YRBG - ECOLI - GREMLIN Contacts

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YRBG - Inner membrane protein YrbG

UniProt:	P45394	Sequences: MLLATALLIVGLLLVVYSADRLVFAASILCRTFGIPPLIIGMTVVSIGTSLPEVIVSLAASLHEQRDLAVGTALGSNIINILLILGLAALVRPFTVHSDVLRRELPLMLLVSVVAGSVLYDGQLSRSDGIFLLFLAVLWLLFIVKLARQAERQGTDSLTREQLAELPRDGGLPVAFLWLGIALIIMPVATRMVVDNATVLANYFAISELTMGLTAIAIGTSLPELATAIAGVRKGENDIAVGNIIGANIFNIVIVLGLPALITPGEIDPLAYSRDYSVMLLVSIIFALLCWRRSPQPGRGVGVLLTGGFIVWLAMLYWLSPILVE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12802
Length:	325 (304)
Sequences:	5330 (3717)
Seq/√Len:	213.2

ECOLI - YRBG CHAA
BACSU - CHAA
HALSA - Q9HS69 Q9HN44
SULSO - Q97YX8 Q97U31

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
121_D	128_D	4.136	1.00
79_I	83_L	4.065	1.00
129_G	260_A	3.924	1.00
79_I	218_I	3.460	1.00
118_V	128_D	3.053	1.00
141_L	145_K	3.022	1.00
43_T	46_S	2.932	1.00
202_N	208_E	2.814	1.00
130_I	134_F	2.659	1.00
65_Q	208_E	2.542	1.00
115_A	252_I	2.498	1.00
113_V	117_S	2.484	1.00
279_M	283_S	2.464	1.00
37_P	236_E	2.413	1.00
89_A	302_G	2.412	1.00
196_N	199_V	2.397	1.00
191_R	195_D	2.391	1.00
172_L	176_F	2.351	1.00
176_F	180_G	2.350	1.00
7_L	196_N	2.233	1.00
133_L	137_V	2.232	1.00
293_R	301_V	2.209	1.00
206_I	210_T	2.159	1.00
136_A	254_I	2.157	1.00
173_P	177_L	2.141	1.00
278_V	282_V	2.095	1.00
90_L	306_T	2.094	1.00
111_V	253_V	2.086	1.00
197_A	216_I	2.059	1.00
8_L	196_N	2.040	1.00
67_D	268_D	2.026	1.00
137_V	141_L	2.005	1.00
188_V	192_M	1.960	1.00
108_M	112_S	1.948	1.00
89_A	297_P	1.929	1.00
18_S	185_I	1.920	1.00
92_R	235_G	1.912	1.00
130_I	261_L	1.895	1.00
17_Y	21_R	1.889	1.00
7_L	192_M	1.857	1.00
117_S	121_D	1.850	1.00
174_V	178_W	1.808	1.00
280_L	284_I	1.808	1.00
117_S	120_Y	1.765	1.00
90_L	303_V	1.747	1.00
49_T	224_E	1.743	1.00
83_L	218_I	1.700	1.00
200_L	204_F	1.683	1.00
82_L	305_L	1.652	1.00
57_S	72_T	1.649	1.00
294_S	301_V	1.629	1.00
310_I	314_A	1.624	1.00
6_A	10_V	1.613	1.00
82_L	282_V	1.605	1.00
298_G	301_V	1.602	1.00
125_S	128_D	1.590	1.00
114_V	118_V	1.556	1.00
280_L	283_S	1.541	1.00
281_L	284_I	1.537	1.00
201_A	211_M	1.530	1.00
5_T	9_I	1.527	1.00
86_G	302_G	1.521	1.00
278_V	283_S	1.520	1.00
110_L	114_V	1.505	1.00
25_A	182_A	1.494	1.00
87_L	229_I	1.475	1.00
147_A	150_A	1.472	1.00
132_L	136_A	1.470	1.00
18_S	189_A	1.466	1.00
28_I	175_A	1.451	1.00
177_L	181_I	1.447	1.00
307_G	311_V	1.442	1.00
25_A	179_L	1.439	1.00
133_L	261_L	1.428	1.00
17_Y	20_D	1.426	1.00
42_M	45_V	1.424	1.00
32_T	172_L	1.410	1.00
8_L	200_L	1.405	1.00
29_L	179_L	1.393	1.00
21_R	178_W	1.392	1.00
126_R	261_L	1.391	1.00
80_N	248_N	1.386	1.00
73_A	256_L	1.381	1.00
307_G	314_A	1.366	1.00
228_A	243_N	1.366	1.00
77_N	251_N	1.360	1.00
251_N	255_V	1.351	1.00
50_S	247_A	1.336	1.00
68_L	212_G	1.327	1.00
47_I	51_L	1.323	1.00
58_L	62_L	1.322	1.00
200_L	203_Y	1.312	1.00
278_V	281_L	1.310	1.00
65_Q	198_T	1.308	1.00
183_L	187_P	1.285	1.00
47_I	250_F	1.284	1.00
171_G	174_V	1.279	1.00
277_S	281_L	1.276	1.00
22_L	186_M	1.276	1.00
11_G	14_L	1.261	1.00
129_G	257_G	1.259	1.00
275_D	312_W	1.258	1.00
55_I	190_T	1.250	1.00
21_R	181_I	1.246	1.00
58_L	262_I	1.241	1.00
59_A	63_H	1.241	1.00
277_S	280_L	1.218	1.00
277_S	282_V	1.217	1.00
29_L	175_A	1.214	1.00
285_I	289_L	1.210	1.00
275_D	278_V	1.194	1.00
300_G	303_V	1.178	1.00
39_I	144_V	1.177	1.00
127_S	314_A	1.169	1.00
45_V	239_I	1.164	1.00
217_A	221_S	1.160	1.00
199_V	203_Y	1.148	1.00
11_G	189_A	1.145	1.00
279_M	282_V	1.142	1.00
199_V	202_N	1.139	1.00
210_T	317_Y	1.135	1.00
14_L	185_I	1.111	1.00
271_A	275_D	1.105	1.00
26_A	45_V	1.102	1.00
76_S	80_N	1.099	1.00
115_A	119_L	1.094	1.00
93_P	299_R	1.093	1.00
126_R	264_P	1.093	1.00
42_M	48_G	1.089	1.00
145_K	149_Q	1.089	1.00
181_I	185_I	1.086	1.00
276_Y	280_L	1.077	1.00
279_M	284_I	1.071	1.00
107_L	113_V	1.070	1.00
67_D	71_G	1.069	1.00
25_A	178_W	1.066	1.00
250_F	254_I	1.059	1.00
206_I	211_M	1.055	1.00
21_R	185_I	1.054	1.00
90_L	302_G	1.054	1.00
300_G	304_L	1.048	1.00
126_R	130_I	1.041	1.00
192_M	196_N	1.035	1.00
20_D	24_F	1.033	1.00
124_L	128_D	1.032	1.00
140_L	144_V	1.027	1.00
14_L	192_M	1.027	1.00
214_T	217_A	1.023	1.00
7_L	195_D	1.013	1.00
73_A	259_P	1.003	1.00
102_R	106_P	1.000	1.00
7_L	10_V	0.998	1.00
221_S	225_L	0.997	1.00
198_T	202_N	0.997	1.00
145_K	148_R	0.993	1.00
54_V	255_V	0.992	1.00
170_G	175_A	0.989	1.00
54_V	58_L	0.988	1.00
54_V	73_A	0.987	1.00
148_R	152_R	0.985	1.00
47_I	136_A	0.985	1.00
166_L	169_D	0.983	1.00
195_D	199_V	0.982	1.00
112_S	116_G	0.979	1.00
202_N	211_M	0.974	1.00
142_F	146_L	0.970	1.00
8_L	193_V	0.968	1.00
290_C	293_R	0.964	1.00
18_S	182_A	0.961	1.00
21_R	24_F	0.960	1.00
227_T	231_G	0.959	1.00
53_E	223_P	0.959	1.00
88_A	232_V	0.955	1.00
114_V	117_S	0.955	1.00
54_V	80_N	0.954	1.00
27_S	236_E	0.951	1.00
15_V	23_V	0.951	1.00
80_N	247_A	0.951	1.00
10_V	13_L	0.944	1.00
53_E	224_E	0.943	0.99
49_T	223_P	0.935	0.99
55_I	187_P	0.934	0.99
277_S	283_S	0.931	0.99
114_V	135_L	0.927	0.99
148_R	151_E	0.926	0.99
273_S	276_Y	0.924	0.99
11_G	196_N	0.923	0.99
36_P	147_A	0.920	0.99
116_G	119_L	0.918	0.99
128_D	131_F	0.914	0.99
88_A	228_A	0.913	0.99
95_T	296_Q	0.913	0.99
26_A	40_I	0.911	0.99
31_R	40_I	0.904	0.99
178_W	182_A	0.904	0.99
301_V	305_L	0.901	0.99
134_F	138_L	0.897	0.99
53_E	220_T	0.894	0.99
19_A	27_S	0.887	0.99
85_L	241_V	0.884	0.99
119_L	267_I	0.884	0.99
107_L	110_L	0.878	0.99
247_A	250_F	0.874	0.99
101_L	105_L	0.871	0.99
178_W	181_I	0.870	0.99
32_T	37_P	0.864	0.99
79_I	82_L	0.863	0.99
76_S	221_S	0.863	0.99
229_I	233_R	0.854	0.99
271_A	274_R	0.853	0.99
274_R	282_V	0.852	0.99
81_I	247_A	0.851	0.99
139_W	249_I	0.848	0.99
174_V	177_L	0.846	0.99
223_P	248_N	0.842	0.99
188_V	191_R	0.836	0.99
76_S	248_N	0.836	0.99
129_G	132_L	0.835	0.99
85_L	297_P	0.835	0.99
60_A	69_A	0.834	0.99
108_M	111_V	0.829	0.99
275_D	283_S	0.827	0.99
187_P	191_R	0.826	0.99
150_A	154_G	0.823	0.99
98_S	102_R	0.820	0.99
107_L	117_S	0.815	0.99
84_I	225_L	0.814	0.99
164_A	167_P	0.812	0.98
184_I	187_P	0.809	0.98
220_T	223_P	0.808	0.98
116_G	276_Y	0.807	0.98
170_G	174_V	0.807	0.98
61_S	259_P	0.804	0.98
313_L	317_Y	0.804	0.98
302_G	306_T	0.802	0.98
109_L	113_V	0.802	0.98
294_S	300_G	0.795	0.98
38_L	42_M	0.793	0.98
192_M	195_D	0.791	0.98
42_M	46_S	0.791	0.98
126_R	133_L	0.786	0.98
185_I	188_V	0.784	0.98
115_A	256_L	0.784	0.98
79_I	225_L	0.780	0.98
112_S	279_M	0.780	0.98
101_L	106_P	0.778	0.98
108_M	245_I	0.776	0.98
96_V	235_G	0.773	0.98
50_S	77_N	0.769	0.98
232_V	237_N	0.768	0.98
78_I	312_W	0.768	0.98
133_L	258_L	0.766	0.98
284_I	289_L	0.764	0.98
110_L	117_S	0.762	0.98
111_V	249_I	0.761	0.98
242_G	246_G	0.760	0.98
275_D	280_L	0.757	0.98
49_T	220_T	0.756	0.98
29_L	176_F	0.756	0.98
55_I	186_M	0.755	0.98
12_L	16_V	0.752	0.98
228_A	240_A	0.749	0.97
223_P	243_N	0.747	0.97
147_A	151_E	0.743	0.97
31_R	37_P	0.741	0.97
135_L	139_W	0.740	0.97
12_L	218_I	0.738	0.97
26_A	231_G	0.733	0.97
19_A	48_G	0.731	0.97
80_N	220_T	0.730	0.97
115_A	118_V	0.729	0.97
111_V	114_V	0.728	0.97
288_L	292_R	0.726	0.97
100_V	104_E	0.726	0.97
28_I	32_T	0.726	0.97
79_I	221_S	0.721	0.97
231_G	239_I	0.721	0.97
108_M	283_S	0.719	0.97
190_T	254_I	0.718	0.97
50_S	248_N	0.714	0.97
118_V	131_F	0.714	0.97
271_A	276_Y	0.706	0.96
133_L	254_I	0.705	0.96
314_A	317_Y	0.704	0.96
46_S	49_T	0.698	0.96
171_G	175_A	0.697	0.96
92_R	95_T	0.697	0.96
50_S	80_N	0.693	0.96
29_L	33_F	0.689	0.96
302_G	305_L	0.687	0.96
139_W	142_F	0.687	0.96
129_G	136_A	0.687	0.96
214_T	313_L	0.686	0.96
69_A	72_T	0.686	0.96
83_L	306_T	0.686	0.96
209_L	212_G	0.685	0.96
221_S	251_N	0.682	0.96
282_V	285_I	0.679	0.95
87_L	225_L	0.677	0.95
178_W	185_I	0.677	0.95
53_E	80_N	0.672	0.95
167_P	170_G	0.669	0.95
176_F	181_I	0.669	0.95
48_G	247_A	0.669	0.95
303_V	307_G	0.669	0.95
224_E	255_V	0.668	0.95
17_Y	24_F	0.666	0.95
136_A	139_W	0.663	0.95
108_M	136_A	0.662	0.95
275_D	279_M	0.661	0.95
46_S	52_P	0.659	0.95
26_A	30_C	0.656	0.95
195_D	198_T	0.652	0.94
84_I	241_V	0.652	0.94
74_L	82_L	0.651	0.94
65_Q	68_L	0.651	0.94
59_A	191_R	0.650	0.94
14_L	17_Y	0.649	0.94
36_P	148_R	0.646	0.94
49_T	52_P	0.645	0.94
77_N	247_A	0.641	0.94
57_S	61_S	0.640	0.94
205_A	216_I	0.637	0.94
121_D	125_S	0.635	0.94
118_V	132_L	0.634	0.94
11_G	19_A	0.634	0.94
208_E	212_G	0.633	0.93
50_S	221_S	0.631	0.93
299_R	302_G	0.629	0.93
306_T	310_I	0.628	0.93
260_A	264_P	0.625	0.93
174_V	181_I	0.625	0.93
197_A	220_T	0.622	0.93
68_L	216_I	0.621	0.93
201_A	212_G	0.617	0.93
304_L	308_G	0.616	0.93
51_L	250_F	0.615	0.92
9_I	13_L	0.614	0.92
138_L	142_F	0.612	0.92
61_S	263_T	0.612	0.92
11_G	214_T	0.610	0.92
186_M	226_A	0.610	0.92
80_N	223_P	0.608	0.92
51_L	55_I	0.606	0.92
163_L	166_L	0.606	0.92
20_D	230_A	0.605	0.92
230_A	233_R	0.603	0.92
238_D	247_A	0.603	0.92
24_F	234_K	0.602	0.92
272_Y	284_I	0.600	0.92
113_V	118_V	0.600	0.92
296_Q	300_G	0.600	0.92
87_L	91_V	0.597	0.91
82_L	283_S	0.594	0.91
286_F	289_L	0.593	0.91
235_G	240_A	0.592	0.91
289_L	292_R	0.590	0.91
254_I	258_L	0.587	0.91
269_P	273_S	0.586	0.91
240_A	256_L	0.586	0.91
53_E	216_I	0.586	0.91
209_L	259_P	0.581	0.90
46_S	50_S	0.581	0.90
88_A	227_T	0.580	0.90
16_V	20_D	0.580	0.90
220_T	243_N	0.580	0.90
135_L	138_L	0.578	0.90
72_T	220_T	0.576	0.90
87_L	306_T	0.575	0.90
77_N	252_I	0.574	0.90
144_V	148_R	0.574	0.90
87_L	90_L	0.573	0.90
57_S	259_P	0.572	0.90
276_Y	279_M	0.572	0.90
94_F	135_L	0.571	0.89
212_G	217_A	0.570	0.89
10_V	14_L	0.568	0.89
74_L	256_L	0.568	0.89
163_L	168_R	0.567	0.89
289_L	305_L	0.565	0.89
221_S	248_N	0.564	0.89
124_L	256_L	0.564	0.89
84_I	221_S	0.564	0.89
86_G	93_P	0.564	0.89
220_T	248_N	0.563	0.89
49_T	243_N	0.561	0.89
281_L	285_I	0.560	0.89
43_T	244_I	0.560	0.89
39_I	143_I	0.559	0.88
82_L	88_A	0.559	0.88
111_V	117_S	0.558	0.88
48_G	183_L	0.554	0.88
63_H	191_R	0.553	0.88
22_L	29_L	0.553	0.88
14_L	189_A	0.551	0.88
113_V	116_G	0.550	0.88
281_L	288_L	0.550	0.88
11_G	192_M	0.550	0.88
80_N	251_N	0.548	0.87
287_A	291_W	0.546	0.87
142_F	152_R	0.545	0.87
185_I	189_A	0.544	0.87
77_N	80_N	0.543	0.87
44_V	179_L	0.541	0.87
141_L	149_Q	0.541	0.87
57_S	248_N	0.538	0.87
36_P	39_I	0.538	0.87
224_E	247_A	0.538	0.87
284_I	291_W	0.538	0.87
40_I	43_T	0.537	0.86
86_G	91_V	0.536	0.86
99_D	103_R	0.534	0.86
16_V	19_A	0.534	0.86
31_R	165_E	0.534	0.86
138_L	145_K	0.532	0.86
223_P	246_G	0.532	0.86
193_V	222_L	0.530	0.86
84_I	219_G	0.529	0.86
211_M	215_A	0.528	0.86
49_T	251_N	0.526	0.85
303_V	308_G	0.526	0.85
84_I	220_T	0.525	0.85
218_I	225_L	0.525	0.85
108_M	115_A	0.523	0.85
82_L	240_A	0.523	0.85
256_L	259_P	0.522	0.85
82_L	86_G	0.521	0.85
165_E	169_D	0.520	0.85
165_E	168_R	0.519	0.85
270_L	274_R	0.519	0.85
105_L	245_I	0.519	0.85
19_A	24_F	0.519	0.85
15_V	18_S	0.518	0.84
81_I	85_L	0.517	0.84
198_T	208_E	0.517	0.84
24_F	59_A	0.516	0.84
29_L	44_V	0.515	0.84
135_L	253_V	0.514	0.84
132_L	253_V	0.513	0.84
186_M	254_I	0.512	0.84
244_I	248_N	0.512	0.84
55_I	59_A	0.511	0.84
208_E	211_M	0.511	0.84
112_S	117_S	0.511	0.84
97_H	238_D	0.508	0.83
107_L	121_D	0.507	0.83
30_C	44_V	0.507	0.83
26_A	44_V	0.504	0.83
23_V	220_T	0.504	0.83
309_F	312_W	0.503	0.83
57_S	221_S	0.502	0.83
136_A	140_L	0.501	0.82
45_V	143_I	0.501	0.82
80_N	243_N	0.501	0.82
101_L	104_E	0.500	0.82
213_L	275_D	0.500	0.82

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
3v5uA	1	0.9077	100	0.19	Contact Map
4k1cA	4	0.9785	100	0.208	Contact Map
4kjrA	3	0.8862	100	0.23	Contact Map
4kppA	1	0.96	100	0.263	Contact Map
3giaA	1	0.4523	35.9	0.947	Contact Map
4rp9A	2	0.4092	32.1	0.948	Contact Map
3o7qA	1	0.4615	30.8	0.949	Contact Map
3l1lA	2	0.4492	17.6	0.954	Contact Map
4pgrA	1	0.44	15.3	0.955	Contact Map
3qe7A	2	0.44	14.7	0.956	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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