LFTR - ECOLI - GREMLIN Contacts

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LFTR - Leucyl/phenylalanyl-tRNA--protein transferase

UniProt:	P0A8P1	Sequences: MRLVQLSRHSIAFPSPEGALREPNGLLALGGDLSPARLLMAYQRGIFPWFSPGDPILWWSPDPRAVLWPESLHISRSMKRFHKRSPYRVTMNYAFGQVIEGCASDREEGTWITRGVVEAYHRLHELGHAHSIEVWREDELVGGMYGVAQGTLFCGESMFSRMENASKTALLVFCEEFIGHGGKLIDCQVLNDHTASLGACEIPRRDYLNYLNQMRLGRLPNNFWVPRCLFSPQE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11112
Length:	234 (203)
Sequences:	2004 (1404)
Seq/√Len:	98.6

ECOLI - LFTR

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
94_A	97_Q	4.757	1.00
71_S	200_C	4.721	1.00
81_F	164_N	3.574	1.00
100_E	117_V	3.523	1.00
136_R	162_M	3.515	1.00
90_T	93_Y	3.202	1.00
96_G	121_H	2.969	1.00
39_L	128_H	2.780	1.00
16_P	208_L	2.733	1.00
35_P	126_L	2.389	1.00
190_L	195_A	2.385	1.00
72_L	174_C	2.348	1.00
177_F	182_G	2.279	1.00
90_T	135_W	2.266	1.00
32_D	37_R	2.248	1.00
40_M	44_R	2.190	1.00
101_G	161_R	2.168	1.00
78_M	171_L	2.146	1.00
176_E	180_H	2.128	1.00
139_E	162_M	2.124	1.00
92_N	130_H	2.097	1.00
77_S	80_R	2.069	1.00
89_V	168_T	2.043	1.00
190_L	201_E	2.018	1.00
88_R	138_D	2.016	1.00
72_L	171_L	1.976	1.00
94_A	135_W	1.955	1.00
74_I	171_L	1.867	1.00
75_S	196_S	1.855	1.00
122_R	125_E	1.763	1.00
89_V	134_V	1.637	1.00
68_W	210_Y	1.620	1.00
120_Y	147_V	1.582	1.00
60_S	204_R	1.579	1.00
65_A	190_L	1.552	1.00
99_I	117_V	1.544	1.00
38_L	147_V	1.541	1.00
148_A	182_G	1.507	1.00
170_L	197_L	1.497	1.00
70_E	178_I	1.494	1.00
96_G	100_E	1.487	1.00
65_A	195_A	1.476	1.00
174_C	178_I	1.454	1.00
75_S	197_L	1.452	1.00
122_R	126_L	1.440	1.00
79_K	83_K	1.437	1.00
97_Q	101_G	1.419	1.00
100_E	114_R	1.410	1.00
51_S	54_D	1.407	1.00
105_D	161_R	1.399	1.00
89_V	172_V	1.398	0.99
91_M	132_I	1.369	0.99
99_I	121_H	1.350	0.99
206_D	210_Y	1.349	0.99
152_L	214_M	1.342	0.99
117_V	121_H	1.326	0.99
95_F	129_A	1.319	0.99
134_V	169_A	1.307	0.99
87_Y	168_T	1.301	0.99
124_H	131_S	1.299	0.99
104_S	161_R	1.286	0.99
38_L	119_A	1.284	0.99
151_T	217_G	1.284	0.99
98_V	159_F	1.270	0.99
34_S	37_R	1.270	0.99
91_M	176_E	1.263	0.99
66_V	202_I	1.261	0.99
87_Y	162_M	1.254	0.99
173_F	177_F	1.227	0.99
151_T	183_K	1.224	0.99
96_G	125_E	1.201	0.98
60_S	208_L	1.179	0.98
183_K	214_M	1.174	0.98
82_H	171_L	1.166	0.98
65_A	191_N	1.157	0.98
72_L	197_L	1.156	0.98
67_L	187_C	1.145	0.98
98_V	140_L	1.136	0.98
175_E	178_I	1.129	0.98
146_G	153_F	1.124	0.98
121_H	125_E	1.121	0.98
202_I	210_Y	1.111	0.97
149_Q	154_C	1.093	0.97
132_I	173_F	1.091	0.97
43_Q	149_Q	1.077	0.97
51_S	113_T	1.075	0.97
88_R	93_Y	1.072	0.97
69_P	174_C	1.065	0.97
206_D	209_N	1.054	0.96
41_A	58_W	1.051	0.96
132_I	144_M	1.045	0.96
116_V	145_Y	1.042	0.96
17_E	205_R	1.040	0.96
87_Y	141_V	1.033	0.96
68_W	200_C	1.016	0.96
187_C	191_N	1.015	0.96
87_Y	136_R	1.014	0.96
68_W	71_S	1.014	0.96
192_D	195_A	1.003	0.95
86_P	136_R	1.003	0.95
101_G	159_F	0.995	0.95
66_V	184_L	0.991	0.95
144_M	173_F	0.986	0.95
50_F	115_G	0.985	0.95
172_V	175_E	0.983	0.95
213_Q	217_G	0.978	0.95
174_C	185_I	0.975	0.95
149_Q	215_R	0.960	0.94
67_L	191_N	0.959	0.94
101_G	105_D	0.958	0.94
65_A	199_A	0.953	0.94
90_T	134_V	0.950	0.94
155_G	158_M	0.939	0.93
103_A	117_V	0.933	0.93
203_P	206_D	0.923	0.93
144_M	185_I	0.922	0.93
136_R	139_E	0.917	0.93
171_L	197_L	0.917	0.93
114_R	118_E	0.900	0.92
51_S	55_P	0.898	0.92
31_G	56_I	0.897	0.92
92_N	180_H	0.888	0.91
65_A	201_E	0.886	0.91
19_A	27_L	0.882	0.91
43_Q	216_L	0.870	0.90
80_R	83_K	0.870	0.90
73_H	197_L	0.861	0.90
116_V	119_A	0.860	0.90
78_M	164_N	0.856	0.90
190_L	199_A	0.855	0.90
100_E	121_H	0.853	0.90
124_H	129_A	0.847	0.89
90_T	131_S	0.843	0.89
139_E	161_R	0.843	0.89
33_L	119_A	0.841	0.89
166_S	193_H	0.832	0.88
50_F	56_I	0.832	0.88
142_G	165_A	0.824	0.88
63_P	203_P	0.823	0.88
170_L	174_C	0.821	0.88
136_R	141_V	0.821	0.88
138_D	141_V	0.820	0.88
100_E	104_S	0.820	0.88
123_L	129_A	0.819	0.88
96_G	117_V	0.817	0.87
141_V	162_M	0.816	0.87
81_F	86_P	0.811	0.87
184_L	210_Y	0.808	0.87
114_R	117_V	0.803	0.87
69_P	185_I	0.801	0.86
70_E	174_C	0.800	0.86
82_H	168_T	0.794	0.86
81_F	163_E	0.791	0.86
72_L	170_L	0.790	0.86
202_I	206_D	0.787	0.85
98_V	101_G	0.782	0.85
81_F	168_T	0.775	0.85
67_L	174_C	0.772	0.84
142_G	160_S	0.771	0.84
124_H	130_H	0.768	0.84
193_H	197_L	0.768	0.84
50_F	54_D	0.766	0.84
87_Y	163_E	0.760	0.83
130_H	148_A	0.757	0.83
154_C	215_R	0.755	0.83
77_S	84_R	0.751	0.83
113_T	116_V	0.750	0.83
68_W	202_I	0.746	0.82
123_L	147_V	0.744	0.82
33_L	58_W	0.743	0.82
66_V	200_C	0.740	0.82
209_N	212_N	0.732	0.81
77_S	81_F	0.732	0.81
24_N	63_P	0.731	0.81
204_R	208_L	0.727	0.81
164_N	167_K	0.722	0.80
160_S	170_L	0.718	0.80
69_P	187_C	0.714	0.79
210_Y	214_M	0.714	0.79
31_G	37_R	0.713	0.79
154_C	207_Y	0.713	0.79
144_M	155_G	0.712	0.79
33_L	41_A	0.704	0.78
69_P	178_I	0.702	0.78
128_H	147_V	0.702	0.78
61_P	204_R	0.695	0.78
30_G	119_A	0.694	0.78
73_H	80_R	0.685	0.77
36_A	126_L	0.685	0.77
116_V	120_Y	0.683	0.76
77_S	196_S	0.680	0.76
162_M	165_A	0.677	0.76
154_C	189_V	0.674	0.75
184_L	214_M	0.666	0.75
153_F	177_F	0.665	0.74
112_I	156_E	0.664	0.74
134_V	138_D	0.662	0.74
160_S	174_C	0.661	0.74
50_F	59_W	0.654	0.73
52_P	113_T	0.650	0.73
47_F	156_E	0.650	0.73
144_M	187_C	0.647	0.72
69_P	184_L	0.646	0.72
35_P	122_R	0.646	0.72
39_L	126_L	0.643	0.72
99_I	112_I	0.643	0.72
55_P	113_T	0.642	0.72
19_A	23_P	0.639	0.72
26_L	57_L	0.637	0.71
141_V	165_A	0.636	0.71
65_A	189_V	0.635	0.71
66_V	210_Y	0.630	0.70
65_A	187_C	0.626	0.70
77_S	193_H	0.626	0.70
155_G	194_T	0.625	0.70
50_F	113_T	0.625	0.70
56_I	116_V	0.618	0.69
19_A	25_G	0.614	0.68
152_L	215_R	0.610	0.68
199_A	204_R	0.607	0.68
22_E	26_L	0.604	0.67
99_I	145_Y	0.603	0.67
49_W	156_E	0.600	0.67
70_E	200_C	0.599	0.67
160_S	163_E	0.599	0.67
62_D	203_P	0.599	0.67
80_R	144_M	0.598	0.66
92_N	173_F	0.597	0.66
145_Y	156_E	0.594	0.66
92_N	124_H	0.591	0.66
89_V	132_I	0.590	0.65
84_R	168_T	0.590	0.65
175_E	179_G	0.590	0.65
151_T	214_M	0.589	0.65
40_M	43_Q	0.588	0.65
61_P	154_C	0.587	0.65
80_R	84_R	0.584	0.65
184_L	202_I	0.582	0.64
112_I	116_V	0.581	0.64
205_R	213_Q	0.579	0.64
86_P	168_T	0.576	0.64
49_W	189_V	0.575	0.63
164_N	171_L	0.573	0.63
134_V	139_E	0.569	0.63
53_G	57_L	0.569	0.63
73_H	163_E	0.567	0.62
77_S	167_K	0.565	0.62
87_Y	165_A	0.564	0.62
33_L	115_G	0.564	0.62
183_K	217_G	0.561	0.62
103_A	110_T	0.561	0.62
19_A	26_L	0.560	0.61
94_A	131_S	0.559	0.61
142_G	169_A	0.557	0.61
61_P	189_V	0.557	0.61
36_A	40_M	0.556	0.61
72_L	178_I	0.556	0.61
115_G	118_E	0.555	0.61
22_E	25_G	0.555	0.61
59_W	204_R	0.553	0.60
78_M	167_K	0.553	0.60
155_G	188_Q	0.552	0.60
171_L	175_E	0.552	0.60
167_K	193_H	0.551	0.60
213_Q	216_L	0.550	0.60
24_N	189_V	0.550	0.60
191_N	199_A	0.550	0.60
95_F	124_H	0.544	0.59
112_I	120_Y	0.543	0.59
78_M	81_F	0.541	0.59
86_P	141_V	0.539	0.59
78_M	168_T	0.539	0.59
158_M	188_Q	0.539	0.59
15_S	18_G	0.538	0.58
132_I	176_E	0.536	0.58
81_F	84_R	0.532	0.58
37_R	55_P	0.529	0.57
194_T	197_L	0.528	0.57
152_L	184_L	0.528	0.57
90_T	94_A	0.527	0.57
161_R	165_A	0.527	0.57
24_N	27_L	0.527	0.57
67_L	199_A	0.527	0.57
160_S	192_D	0.525	0.57
67_L	197_L	0.524	0.56
118_E	209_N	0.522	0.56
42_Y	156_E	0.520	0.56
63_P	201_E	0.518	0.56
122_R	205_R	0.518	0.56
160_S	194_T	0.517	0.55
27_L	46_I	0.516	0.55
147_V	170_L	0.514	0.55
34_S	119_A	0.514	0.55
62_D	205_R	0.511	0.55
122_R	209_N	0.510	0.54
152_L	211_L	0.510	0.54
39_L	43_Q	0.509	0.54
86_P	134_V	0.508	0.54
101_G	165_A	0.506	0.54
203_P	209_N	0.506	0.54
151_T	181_G	0.505	0.54
50_F	57_L	0.503	0.53
32_D	56_I	0.503	0.53
156_E	188_Q	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
2cxaA	1	0.9701	100	0.018	Contact Map
3gkrA	1	0.9231	87.8	0.944	Contact Map
2o28A	2	0.6966	61.9	0.956	Contact Map
2dxqA	2	0.5427	41.6	0.96	Contact Map
4jxqA	2	0.6368	39.7	0.961	Contact Map
3i3gA	2	0.5385	29.8	0.963	Contact Map
4zbgA	1	0.5855	27.2	0.964	Contact Map
4evyA	2	0.5427	27.2	0.964	Contact Map
4ehiA	2	0.3504	27.1	0.964	Contact Map
1s3zA	2	0.5299	26.2	0.964	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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