YBIR - ECOLI - GREMLIN Contacts

Home
GREMLIN
- Submit - Monomer
- Submit - Complex
Contacts
Metagenomics
- Contacts
- Structures
Structures
- List
Old Projects
- Complexes (2014)
- PFAM (2013)

YBIR - Inner membrane protein YbiR

UniProt:	P75788	Sequences: MSLPFLRTLQGDRFFQLLILVGIGLSFFVPFAPKSWPAAIDWHTIITLSGLMLLTKGVELSGYFDVLGRKMVRRFATERRLAMFMVLAAALLSTFLTNDVALFIVVPLTITLKRLCEIPVNRLIIFEALAVNAGSLLTPIGNPQNILIWGRSGLSFAGFIAQMAPLAGAMMLTLLLLCWCCFPGKAMQYHTGVQTPEWKPRLVWSCLGLYIVFLTALEFKQELWGLVIVAAGFALLARRVVLSVDWTLLLVFMAMFIDVHLLTQLPALQGVLGNVSHLSEPGLWLTAIGLSQVISNVPSTILLLNYVPPSLLLVWAVNVGGFGLLPGSLANLIALRMANDRRIWWRFHLYSIPMLLWAALVGYVLLVILPAN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13323
Length:	372 (350)
Sequences:	4483 (2993)
Seq/√Len:	160.0

ECOLI - YBIR ARSB YBHI TTDT CITT YFJV
BACSU - YDFA YWRK YFLS
SULSO - Q980X8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
325_L	335_L	3.419	1.00
202_L	206_C	3.244	1.00
77_T	80_R	3.219	1.00
109_T	127_E	3.195	1.00
70_K	74_R	3.141	1.00
346_R	349_L	2.837	1.00
35_S	264_Q	2.748	1.00
209_L	216_A	2.483	1.00
134_G	171_M	2.421	1.00
49_S	249_L	2.416	1.00
102_L	131_V	2.385	1.00
208_G	212_V	2.376	1.00
201_R	205_S	2.368	1.00
213_F	216_A	2.325	1.00
351_S	355_L	2.319	1.00
102_L	334_A	2.302	1.00
206_C	214_L	2.295	1.00
209_L	212_V	2.257	1.00
206_C	212_V	2.228	1.00
66_V	70_K	2.207	1.00
206_C	210_Y	2.160	1.00
288_I	359_A	2.159	1.00
204_W	208_G	2.127	1.00
205_S	215_T	2.127	1.00
211_I	214_L	2.124	1.00
211_I	215_T	2.070	1.00
124_I	334_A	2.068	1.00
208_G	215_T	2.052	1.00
155_S	158_G	2.048	1.00
207_L	215_T	2.016	1.00
204_W	212_V	1.993	1.00
212_V	216_A	1.983	1.00
212_V	215_T	1.979	1.00
147_L	304_L	1.967	1.00
206_C	213_F	1.943	1.00
292_Q	323_G	1.938	1.00
205_S	212_V	1.929	1.00
139_P	149_W	1.925	1.00
60_L	239_R	1.911	1.00
207_L	211_I	1.910	1.00
210_Y	213_F	1.892	1.00
110_I	343_I	1.892	1.00
219_F	222_E	1.888	1.00
157_A	161_A	1.869	1.00
208_G	211_I	1.850	1.00
205_S	216_A	1.832	1.00
352_I	355_L	1.822	1.00
201_R	216_A	1.814	1.00
205_S	209_L	1.809	1.00
135_S	142_N	1.797	1.00
312_L	316_A	1.781	1.00
89_A	105_V	1.776	1.00
208_G	214_L	1.770	1.00
205_S	208_G	1.740	1.00
201_R	212_V	1.737	1.00
202_L	205_S	1.732	1.00
66_V	69_R	1.729	1.00
237_A	240_V	1.710	1.00
269_Q	273_G	1.694	1.00
210_Y	214_L	1.674	1.00
206_C	216_A	1.642	1.00
205_S	214_L	1.639	1.00
203_V	206_C	1.638	1.00
201_R	215_T	1.636	1.00
87_L	171_M	1.633	1.00
226_L	229_V	1.626	1.00
200_P	204_W	1.617	1.00
285_L	363_Y	1.615	1.00
114_R	341_R	1.611	1.00
203_V	207_L	1.594	1.00
176_L	180_C	1.586	1.00
119_P	185_K	1.576	1.00
204_W	215_T	1.570	1.00
158_G	161_A	1.564	1.00
347_F	351_S	1.559	1.00
69_R	73_R	1.539	1.00
79_R	179_W	1.535	1.00
164_A	168_G	1.531	1.00
169_A	365_L	1.524	1.00
348_H	352_I	1.518	1.00
220_K	223_L	1.517	1.00
136_L	167_A	1.513	1.00
205_S	213_F	1.511	1.00
197_E	200_P	1.478	1.00
202_L	214_L	1.474	1.00
201_R	211_I	1.459	1.00
203_V	214_L	1.451	1.00
106_V	124_I	1.445	1.00
32_A	35_S	1.433	1.00
231_A	235_L	1.426	1.00
289_G	293_V	1.417	1.00
201_R	204_W	1.415	1.00
128_A	334_A	1.413	1.00
229_V	233_F	1.413	1.00
312_L	366_L	1.412	1.00
201_R	214_L	1.410	1.00
203_V	216_A	1.401	1.00
182_F	350_Y	1.400	1.00
176_L	179_W	1.391	1.00
58_V	63_Y	1.386	1.00
207_L	214_L	1.376	1.00
232_G	236_L	1.367	1.00
36_W	39_A	1.367	1.00
203_V	215_T	1.363	1.00
209_L	213_F	1.353	1.00
325_L	332_L	1.350	1.00
65_D	69_R	1.333	1.00
97_T	100_V	1.330	1.00
75_F	84_F	1.315	1.00
18_L	25_L	1.307	1.00
230_A	234_A	1.307	1.00
345_W	348_H	1.301	1.00
26_S	29_V	1.293	1.00
113_K	123_L	1.290	1.00
227_V	231_A	1.290	1.00
218_E	223_L	1.289	1.00
285_L	289_G	1.289	1.00
21_V	25_L	1.284	1.00
22_G	25_L	1.283	1.00
204_W	214_L	1.283	1.00
170_M	358_A	1.282	1.00
15_F	18_L	1.277	1.00
204_W	210_Y	1.257	1.00
203_V	213_F	1.257	1.00
198_W	209_L	1.250	1.00
345_W	349_L	1.247	1.00
37_P	41_D	1.243	1.00
36_W	40_I	1.241	1.00
270_G	273_G	1.238	1.00
177_L	357_W	1.226	1.00
21_V	26_S	1.222	1.00
172_L	176_L	1.221	1.00
353_P	356_L	1.216	1.00
144_Q	318_N	1.209	1.00
352_I	356_L	1.191	1.00
173_T	361_V	1.191	1.00
218_E	221_Q	1.190	1.00
33_P	36_W	1.183	1.00
206_C	209_L	1.180	1.00
129_L	354_M	1.179	1.00
286_T	290_L	1.178	1.00
360_L	364_V	1.175	1.00
201_R	208_G	1.172	1.00
83_M	179_W	1.172	1.00
193_V	198_W	1.170	1.00
201_R	209_L	1.169	1.00
34_K	38_A	1.167	1.00
287_A	313_L	1.163	1.00
33_P	37_P	1.162	1.00
356_L	360_L	1.162	1.00
83_M	175_L	1.162	1.00
32_A	36_W	1.152	1.00
182_F	185_K	1.147	1.00
161_A	165_P	1.147	1.00
60_L	243_S	1.147	1.00
206_C	215_T	1.146	1.00
207_L	210_Y	1.146	1.00
86_V	126_F	1.137	1.00
204_W	207_L	1.131	1.00
122_R	178_C	1.119	1.00
201_R	210_Y	1.113	1.00
197_E	201_R	1.113	1.00
125_I	350_Y	1.100	1.00
18_L	22_G	1.100	1.00
252_F	321_G	1.098	1.00
70_K	73_R	1.094	1.00
203_V	208_G	1.094	1.00
22_G	26_S	1.088	0.99
209_L	215_T	1.085	0.99
25_L	29_V	1.078	0.99
270_G	274_N	1.078	0.99
19_I	23_I	1.077	0.99
34_K	40_I	1.077	0.99
300_T	317_V	1.077	0.99
76_A	80_R	1.074	0.99
88_A	92_L	1.070	0.99
53_L	241_V	1.067	0.99
210_Y	215_T	1.066	0.99
99_D	142_N	1.044	0.99
91_L	95_F	1.043	0.99
106_V	334_A	1.040	0.99
64_F	68_G	1.036	0.99
87_L	91_L	1.025	0.99
202_L	213_F	1.020	0.99
323_G	355_L	1.020	0.99
202_L	208_G	1.019	0.99
92_L	101_A	1.018	0.99
355_L	359_A	1.015	0.99
222_E	226_L	1.010	0.99
199_K	205_S	1.010	0.99
59_E	243_S	1.008	0.99
202_L	215_T	1.006	0.99
143_P	256_F	1.001	0.99
199_K	203_V	0.995	0.99
18_L	26_S	0.983	0.99
18_L	27_F	0.977	0.99
287_A	317_V	0.975	0.99
207_L	213_F	0.974	0.99
180_C	184_G	0.973	0.99
50_G	226_L	0.965	0.99
199_K	210_Y	0.962	0.99
291_S	317_V	0.961	0.99
274_N	278_L	0.960	0.99
121_N	346_R	0.960	0.99
23_I	26_S	0.954	0.99
316_A	320_G	0.953	0.99
204_W	216_A	0.952	0.99
38_A	41_D	0.945	0.99
292_Q	295_S	0.942	0.99
287_A	316_A	0.939	0.98
193_V	200_P	0.935	0.98
23_I	27_F	0.933	0.98
17_L	21_V	0.931	0.98
124_I	338_A	0.928	0.98
274_N	277_H	0.922	0.98
348_H	351_S	0.922	0.98
56_K	59_E	0.918	0.98
204_W	213_F	0.915	0.98
44_T	51_L	0.914	0.98
25_L	30_P	0.904	0.98
226_L	233_F	0.898	0.98
99_D	135_S	0.896	0.98
273_G	277_H	0.896	0.98
163_M	314_V	0.895	0.98
201_R	207_L	0.892	0.98
138_T	141_G	0.891	0.98
97_T	135_S	0.890	0.98
21_V	36_W	0.888	0.98
208_G	216_A	0.885	0.98
199_K	216_A	0.884	0.98
349_L	352_I	0.881	0.98
321_G	331_N	0.880	0.98
325_L	344_W	0.877	0.98
166_L	315_W	0.876	0.98
199_K	202_L	0.875	0.98
24_G	28_F	0.873	0.98
136_L	163_M	0.871	0.98
200_P	216_A	0.869	0.97
226_L	232_G	0.867	0.97
85_M	109_T	0.867	0.97
18_L	21_V	0.867	0.97
42_W	49_S	0.866	0.97
203_V	210_Y	0.865	0.97
35_S	38_A	0.862	0.97
100_V	251_V	0.862	0.97
147_L	297_V	0.860	0.97
314_V	317_V	0.857	0.97
137_L	167_A	0.855	0.97
203_V	211_I	0.846	0.97
144_Q	297_V	0.844	0.97
287_A	303_L	0.843	0.97
50_G	230_A	0.842	0.97
260_H	264_Q	0.841	0.97
337_M	341_R	0.835	0.97
62_G	65_D	0.835	0.97
348_H	355_L	0.835	0.97
173_T	177_L	0.833	0.97
34_K	37_P	0.831	0.97
261_L	265_L	0.828	0.97
106_V	337_M	0.828	0.97
363_Y	367_V	0.828	0.97
225_G	230_A	0.824	0.97
203_V	209_L	0.823	0.97
299_S	303_L	0.818	0.96
31_F	36_W	0.811	0.96
134_G	141_G	0.811	0.96
169_A	361_V	0.811	0.96
278_L	282_G	0.805	0.96
207_L	216_A	0.804	0.96
26_S	36_W	0.800	0.96
49_S	53_L	0.800	0.96
225_G	229_V	0.799	0.96
125_I	129_L	0.797	0.96
205_S	210_Y	0.793	0.96
93_S	297_V	0.792	0.96
268_L	278_L	0.788	0.96
142_N	145_N	0.786	0.95
198_W	205_S	0.783	0.95
68_G	71_M	0.782	0.95
129_L	174_L	0.781	0.95
131_V	330_A	0.781	0.95
130_A	171_M	0.776	0.95
182_F	186_A	0.775	0.95
19_I	22_G	0.774	0.95
364_V	367_V	0.773	0.95
51_L	55_T	0.770	0.95
167_A	171_M	0.761	0.95
202_L	211_I	0.760	0.95
210_Y	216_A	0.756	0.94
297_V	329_L	0.756	0.94
160_I	164_A	0.753	0.94
16_Q	26_S	0.752	0.94
136_L	319_V	0.747	0.94
180_C	183_P	0.747	0.94
136_L	318_N	0.745	0.94
211_I	216_A	0.745	0.94
42_W	46_I	0.744	0.94
207_L	212_V	0.743	0.94
26_S	33_P	0.743	0.94
299_S	302_L	0.741	0.94
96_L	124_I	0.741	0.94
50_G	54_L	0.732	0.93
232_G	235_L	0.732	0.93
37_P	40_I	0.725	0.93
188_Q	191_T	0.724	0.93
238_R	241_V	0.722	0.93
17_L	22_G	0.722	0.93
19_I	25_L	0.720	0.93
78_E	82_A	0.719	0.93
20_L	27_F	0.718	0.93
228_I	232_G	0.718	0.93
288_I	355_L	0.718	0.93
344_W	355_L	0.717	0.93
20_L	26_S	0.717	0.93
300_T	304_L	0.716	0.93
69_R	72_V	0.716	0.93
15_F	19_I	0.715	0.93
98_N	142_N	0.712	0.92
144_Q	295_S	0.712	0.92
66_V	73_R	0.711	0.92
218_E	222_E	0.707	0.92
141_G	321_G	0.704	0.92
134_G	252_F	0.703	0.92
45_I	253_M	0.702	0.92
39_A	260_H	0.702	0.92
47_T	51_L	0.701	0.92
26_S	31_F	0.701	0.92
44_T	54_L	0.700	0.92
328_S	331_N	0.699	0.92
219_F	223_L	0.698	0.92
86_V	178_C	0.698	0.92
285_L	359_A	0.697	0.92
88_A	131_V	0.694	0.91
159_F	163_M	0.691	0.91
238_R	242_L	0.686	0.91
140_I	156_F	0.685	0.91
245_D	252_F	0.685	0.91
199_K	209_L	0.681	0.91
113_K	120_V	0.681	0.91
149_W	156_F	0.678	0.91
99_D	145_N	0.678	0.91
16_Q	20_L	0.675	0.90
28_F	31_F	0.674	0.90
296_N	326_P	0.673	0.90
295_S	321_G	0.672	0.90
239_R	242_L	0.671	0.90
314_V	331_N	0.670	0.90
68_G	73_R	0.669	0.90
49_S	244_V	0.665	0.90
199_K	214_L	0.665	0.90
349_L	353_P	0.665	0.90
322_F	331_N	0.662	0.89
229_V	232_G	0.661	0.89
46_I	50_G	0.660	0.89
328_S	332_L	0.660	0.89
99_D	333_I	0.659	0.89
262_L	265_L	0.657	0.89
59_E	111_T	0.654	0.89
143_P	331_N	0.653	0.89
151_R	304_L	0.652	0.89
296_N	321_G	0.649	0.89
351_S	354_M	0.647	0.88
268_L	272_L	0.647	0.88
118_I	123_L	0.646	0.88
51_L	100_V	0.644	0.88
344_W	348_H	0.642	0.88
193_V	199_K	0.642	0.88
278_L	281_P	0.640	0.88
20_L	24_G	0.640	0.88
19_I	26_S	0.636	0.88
344_W	347_F	0.636	0.88
80_R	114_R	0.635	0.87
313_L	334_A	0.635	0.87
355_L	362_G	0.634	0.87
318_N	321_G	0.633	0.87
252_F	296_N	0.630	0.87
99_D	107_P	0.630	0.87
323_G	352_I	0.630	0.87
204_W	211_I	0.629	0.87
275_V	282_G	0.628	0.87
351_S	362_G	0.627	0.87
98_N	143_P	0.626	0.87
64_F	73_R	0.625	0.87
25_L	261_L	0.624	0.87
198_W	215_T	0.624	0.87
289_G	323_G	0.623	0.86
16_Q	19_I	0.622	0.86
65_D	68_G	0.622	0.86
86_V	130_A	0.621	0.86
135_S	144_Q	0.621	0.86
198_W	201_R	0.621	0.86
266_P	269_Q	0.620	0.86
169_A	364_V	0.618	0.86
319_V	358_A	0.618	0.86
202_L	209_L	0.617	0.86
199_K	204_W	0.617	0.86
15_F	26_S	0.617	0.86
48_L	52_M	0.617	0.86
200_P	215_T	0.614	0.86
143_P	321_G	0.614	0.86
291_S	295_S	0.613	0.86
270_G	280_E	0.613	0.86
24_G	27_F	0.613	0.86
344_W	351_S	0.610	0.85
203_V	212_V	0.609	0.85
359_A	362_G	0.609	0.85
90_A	129_L	0.608	0.85
201_R	206_C	0.607	0.85
147_L	301_I	0.605	0.85
230_A	233_F	0.605	0.85
318_N	331_N	0.604	0.85
166_L	170_M	0.603	0.85
247_T	250_L	0.603	0.85
31_F	38_A	0.602	0.85
169_A	362_G	0.601	0.84
109_T	113_K	0.599	0.84
62_G	68_G	0.599	0.84
295_S	302_L	0.599	0.84
48_L	134_G	0.597	0.84
132_N	328_S	0.591	0.83
202_L	216_A	0.591	0.83
269_Q	272_L	0.590	0.83
290_L	293_V	0.590	0.83
252_F	256_F	0.590	0.83
144_Q	292_Q	0.590	0.83
145_N	298_P	0.587	0.83
208_G	213_F	0.585	0.83
248_L	333_I	0.585	0.83
97_T	295_S	0.584	0.83
252_F	297_V	0.582	0.82
130_A	134_G	0.581	0.82
48_L	97_T	0.580	0.82
98_N	330_A	0.579	0.82
142_N	292_Q	0.577	0.82
100_V	322_F	0.577	0.82
331_N	334_A	0.576	0.82
187_M	190_H	0.575	0.82
97_T	297_V	0.575	0.82
44_T	52_M	0.575	0.82
290_L	299_S	0.575	0.82
128_A	351_S	0.573	0.82
21_V	24_G	0.572	0.81
141_G	256_F	0.572	0.81
183_P	186_A	0.571	0.81
129_L	133_A	0.570	0.81
142_N	318_N	0.569	0.81
247_T	339_N	0.569	0.81
44_T	299_S	0.567	0.81
32_A	39_A	0.564	0.81
35_S	39_A	0.563	0.80
294_I	299_S	0.561	0.80
316_A	324_L	0.560	0.80
90_A	171_M	0.559	0.80
73_R	193_V	0.559	0.80
218_E	225_G	0.558	0.80
62_G	69_R	0.558	0.80
40_I	253_M	0.557	0.80
113_K	117_E	0.556	0.80
51_L	97_T	0.556	0.80
173_T	360_L	0.555	0.79
143_P	322_F	0.553	0.79
64_F	71_M	0.553	0.79
354_M	359_A	0.551	0.79
348_H	354_M	0.551	0.79
233_F	236_L	0.550	0.79
318_N	328_S	0.549	0.79
141_G	331_N	0.549	0.79
64_F	67_L	0.548	0.79
294_I	298_P	0.545	0.78
322_F	358_A	0.544	0.78
334_A	338_A	0.544	0.78
142_N	298_P	0.543	0.78
359_A	363_Y	0.542	0.78
200_P	209_L	0.541	0.78
179_W	184_G	0.541	0.78
317_V	320_G	0.540	0.78
355_L	358_A	0.540	0.78
173_T	357_W	0.539	0.77
198_W	212_V	0.537	0.77
327_G	332_L	0.537	0.77
352_I	362_G	0.535	0.77
62_G	66_V	0.535	0.77
202_L	212_V	0.535	0.77
158_G	162_Q	0.534	0.77
248_L	336_R	0.533	0.77
318_N	329_L	0.533	0.77
315_W	319_V	0.533	0.77
319_V	322_F	0.532	0.77
353_P	357_W	0.531	0.76
39_A	263_T	0.526	0.76
315_W	362_G	0.525	0.76
156_F	160_I	0.524	0.75
72_V	112_L	0.524	0.75
273_G	278_L	0.523	0.75
130_A	141_G	0.519	0.75
222_E	227_V	0.519	0.75
90_A	94_T	0.518	0.75
193_V	210_Y	0.518	0.75
193_V	197_E	0.518	0.75
61_S	64_F	0.518	0.75
90_A	331_N	0.516	0.74
126_F	174_L	0.515	0.74
135_S	299_S	0.513	0.74
259_V	330_A	0.512	0.74
26_S	30_P	0.512	0.74
225_G	233_F	0.512	0.74
276_S	280_E	0.510	0.74
146_I	316_A	0.509	0.73
197_E	211_I	0.508	0.73
42_W	50_G	0.508	0.73
248_L	328_S	0.506	0.73
97_T	142_N	0.506	0.73
86_V	100_V	0.506	0.73
59_E	65_D	0.504	0.73
25_L	28_F	0.504	0.73
97_T	103_F	0.504	0.73
129_L	322_F	0.504	0.73
197_E	215_T	0.504	0.73
123_L	338_A	0.502	0.72
133_A	170_M	0.502	0.72
324_L	348_H	0.502	0.72
82_A	178_C	0.501	0.72
144_Q	333_I	0.501	0.72
304_L	308_P	0.501	0.72
288_I	302_L	0.500	0.72

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
4f35D	2	0.9704	100	0.484	Contact Map
4r1iA	2	0.9866	99.7	0.768	Contact Map
4r0cA	3	0.9812	99.6	0.777	Contact Map
3aqpA	1	0.3817	16.9	0.962	Contact Map
3w9iA	3	0.3978	14.1	0.963	Contact Map
2mfrA	1	0.1532	10.4	0.965	Contact Map
3zojA	3	0.4382	8.9	0.966	Contact Map
4wgvA	2	0.5565	6	0.969	Contact Map
3ne5A	3	0.3091	5.5	0.969	Contact Map
4mt1A	3	0.3978	5.5	0.969	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.

Page generated in 0.0111 seconds.