YRRI - BACSU - GREMLIN Contacts

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YRRI - UPF0118 membrane protein YrrI

UniProt:	O34472	Sequences: MLQKPVQLLLWVAICLLVLLTVYVFFMLDMLWSPFWLVIKTIFIPLIISIFISYLLLPVTEWLHGKGLPRTLSILVIYVLFFGGIGWALYKGVPVLIVQLTDLSENIPMFAETYNGLLLHVHNHTDDWPDGMHHRIDKMIRQTEAFFAGTIEGAISGIRNVLDYFLIAATIPFLVFYMVKDIELMKKTVWYLTPKSWRKRGSAFLRDVDDSLGDYIRGQLLVCLILGVIAGISFWVFGLPYPLILGLISGVTNVIPYFGPFIGAVPALLIAMTISVKAVLVVVITVFILQFMEGNILSPFIVGRSLKMHPVVIMLALLAGGELAGIVGMILAVPATAVLKVMMIHFLRMRTEH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	353 (325)
Sequences:	10950 (8503)
Seq/√Len:	471.7

ECOLI - PERM YDIK TQSA YHHT
BACSU - YRRI YUBA YUEF YTVI YDBI
HALSA - Q9HPX5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
231_G	246_G	5.231	1.00
233_S	285_T	4.874	1.00
62_W	66_K	4.439	1.00
316_A	336_T	3.143	1.00
64_H	70_R	3.070	1.00
54_Y	209_D	3.008	1.00
227_G	250_G	2.836	1.00
280_L	284_I	2.782	1.00
277_K	281_V	2.591	1.00
231_G	235_W	2.528	1.00
227_G	246_G	2.525	1.00
69_P	72_L	2.518	1.00
62_W	65_G	2.480	1.00
52_I	175_V	2.437	1.00
68_L	76_V	2.209	1.00
340_K	344_I	2.182	1.00
268_L	283_V	2.165	1.00
234_F	239_L	2.136	1.00
49_S	175_V	2.056	1.00
106_N	109_M	2.056	1.00
220_L	254_V	1.950	1.00
218_G	301_I	1.945	1.00
176_F	180_K	1.918	1.00
203_A	345_H	1.878	1.00
268_L	279_V	1.860	1.00
281_V	284_I	1.855	1.00
193_T	201_G	1.841	1.00
115_N	119_L	1.829	1.00
71_T	75_L	1.828	1.00
207_D	345_H	1.809	1.00
284_I	288_I	1.800	1.00
57_L	70_R	1.792	1.00
230_A	249_S	1.758	1.00
57_L	61_E	1.754	1.00
232_I	235_W	1.743	1.00
248_I	252_T	1.730	1.00
60_T	77_I	1.727	1.00
171_I	175_V	1.723	1.00
181_D	309_H	1.720	1.00
74_I	176_F	1.713	1.00
300_F	304_R	1.706	1.00
208_V	338_V	1.696	1.00
174_L	311_V	1.679	1.00
231_G	242_P	1.665	1.00
60_T	74_I	1.659	1.00
190_W	202_S	1.643	1.00
125_T	128_W	1.640	1.00
242_P	246_G	1.633	1.00
276_V	279_V	1.629	1.00
74_I	78_Y	1.619	1.00
37_L	40_K	1.613	1.00
235_W	242_P	1.603	1.00
226_L	253_N	1.598	1.00
59_V	77_I	1.591	1.00
240_P	274_I	1.590	1.00
71_T	180_K	1.588	1.00
229_I	289_L	1.587	1.00
174_L	178_M	1.584	1.00
278_A	281_V	1.582	1.00
60_T	70_R	1.577	1.00
271_A	282_V	1.575	1.00
23_Y	27_M	1.574	1.00
321_G	329_M	1.556	1.00
131_G	134_H	1.555	1.00
46_L	315_L	1.545	1.00
117_L	120_H	1.538	1.00
86_G	90_Y	1.533	1.00
134_H	138_K	1.530	1.00
276_V	280_L	1.495	1.00
230_A	289_L	1.493	1.00
252_T	263_G	1.482	1.00
63_L	80_L	1.472	1.00
187_K	191_Y	1.471	1.00
297_L	301_I	1.459	1.00
138_K	141_R	1.435	1.00
101_T	105_E	1.425	1.00
116_G	120_H	1.401	1.00
277_K	280_L	1.400	1.00
120_H	124_H	1.390	1.00
264_A	268_L	1.385	1.00
30_M	34_P	1.383	1.00
119_L	122_H	1.357	1.00
68_L	72_L	1.351	1.00
271_A	279_V	1.346	1.00
130_D	134_H	1.342	1.00
113_T	116_G	1.340	1.00
222_V	293_E	1.335	1.00
56_L	179_V	1.326	1.00
292_M	297_L	1.307	1.00
194_P	198_R	1.298	1.00
245_L	267_A	1.297	1.00
283_V	287_F	1.296	1.00
267_A	282_V	1.285	1.00
93_V	97_I	1.274	1.00
49_S	171_I	1.274	1.00
290_Q	294_G	1.266	1.00
317_L	329_M	1.252	1.00
233_S	237_F	1.247	1.00
117_L	121_V	1.247	1.00
211_S	337_A	1.242	1.00
71_T	176_F	1.241	1.00
82_F	86_G	1.239	1.00
60_T	179_V	1.238	1.00
56_L	81_F	1.235	1.00
133_H	137_D	1.233	1.00
109_M	112_E	1.231	1.00
312_V	336_T	1.230	1.00
223_C	253_N	1.216	1.00
287_F	291_F	1.216	1.00
136_I	139_M	1.215	1.00
132_M	135_R	1.214	1.00
186_K	190_W	1.209	1.00
75_L	79_V	1.207	1.00
57_L	182_I	1.200	1.00
45_P	49_S	1.199	1.00
316_A	320_G	1.194	1.00
112_E	115_N	1.191	1.00
108_P	112_E	1.190	1.00
226_L	289_L	1.187	1.00
131_G	135_R	1.187	1.00
60_T	73_S	1.180	1.00
246_G	250_G	1.172	1.00
281_V	285_T	1.171	1.00
320_G	324_A	1.161	1.00
181_D	184_L	1.161	1.00
68_L	73_S	1.157	1.00
73_S	77_I	1.156	1.00
29_D	33_S	1.155	1.00
129_P	133_H	1.153	1.00
142_Q	145_A	1.152	1.00
104_S	108_P	1.151	1.00
59_V	62_W	1.151	1.00
239_L	271_A	1.148	1.00
188_T	191_Y	1.147	1.00
232_I	236_V	1.145	1.00
52_I	171_I	1.144	1.00
26_F	30_M	1.142	1.00
109_M	113_T	1.137	1.00
237_F	282_V	1.132	1.00
70_R	183_E	1.129	1.00
134_H	137_D	1.129	1.00
118_L	122_H	1.128	1.00
294_G	298_S	1.125	1.00
207_D	344_I	1.113	1.00
204_F	342_M	1.112	1.00
217_R	221_L	1.111	1.00
46_L	174_L	1.110	1.00
60_T	64_H	1.109	1.00
222_V	226_L	1.107	1.00
234_F	249_S	1.102	1.00
53_S	178_M	1.067	1.00
226_L	230_A	1.065	1.00
130_D	133_H	1.061	1.00
327_V	331_L	1.061	1.00
320_G	336_T	1.061	1.00
64_H	73_S	1.059	1.00
33_S	37_L	1.052	1.00
48_I	171_I	1.052	1.00
285_T	289_L	1.049	1.00
135_R	138_K	1.049	1.00
231_G	243_L	1.043	1.00
214_D	218_G	1.042	1.00
227_G	231_G	1.039	1.00
339_L	343_M	1.038	1.00
50_I	178_M	1.037	1.00
296_I	300_F	1.037	1.00
220_L	224_L	1.034	1.00
24_V	28_L	1.032	1.00
222_V	297_L	1.031	1.00
219_Q	298_S	1.029	1.00
164_Y	168_A	1.021	1.00
170_T	174_L	1.019	1.00
174_L	315_L	1.017	1.00
233_S	289_L	1.015	1.00
190_W	198_R	1.012	1.00
138_K	142_Q	1.009	1.00
72_L	75_L	1.005	1.00
49_S	53_S	1.004	1.00
226_L	260_P	1.003	1.00
117_L	122_H	1.002	1.00
272_M	279_V	1.002	1.00
63_L	77_I	1.002	1.00
34_P	38_V	0.990	1.00
78_Y	175_V	0.990	1.00
154_A	158_I	0.988	1.00
139_M	142_Q	0.980	1.00
224_L	250_G	0.973	1.00
312_V	340_K	0.967	1.00
228_V	232_I	0.967	1.00
214_D	305_S	0.963	1.00
250_G	254_V	0.959	1.00
137_D	141_R	0.959	1.00
146_F	150_T	0.956	1.00
141_R	145_A	0.955	1.00
293_E	298_S	0.954	1.00
237_F	278_A	0.952	1.00
316_A	332_A	0.950	1.00
157_G	161_V	0.947	1.00
270_I	274_I	0.945	1.00
203_A	207_D	0.943	1.00
35_F	39_I	0.942	1.00
116_G	119_L	0.942	1.00
221_L	225_I	0.939	1.00
97_I	100_L	0.937	1.00
222_V	298_S	0.937	1.00
237_F	285_T	0.935	1.00
143_T	146_F	0.933	1.00
42_I	319_A	0.930	1.00
145_A	148_A	0.930	1.00
147_F	151_I	0.918	1.00
225_I	229_I	0.915	1.00
234_F	282_V	0.913	1.00
288_I	292_M	0.911	1.00
234_F	245_L	0.910	1.00
49_S	174_L	0.908	1.00
332_A	336_T	0.905	1.00
182_I	186_K	0.901	1.00
248_I	263_G	0.901	1.00
90_Y	94_P	0.900	1.00
61_E	64_H	0.899	1.00
246_G	249_S	0.899	1.00
253_N	260_P	0.899	1.00
275_S	278_A	0.897	1.00
124_H	127_D	0.897	1.00
101_T	104_S	0.895	1.00
118_L	124_H	0.894	1.00
290_Q	293_E	0.894	1.00
292_M	296_I	0.890	1.00
262_I	266_P	0.886	1.00
241_Y	244_I	0.886	1.00
222_V	253_N	0.882	1.00
102_D	105_E	0.875	1.00
228_V	231_G	0.868	1.00
56_L	77_I	0.868	1.00
98_V	102_D	0.866	1.00
150_T	153_G	0.863	1.00
61_E	65_G	0.856	1.00
113_T	117_L	0.852	1.00
147_F	150_T	0.847	1.00
32_W	35_F	0.843	1.00
342_M	346_F	0.841	1.00
279_V	283_V	0.839	1.00
107_I	111_A	0.834	1.00
291_F	295_N	0.832	1.00
282_V	286_V	0.831	1.00
204_F	345_H	0.827	1.00
302_V	313_I	0.826	1.00
233_S	281_V	0.826	1.00
315_L	319_A	0.818	1.00
230_A	234_F	0.817	1.00
122_H	125_T	0.817	1.00
245_L	270_I	0.816	1.00
188_T	192_L	0.815	1.00
89_L	93_V	0.814	1.00
106_N	110_F	0.814	1.00
121_V	124_H	0.810	1.00
112_E	116_G	0.808	1.00
61_E	183_E	0.807	1.00
210_D	214_D	0.806	1.00
308_M	336_T	0.805	1.00
235_W	238_G	0.804	1.00
141_R	144_E	0.803	1.00
84_G	88_A	0.802	1.00
226_L	298_S	0.799	1.00
124_H	128_W	0.797	1.00
63_L	68_L	0.797	1.00
224_L	228_V	0.796	1.00
235_W	246_G	0.791	1.00
223_C	254_V	0.790	1.00
272_M	276_V	0.789	1.00
253_N	298_S	0.787	1.00
46_L	178_M	0.787	1.00
119_L	123_N	0.782	1.00
303_G	313_I	0.780	1.00
200_R	345_H	0.779	1.00
223_C	227_G	0.775	1.00
140_I	144_E	0.773	1.00
184_L	187_K	0.769	1.00
121_V	125_T	0.769	1.00
249_S	286_V	0.768	1.00
269_L	273_T	0.765	1.00
298_S	302_V	0.763	1.00
137_D	140_I	0.760	1.00
222_V	302_V	0.760	1.00
53_S	175_V	0.759	1.00
158_I	162_L	0.758	1.00
62_W	67_G	0.757	1.00
122_H	126_D	0.753	1.00
207_D	341_V	0.750	1.00
175_V	179_V	0.750	1.00
119_L	125_T	0.747	1.00
225_I	297_L	0.744	1.00
160_N	163_D	0.742	1.00
22_V	26_F	0.741	1.00
163_D	167_I	0.734	1.00
221_L	301_I	0.732	1.00
114_Y	117_L	0.732	1.00
249_S	253_N	0.730	1.00
200_R	203_A	0.730	1.00
190_W	193_T	0.730	1.00
100_L	104_S	0.729	1.00
193_T	197_W	0.729	1.00
102_D	106_N	0.723	1.00
56_L	59_V	0.723	1.00
69_P	73_S	0.721	1.00
184_L	188_T	0.718	1.00
96_L	100_L	0.716	1.00
30_M	33_S	0.715	1.00
268_L	272_M	0.714	1.00
219_Q	253_N	0.713	1.00
310_P	314_M	0.712	1.00
80_L	83_G	0.712	1.00
306_L	333_V	0.710	1.00
194_P	197_W	0.710	1.00
227_G	243_L	0.709	1.00
120_H	123_N	0.708	1.00
95_V	98_V	0.707	1.00
199_K	203_A	0.705	1.00
320_G	335_A	0.704	1.00
78_Y	176_F	0.703	1.00
142_Q	146_F	0.702	1.00
263_G	267_A	0.699	1.00
145_A	149_G	0.698	1.00
84_G	87_W	0.697	1.00
34_P	37_L	0.693	1.00
211_S	214_D	0.692	1.00
63_L	73_S	0.692	1.00
198_R	202_S	0.686	1.00
298_S	301_I	0.686	1.00
207_D	211_S	0.686	1.00
201_G	205_L	0.685	1.00
219_Q	223_C	0.685	1.00
91_K	95_V	0.684	1.00
151_I	154_A	0.684	1.00
48_I	52_I	0.683	1.00
249_S	263_G	0.682	1.00
208_V	341_V	0.681	1.00
118_L	123_N	0.680	1.00
53_S	57_L	0.679	1.00
166_L	170_T	0.675	1.00
202_S	206_R	0.675	1.00
57_L	179_V	0.671	1.00
45_P	303_G	0.670	1.00
23_Y	28_L	0.670	1.00
213_G	217_R	0.668	1.00
223_C	226_L	0.667	1.00
223_C	250_G	0.665	1.00
130_D	135_R	0.663	1.00
257_Y	310_P	0.662	1.00
87_W	91_K	0.661	1.00
336_T	340_K	0.658	1.00
222_V	301_I	0.657	1.00
226_L	290_Q	0.657	1.00
139_M	143_T	0.655	1.00
63_L	76_V	0.654	1.00
239_L	274_I	0.653	1.00
27_M	30_M	0.651	1.00
77_I	81_F	0.649	1.00
212_L	215_Y	0.648	1.00
291_F	294_G	0.648	1.00
28_L	32_W	0.648	1.00
187_K	202_S	0.647	1.00
64_H	69_P	0.645	1.00
260_P	263_G	0.644	1.00
56_L	175_V	0.644	1.00
226_L	293_E	0.643	1.00
148_A	152_E	0.643	1.00
144_E	148_A	0.643	1.00
263_G	290_Q	0.640	1.00
155_I	159_R	0.639	1.00
230_A	246_G	0.639	1.00
45_P	167_I	0.636	1.00
136_I	140_I	0.635	1.00
313_I	333_V	0.635	1.00
227_G	247_L	0.631	1.00
219_Q	222_V	0.629	0.99
317_L	333_V	0.626	0.99
92_G	96_L	0.623	0.99
229_I	233_S	0.622	0.99
248_I	266_P	0.621	0.99
240_P	243_L	0.617	0.99
221_L	224_L	0.616	0.99
149_G	152_E	0.615	0.99
237_F	281_V	0.614	0.99
114_Y	118_L	0.613	0.99
33_S	36_W	0.612	0.99
53_S	179_V	0.612	0.99
249_S	260_P	0.612	0.99
326_I	329_M	0.612	0.99
207_D	210_D	0.609	0.99
105_E	109_M	0.608	0.99
204_F	208_V	0.607	0.99
140_I	143_T	0.607	0.99
297_L	300_F	0.606	0.99
264_A	286_V	0.604	0.99
123_N	126_D	0.602	0.99
97_I	101_T	0.601	0.99
74_I	180_K	0.600	0.99
214_D	217_R	0.599	0.99
160_N	164_Y	0.595	0.99
94_P	334_P	0.594	0.99
170_T	318_L	0.592	0.99
187_K	190_W	0.591	0.99
32_W	36_W	0.590	0.99
230_A	250_G	0.590	0.99
264_A	287_F	0.588	0.99
250_G	257_Y	0.587	0.99
274_I	278_A	0.587	0.99
222_V	260_P	0.587	0.99
178_M	311_V	0.584	0.99
153_G	157_G	0.584	0.99
95_V	99_Q	0.583	0.99
135_R	139_M	0.583	0.99
105_E	108_P	0.583	0.99
86_G	89_L	0.581	0.99
174_L	318_L	0.579	0.99
64_H	67_G	0.579	0.99
188_T	312_V	0.579	0.99
38_V	41_T	0.578	0.99
219_Q	254_V	0.577	0.99
70_R	74_I	0.576	0.99
263_G	333_V	0.574	0.99
85_I	89_L	0.573	0.99
99_Q	102_D	0.573	0.99
107_I	110_F	0.573	0.99
218_G	337_A	0.571	0.99
208_V	212_L	0.571	0.99
215_Y	334_P	0.571	0.99
151_I	155_I	0.568	0.99
129_P	135_R	0.568	0.99
253_N	293_E	0.568	0.99
309_H	340_K	0.567	0.99
219_Q	293_E	0.566	0.99
260_P	290_Q	0.563	0.99
295_N	318_L	0.563	0.99
226_L	229_I	0.559	0.99
164_Y	167_I	0.556	0.99
237_F	289_L	0.555	0.99
25_F	29_D	0.555	0.99
230_A	285_T	0.555	0.99
324_A	328_G	0.554	0.99
45_P	54_Y	0.553	0.99
30_M	37_L	0.553	0.99
288_I	291_F	0.549	0.99
265_V	269_L	0.548	0.99
27_M	31_L	0.547	0.99
168_A	172_P	0.547	0.99
304_R	307_K	0.547	0.99
303_G	307_K	0.546	0.99
235_W	243_L	0.545	0.99
206_R	210_D	0.545	0.99
102_D	241_Y	0.542	0.99
35_F	339_L	0.540	0.98
156_S	159_R	0.537	0.98
300_F	307_K	0.537	0.98
308_M	313_I	0.537	0.98
35_F	38_V	0.534	0.98
226_L	250_G	0.533	0.98
56_L	60_T	0.531	0.98
218_G	305_S	0.530	0.98
79_V	83_G	0.529	0.98
227_G	264_A	0.528	0.98
219_Q	297_L	0.527	0.98
250_G	253_N	0.525	0.98
239_L	242_P	0.524	0.98
177_Y	181_D	0.524	0.98
261_F	264_A	0.521	0.98
321_G	334_P	0.520	0.98
263_G	330_I	0.519	0.98
198_R	201_G	0.518	0.98
217_R	305_S	0.517	0.98
146_F	149_G	0.517	0.98
243_L	246_G	0.517	0.98
162_L	166_L	0.516	0.98
275_S	279_V	0.515	0.98
211_S	341_V	0.515	0.98
161_V	165_F	0.515	0.98
253_N	290_Q	0.511	0.98
230_A	233_S	0.511	0.98
284_I	287_F	0.510	0.98
300_F	303_G	0.509	0.98
263_G	334_P	0.507	0.98
253_N	263_G	0.504	0.98
23_Y	26_F	0.504	0.98
149_G	153_G	0.503	0.98
320_G	332_A	0.503	0.98
31_L	34_P	0.502	0.98
148_A	151_I	0.500	0.98

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
3tx3A	2	0.5609	25	0.953	Contact Map
4b19A	1	0.085	16.3	0.957	Contact Map
2kv5A	1	0.0878	15.7	0.957	Contact Map
4lz6A	1	0.898	11.8	0.96	Contact Map
3bz1X	1	0.1048	11.3	0.96	Contact Map
4tkrA	2	0.3059	9.4	0.961	Contact Map
3mktA	1	0.9773	7.8	0.963	Contact Map
3rlbA	1	0.3286	6.6	0.964	Contact Map
4bgnA	3	0.2805	6.5	0.964	Contact Map
3w4tA	1	0.8895	6.3	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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