YIBH - ECOLI - GREMLIN Contacts

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YIBH - Inner membrane protein YibH

UniProt:	P0AFV0	Sequences: MDLLIVLTYVALAWAVFKIFRIPVNQWTLATAALGGVFLVSGLILLMNYNHPYTFTAQKAVIAIPITPQVTGIVTEVTDKNNQLIQKGEVLFKLDPVRYQARVDRLQADLMTATHNIKTLRAQLTEAQANTTQVSAERDRLFKNYQRYLKGSQAAVNPFSERDIDDARQNFLAQDALVKGSVAEQAQIQSQLDSMVNGEQSQIVSLRAQLTEAKYNLEQTVIRAPSNGYVTQVLIRPGTYAAALPLRPVMVFIPEQKRQIVAQFRQNSLLRLKPGDDAEVVFNALPGQVFHGKLTSILPVVPGGSYQAQGVLQSLTVVPGTDGVLGTIELDPNDDIDALPDGIYAQVAVYSDHFSHVSVMRKVLLRMTSWMHYLYLDH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11764
Length:	378 (317)
Sequences:	18569 (14688)
Seq/√Len:	824.9

ECOLI - YIBH YIAV EMRK EMRA YHII YBHG MDTN MACA AAEA ACRE ACRA YDHJ MDTA MDTE CUSB
BACSU - YVRP YKNX

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
76_E	93_K	3.310	1.00
86_Q	227_N	3.287	1.00
90_V	221_V	3.017	1.00
295_T	329_E	2.735	1.00
292_G	328_I	2.580	1.00
142_F	146_Q	2.531	1.00
93_K	221_V	2.382	1.00
107_Q	214_K	2.378	1.00
168_R	172_L	2.377	1.00
277_D	291_H	2.370	1.00
149_L	168_R	2.336	1.00
78_T	93_K	2.293	1.00
148_Y	159_F	2.266	1.00
86_Q	89_E	2.240	1.00
96_P	100_Q	2.190	1.00
148_Y	167_A	2.165	1.00
103_V	210_L	2.129	1.00
149_L	153_Q	2.121	1.00
142_F	175_D	2.114	1.00
171_F	175_D	2.095	1.00
90_V	223_R	2.081	1.00
69_Q	219_Q	2.043	1.00
87_K	227_N	2.037	1.00
84_L	229_Y	2.000	1.00
114_T	207_R	1.965	1.00
145_Y	164_I	1.896	1.00
78_T	90_V	1.896	1.00
261_V	325_L	1.893	1.00
152_S	161_E	1.888	1.00
293_K	331_D	1.870	1.00
142_F	171_F	1.869	1.00
135_S	182_V	1.867	1.00
163_D	166_D	1.853	1.00
279_E	291_H	1.851	1.00
293_K	329_E	1.839	1.00
145_Y	149_L	1.834	1.00
277_D	293_K	1.815	1.00
161_E	165_D	1.814	1.00
259_Q	327_T	1.806	1.00
279_E	289_V	1.792	1.00
104_D	107_Q	1.782	1.00
231_T	253_I	1.742	1.00
278_A	328_I	1.729	1.00
103_V	214_K	1.729	1.00
152_S	164_I	1.722	1.00
262_A	347_V	1.721	1.00
138_R	171_F	1.683	1.00
41_S	45_L	1.665	1.00
110_L	210_L	1.660	1.00
80_K	83_Q	1.660	1.00
135_S	178_V	1.651	1.00
100_Q	217_L	1.635	1.00
145_Y	171_F	1.620	1.00
204_V	207_R	1.600	1.00
103_V	107_Q	1.591	1.00
296_S	327_T	1.570	1.00
40_V	44_I	1.557	1.00
102_R	105_R	1.556	1.00
211_T	214_K	1.552	1.00
140_R	144_N	1.547	1.00
100_Q	104_D	1.517	1.00
110_L	114_T	1.512	1.00
164_I	168_R	1.510	1.00
125_T	128_Q	1.507	1.00
262_A	328_I	1.507	1.00
128_Q	189_Q	1.505	1.00
224_A	252_F	1.499	1.00
60_A	261_V	1.484	1.00
145_Y	168_R	1.483	1.00
111_M	114_T	1.478	1.00
260_I	345_A	1.475	1.00
72_G	94_L	1.473	1.00
92_F	222_I	1.451	1.00
105_R	209_Q	1.451	1.00
107_Q	210_L	1.449	1.00
75_T	95_D	1.449	1.00
138_R	142_F	1.441	1.00
175_D	179_K	1.438	1.00
132_T	135_S	1.434	1.00
172_L	175_D	1.422	1.00
301_V	324_V	1.421	1.00
74_V	235_I	1.415	1.00
166_D	170_N	1.413	1.00
110_L	207_R	1.411	1.00
74_V	92_F	1.395	1.00
179_K	182_V	1.382	1.00
131_T	178_V	1.379	1.00
279_E	350_Y	1.374	1.00
75_T	93_K	1.372	1.00
144_N	166_D	1.359	1.00
39_L	43_L	1.358	1.00
210_L	214_K	1.357	1.00
131_T	185_Q	1.353	1.00
84_L	255_E	1.337	1.00
212_E	216_N	1.335	1.00
170_N	173_A	1.334	1.00
41_S	44_I	1.331	1.00
186_A	189_Q	1.327	1.00
242_A	247_R	1.322	1.00
147_R	165_D	1.321	1.00
42_G	46_L	1.319	1.00
139_D	143_K	1.315	1.00
257_K	329_E	1.308	1.00
102_R	212_E	1.307	1.00
120_L	123_Q	1.301	1.00
138_R	175_D	1.295	1.00
116_N	119_T	1.293	1.00
146_Q	150_K	1.287	1.00
110_L	203_I	1.286	1.00
141_L	174_Q	1.284	1.00
178_V	182_V	1.282	1.00
138_R	178_V	1.271	1.00
103_V	217_L	1.267	1.00
153_Q	156_V	1.263	1.00
197_N	200_Q	1.256	1.00
135_S	139_D	1.254	1.00
76_E	237_P	1.253	1.00
90_V	93_K	1.253	1.00
288_Q	338_A	1.250	1.00
128_Q	185_Q	1.246	1.00
91_L	250_M	1.245	1.00
214_K	218_E	1.235	1.00
149_L	164_I	1.234	1.00
207_R	211_T	1.231	1.00
265_R	268_S	1.231	1.00
230_V	250_M	1.225	1.00
102_R	216_N	1.216	1.00
117_I	200_Q	1.214	1.00
65_P	248_P	1.201	1.00
146_Q	149_L	1.200	1.00
282_F	345_A	1.193	1.00
162_R	166_D	1.172	1.00
99_Y	220_T	1.172	1.00
79_D	89_E	1.169	1.00
150_K	156_V	1.159	1.00
291_H	331_D	1.149	1.00
83_Q	89_E	1.136	1.00
264_F	272_L	1.131	1.00
59_K	260_I	1.127	1.00
107_Q	111_M	1.127	1.00
131_T	182_V	1.125	1.00
150_K	153_Q	1.125	1.00
279_E	348_A	1.121	1.00
105_R	109_D	1.117	1.00
165_D	168_R	1.114	1.00
40_V	43_L	1.105	1.00
64_I	226_S	1.095	1.00
294_L	326_G	1.095	1.00
215_Y	219_Q	1.091	1.00
109_D	205_S	1.089	1.00
170_N	174_Q	1.087	1.00
261_V	327_T	1.084	1.00
96_P	220_T	1.084	1.00
281_V	348_A	1.080	1.00
133_Q	177_L	1.079	1.00
185_Q	189_Q	1.079	1.00
63_A	251_V	1.076	1.00
144_N	162_R	1.075	1.00
117_I	203_I	1.066	1.00
68_P	222_I	1.065	1.00
202_Q	205_S	1.061	1.00
228_G	252_F	1.061	1.00
38_F	42_G	1.058	1.00
198_G	202_Q	1.055	1.00
137_E	173_A	1.052	1.00
241_A	249_V	1.051	1.00
65_P	251_V	1.051	1.00
109_D	112_T	1.042	1.00
264_F	326_G	1.042	1.00
334_D	338_A	1.040	1.00
272_L	349_V	1.039	1.00
116_N	202_Q	1.038	1.00
134_V	174_Q	1.036	1.00
104_D	211_T	1.031	1.00
114_T	118_K	1.018	1.00
272_L	294_L	1.017	1.00
280_V	330_L	1.007	1.00
139_D	142_F	1.001	1.00
131_T	135_S	0.998	1.00
77_V	92_F	0.987	1.00
71_T	243_A	0.982	1.00
81_N	232_Q	0.982	1.00
233_V	236_R	0.981	1.00
281_V	289_V	0.980	1.00
77_V	237_P	0.979	1.00
143_K	165_D	0.979	1.00
79_D	250_M	0.974	1.00
92_F	249_V	0.973	1.00
173_A	177_L	0.970	1.00
224_A	227_N	0.970	1.00
232_Q	251_V	0.969	1.00
200_Q	204_V	0.966	1.00
119_T	195_M	0.964	1.00
263_Q	325_L	0.960	1.00
143_K	146_Q	0.956	1.00
254_P	257_K	0.955	1.00
112_T	202_Q	0.951	1.00
29_L	33_A	0.948	1.00
84_L	227_N	0.946	1.00
112_T	116_N	0.943	1.00
114_T	203_I	0.931	1.00
106_L	206_L	0.931	1.00
69_Q	73_I	0.930	1.00
144_N	148_Y	0.928	1.00
113_A	116_N	0.923	1.00
73_I	240_Y	0.918	1.00
62_I	254_P	0.916	1.00
80_K	233_V	0.915	1.00
298_L	325_L	0.913	1.00
264_F	349_V	0.910	1.00
68_P	241_A	0.908	1.00
108_A	208_A	0.904	1.00
43_L	46_L	0.904	1.00
57_A	260_I	0.903	1.00
273_K	276_D	0.899	1.00
203_I	207_R	0.897	1.00
37_V	41_S	0.896	1.00
27_W	31_T	0.895	1.00
183_A	186_A	0.894	1.00
101_A	215_Y	0.891	1.00
113_A	206_L	0.882	1.00
71_T	242_A	0.879	1.00
134_V	137_E	0.878	1.00
177_L	180_G	0.876	1.00
128_Q	132_T	0.876	1.00
103_V	213_A	0.872	1.00
148_Y	163_D	0.870	1.00
167_A	170_N	0.868	1.00
159_F	163_D	0.866	1.00
209_Q	212_E	0.865	1.00
102_R	106_L	0.858	1.00
260_I	347_V	0.858	1.00
137_E	140_R	0.856	1.00
97_V	215_Y	0.855	1.00
205_S	209_Q	0.855	1.00
350_Y	353_H	0.847	1.00
196_V	200_Q	0.845	1.00
109_D	113_A	0.840	1.00
269_L	324_V	0.838	1.00
213_A	216_N	0.837	1.00
92_F	250_M	0.836	1.00
102_R	213_A	0.834	1.00
180_G	184_E	0.834	1.00
233_V	250_M	0.834	1.00
85_I	91_L	0.833	1.00
139_D	172_L	0.831	1.00
354_F	357_V	0.821	1.00
168_R	171_F	0.821	1.00
280_V	345_A	0.821	1.00
263_Q	323_G	0.819	1.00
130_N	133_Q	0.818	1.00
260_I	280_V	0.818	1.00
280_V	292_G	0.817	1.00
259_Q	295_T	0.816	1.00
184_E	187_Q	0.814	1.00
96_P	221_V	0.812	1.00
43_L	47_M	0.811	1.00
106_L	109_D	0.811	1.00
215_Y	218_E	0.810	1.00
109_D	209_Q	0.807	1.00
93_K	96_P	0.802	1.00
294_L	328_I	0.802	1.00
285_L	290_F	0.801	1.00
152_S	159_F	0.788	1.00
74_V	241_A	0.786	1.00
101_A	208_A	0.782	1.00
199_E	202_Q	0.782	1.00
75_T	96_P	0.780	1.00
75_T	78_T	0.775	1.00
157_N	161_E	0.771	1.00
130_N	184_E	0.770	1.00
62_I	236_R	0.769	1.00
127_A	130_N	0.767	1.00
79_D	230_V	0.767	1.00
26_Q	30_A	0.766	1.00
182_V	186_A	0.766	1.00
130_N	180_G	0.755	1.00
71_T	240_Y	0.754	1.00
111_M	204_V	0.753	1.00
106_L	213_A	0.750	1.00
181_S	184_E	0.748	1.00
59_K	258_R	0.746	1.00
69_Q	98_R	0.743	1.00
45_L	48_N	0.741	1.00
99_Y	213_A	0.740	1.00
208_A	211_T	0.738	1.00
174_Q	177_L	0.736	1.00
206_L	210_L	0.736	1.00
234_L	251_V	0.735	1.00
206_L	209_Q	0.735	1.00
218_E	223_R	0.734	1.00
114_T	117_I	0.733	1.00
68_P	249_V	0.730	1.00
134_V	181_S	0.730	1.00
33_A	37_V	0.728	1.00
134_V	177_L	0.727	1.00
73_I	95_D	0.726	1.00
66_I	250_M	0.726	1.00
44_I	48_N	0.724	1.00
282_F	285_L	0.722	1.00
46_L	49_Y	0.720	1.00
118_K	121_R	0.716	1.00
123_Q	187_Q	0.715	1.00
133_Q	137_E	0.713	1.00
24_V	27_W	0.712	1.00
87_K	225_P	0.712	1.00
113_A	199_E	0.712	1.00
26_Q	37_V	0.709	1.00
278_A	292_G	0.709	1.00
107_Q	110_L	0.707	1.00
281_V	287_G	0.706	1.00
66_I	225_P	0.706	1.00
28_T	32_A	0.706	1.00
124_L	189_Q	0.704	1.00
54_T	346_Q	0.701	1.00
113_A	117_I	0.700	1.00
137_E	170_N	0.699	1.00
274_P	297_I	0.698	1.00
277_D	350_Y	0.695	1.00
159_F	164_I	0.694	1.00
101_A	104_D	0.692	1.00
195_M	198_G	0.685	1.00
126_E	130_N	0.684	1.00
226_S	252_F	0.683	1.00
78_T	89_E	0.682	1.00
169_Q	173_A	0.679	1.00
148_Y	162_R	0.678	1.00
79_D	83_Q	0.678	1.00
137_E	177_L	0.677	1.00
134_V	178_V	0.676	1.00
27_W	30_A	0.676	1.00
202_Q	206_L	0.675	1.00
163_D	167_A	0.675	1.00
122_A	125_T	0.674	1.00
281_V	346_Q	0.672	1.00
259_Q	329_E	0.672	1.00
120_L	124_L	0.669	1.00
140_R	166_D	0.668	1.00
302_P	325_L	0.667	1.00
97_V	218_E	0.666	1.00
181_S	185_Q	0.666	1.00
98_R	102_R	0.662	1.00
174_Q	178_V	0.659	1.00
222_I	249_V	0.658	1.00
123_Q	126_E	0.656	1.00
100_Q	103_V	0.653	1.00
286_P	290_F	0.652	1.00
26_Q	29_L	0.652	1.00
161_E	164_I	0.652	1.00
115_H	118_K	0.649	1.00
262_A	349_V	0.642	1.00
141_L	170_N	0.641	1.00
67_T	240_Y	0.640	1.00
284_A	343_I	0.639	1.00
175_D	178_V	0.638	1.00
218_E	221_V	0.638	1.00
149_L	152_S	0.636	1.00
199_E	203_I	0.633	1.00
276_D	351_S	0.632	1.00
39_L	42_G	0.630	1.00
186_A	190_S	0.628	1.00
92_F	233_V	0.625	1.00
229_Y	255_E	0.624	1.00
70_V	216_N	0.624	1.00
137_E	141_L	0.624	1.00
25_N	28_T	0.623	1.00
332_P	337_D	0.622	1.00
79_D	233_V	0.621	1.00
121_R	125_T	0.621	1.00
98_R	216_N	0.621	1.00
176_A	179_K	0.618	1.00
64_I	252_F	0.618	1.00
303_G	322_D	0.617	1.00
258_R	341_D	0.616	1.00
43_L	357_V	0.616	1.00
144_N	167_A	0.616	1.00
135_S	138_R	0.615	1.00
184_E	188_I	0.614	1.00
280_V	328_I	0.613	1.00
266_Q	344_Y	0.612	1.00
141_L	167_A	0.610	1.00
124_L	128_Q	0.610	1.00
36_G	40_V	0.609	1.00
31_T	38_F	0.607	1.00
136_A	139_D	0.605	1.00
248_P	251_V	0.605	1.00
162_R	165_D	0.604	1.00
106_L	110_L	0.604	1.00
96_P	217_L	0.603	1.00
295_T	327_T	0.601	1.00
280_V	347_V	0.599	1.00
81_N	233_V	0.597	1.00
49_Y	52_P	0.595	1.00
138_R	174_Q	0.594	1.00
68_P	71_T	0.594	1.00
129_A	132_T	0.593	1.00
324_V	343_I	0.593	1.00
25_N	29_L	0.592	1.00
216_N	219_Q	0.591	1.00
106_L	210_L	0.589	1.00
152_S	157_N	0.588	1.00
179_K	183_A	0.588	1.00
301_V	322_D	0.587	1.00
131_T	181_S	0.586	1.00
328_I	347_V	0.586	1.00
147_R	162_R	0.583	1.00
262_A	326_G	0.583	1.00
110_L	206_L	0.579	1.00
160_S	163_D	0.578	1.00
99_Y	216_N	0.577	1.00
55_F	59_K	0.577	1.00
140_R	169_Q	0.575	1.00
26_Q	41_S	0.575	1.00
98_R	219_Q	0.573	1.00
68_P	92_F	0.571	1.00
126_E	184_E	0.570	1.00
136_A	140_R	0.570	1.00
109_D	206_L	0.569	1.00
54_T	348_A	0.568	1.00
58_Q	261_V	0.567	1.00
274_P	295_T	0.566	1.00
59_K	339_L	0.566	1.00
47_M	50_N	0.564	1.00
340_P	343_I	0.562	1.00
207_R	210_L	0.562	1.00
302_P	305_S	0.561	1.00
127_A	181_S	0.560	1.00
140_R	143_K	0.554	1.00
38_F	41_S	0.554	1.00
201_S	204_V	0.552	1.00
146_Q	171_F	0.549	1.00
285_L	343_I	0.547	1.00
278_A	347_V	0.545	1.00
144_N	170_N	0.543	1.00
161_E	168_R	0.543	1.00
88_G	223_R	0.539	1.00
44_I	47_M	0.538	1.00
64_I	68_P	0.536	1.00
275_G	293_K	0.534	1.00
282_F	339_L	0.534	1.00
115_H	119_T	0.533	1.00
147_R	151_G	0.532	1.00
234_L	248_P	0.531	1.00
119_T	123_Q	0.531	1.00
177_L	181_S	0.530	1.00
74_V	77_V	0.530	1.00
209_Q	213_A	0.529	1.00
217_L	220_T	0.528	1.00
283_N	346_Q	0.527	1.00
30_A	34_L	0.527	1.00
127_A	131_T	0.527	1.00
260_I	330_L	0.527	1.00
98_R	215_Y	0.526	1.00
105_R	212_E	0.526	1.00
182_V	185_Q	0.522	1.00
137_E	174_Q	0.522	1.00
81_N	327_T	0.521	1.00
141_L	144_N	0.521	1.00
85_I	224_A	0.521	1.00
231_T	299_P	0.520	1.00
61_V	259_Q	0.517	1.00
264_F	347_V	0.516	1.00
143_K	161_E	0.514	1.00
109_D	202_Q	0.514	1.00
211_T	215_Y	0.511	1.00
104_D	208_A	0.511	1.00
77_V	233_V	0.509	1.00
263_Q	304_G	0.507	1.00
285_L	288_Q	0.507	1.00
229_Y	340_P	0.506	1.00
104_D	108_A	0.505	1.00
142_F	145_Y	0.503	1.00
99_Y	103_V	0.502	1.00
195_M	199_E	0.501	1.00
253_I	341_D	0.501	1.00
165_D	169_Q	0.500	1.00

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
4tkoB	1	0.7407	100	0.351	Contact Map
4dk0A	5	0.7593	100	0.369	Contact Map
3fppA	3	0.6958	100	0.381	Contact Map
3lnnA	6	0.7804	100	0.416	Contact Map
2f1mA	2	0.619	100	0.424	Contact Map
4l8jA	2	0.7011	100	0.449	Contact Map
1vf7A	5	0.6005	100	0.451	Contact Map
3ne5B	3	0.6958	100	0.474	Contact Map
4kkuA	1	0.537	100	0.525	Contact Map
2k32A	1	0.3042	99.8	0.693	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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