CYDB - BACSU - GREMLIN Contacts

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CYDB - Cytochrome bd ubiquinol oxidase subunit 2

UniProt:	P94365	Sequences: MASLHDLWFILVAVLFVGFFFLEGFDFGVGMATRFLGHNELERRVLINTIGPFWDANEVWLLTGAGAIFAAFPNWYATMLSGYYIPFVIVLLALMGRGVAFEFRGKVDHLKWVKVWDWVVFFGSLIPPFVLGVLFTTLFRGMPIDADMNIHAHVSDYINVYSILGGVTVTLLCFQHGLMFITLRTIGDLQNRARKMAQKIMGVVFVAVLAFAALSAYQTDMFTRRGEITIPLAVLIVICFMLAAVFIRKKKDGWTFGMTGAGLALTVGMIFISLFPRVMVSSLHSAYDLTVANASSGDYSLKVMSIAALTLLPFVIGSQIWSYYVFRKRVSHKEPMTY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	338 (322)
Sequences:	3257 (2011)
Seq/√Len:	112.1

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
159_N	162_S	3.437	1.00
31_M	174_F	3.422	1.00
125_L	170_T	3.210	1.00
324_Y	327_R	3.067	1.00
83_Y	142_M	3.024	1.00
308_A	312_L	2.831	1.00
232_L	272_I	2.825	1.00
239_C	261_A	2.737	1.00
42_E	192_R	2.667	1.00
129_F	170_T	2.630	1.00
298_D	302_K	2.600	1.00
129_F	166_G	2.574	1.00
21_F	260_G	2.544	1.00
161_Y	215_S	2.533	1.00
174_F	200_I	2.475	1.00
195_K	199_K	2.430	1.00
171_L	207_A	2.418	1.00
44_R	48_N	2.359	1.00
31_M	170_T	2.274	1.00
10_I	14_V	2.218	1.00
104_R	117_D	2.213	1.00
89_I	130_V	2.157	1.00
198_Q	248_R	2.150	1.00
179_M	197_A	2.146	1.00
29_V	46_L	2.133	1.00
251_K	254_W	2.118	1.00
128_P	169_V	2.102	1.00
45_V	330_V	2.100	1.00
186_I	331_S	2.079	1.00
317_G	320_I	2.069	1.00
14_V	18_G	2.033	1.00
5_H	295_S	2.030	1.00
16_F	68_I	2.028	1.00
171_L	203_V	1.990	1.00
133_V	166_G	1.969	1.00
306_I	310_T	1.967	1.00
197_A	247_I	1.955	1.00
194_R	198_Q	1.951	1.00
167_V	171_L	1.949	1.00
136_T	165_G	1.922	1.00
153_H	156_D	1.908	1.00
221_M	224_R	1.894	1.00
46_L	181_I	1.886	1.00
71_A	304_M	1.883	1.00
163_I	167_V	1.868	1.00
121_F	125_L	1.866	1.00
320_I	324_Y	1.860	1.00
128_P	173_C	1.841	1.00
7_L	305_S	1.799	1.00
118_W	122_F	1.778	1.00
96_G	119_V	1.774	1.00
178_L	197_A	1.762	1.00
209_L	237_V	1.742	1.00
55_D	102_E	1.735	1.00
277_R	290_T	1.733	1.00
115_V	118_W	1.730	1.00
140_R	159_N	1.710	1.00
246_F	258_M	1.695	1.00
123_G	127_P	1.694	1.00
40_E	113_V	1.676	1.00
238_I	242_L	1.666	1.00
240_F	262_G	1.650	1.00
220_D	223_T	1.613	1.00
167_V	207_A	1.598	1.00
47_I	101_F	1.586	1.00
241_M	245_V	1.559	1.00
208_V	269_M	1.549	1.00
208_V	266_T	1.531	1.00
190_Q	252_D	1.529	1.00
119_V	123_G	1.518	1.00
90_V	131_L	1.511	1.00
176_H	260_G	1.510	1.00
82_G	142_M	1.494	1.00
168_T	207_A	1.472	1.00
130_V	158_I	1.471	1.00
311_L	314_F	1.464	1.00
25_F	323_Y	1.447	1.00
93_A	123_G	1.443	1.00
12_V	67_A	1.435	1.00
206_V	210_A	1.423	1.00
27_F	128_P	1.412	1.00
239_C	258_M	1.409	1.00
139_F	274_L	1.407	1.00
239_C	265_L	1.405	1.00
229_T	272_I	1.402	1.00
242_L	258_M	1.401	1.00
31_M	125_L	1.398	1.00
202_G	206_V	1.372	1.00
229_T	233_A	1.370	1.00
214_L	218_Q	1.369	1.00
302_K	306_I	1.357	1.00
172_L	263_L	1.353	1.00
29_V	50_I	1.346	1.00
305_S	309_L	1.344	1.00
235_L	265_L	1.333	1.00
182_T	190_Q	1.328	1.00
233_A	269_M	1.325	1.00
145_D	151_H	1.313	1.00
87_F	134_L	1.310	1.00
43_R	117_D	1.297	0.99
93_A	126_I	1.287	0.99
78_T	279_M	1.285	0.99
188_D	191_N	1.283	0.99
137_T	162_S	1.281	0.99
130_V	133_V	1.278	0.99
221_M	225_R	1.274	0.99
45_V	189_L	1.271	0.99
5_H	301_L	1.270	0.99
25_F	53_F	1.262	0.99
220_D	224_R	1.250	0.99
101_F	116_W	1.247	0.99
83_Y	86_P	1.245	0.99
213_A	217_Y	1.244	0.99
136_T	211_F	1.243	0.99
201_M	243_A	1.243	0.99
183_L	253_G	1.238	0.99
34_R	121_F	1.229	0.99
42_E	332_H	1.225	0.99
15_L	18_G	1.224	0.99
8_W	71_A	1.224	0.99
129_F	133_V	1.223	0.99
114_K	118_W	1.223	0.99
39_N	42_E	1.213	0.99
6_D	292_A	1.210	0.99
25_F	256_F	1.203	0.99
75_W	79_M	1.195	0.99
297_G	300_S	1.191	0.99
164_L	214_L	1.185	0.99
227_E	231_P	1.182	0.99
83_Y	137_T	1.182	0.99
30_G	124_S	1.177	0.99
41_L	332_H	1.177	0.99
194_R	250_K	1.175	0.99
88_V	92_L	1.174	0.99
175_Q	201_M	1.166	0.99
205_F	240_F	1.157	0.99
29_V	181_I	1.157	0.99
172_L	266_T	1.155	0.99
86_P	133_V	1.135	0.99
107_V	112_W	1.130	0.99
243_A	258_M	1.128	0.98
235_L	239_C	1.124	0.98
45_V	48_N	1.123	0.98
18_G	316_I	1.121	0.98
32_A	178_L	1.119	0.98
298_D	301_L	1.106	0.98
299_Y	302_K	1.103	0.98
68_I	75_W	1.097	0.98
115_V	119_V	1.095	0.98
169_V	173_C	1.079	0.98
299_Y	303_V	1.073	0.98
17_V	264_A	1.072	0.98
209_L	213_A	1.047	0.98
65_A	80_L	1.044	0.97
83_Y	279_M	1.043	0.97
179_M	255_T	1.039	0.97
15_L	63_T	1.036	0.97
75_W	278_V	1.034	0.97
222_F	225_R	1.032	0.97
196_M	199_K	1.031	0.97
53_F	180_F	1.023	0.97
142_M	279_M	1.022	0.97
229_T	232_L	1.013	0.97
205_F	244_A	1.011	0.97
41_L	45_V	1.007	0.97
131_L	173_C	1.005	0.97
122_F	126_I	1.000	0.97
17_V	267_V	0.992	0.97
245_V	249_K	0.991	0.97
39_N	332_H	0.989	0.97
190_Q	194_R	0.989	0.97
179_M	259_T	0.982	0.96
74_N	148_M	0.970	0.96
175_Q	197_A	0.968	0.96
205_F	209_L	0.966	0.96
137_T	157_Y	0.962	0.96
175_Q	179_M	0.962	0.96
176_H	259_T	0.961	0.96
11_L	66_G	0.960	0.96
31_M	121_F	0.960	0.96
45_V	185_T	0.959	0.96
234_V	238_I	0.957	0.96
182_T	194_R	0.949	0.96
33_T	121_F	0.929	0.95
33_T	47_I	0.925	0.95
9_F	13_A	0.924	0.95
44_R	105_G	0.924	0.95
45_V	332_H	0.920	0.95
205_F	237_V	0.913	0.95
44_R	47_I	0.911	0.95
14_V	66_G	0.909	0.94
246_F	254_W	0.908	0.94
196_M	200_I	0.907	0.94
126_I	130_V	0.906	0.94
220_D	225_R	0.904	0.94
232_L	235_L	0.903	0.94
188_D	192_R	0.902	0.94
107_V	110_L	0.902	0.94
23_E	27_F	0.897	0.94
125_L	129_F	0.897	0.94
277_R	281_S	0.892	0.94
201_M	244_A	0.891	0.94
143_P	282_S	0.885	0.94
270_I	274_L	0.884	0.94
56_A	322_S	0.882	0.94
150_I	156_D	0.880	0.93
65_A	76_Y	0.872	0.93
15_L	66_G	0.864	0.93
8_W	304_M	0.864	0.93
253_G	257_G	0.863	0.93
86_P	157_Y	0.861	0.93
36_L	46_L	0.860	0.93
228_I	272_I	0.855	0.92
202_G	244_A	0.854	0.92
191_N	194_R	0.853	0.92
105_G	113_V	0.851	0.92
119_V	122_F	0.847	0.92
219_T	223_T	0.842	0.92
20_F	319_Q	0.841	0.92
180_F	327_R	0.839	0.92
133_V	163_I	0.836	0.92
78_T	144_I	0.835	0.92
79_M	142_M	0.831	0.91
14_V	312_L	0.831	0.91
11_L	14_V	0.829	0.91
20_F	131_L	0.826	0.91
164_L	210_A	0.826	0.91
232_L	269_M	0.825	0.91
30_G	128_P	0.824	0.91
290_T	293_N	0.822	0.91
138_L	279_M	0.821	0.91
90_V	130_V	0.819	0.91
296_S	300_S	0.818	0.91
80_L	87_F	0.817	0.91
310_T	314_F	0.816	0.91
203_V	206_V	0.815	0.91
175_Q	259_T	0.813	0.90
195_K	198_Q	0.812	0.90
93_A	127_P	0.809	0.90
36_L	193_A	0.809	0.90
191_N	250_K	0.808	0.90
189_L	193_A	0.806	0.90
157_Y	160_V	0.805	0.90
108_D	115_V	0.805	0.90
128_P	131_L	0.799	0.90
25_F	184_R	0.797	0.90
95_M	295_S	0.794	0.89
233_A	240_F	0.793	0.89
81_S	84_Y	0.792	0.89
31_M	124_S	0.790	0.89
69_F	76_Y	0.785	0.89
191_N	195_K	0.779	0.88
38_H	42_E	0.777	0.88
129_F	163_I	0.777	0.88
171_L	200_I	0.774	0.88
23_E	184_R	0.772	0.88
48_N	51_G	0.772	0.88
226_G	229_T	0.771	0.88
98_G	101_F	0.770	0.88
264_A	268_G	0.769	0.88
171_L	204_V	0.768	0.88
321_W	325_V	0.762	0.87
13_A	271_F	0.761	0.87
236_I	240_F	0.761	0.87
118_W	121_F	0.755	0.87
168_T	208_V	0.752	0.87
135_F	270_I	0.751	0.87
232_L	265_L	0.749	0.86
75_W	78_T	0.746	0.86
289_L	293_N	0.745	0.86
66_G	312_L	0.743	0.86
16_F	64_G	0.735	0.85
65_A	304_M	0.734	0.85
144_I	279_M	0.733	0.85
175_Q	243_A	0.733	0.85
17_V	21_F	0.731	0.85
257_G	261_A	0.726	0.85
212_A	269_M	0.722	0.84
144_I	148_M	0.717	0.84
125_L	128_P	0.716	0.84
219_T	222_F	0.713	0.84
183_L	256_F	0.713	0.84
116_W	119_V	0.712	0.84
32_A	174_F	0.705	0.83
74_N	294_A	0.705	0.83
185_T	329_R	0.704	0.83
110_L	113_V	0.704	0.83
165_G	211_F	0.703	0.83
49_T	180_F	0.702	0.83
190_Q	329_R	0.700	0.82
82_G	86_P	0.697	0.82
200_I	203_V	0.697	0.82
11_L	312_L	0.695	0.82
179_M	243_A	0.694	0.82
89_I	126_I	0.693	0.82
11_L	308_A	0.691	0.82
38_H	192_R	0.690	0.82
245_V	248_R	0.686	0.81
53_F	322_S	0.685	0.81
241_M	244_A	0.685	0.81
199_K	202_G	0.682	0.81
21_F	264_A	0.681	0.81
289_L	294_A	0.678	0.80
303_V	307_A	0.678	0.80
233_A	237_V	0.678	0.80
178_L	182_T	0.678	0.80
319_Q	322_S	0.677	0.80
48_N	106_K	0.676	0.80
54_W	76_Y	0.676	0.80
19_F	27_F	0.675	0.80
48_N	105_G	0.674	0.80
46_L	107_V	0.674	0.80
98_G	269_M	0.673	0.80
232_L	268_G	0.673	0.80
181_I	193_A	0.673	0.80
123_G	128_P	0.671	0.80
27_F	98_G	0.671	0.80
85_I	89_I	0.671	0.80
55_D	318_S	0.670	0.80
100_A	119_V	0.670	0.80
305_S	329_R	0.670	0.80
67_A	70_A	0.669	0.80
12_V	307_A	0.669	0.80
109_H	112_W	0.669	0.80
216_A	230_I	0.669	0.80
217_Y	250_K	0.668	0.79
243_A	262_G	0.668	0.79
108_D	112_W	0.667	0.79
219_T	225_R	0.667	0.79
182_T	247_I	0.666	0.79
305_S	308_A	0.665	0.79
198_Q	201_M	0.664	0.79
207_A	211_F	0.663	0.79
226_G	230_I	0.661	0.79
261_A	265_L	0.661	0.79
320_I	327_R	0.657	0.78
231_P	236_I	0.656	0.78
129_F	167_V	0.656	0.78
192_R	195_K	0.656	0.78
105_G	108_D	0.655	0.78
268_G	272_I	0.654	0.78
178_L	196_M	0.650	0.78
20_F	173_C	0.648	0.77
237_V	242_L	0.646	0.77
312_L	317_G	0.643	0.77
242_L	246_F	0.643	0.77
231_P	238_I	0.642	0.77
42_E	45_V	0.642	0.77
122_F	331_S	0.641	0.77
198_Q	202_G	0.641	0.77
26_D	29_V	0.641	0.77
35_F	196_M	0.640	0.77
144_I	281_S	0.639	0.76
37_G	42_E	0.635	0.76
194_R	197_A	0.633	0.76
113_V	117_D	0.633	0.76
27_F	94_L	0.631	0.76
132_G	166_G	0.630	0.75
14_V	308_A	0.624	0.75
216_A	225_R	0.624	0.75
154_V	157_Y	0.619	0.74
37_G	46_L	0.618	0.74
9_F	291_V	0.618	0.74
265_L	272_I	0.617	0.74
95_M	100_A	0.615	0.74
32_A	181_I	0.614	0.74
47_I	105_G	0.610	0.73
55_D	58_E	0.607	0.73
236_I	239_C	0.607	0.73
46_L	189_L	0.607	0.73
234_V	248_R	0.606	0.73
49_T	331_S	0.605	0.72
29_V	33_T	0.604	0.72
134_L	208_V	0.600	0.72
275_F	301_L	0.599	0.72
110_L	114_K	0.599	0.72
6_D	275_F	0.597	0.71
317_G	322_S	0.597	0.71
15_L	67_A	0.597	0.71
6_D	291_V	0.593	0.71
50_I	101_F	0.591	0.71
5_H	298_D	0.590	0.71
63_T	307_A	0.590	0.71
80_L	304_M	0.588	0.70
262_G	266_T	0.587	0.70
205_F	229_T	0.584	0.70
224_R	228_I	0.583	0.70
27_F	30_G	0.581	0.69
30_G	35_F	0.580	0.69
12_V	196_M	0.580	0.69
242_L	254_W	0.578	0.69
19_F	326_F	0.578	0.69
246_F	251_K	0.577	0.69
87_F	263_L	0.576	0.69
9_F	77_A	0.576	0.69
198_Q	249_K	0.576	0.69
106_K	319_Q	0.576	0.69
175_Q	200_I	0.572	0.68
64_G	68_I	0.571	0.68
20_F	267_V	0.571	0.68
233_A	236_I	0.571	0.68
230_I	237_V	0.570	0.68
182_T	252_D	0.570	0.68
195_K	238_I	0.569	0.68
12_V	75_W	0.568	0.68
13_A	296_S	0.566	0.67
31_M	93_A	0.566	0.67
306_I	309_L	0.565	0.67
42_E	46_L	0.562	0.67
98_G	103_F	0.561	0.67
65_A	87_F	0.560	0.67
89_I	92_L	0.559	0.66
151_H	155_S	0.556	0.66
63_T	67_A	0.556	0.66
312_L	316_I	0.555	0.66
17_V	268_G	0.552	0.65
15_L	304_M	0.552	0.65
167_V	192_R	0.549	0.65
90_V	172_L	0.549	0.65
11_L	15_L	0.548	0.65
193_A	197_A	0.547	0.65
143_P	156_D	0.547	0.65
137_T	159_N	0.545	0.65
109_H	115_V	0.545	0.65
17_V	260_G	0.545	0.65
136_T	328_K	0.545	0.65
101_F	269_M	0.543	0.64
40_E	117_D	0.542	0.64
181_I	185_T	0.541	0.64
143_P	152_A	0.540	0.64
14_V	62_L	0.540	0.64
160_V	214_L	0.537	0.63
120_V	124_S	0.537	0.63
174_F	178_L	0.537	0.63
145_D	149_N	0.536	0.63
42_E	188_D	0.536	0.63
167_V	202_G	0.535	0.63
52_P	308_A	0.534	0.63
278_V	291_V	0.533	0.63
43_R	104_R	0.531	0.63
9_F	304_M	0.530	0.62
243_A	247_I	0.530	0.62
80_L	84_Y	0.529	0.62
263_L	266_T	0.529	0.62
179_M	247_I	0.529	0.62
216_A	227_E	0.529	0.62
210_A	214_L	0.529	0.62
145_D	148_M	0.529	0.62
43_R	113_V	0.528	0.62
51_G	71_A	0.528	0.62
269_M	296_S	0.526	0.62
239_C	242_L	0.526	0.62
125_L	174_F	0.525	0.62
206_V	238_I	0.525	0.62
156_D	162_S	0.524	0.62
289_L	295_S	0.522	0.61
54_W	97_R	0.520	0.61
97_R	124_S	0.519	0.61
128_P	138_L	0.518	0.61
39_N	188_D	0.518	0.61
10_I	309_L	0.518	0.61
161_Y	273_S	0.517	0.60
34_R	118_W	0.517	0.60
152_A	155_S	0.517	0.60
229_T	236_I	0.516	0.60
194_R	252_D	0.516	0.60
137_T	160_V	0.516	0.60
158_I	162_S	0.515	0.60
176_H	256_F	0.511	0.60
57_N	60_W	0.511	0.60
258_M	261_A	0.510	0.59
52_P	94_L	0.509	0.59
49_T	53_F	0.507	0.59
128_P	170_T	0.506	0.59
240_F	244_A	0.506	0.59
175_Q	204_V	0.505	0.59
39_N	206_V	0.505	0.59
314_F	321_W	0.504	0.59
31_M	128_P	0.503	0.58
129_F	136_T	0.501	0.58
269_M	273_S	0.501	0.58
237_V	240_F	0.500	0.58
125_L	261_A	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
4tphA	2	0.8491	18.8	0.969	Contact Map
3wdoA	1	0.8787	18.7	0.969	Contact Map
3wajA	1	0.6716	16.4	0.97	Contact Map
2mgyA	1	0.497	13.9	0.971	Contact Map
2mfrA	1	0.1568	13.7	0.971	Contact Map
3j1zP	8	0.4201	7.9	0.974	Contact Map
4nv5A	1	0.6036	7.6	0.974	Contact Map
2m20A	2	0.1213	7.5	0.974	Contact Map
1fftB	1	0.1568	7	0.974	Contact Map
1fftC	1	0.4201	6.2	0.975	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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