YDBI - BACSU - GREMLIN Contacts

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YDBI - UPF0118 membrane protein YdbI

UniProt:	P96604	Sequences: MAALVKFFQHPGVRRFSIFVVLTGVLYLFKSMINLILLTFIFTFLMDRLELVVRQFVSQFFRVSQRVVITFLYMLLAVLLTVGGFVFYPVVAAQIQQLVKQIKHIAYHPDSIPFFDEITSVFGDINISSYVKEGFNVVYTYLADISTFGLQVVMALILSMFFLFEKKRLSEFMAKFKTSKLRVFYEEIAFFGSKFARTFGKVLEAQFIIALVNCILTFIALWIMHFPQLFGLSIMVFFLGLIPVAGVVISLIPLSIIAYSTGGGMYVLYIVLVIFAIHAIETYFLNPKLMSAKTELPIFFTFTVLIFSEHFFGIWGLIIGIPIFVFLLDILDVTNKEDRSKGPRENSDKK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	350 (315)
Sequences:	10931 (8468)
Seq/√Len:	477.1

ECOLI - TQSA YDIK YHHT PERM
BACSU - YDBI YTVI YUEF YUBA YRRI
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
220_A	273_V	5.039	1.00
218_F	233_S	4.953	1.00
52_V	56_F	4.829	1.00
304_V	324_F	3.136	1.00
44_F	196_A	2.851	1.00
54_R	65_Q	2.820	1.00
214_C	237_F	2.668	1.00
265_M	269_Y	2.617	1.00
64_S	67_V	2.493	1.00
42_F	159_S	2.464	1.00
268_L	272_L	2.464	1.00
218_F	222_W	2.413	1.00
52_V	55_Q	2.366	1.00
255_S	271_V	2.360	1.00
214_C	233_S	2.322	1.00
63_V	71_F	2.160	1.00
328_L	332_D	2.122	1.00
23_T	27_Y	2.087	1.00
221_L	226_F	2.025	1.00
190_F	333_V	1.965	1.00
255_S	267_V	1.940	1.00
47_D	51_L	1.928	1.00
101_Q	104_H	1.876	1.00
272_L	276_A	1.863	1.00
39_T	159_S	1.860	1.00
207_F	241_L	1.832	1.00
24_G	28_L	1.825	1.00
205_A	289_L	1.798	1.00
160_M	164_F	1.794	1.00
194_K	333_V	1.794	1.00
269_Y	272_L	1.755	1.00
235_M	239_L	1.723	1.00
195_F	326_F	1.722	1.00
50_E	72_L	1.715	1.00
66_R	70_T	1.706	1.00
69_I	160_M	1.692	1.00
117_E	120_S	1.679	1.00
217_T	236_V	1.678	1.00
229_L	233_S	1.671	1.00
50_E	69_I	1.662	1.00
174_A	189_A	1.657	1.00
219_I	222_W	1.656	1.00
107_Y	110_D	1.646	1.00
217_T	277_I	1.642	1.00
263_G	266_Y	1.642	1.00
47_D	65_Q	1.637	1.00
158_L	299_F	1.634	1.00
112_I	115_F	1.597	1.00
81_T	85_F	1.590	1.00
288_K	292_A	1.581	1.00
69_I	73_Y	1.580	1.00
119_T	123_G	1.576	1.00
66_R	164_F	1.574	1.00
155_A	159_S	1.567	1.00
222_W	229_L	1.563	1.00
227_P	261_T	1.555	1.00
111_S	115_F	1.554	1.00
266_Y	269_Y	1.550	1.00
218_F	229_L	1.548	1.00
99_V	103_K	1.536	1.00
94_Q	99_V	1.535	1.00
165_E	297_P	1.530	1.00
36_I	303_T	1.521	1.00
177_K	188_I	1.519	1.00
108_H	111_S	1.502	1.00
50_E	65_Q	1.486	1.00
216_L	277_I	1.482	1.00
285_L	289_L	1.481	1.00
49_L	72_L	1.471	1.00
110_D	114_F	1.450	1.00
19_F	23_T	1.449	1.00
239_L	250_S	1.432	1.00
104_H	108_H	1.426	1.00
309_E	317_L	1.423	1.00
213_N	240_G	1.421	1.00
53_V	75_L	1.420	1.00
63_V	67_V	1.390	1.00
121_V	124_D	1.373	1.00
104_H	107_Y	1.372	1.00
120_S	123_G	1.368	1.00
158_L	162_F	1.366	1.00
46_M	163_L	1.363	1.00
275_F	279_A	1.351	1.00
96_Q	100_K	1.340	1.00
232_L	254_L	1.320	1.00
171_E	175_K	1.318	1.00
258_A	270_I	1.317	1.00
265_M	268_L	1.310	1.00
251_L	255_S	1.303	1.00
126_N	129_S	1.301	1.00
39_T	155_A	1.289	1.00
77_A	81_T	1.273	1.00
220_A	269_Y	1.260	1.00
108_H	112_I	1.260	1.00
122_F	125_I	1.255	1.00
103_K	107_Y	1.255	1.00
254_L	270_I	1.249	1.00
271_V	275_F	1.232	1.00
220_A	224_M	1.229	1.00
305_L	317_L	1.227	1.00
50_E	163_L	1.225	1.00
27_Y	30_K	1.224	1.00
209_I	281_E	1.202	1.00
165_E	168_R	1.196	1.00
178_T	182_R	1.193	1.00
120_S	124_D	1.191	1.00
13_V	17_S	1.190	1.00
204_E	208_I	1.187	1.00
280_I	285_L	1.181	1.00
93_A	97_Q	1.181	1.00
70_T	74_M	1.178	1.00
24_G	27_Y	1.174	1.00
213_N	277_I	1.170	1.00
49_L	52_V	1.168	1.00
43_T	162_F	1.168	1.00
226_F	258_A	1.167	1.00
96_Q	99_V	1.166	1.00
20_V	24_G	1.163	1.00
12_G	16_F	1.155	1.00
35_L	39_T	1.155	1.00
198_T	325_V	1.152	1.00
102_I	105_I	1.151	1.00
194_K	332_D	1.146	1.00
46_M	76_L	1.145	1.00
300_F	324_F	1.142	1.00
88_Y	92_A	1.139	1.00
50_E	68_V	1.139	1.00
278_H	282_T	1.136	1.00
47_D	166_K	1.135	1.00
117_E	121_V	1.134	1.00
42_F	155_A	1.131	1.00
233_S	237_F	1.130	1.00
168_R	171_E	1.128	1.00
101_Q	105_I	1.127	1.00
264_G	267_V	1.126	1.00
219_I	223_I	1.126	1.00
67_V	70_T	1.125	1.00
68_V	72_L	1.121	1.00
118_I	121_V	1.113	1.00
65_Q	167_K	1.112	1.00
66_R	160_M	1.112	1.00
224_M	273_V	1.111	1.00
116_D	120_S	1.109	1.00
259_Y	267_V	1.108	1.00
308_S	312_F	1.107	1.00
264_G	268_L	1.107	1.00
267_V	271_V	1.106	1.00
191_F	330_I	1.104	1.00
97_Q	100_K	1.100	1.00
258_A	267_V	1.090	1.00
179_S	182_R	1.087	1.00
50_E	54_R	1.083	1.00
210_A	240_G	1.079	1.00
107_Y	111_S	1.074	1.00
315_W	319_I	1.071	1.00
127_I	130_Y	1.070	1.00
15_R	19_F	1.066	1.00
129_S	132_K	1.064	1.00
54_R	68_V	1.060	1.00
209_I	285_L	1.060	1.00
105_I	109_P	1.057	1.00
190_F	194_K	1.053	1.00
304_V	308_S	1.047	1.00
39_T	43_T	1.042	1.00
23_T	26_L	1.039	1.00
36_I	158_L	1.039	1.00
218_F	230_F	1.033	1.00
224_M	266_Y	1.030	1.00
220_A	277_I	1.028	1.00
63_V	68_V	1.028	1.00
207_F	211_L	1.021	1.00
73_Y	159_S	1.017	1.00
158_L	303_T	1.017	1.00
40_F	162_F	1.013	1.00
130_Y	134_G	1.012	1.00
224_M	270_I	1.012	1.00
38_L	155_A	1.002	1.00
111_S	114_F	0.994	1.00
211_L	237_F	0.992	1.00
214_C	218_F	0.990	1.00
148_F	152_V	0.988	1.00
142_L	146_S	0.985	1.00
208_I	212_V	0.985	1.00
257_I	261_T	0.981	1.00
206_Q	286_N	0.981	1.00
138_V	142_L	0.974	1.00
201_K	293_K	0.973	1.00
52_V	62_R	0.970	1.00
221_L	232_L	0.967	1.00
172_F	175_K	0.966	1.00
174_A	178_T	0.965	1.00
201_K	205_A	0.964	1.00
308_S	324_F	0.963	1.00
85_F	89_P	0.960	1.00
284_F	288_K	0.952	1.00
209_I	213_N	0.950	1.00
221_L	236_V	0.950	1.00
154_M	158_L	0.948	1.00
18_I	22_L	0.940	1.00
174_A	182_R	0.939	1.00
213_N	247_V	0.938	1.00
304_V	320_G	0.937	1.00
90_V	93_A	0.935	1.00
121_V	125_I	0.933	1.00
116_D	119_T	0.930	1.00
273_V	277_I	0.928	1.00
269_Y	273_V	0.928	1.00
106_A	110_D	0.928	1.00
282_T	286_N	0.927	1.00
51_L	54_R	0.927	1.00
300_F	328_L	0.927	1.00
166_K	170_S	0.925	1.00
280_I	284_F	0.922	1.00
221_L	270_I	0.920	1.00
129_S	133_E	0.917	1.00
14_R	28_L	0.915	1.00
237_F	241_L	0.914	1.00
215_I	219_I	0.914	1.00
131_V	134_G	0.912	1.00
235_M	250_S	0.909	1.00
53_V	72_L	0.909	1.00
233_S	236_V	0.905	1.00
278_H	281_E	0.904	1.00
90_V	94_Q	0.904	1.00
330_I	334_T	0.901	1.00
249_I	253_P	0.901	1.00
213_N	217_T	0.898	1.00
327_L	331_L	0.897	1.00
16_F	20_V	0.894	1.00
276_A	280_I	0.881	1.00
228_Q	231_G	0.881	1.00
215_I	218_F	0.877	1.00
93_A	96_Q	0.874	1.00
128_S	132_K	0.872	1.00
178_T	181_L	0.866	1.00
290_M	301_T	0.864	1.00
197_R	201_K	0.862	1.00
32_M	307_F	0.854	1.00
281_E	286_N	0.854	1.00
46_M	72_L	0.853	1.00
170_S	174_A	0.851	1.00
209_I	286_N	0.850	1.00
56_F	62_R	0.848	1.00
224_M	269_Y	0.846	1.00
79_L	83_G	0.844	1.00
134_G	137_V	0.843	1.00
259_Y	264_G	0.840	1.00
222_W	225_H	0.839	1.00
51_L	55_Q	0.837	1.00
141_Y	145_I	0.833	1.00
222_W	233_S	0.833	1.00
256_I	260_S	0.830	1.00
39_T	158_L	0.829	1.00
303_T	307_F	0.828	1.00
251_L	274_I	0.826	1.00
109_P	112_I	0.825	1.00
168_R	172_F	0.824	1.00
94_Q	97_Q	0.823	1.00
97_Q	101_Q	0.818	1.00
15_R	18_I	0.814	1.00
320_G	324_F	0.812	1.00
14_R	18_I	0.812	1.00
177_K	181_L	0.811	1.00
217_T	221_L	0.811	1.00
95_I	99_V	0.810	1.00
212_V	285_L	0.805	1.00
211_L	215_I	0.800	1.00
191_F	333_V	0.799	1.00
18_I	25_V	0.797	1.00
209_I	240_G	0.792	1.00
36_I	162_F	0.787	1.00
232_L	257_I	0.775	1.00
279_A	283_Y	0.775	1.00
258_A	263_G	0.769	1.00
212_V	216_L	0.769	1.00
296_L	324_F	0.765	1.00
308_S	323_I	0.764	1.00
144_D	147_T	0.764	1.00
210_A	241_L	0.763	1.00
210_A	214_C	0.762	1.00
187_E	333_V	0.762	1.00
240_G	247_V	0.760	1.00
213_N	286_N	0.758	1.00
17_S	21_V	0.758	1.00
56_F	63_V	0.751	1.00
20_V	27_Y	0.749	1.00
53_V	68_V	0.744	1.00
194_K	329_D	0.742	1.00
20_V	23_T	0.741	1.00
236_V	240_G	0.740	1.00
189_A	193_S	0.740	1.00
236_V	250_S	0.740	1.00
21_V	25_V	0.739	1.00
255_S	259_Y	0.739	1.00
279_A	282_T	0.736	1.00
43_T	159_S	0.735	1.00
25_V	29_F	0.735	1.00
209_I	290_M	0.733	1.00
54_R	62_R	0.730	1.00
159_S	163_L	0.728	1.00
195_F	329_D	0.726	1.00
187_E	190_F	0.724	1.00
100_K	104_H	0.723	1.00
208_I	289_L	0.721	1.00
53_V	63_V	0.715	1.00
43_T	47_D	0.711	1.00
172_F	176_F	0.711	1.00
51_L	167_K	0.709	1.00
188_I	192_G	0.707	1.00
261_T	266_Y	0.707	1.00
134_G	138_V	0.703	1.00
64_S	68_V	0.702	1.00
54_R	64_S	0.699	1.00
147_T	151_Q	0.699	1.00
291_S	301_T	0.697	1.00
13_V	18_I	0.694	1.00
16_F	19_F	0.693	1.00
217_T	233_S	0.691	1.00
240_G	286_N	0.688	1.00
176_F	331_L	0.685	1.00
25_V	28_L	0.685	1.00
208_I	211_L	0.683	1.00
135_F	138_V	0.680	1.00
171_E	174_A	0.678	1.00
324_F	328_L	0.672	1.00
200_G	204_E	0.671	1.00
198_T	201_K	0.670	1.00
133_E	137_V	0.669	1.00
75_L	78_V	0.669	1.00
244_V	298_I	0.668	1.00
174_A	177_K	0.667	1.00
286_N	290_M	0.665	1.00
214_C	234_I	0.662	1.00
247_V	278_H	0.661	1.00
194_K	198_T	0.660	1.00
294_T	321_I	0.659	1.00
301_T	321_I	0.656	1.00
84_G	88_Y	0.655	1.00
171_E	189_A	0.651	1.00
217_T	273_V	0.649	1.00
35_L	151_Q	0.648	1.00
133_E	136_N	0.648	1.00
91_V	95_I	0.647	1.00
240_G	281_E	0.646	1.00
250_S	254_L	0.644	1.00
47_D	163_L	0.644	1.00
22_L	25_V	0.643	1.00
92_A	95_I	0.642	1.00
82_V	86_V	0.641	1.00
286_N	289_L	0.641	1.00
191_F	195_F	0.639	1.00
73_Y	160_M	0.637	1.00
139_Y	143_A	0.635	1.00
126_N	130_Y	0.633	1.00
92_A	96_Q	0.629	1.00
314_I	317_L	0.627	1.00
79_L	82_V	0.626	1.00
126_N	131_V	0.626	1.00
46_M	49_L	0.625	0.99
152_V	156_L	0.622	0.99
87_F	91_V	0.619	0.99
193_S	197_R	0.619	0.99
118_I	125_I	0.617	0.99
214_C	230_F	0.616	0.99
19_F	22_L	0.616	0.99
35_L	291_S	0.613	0.99
137_V	141_Y	0.613	0.99
46_M	159_S	0.613	0.99
172_F	300_F	0.612	0.99
144_D	148_F	0.609	0.99
154_M	306_I	0.608	0.99
132_K	136_N	0.605	0.99
298_I	302_F	0.602	0.99
130_Y	133_E	0.601	0.99
119_T	122_F	0.598	0.99
43_T	163_L	0.597	0.99
21_V	24_G	0.597	0.99
38_L	42_F	0.596	0.99
206_Q	240_G	0.596	0.99
105_I	108_H	0.595	0.99
131_V	135_F	0.595	0.99
210_A	237_F	0.595	0.99
80_L	84_G	0.594	0.99
109_P	113_P	0.593	0.99
312_F	316_G	0.587	0.99
210_A	213_N	0.587	0.99
53_V	71_F	0.586	0.99
170_S	193_S	0.583	0.99
74_M	78_V	0.582	0.99
148_F	151_Q	0.581	0.99
236_V	274_I	0.579	0.99
226_F	229_L	0.579	0.99
213_N	281_E	0.577	0.99
186_E	190_F	0.576	0.99
285_L	288_K	0.575	0.99
288_K	295_E	0.574	0.99
235_M	253_P	0.574	0.99
86_V	90_V	0.573	0.99
161_F	165_E	0.572	0.99
69_I	164_F	0.572	0.99
105_I	112_I	0.571	0.99
236_V	247_V	0.570	0.99
78_V	81_T	0.568	0.99
206_Q	210_A	0.568	0.99
22_L	26_L	0.568	0.99
213_N	278_H	0.567	0.99
150_L	154_M	0.566	0.99
194_K	197_R	0.564	0.99
226_F	261_T	0.563	0.99
217_T	237_F	0.561	0.99
35_L	44_F	0.560	0.99
247_V	250_S	0.558	0.99
106_A	112_I	0.558	0.99
204_E	293_K	0.558	0.99
258_A	266_Y	0.557	0.99
209_I	289_L	0.555	0.99
291_S	295_E	0.555	0.99
239_L	253_P	0.554	0.99
222_W	230_F	0.554	0.99
198_T	329_D	0.554	0.99
117_E	122_F	0.551	0.99
210_A	274_I	0.550	0.99
249_I	278_H	0.550	0.99
25_V	327_L	0.549	0.99
221_L	233_S	0.546	0.99
12_G	15_R	0.544	0.99
201_K	204_E	0.543	0.99
162_F	299_F	0.542	0.99
82_V	85_F	0.542	0.99
142_L	145_I	0.540	0.99
292_A	295_E	0.539	0.99
118_I	122_F	0.536	0.98
204_E	207_F	0.534	0.98
65_Q	69_I	0.532	0.98
296_L	301_T	0.532	0.98
170_S	192_G	0.531	0.98
251_L	271_V	0.530	0.98
169_L	172_F	0.528	0.98
206_Q	209_I	0.528	0.98
209_I	291_S	0.527	0.98
147_T	283_Y	0.526	0.98
17_S	20_V	0.526	0.98
237_F	244_V	0.524	0.98
213_N	216_L	0.523	0.98
13_V	16_F	0.520	0.98
173_M	176_F	0.519	0.98
94_Q	101_Q	0.519	0.98
177_K	182_R	0.518	0.98
199_F	202_V	0.517	0.98
216_L	220_A	0.517	0.98
206_Q	241_L	0.517	0.98
99_V	102_I	0.515	0.98
72_L	76_L	0.515	0.98
226_F	254_L	0.514	0.98
214_C	251_L	0.514	0.98
103_K	106_A	0.511	0.98
135_F	139_Y	0.511	0.98
40_F	166_K	0.511	0.98
205_A	325_V	0.510	0.98
305_L	321_I	0.509	0.98
254_L	258_A	0.509	0.98
118_I	123_G	0.508	0.98
140_T	143_A	0.507	0.98
213_N	237_F	0.506	0.98
198_T	326_F	0.505	0.98
221_L	274_I	0.503	0.98
101_Q	227_P	0.502	0.98
158_L	306_I	0.501	0.98
259_Y	268_L	0.501	0.98
237_F	240_G	0.501	0.98
81_T	84_G	0.500	0.98
297_P	300_F	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
3w4tA	1	0.8657	58.3	0.941	Contact Map
4rp9A	2	0.88	36.1	0.948	Contact Map
4r0cA	3	0.62	34	0.949	Contact Map
4humA	1	0.8943	29.6	0.951	Contact Map
4ltoA	3	0.32	23.3	0.953	Contact Map
3mktA	1	0.8914	21.9	0.954	Contact Map
2kv5A	1	0.0943	18.3	0.955	Contact Map
4lz6A	1	0.8971	15	0.957	Contact Map
4tkrA	2	0.3171	13.9	0.958	Contact Map
4p6vB	1	0.1686	13.5	0.958	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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