YUEF - BACSU - GREMLIN Contacts

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YUEF - UPF0118 membrane protein YueF

UniProt:	O32095	Sequences: MLKSKVHFWTLQILFVLLIIFVATKVSFVFQPFIVFISTLFFPMLIAGILYFIFNPVVRLLEKKIPRTLSILLIYLLFIGLLAFISASVGPIITAQVTGLFNNLPDYIKQIQALTKDLSHSQWFTWMMNQDYVSISKIEQSLTSFLQNLPQNITSSLSAVFGVVTNITLVIITVPFILFYMLKDGHRFPHLAVKILPASYRTEGLKIFKDLSDTLAAYFQGQLLICLFVGTACFIGYLIAGLPYALILGIVMAITNIIPYVGPFLGAAPAVIVGFMDSPAKALFAIIVVVIVQQLDGNLLSPLVIGKRLNTHPLTIILLLIGAGSFGGILGMILAVPVYAVVKAFFLNIVRLIKLRQRSRLEENAKPAE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	369 (325)
Sequences:	10931 (8499)
Seq/√Len:	471.5

ECOLI - YDIK PERM YHHT TQSA
BACSU - YUEF YUBA YTVI YRRI 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
234_F	249_G	5.159	1.00
236_G	288_V	4.977	1.00
319_L	339_Y	3.257	1.00
62_E	67_R	3.090	1.00
283_L	287_I	2.922	1.00
52_F	212_S	2.912	1.00
230_G	253_A	2.859	1.00
66_P	69_L	2.810	1.00
280_A	284_F	2.711	1.00
234_F	238_L	2.611	1.00
230_G	249_G	2.552	1.00
50_L	178_L	2.424	1.00
103_N	106_D	2.340	1.00
343_K	347_L	2.255	1.00
65_I	73_L	2.241	1.00
60_L	63_K	2.230	1.00
271_V	286_I	2.193	1.00
21_F	25_K	1.980	1.00
55_N	59_R	1.980	1.00
237_Y	242_L	1.975	1.00
210_D	348_N	1.937	1.00
206_K	348_N	1.934	1.00
47_A	178_L	1.909	1.00
223_L	257_I	1.897	1.00
174_V	178_L	1.874	1.00
134_S	137_K	1.858	1.00
114_L	117_D	1.858	1.00
221_G	304_V	1.840	1.00
245_A	249_G	1.804	1.00
233_C	252_M	1.802	1.00
284_F	287_I	1.800	1.00
179_F	183_K	1.798	1.00
251_V	255_T	1.793	1.00
58_V	74_I	1.792	1.00
68_T	72_L	1.761	1.00
211_L	341_V	1.746	1.00
193_V	205_L	1.743	1.00
55_N	67_R	1.739	1.00
271_V	282_A	1.735	1.00
71_I	75_Y	1.731	1.00
58_V	71_I	1.679	1.00
57_V	74_I	1.673	1.00
68_T	183_K	1.661	1.00
303_L	307_K	1.659	1.00
235_I	238_L	1.654	1.00
71_I	179_F	1.651	1.00
141_S	144_S	1.645	1.00
58_V	67_R	1.644	1.00
61_L	77_L	1.630	1.00
35_V	38_S	1.627	1.00
83_A	87_A	1.625	1.00
196_L	204_G	1.621	1.00
238_L	245_A	1.618	1.00
287_I	291_I	1.609	1.00
177_I	314_L	1.608	1.00
184_D	312_H	1.608	1.00
28_F	32_P	1.602	1.00
113_A	117_D	1.597	1.00
234_F	245_A	1.588	1.00
98_T	102_N	1.580	1.00
274_G	285_A	1.580	1.00
112_Q	116_K	1.577	1.00
44_M	318_L	1.569	1.00
324_G	332_M	1.546	1.00
281_K	284_F	1.526	1.00
243_P	277_D	1.515	1.00
177_I	181_M	1.513	1.00
300_L	304_V	1.513	1.00
143_T	147_Q	1.510	1.00
229_V	256_N	1.507	1.00
113_A	116_K	1.506	1.00
116_K	119_S	1.502	1.00
135_I	138_I	1.485	1.00
109_K	112_Q	1.474	1.00
233_C	292_V	1.473	1.00
137_K	140_Q	1.467	1.00
290_V	294_Q	1.461	1.00
255_T	266_G	1.459	1.00
295_L	300_L	1.432	1.00
132_Y	136_S	1.426	1.00
267_A	271_V	1.405	1.00
54_F	182_L	1.393	1.00
149_L	153_I	1.387	1.00
236_G	240_A	1.384	1.00
130_Q	134_S	1.375	1.00
114_L	118_L	1.371	1.00
274_G	282_A	1.363	1.00
137_K	141_S	1.362	1.00
140_Q	143_T	1.360	1.00
280_A	283_L	1.356	1.00
286_I	290_V	1.340	1.00
106_D	110_Q	1.326	1.00
214_T	340_A	1.324	1.00
115_T	119_S	1.322	1.00
232_A	292_V	1.306	1.00
117_D	121_S	1.304	1.00
144_S	148_N	1.278	1.00
248_L	270_A	1.273	1.00
320_L	332_M	1.262	1.00
90_G	94_T	1.255	1.00
235_I	239_I	1.249	1.00
284_F	288_V	1.248	1.00
54_F	78_F	1.236	1.00
106_D	109_K	1.236	1.00
105_P	109_K	1.236	1.00
242_L	274_G	1.235	1.00
47_A	174_V	1.234	1.00
101_F	105_P	1.230	1.00
57_V	60_L	1.229	1.00
79_I	83_A	1.223	1.00
270_A	285_A	1.221	1.00
116_K	120_H	1.218	1.00
43_P	47_A	1.211	1.00
184_D	187_R	1.208	1.00
145_F	148_N	1.207	1.00
27_S	31_Q	1.206	1.00
190_H	194_K	1.206	1.00
139_E	142_L	1.203	1.00
65_I	70_S	1.203	1.00
32_P	36_F	1.201	1.00
58_V	70_S	1.199	1.00
55_N	185_G	1.198	1.00
118_L	121_S	1.193	1.00
293_Q	297_G	1.192	1.00
240_A	285_A	1.189	1.00
157_L	161_F	1.187	1.00
114_L	119_S	1.184	1.00
210_D	347_L	1.183	1.00
110_Q	113_A	1.181	1.00
225_I	296_D	1.175	1.00
220_Q	224_L	1.169	1.00
207_I	345_F	1.161	1.00
58_V	62_E	1.160	1.00
68_T	179_F	1.158	1.00
50_L	174_V	1.153	1.00
229_V	292_V	1.151	1.00
67_R	186_H	1.146	1.00
191_L	194_K	1.145	1.00
315_T	339_Y	1.143	1.00
24_T	28_F	1.136	1.00
133_V	137_K	1.134	1.00
58_V	182_L	1.131	1.00
103_N	107_Y	1.131	1.00
48_G	181_M	1.128	1.00
319_L	323_A	1.122	1.00
51_Y	181_M	1.118	1.00
69_L	72_L	1.116	1.00
249_G	253_A	1.115	1.00
65_I	69_L	1.108	1.00
134_S	138_I	1.107	1.00
185_G	189_P	1.101	1.00
187_R	190_H	1.100	1.00
46_I	174_V	1.100	1.00
72_L	76_L	1.094	1.00
291_I	295_L	1.090	1.00
70_S	74_I	1.085	1.00
323_A	327_G	1.081	1.00
117_D	120_H	1.080	1.00
275_F	282_A	1.075	1.00
121_S	124_F	1.071	1.00
223_L	227_L	1.065	1.00
197_P	201_R	1.063	1.00
95_A	99_G	1.062	1.00
44_M	177_I	1.056	1.00
62_E	70_S	1.053	1.00
234_F	246_L	1.048	1.00
330_L	334_L	1.045	1.00
177_I	318_L	1.036	1.00
161_F	165_T	1.032	1.00
47_A	51_Y	1.030	1.00
226_C	256_N	1.027	1.00
297_G	301_S	1.024	1.00
323_A	339_Y	1.023	1.00
133_V	136_S	1.019	1.00
295_L	299_L	1.019	1.00
206_K	210_D	1.017	1.00
99_G	102_N	1.017	1.00
222_Q	301_S	1.009	1.00
224_L	228_F	1.009	1.00
237_Y	248_L	1.009	1.00
288_V	292_V	1.007	1.00
319_L	335_A	1.007	1.00
299_L	303_L	1.001	1.00
31_Q	35_V	0.999	1.00
227_L	253_A	0.998	1.00
33_F	37_I	0.992	1.00
135_I	139_E	0.990	1.00
230_G	234_F	0.988	1.00
87_A	91_P	0.987	1.00
253_A	257_I	0.986	1.00
60_L	64_K	0.985	1.00
173_T	177_I	0.982	1.00
229_V	263_P	0.974	1.00
229_V	233_C	0.968	1.00
94_T	97_V	0.967	1.00
136_S	140_Q	0.966	1.00
136_S	139_E	0.964	1.00
75_Y	178_L	0.963	1.00
315_T	343_K	0.962	1.00
187_R	191_L	0.962	1.00
40_L	322_G	0.960	1.00
225_I	229_V	0.959	1.00
251_V	266_G	0.957	1.00
59_R	62_E	0.951	1.00
61_L	74_I	0.948	1.00
134_S	139_E	0.946	1.00
110_Q	114_L	0.945	1.00
240_A	281_K	0.941	1.00
342_V	346_F	0.939	1.00
47_A	177_I	0.936	1.00
231_T	235_I	0.935	1.00
98_T	101_F	0.935	1.00
148_N	151_Q	0.932	1.00
217_A	221_G	0.928	1.00
22_V	26_V	0.926	1.00
237_Y	252_M	0.926	1.00
141_S	145_F	0.926	1.00
202_T	206_K	0.923	1.00
189_P	193_V	0.923	1.00
225_I	300_L	0.919	1.00
160_V	164_V	0.917	1.00
92_I	95_A	0.913	1.00
130_Q	133_V	0.912	1.00
213_D	217_A	0.910	1.00
237_Y	285_A	0.908	1.00
146_L	149_L	0.904	1.00
150_P	154_T	0.899	1.00
236_G	292_V	0.897	1.00
244_Y	247_I	0.894	1.00
193_V	201_R	0.893	1.00
167_I	171_I	0.892	1.00
228_F	232_A	0.885	1.00
273_V	277_D	0.883	1.00
30_F	33_F	0.882	1.00
231_T	234_F	0.879	1.00
282_A	286_I	0.877	1.00
217_A	308_R	0.872	1.00
265_L	269_P	0.871	1.00
225_I	301_S	0.871	1.00
207_I	348_N	0.868	1.00
142_L	145_F	0.866	1.00
99_G	103_N	0.859	1.00
140_Q	144_S	0.854	1.00
335_A	339_Y	0.850	1.00
249_G	252_M	0.848	1.00
153_I	157_L	0.847	1.00
104_L	108_I	0.847	1.00
305_I	316_I	0.843	1.00
228_F	300_L	0.841	1.00
119_S	125_T	0.833	1.00
345_F	349_I	0.833	1.00
115_T	121_S	0.832	1.00
318_L	322_G	0.832	1.00
131_D	135_I	0.829	1.00
61_L	70_S	0.829	1.00
32_P	35_V	0.829	1.00
238_L	241_G	0.816	1.00
294_Q	298_N	0.816	1.00
20_I	24_T	0.810	1.00
96_Q	99_G	0.805	1.00
227_L	231_T	0.801	1.00
256_N	263_P	0.801	1.00
229_V	301_S	0.794	1.00
54_F	74_I	0.791	1.00
248_L	273_V	0.790	1.00
252_M	266_G	0.786	1.00
148_N	152_N	0.785	1.00
296_D	301_S	0.785	1.00
233_C	237_Y	0.785	1.00
226_C	257_I	0.780	1.00
226_C	230_G	0.778	1.00
252_M	289_V	0.774	1.00
275_F	279_P	0.771	1.00
279_P	282_A	0.770	1.00
236_G	284_F	0.768	1.00
191_L	195_I	0.765	1.00
107_Y	111_I	0.763	1.00
271_V	275_F	0.762	1.00
205_L	209_K	0.757	1.00
156_S	160_V	0.757	1.00
240_A	288_V	0.753	1.00
238_L	249_G	0.752	1.00
44_M	181_M	0.751	1.00
216_A	220_Q	0.749	1.00
24_T	27_S	0.746	1.00
163_V	166_N	0.746	1.00
86_S	90_G	0.745	1.00
153_I	156_S	0.745	1.00
152_N	155_S	0.744	1.00
102_N	106_D	0.744	1.00
178_L	182_L	0.743	1.00
225_I	256_N	0.743	1.00
55_N	182_L	0.743	1.00
144_S	147_Q	0.742	1.00
20_I	23_A	0.741	1.00
210_D	344_A	0.733	1.00
307_K	310_N	0.733	1.00
84_F	88_S	0.728	1.00
59_R	63_K	0.723	1.00
149_L	152_N	0.722	1.00
210_D	214_T	0.719	1.00
272_I	276_M	0.718	1.00
214_T	217_A	0.717	1.00
81_L	85_I	0.716	1.00
51_Y	178_L	0.714	1.00
204_G	208_F	0.713	1.00
293_Q	296_D	0.712	1.00
104_L	107_Y	0.710	1.00
301_S	305_I	0.709	1.00
276_M	279_P	0.708	1.00
266_G	270_A	0.708	1.00
278_S	281_K	0.708	1.00
115_T	118_L	0.706	1.00
152_N	156_S	0.703	1.00
28_F	31_Q	0.703	1.00
207_I	211_L	0.700	1.00
233_C	249_G	0.695	1.00
313_P	317_I	0.691	1.00
252_M	256_N	0.690	1.00
197_P	200_Y	0.690	1.00
92_I	96_Q	0.689	1.00
46_I	50_L	0.683	1.00
61_L	73_L	0.683	1.00
203_E	206_K	0.683	1.00
51_Y	55_N	0.682	1.00
224_L	304_V	0.681	1.00
154_T	157_L	0.680	1.00
306_G	316_I	0.679	1.00
61_L	65_I	0.679	1.00
62_E	66_P	0.679	1.00
311_T	339_Y	0.678	1.00
224_L	227_L	0.678	1.00
111_I	114_L	0.676	1.00
230_G	250_I	0.675	1.00
211_L	344_A	0.675	1.00
102_N	105_P	0.675	1.00
138_I	141_S	0.674	1.00
163_V	167_I	0.673	1.00
25_K	28_F	0.673	1.00
291_I	294_Q	0.672	1.00
316_I	336_V	0.671	1.00
54_F	57_V	0.670	1.00
323_A	338_V	0.667	1.00
93_I	97_V	0.666	1.00
147_Q	151_Q	0.664	1.00
203_E	348_N	0.660	1.00
145_F	149_L	0.658	1.00
139_E	143_T	0.657	1.00
329_I	332_M	0.657	1.00
66_P	70_S	0.656	1.00
21_F	26_V	0.655	1.00
225_I	305_I	0.650	1.00
267_A	289_V	0.649	1.00
230_G	246_L	0.646	1.00
132_Y	135_I	0.645	1.00
88_S	92_I	0.641	1.00
189_P	209_K	0.641	1.00
217_A	220_Q	0.639	1.00
59_R	186_H	0.637	1.00
25_K	29_V	0.637	1.00
54_F	178_L	0.633	1.00
151_Q	155_S	0.632	1.00
167_I	170_V	0.631	1.00
125_T	134_S	0.630	1.00
158_S	162_G	0.627	0.99
166_N	170_V	0.626	0.99
210_D	213_D	0.624	0.99
198_A	201_R	0.624	0.99
81_L	84_F	0.623	0.99
97_V	105_P	0.618	0.99
242_L	245_A	0.618	0.99
256_N	301_S	0.616	0.99
309_L	336_V	0.613	0.99
200_Y	204_G	0.613	0.99
303_L	306_G	0.612	0.99
97_V	101_F	0.610	0.99
240_A	284_F	0.607	0.99
294_Q	297_G	0.605	0.99
23_A	27_S	0.605	0.99
190_H	193_V	0.604	0.99
171_I	175_P	0.603	0.99
339_Y	343_K	0.600	0.99
327_G	331_G	0.600	0.99
311_T	316_I	0.599	0.99
226_C	229_V	0.598	0.99
191_L	315_T	0.597	0.99
80_G	83_A	0.597	0.99
232_A	236_G	0.596	0.99
260_Y	313_P	0.595	0.99
277_D	281_K	0.594	0.99
111_I	115_T	0.594	0.99
150_P	153_I	0.593	0.99
154_T	158_S	0.593	0.99
301_S	304_V	0.592	0.99
158_S	161_F	0.591	0.99
229_V	293_Q	0.590	0.99
220_Q	308_R	0.588	0.99
26_V	30_F	0.586	0.99
82_L	86_S	0.584	0.99
75_Y	179_F	0.582	0.99
287_I	290_V	0.581	0.99
51_Y	182_L	0.580	0.99
196_L	200_Y	0.580	0.99
222_Q	256_N	0.579	0.99
36_F	39_T	0.579	0.99
251_V	269_P	0.577	0.99
181_M	314_L	0.577	0.99
306_G	310_N	0.576	0.99
169_L	173_T	0.574	0.99
346_F	350_V	0.574	0.99
317_I	321_I	0.574	0.99
225_I	306_G	0.574	0.99
240_A	292_V	0.573	0.99
21_F	24_T	0.573	0.99
93_I	247_I	0.573	0.99
139_E	145_F	0.572	0.99
94_T	98_T	0.571	0.99
173_T	321_I	0.570	0.99
300_L	303_L	0.567	0.99
180_Y	184_D	0.567	0.99
89_V	93_I	0.563	0.99
243_P	246_L	0.563	0.99
166_N	298_N	0.563	0.99
43_P	170_V	0.561	0.99
190_H	205_L	0.561	0.99
30_F	34_I	0.561	0.99
263_P	266_G	0.560	0.99
222_Q	226_C	0.560	0.99
143_T	146_L	0.559	0.99
275_F	278_S	0.558	0.99
252_M	263_P	0.555	0.99
267_A	282_A	0.555	0.99
77_L	80_G	0.555	0.99
188_F	191_L	0.554	0.99
93_I	96_Q	0.554	0.99
225_I	263_P	0.553	0.99
53_I	219_F	0.551	0.99
209_K	213_D	0.550	0.99
215_L	218_Y	0.548	0.99
71_I	183_K	0.547	0.99
195_I	346_F	0.547	0.99
160_V	163_V	0.547	0.99
320_L	336_V	0.546	0.99
135_I	141_S	0.544	0.99
221_G	340_A	0.543	0.99
161_F	164_V	0.542	0.99
229_V	296_D	0.542	0.99
22_V	25_K	0.542	0.99
285_A	289_V	0.539	0.98
83_A	86_S	0.539	0.98
211_L	214_T	0.536	0.98
256_N	296_D	0.536	0.98
115_T	120_H	0.536	0.98
109_K	113_A	0.535	0.98
226_C	253_A	0.535	0.98
177_I	321_I	0.534	0.98
124_F	131_D	0.534	0.98
42_F	45_L	0.533	0.98
266_G	336_V	0.532	0.98
225_I	304_V	0.531	0.98
253_A	260_Y	0.531	0.98
33_F	342_V	0.531	0.98
267_A	290_V	0.530	0.98
221_G	308_R	0.529	0.98
229_V	232_A	0.528	0.98
193_V	196_L	0.528	0.98
214_T	344_A	0.527	0.98
228_F	296_D	0.523	0.98
303_L	310_N	0.523	0.98
269_P	272_I	0.523	0.98
133_V	138_I	0.521	0.98
192_A	195_I	0.521	0.98
263_P	293_Q	0.519	0.98
222_Q	257_I	0.518	0.98
29_V	32_P	0.517	0.98
54_F	58_V	0.516	0.98
131_D	134_S	0.516	0.98
222_Q	225_I	0.515	0.98
48_G	185_G	0.513	0.98
242_L	277_D	0.511	0.98
344_A	348_N	0.510	0.98
111_I	118_L	0.506	0.98
285_A	288_V	0.505	0.98
237_Y	289_V	0.502	0.98
233_C	236_G	0.500	0.98
283_L	288_V	0.500	0.98
108_I	112_Q	0.500	0.98
232_A	296_D	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
4humA	1	0.9729	46.7	0.948	Contact Map
3mktA	1	0.9783	44.3	0.948	Contact Map
3w4tA	1	0.8726	43.6	0.948	Contact Map
4ltoA	3	0.3035	40.8	0.949	Contact Map
3tx3A	2	0.5827	29.1	0.953	Contact Map
4lz6A	1	0.8699	19	0.957	Contact Map
2cfqA	1	0.9566	18.3	0.957	Contact Map
2kv5A	1	0.0894	17.4	0.958	Contact Map
4tkrA	2	0.3144	17.1	0.958	Contact Map
4rp9A	2	0.8238	14.1	0.959	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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