	0.75
30_V	37_A	0.673	0.75
80_E	95_A	0.673	0.75
36_Q	53_E	0.671	0.75
21_P	123_I	0.650	0.73
87_N	90_F	0.646	0.72
33_G	38_F	0.645	0.72
33_G	58_S	0.641	0.72
139_D	153_P	0.641	0.72
34_K	37_A	0.639	0.71
177_D	184_V	0.638	0.71
35_G	55_T	0.637	0.71
35_G	38_F	0.637	0.71
13_L	64_G	0.635	0.71
46_L	116_T	0.634	0.71
16_M	21_P	0.633	0.71
69_D	114_I	0.630	0.70
73_T	92_Q	0.625	0.70
31_K	55_T	0.625	0.70
29_F	33_G	0.625	0.70
74_Y	83_H	0.624	0.70
42_K	51_R	0.621	0.69
7_N	39_A	0.616	0.69
74_Y	104_A	0.613	0.68
84_F	115_V	0.612	0.68
153_P	161_V	0.611	0.68
84_F	113_C	0.610	0.68
108_L	133_L	0.604	0.67
36_Q	57_K	0.604	0.67
150_G	153_P	0.603	0.67
54_K	62_A	0.600	0.67
86_N	93_L	0.594	0.66
24_V	27_S	0.592	0.66
66_D	120_G	0.591	0.65
15_I	54_K	0.588	0.65
6_S	62_A	0.585	0.65
20_E	48_T	0.584	0.65
167_F	186_R	0.582	0.64
67_V	116_T	0.579	0.64
114_I	126_T	0.579	0.64
85_M	90_F	0.579	0.64
111_A	128_P	0.578	0.64
134_E	172_E	0.574	0.63
140_P	147_A	0.573	0.63
131_V	178_T	0.573	0.63
56_F	95_A	0.572	0.63
111_A	131_V	0.571	0.63
23_A	69_D	0.570	0.63
80_E	96_D	0.568	0.62
141_G	150_G	0.566	0.62
140_P	154_A	0.566	0.62
9_F	59_T	0.564	0.62
140_P	169_Q	0.563	0.62
105_K	158_T	0.562	0.62
6_S	60_D	0.561	0.61
31_K	35_G	0.559	0.61
113_C	125_V	0.558	0.61
31_K	44_R	0.558	0.61
46_L	124_S	0.557	0.61
116_T	124_S	0.556	0.61
141_G	153_P	0.550	0.60
75_L	110_Q	0.549	0.60
141_G	145_D	0.548	0.60
156_L	162_V	0.547	0.60
28_E	41_V	0.547	0.60
44_R	51_R	0.545	0.59
98_K	101_G	0.545	0.59
55_T	149_T	0.545	0.59
139_D	150_G	0.544	0.59
21_P	119_N	0.543	0.59
130_F	179_R	0.536	0.58
73_T	85_M	0.536	0.58
70_M	120_G	0.535	0.58
80_E	98_K	0.535	0.58
45_R	121_Q	0.534	0.58
15_I	52_V	0.528	0.57
139_D	151_G	0.528	0.57
131_V	158_T	0.525	0.56
135_I	172_E	0.523	0.56
149_T	167_F	0.522	0.56
14_K	23_A	0.521	0.56
26_A	59_T	0.518	0.55
8_D	39_A	0.518	0.55
22_Y	60_D	0.517	0.55
95_A	124_S	0.515	0.55
105_K	161_V	0.509	0.54
79_G	83_H	0.508	0.54
30_V	33_G	0.508	0.54
7_N	62_A	0.507	0.54
71_N	126_T	0.503	0.53
148_G	151_G	0.502	0.53
58_S	73_T	0.501	0.53
151_G	170_I	0.500	0.53

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
3treA	1	0.6862	100	0.045	Contact Map
3a5zB	1	0.7128	100	0.048	Contact Map
3oyyA	1	0.9894	100	0.051	Contact Map
1ybyA	2	0.9628	100	0.07	Contact Map
1uebA	1	0.9787	100	0.07	Contact Map
1bkbA	3	0.6862	100	0.508	Contact Map
1iz6A	1	0.6915	100	0.515	Contact Map
2eifA	1	0.6649	100	0.516	Contact Map
3er0A	1	0.7234	100	0.519	Contact Map
3hksA	1	0.7234	100	0.525	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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