CYDB - ECOLI - GREMLIN Contacts

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CYDB - Cytochrome bd-I ubiquinol oxidase subunit 2

UniProt:	P0ABK2	Sequences: MIDYEVLRFIWWLLVGVLLIGFAVTDGFDMGVGMLTRFLGRNDTERRIMINSIAPHWDGNQVWLITAGGALFAAWPMVYAAAFSGFYVAMILVLASLFFRPVGFDYRSKIEETRWRNMWDWGIFIGSFVPPLVIGVAFGNLLQGVPFNVDEYLRLYYTGNFFQLLNPFGLLAGVVSVGMIITQGATYLQMRTVGELHLRTRATAQVAALVTLVCFALAGVWVMYGIDGYVVKSTMDHYAASNPLNKEVVREAGAWLVNFNNTPILWAIPALGVVLPLLTILTARMDKAAWAFVFSSLTLACIILTAGIAMFPFVMPSSTMMNASLTMWDATSSQLTLNVMTWVAVVLVPIILLYTAWCYWKMFGRITKEDIERNTHSLY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10174
Length:	379 (325)
Sequences:	3274 (2019)
Seq/√Len:	112.0

ECOLI - CYDB APPB
BACSU - CYDB YTHB
HALSA - O54596

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
166_N	169_G	3.530	1.00
34_M	181_I	3.468	1.00
128_F	177_V	3.155	1.00
360_W	363_F	2.980	1.00
86_F	145_V	2.878	1.00
275_L	297_L	2.812	1.00
344_A	348_V	2.738	1.00
132_L	177_V	2.722	1.00
181_I	207_A	2.700	1.00
268_I	308_I	2.683	1.00
24_V	296_S	2.655	1.00
45_E	199_R	2.625	1.00
202_A	206_V	2.620	1.00
334_Q	338_N	2.596	1.00
168_F	222_V	2.590	1.00
132_L	173_G	2.589	1.00
34_M	177_V	2.549	1.00
205_Q	284_R	2.407	1.00
47_R	51_N	2.310	1.00
107_R	120_D	2.272	1.00
32_V	49_M	2.255	1.00
13_L	17_V	2.206	1.00
178_G	214_C	2.184	1.00
92_L	133_V	2.182	1.00
193_V	367_T	2.149	1.00
287_K	290_W	2.134	1.00
186_T	204_A	2.111	1.00
48_I	366_I	2.072	1.00
131_P	176_S	2.044	1.00
19_L	71_L	2.026	1.00
353_L	356_A	2.024	1.00
342_W	346_V	2.015	1.00
8_R	331_T	2.012	1.00
174_V	178_G	2.007	1.00
136_V	173_G	1.972	1.00
356_A	360_W	1.947	1.00
160_N	163_Q	1.932	1.00
139_G	172_A	1.894	1.00
178_G	210_V	1.887	1.00
124_F	128_F	1.881	1.00
99_F	122_G	1.867	1.00
74_A	340_M	1.865	1.00
204_A	283_A	1.855	1.00
118_M	121_W	1.854	1.00
43_D	116_R	1.842	1.00
49_M	188_L	1.839	1.00
131_P	180_I	1.824	1.00
17_V	21_G	1.823	1.00
170_L	174_V	1.806	1.00
313_F	326_T	1.785	1.00
10_I	341_T	1.772	1.00
58_D	105_D	1.758	1.00
126_G	130_P	1.753	1.00
143_Q	166_N	1.742	1.00
216_A	273_V	1.741	1.00
282_T	294_F	1.734	1.00
121_W	125_I	1.734	1.00
274_V	278_L	1.698	1.00
185_A	204_A	1.669	1.00
276_P	298_T	1.642	1.00
42_N	45_E	1.627	1.00
148_N	158_T	1.627	1.00
183_Q	296_S	1.593	1.00
50_I	104_F	1.581	1.00
341_T	345_V	1.558	1.00
215_F	305_T	1.557	1.00
215_F	302_I	1.536	1.00
122_G	126_G	1.535	1.00
35_L	185_A	1.513	1.00
174_V	214_C	1.507	1.00
93_V	134_I	1.496	1.00
275_L	301_C	1.493	1.00
271_L	301_C	1.492	1.00
34_M	128_F	1.475	1.00
259_F	263_P	1.465	1.00
197_H	288_A	1.459	1.00
32_V	188_L	1.453	1.00
175_V	214_C	1.452	1.00
347_L	350_I	1.451	1.00
96_S	126_G	1.450	1.00
201_R	205_Q	1.431	1.00
133_V	165_L	1.430	1.00
48_I	196_L	1.426	1.00
142_L	310_M	1.416	1.00
28_F	359_Y	1.413	1.00
275_L	294_F	1.411	1.00
81_A	315_M	1.410	1.00
96_S	129_V	1.404	1.00
338_N	342_W	1.374	1.00
90_M	137_A	1.373	1.00
15_V	70_A	1.370	1.00
85_G	145_V	1.366	1.00
46_R	120_D	1.364	1.00
208_A	279_T	1.344	1.00
32_V	53_I	1.328	1.00
179_M	299_L	1.321	1.00
30_M	131_P	1.318	1.00
189_Q	197_H	1.304	0.99
117_N	121_W	1.304	0.99
132_L	136_V	1.300	0.99
213_V	217_L	1.300	0.99
44_T	368_K	1.298	0.99
221_W	225_G	1.298	0.99
190_M	289_A	1.291	0.99
209_L	213_V	1.290	0.99
18_L	21_G	1.289	0.99
140_N	169_G	1.280	0.99
86_F	89_A	1.279	0.99
8_R	337_L	1.268	0.99
45_E	368_K	1.263	0.99
195_E	198_L	1.259	0.99
212_L	276_P	1.258	0.99
28_F	56_H	1.253	0.99
133_V	136_V	1.251	0.99
91_I	95_A	1.243	0.99
186_T	291_A	1.240	0.99
278_L	294_F	1.234	0.99
28_F	292_F	1.234	0.99
33_G	127_S	1.233	0.99
220_V	224_Y	1.227	0.99
11_W	74_A	1.227	0.99
9_F	328_W	1.223	0.99
37_R	124_F	1.221	0.99
269_P	305_T	1.212	0.99
104_F	119_W	1.210	0.99
179_M	302_I	1.203	0.99
279_T	294_F	1.198	0.99
139_G	218_A	1.198	0.99
223_M	256_L	1.194	0.99
86_F	140_N	1.186	0.99
171_L	221_W	1.180	0.99
34_M	124_F	1.173	0.99
265_L	308_I	1.150	0.99
263_P	267_A	1.147	0.99
208_A	280_I	1.142	0.99
114_R	118_M	1.139	0.99
333_S	336_T	1.135	0.99
20_I	300_A	1.135	0.99
334_Q	337_L	1.130	0.99
71_L	78_V	1.121	0.98
118_M	122_G	1.120	0.98
78_V	314_V	1.114	0.98
39_L	200_T	1.105	0.98
201_R	286_D	1.105	0.98
182_T	208_A	1.104	0.98
176_S	180_I	1.100	0.98
164_L	167_P	1.097	0.98
78_V	82_A	1.094	0.98
56_H	187_Y	1.083	0.98
48_I	51_N	1.078	0.98
335_L	339_V	1.075	0.98
20_I	303_I	1.067	0.98
335_L	338_N	1.058	0.98
125_I	129_V	1.057	0.98
281_L	285_M	1.057	0.98
89_A	136_V	1.054	0.98
317_S	324_S	1.048	0.98
12_W	16_G	1.042	0.97
41_R	45_E	1.035	0.97
86_F	315_M	1.035	0.97
110_I	115_W	1.034	0.97
203_T	206_V	1.025	0.97
183_Q	295_S	1.022	0.97
313_F	317_S	1.022	0.97
189_Q	201_R	1.021	0.97
346_V	350_I	1.019	0.97
44_T	48_I	1.017	0.97
18_L	66_T	1.017	0.97
145_V	315_M	1.009	0.97
277_L	281_L	1.006	0.97
157_Y	163_Q	0.992	0.97
68_G	83_F	0.976	0.96
261_N	265_L	0.972	0.96
195_E	199_R	0.970	0.96
134_I	180_I	0.965	0.96
17_V	69_G	0.963	0.96
81_A	147_F	0.963	0.96
265_L	268_I	0.963	0.96
140_N	164_L	0.963	0.96
268_I	301_C	0.961	0.96
141_L	315_M	0.960	0.96
48_I	192_T	0.960	0.96
182_T	186_T	0.952	0.96
39_L	49_M	0.946	0.96
264_I	308_I	0.945	0.95
42_N	368_K	0.944	0.95
108_S	116_R	0.944	0.95
175_V	215_F	0.940	0.95
36_T	50_I	0.940	0.95
190_M	292_F	0.939	0.95
313_F	324_S	0.933	0.95
47_R	108_S	0.923	0.95
68_G	79_Y	0.921	0.95
138_F	306_A	0.921	0.95
186_T	295_S	0.921	0.95
178_G	207_A	0.921	0.95
212_L	216_A	0.920	0.95
129_V	133_V	0.918	0.95
36_T	124_F	0.914	0.95
182_T	204_A	0.912	0.95
306_A	310_M	0.912	0.95
17_V	348_V	0.910	0.94
203_T	207_A	0.909	0.94
189_Q	283_A	0.904	0.94
128_F	132_L	0.903	0.94
47_R	50_I	0.900	0.94
282_T	290_W	0.899	0.94
268_I	272_G	0.896	0.94
212_L	273_V	0.895	0.94
83_F	90_M	0.893	0.94
59_G	358_C	0.892	0.94
11_W	340_M	0.892	0.94
26_D	30_M	0.891	0.94
21_G	352_L	0.879	0.93
34_M	127_S	0.878	0.93
271_L	275_L	0.876	0.93
48_I	368_K	0.874	0.93
182_T	279_T	0.865	0.93
187_Y	363_F	0.854	0.92
332_S	336_T	0.852	0.92
202_A	205_Q	0.848	0.92
258_N	261_N	0.847	0.92
14_L	17_V	0.847	0.92
197_H	201_R	0.845	0.92
23_A	355_T	0.843	0.92
69_G	348_V	0.840	0.92
178_G	211_T	0.837	0.92
121_W	124_F	0.833	0.91
289_A	293_V	0.832	0.91
136_V	170_L	0.830	0.91
84_S	87_Y	0.828	0.91
198_L	202_A	0.820	0.91
132_L	170_L	0.817	0.91
268_I	271_L	0.812	0.90
40_G	49_M	0.812	0.90
98_F	331_T	0.812	0.90
51_N	54_A	0.811	0.90
150_D	156_Y	0.809	0.90
212_L	280_I	0.808	0.90
216_A	220_V	0.808	0.90
209_L	280_I	0.806	0.90
114_R	117_N	0.804	0.90
14_L	69_G	0.802	0.90
101_P	104_F	0.801	0.90
198_L	286_D	0.795	0.89
93_V	133_V	0.791	0.89
18_L	69_G	0.791	0.89
265_L	269_P	0.791	0.89
219_G	269_P	0.791	0.89
96_S	130_P	0.788	0.89
326_T	329_D	0.788	0.89
82_A	145_V	0.787	0.89
198_L	201_R	0.786	0.89
171_L	217_L	0.784	0.89
300_A	304_L	0.784	0.89
115_W	118_M	0.783	0.89
210_V	213_V	0.781	0.89
24_V	300_A	0.774	0.88
92_L	129_V	0.773	0.88
278_L	282_T	0.773	0.88
72_F	79_Y	0.773	0.88
182_T	295_S	0.772	0.88
33_G	131_P	0.771	0.88
89_A	164_L	0.769	0.88
298_T	302_I	0.769	0.88
147_F	315_M	0.768	0.88
357_W	361_K	0.762	0.87
28_F	191_R	0.760	0.87
78_V	81_A	0.759	0.87
85_G	89_A	0.759	0.87
293_V	297_L	0.756	0.87
325_L	329_D	0.754	0.87
268_I	305_T	0.752	0.87
58_D	354_Y	0.752	0.87
122_G	125_I	0.749	0.86
279_T	282_T	0.747	0.86
131_P	134_I	0.747	0.86
15_V	343_V	0.744	0.86
185_A	203_T	0.744	0.86
30_M	101_P	0.741	0.86
108_S	111_E	0.738	0.86
219_G	305_T	0.738	0.86
192_T	365_R	0.737	0.86
206_V	209_L	0.735	0.85
49_M	110_I	0.733	0.85
26_D	191_R	0.733	0.85
52_S	187_Y	0.731	0.85
339_V	343_V	0.731	0.85
35_L	188_L	0.730	0.85
23_A	180_I	0.730	0.85
188_L	200_T	0.730	0.85
273_V	277_L	0.730	0.85
325_L	330_A	0.725	0.85
297_L	301_C	0.723	0.84
116_R	120_D	0.721	0.84
30_M	97_L	0.720	0.84
128_F	131_P	0.715	0.84
186_T	279_T	0.710	0.83
51_N	108_S	0.710	0.83
12_W	327_M	0.710	0.83
126_G	131_P	0.705	0.83
35_L	181_I	0.703	0.83
110_I	113_T	0.701	0.83
19_L	67_A	0.699	0.82
57_W	79_Y	0.697	0.82
20_I	24_V	0.696	0.82
324_S	329_D	0.694	0.82
20_I	296_S	0.691	0.82
132_L	174_V	0.684	0.81
188_L	192_T	0.684	0.81
353_L	358_C	0.684	0.81
38_F	203_T	0.683	0.81
119_W	122_G	0.683	0.81
101_P	305_T	0.681	0.81
113_T	116_R	0.680	0.81
272_G	276_P	0.680	0.81
70_A	73_A	0.679	0.81
182_T	207_A	0.677	0.80
146_P	163_Q	0.672	0.80
45_E	195_E	0.670	0.80
305_T	332_S	0.668	0.79
111_E	118_M	0.667	0.79
147_F	317_S	0.666	0.79
263_P	266_W	0.665	0.79
40_G	45_E	0.665	0.79
199_R	202_A	0.662	0.79
197_H	365_R	0.659	0.79
186_T	283_A	0.658	0.78
159_G	162_F	0.657	0.78
279_T	298_T	0.656	0.78
301_C	308_I	0.655	0.78
223_M	266_W	0.655	0.78
29_D	32_V	0.653	0.78
341_T	344_A	0.652	0.78
18_L	340_M	0.647	0.77
50_I	108_S	0.645	0.77
98_F	103_G	0.644	0.77
14_L	344_A	0.643	0.77
77_M	330_A	0.643	0.77
17_V	344_A	0.641	0.77
14_L	348_V	0.638	0.76
111_E	115_W	0.638	0.76
49_M	196_L	0.634	0.76
8_R	334_Q	0.634	0.76
356_A	363_F	0.633	0.76
205_Q	208_A	0.631	0.75
88_V	92_L	0.630	0.75
16_G	307_G	0.629	0.75
56_H	358_C	0.627	0.75
273_V	280_I	0.626	0.75
192_T	292_F	0.625	0.75
43_D	120_D	0.624	0.75
213_V	274_V	0.623	0.75
181_I	185_A	0.623	0.75
185_A	189_Q	0.623	0.75
92_L	95_A	0.622	0.74
196_L	200_T	0.620	0.74
23_A	134_I	0.619	0.74
22_F	362_M	0.619	0.74
68_G	340_M	0.618	0.74
279_T	295_S	0.617	0.74
277_L	280_I	0.616	0.74
355_T	358_C	0.613	0.73
270_A	284_R	0.612	0.73
341_T	365_R	0.612	0.73
174_V	199_R	0.612	0.73
66_T	343_V	0.611	0.73
58_D	61_Q	0.610	0.73
270_A	274_V	0.609	0.73
348_V	352_L	0.606	0.73
135_G	173_G	0.606	0.73
103_G	122_G	0.606	0.73
342_W	345_V	0.605	0.72
125_I	367_T	0.605	0.72
278_L	281_L	0.602	0.72
164_L	169_G	0.601	0.72
41_R	199_R	0.599	0.72
15_V	203_T	0.598	0.72
53_I	104_F	0.597	0.71
12_W	80_A	0.596	0.71
140_N	167_P	0.596	0.71
93_V	179_M	0.596	0.71
170_L	324_S	0.593	0.71
101_P	106_Y	0.593	0.71
34_M	96_S	0.592	0.71
22_F	30_M	0.591	0.71
109_K	355_T	0.591	0.71
67_A	71_L	0.590	0.71
66_T	70_A	0.590	0.71
14_L	18_L	0.589	0.70
304_L	308_I	0.586	0.70
123_I	127_S	0.586	0.70
15_V	78_V	0.584	0.70
52_S	367_T	0.583	0.70
20_I	304_L	0.582	0.70
45_E	49_M	0.582	0.70
51_N	109_K	0.582	0.70
45_E	48_I	0.581	0.69
217_L	266_W	0.580	0.69
148_N	156_Y	0.579	0.69
9_F	311_F	0.578	0.69
161_F	164_L	0.577	0.69
207_A	210_V	0.576	0.69
348_V	353_L	0.575	0.69
211_T	302_I	0.572	0.68
259_F	262_T	0.572	0.68
46_R	116_R	0.571	0.68
189_Q	291_A	0.570	0.68
163_Q	169_G	0.568	0.68
49_M	195_E	0.568	0.68
68_G	90_M	0.567	0.68
181_I	203_T	0.565	0.67
90_M	299_L	0.561	0.67
205_Q	285_M	0.561	0.67
179_M	298_T	0.560	0.67
80_A	141_L	0.559	0.66
18_L	70_A	0.557	0.66
201_R	288_A	0.557	0.66
17_V	65_I	0.557	0.66
83_F	87_Y	0.553	0.66
138_F	218_A	0.551	0.65
189_Q	288_A	0.551	0.65
16_G	303_I	0.550	0.65
290_W	293_V	0.549	0.65
260_N	266_W	0.548	0.65
33_G	100_R	0.547	0.65
77_M	325_L	0.547	0.65
148_N	151_E	0.546	0.65
113_T	117_N	0.545	0.64
172_A	218_A	0.545	0.64
55_P	344_A	0.544	0.64
49_M	170_L	0.543	0.64
68_G	354_Y	0.541	0.64
37_R	121_W	0.541	0.64
286_D	289_A	0.539	0.64
182_T	211_T	0.538	0.63
139_G	169_G	0.538	0.63
227_D	256_L	0.535	0.63
267_A	270_A	0.533	0.63
215_F	274_V	0.533	0.63
77_M	151_E	0.532	0.63
117_N	261_N	0.531	0.62
165_L	169_G	0.531	0.62
259_F	269_P	0.530	0.62
52_S	64_L	0.528	0.62
23_A	176_S	0.527	0.62
12_W	340_M	0.526	0.62
167_P	171_L	0.526	0.62
198_L	297_L	0.523	0.61
46_R	107_R	0.523	0.61
49_M	52_S	0.523	0.61
314_V	327_M	0.522	0.61
276_P	280_I	0.522	0.61
8_R	328_W	0.522	0.61
285_M	345_V	0.522	0.61
273_V	278_L	0.521	0.61
64_L	134_I	0.521	0.61
254_A	309_A	0.520	0.61
311_F	337_L	0.519	0.61
54_A	74_A	0.518	0.61
9_F	13_L	0.518	0.61
19_L	176_S	0.517	0.60
12_W	19_L	0.517	0.60
220_V	223_M	0.517	0.60
27_G	60_N	0.516	0.60
139_G	364_G	0.516	0.60
14_L	341_T	0.515	0.60
169_G	172_A	0.515	0.60
9_F	327_M	0.513	0.60
88_V	191_R	0.513	0.60
15_V	307_G	0.512	0.60
142_L	306_A	0.511	0.60
110_I	114_R	0.511	0.60
168_F	309_A	0.511	0.60
195_E	202_A	0.509	0.59
37_R	117_N	0.509	0.59
44_T	274_V	0.509	0.59
46_R	176_S	0.507	0.59
14_L	340_M	0.506	0.59
80_A	84_S	0.506	0.59
73_A	79_Y	0.505	0.59
73_A	349_P	0.504	0.59
272_G	275_L	0.503	0.58
60_N	63_W	0.503	0.58
72_F	80_A	0.502	0.58
62_V	65_I	0.501	0.58
68_G	165_L	0.501	0.58
130_P	138_F	0.500	0.58

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
3wajA	1	0.6966	57	0.965	Contact Map
2mfrA	1	0.1504	49.6	0.967	Contact Map
4b4aA	1	0.533	21.8	0.973	Contact Map
2m20A	2	0.1214	15.1	0.974	Contact Map
2l8sA	1	0.1214	14.8	0.975	Contact Map
2kncA	1	0.1372	11.8	0.976	Contact Map
2m3eA	1	0.1266	10.6	0.976	Contact Map
3wdoA	1	0.8074	10.5	0.976	Contact Map
3rkoM	1	0.2797	9.7	0.977	Contact Map
1pw4A	1	0.7968	8.9	0.977	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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