APPB - ECOLI - GREMLIN Contacts

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APPB - Cytochrome bd-II ubiquinol oxidase subunit 2

UniProt:	P26458	Sequences: MFDYETLRFIWWLLIGVILVVFMISDGFDMGIGCLLPLVARNDDERRIVINSVGAHWEGNQVWLILAGGALFAAWPRVYAAAFSGFYVAMILVLCSLFFRPLAFDYRGKIADARWRKMWDAGLVIGSLVPPVVFGIAFGNLLLGVPFAFTPQLRVEYLGSFWQLLTPFPLLCGLLSLGMVILQGGVWLQLKTVGVIHLRSQLATKRAALLVMLCFLLAGYWLWVGIDGFVLLAQDANGPSNPLMKLVAVLPGAWMNNFVESPVLWIFPLLGFFCPLLTVMAIYRGRPGWGFLMASLMQFGVIFTAGITLFPFVMPSSVSPISSLTLWDSTSSQLTLSIMLVIVLIFLPIVLLYTLWSYYKMWGRMTTETLRRNENELY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11379
Length:	378 (324)
Sequences:	3272 (1998)
Seq/√Len:	111.0

ECOLI - APPB CYDB
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_T	169_P	3.528	1.00
34_C	181_I	3.409	1.00
128_L	177_L	3.165	1.00
86_F	145_V	3.002	1.00
359_Y	362_W	2.975	1.00
274_C	296_L	2.807	1.00
343_V	347_L	2.807	1.00
132_V	177_L	2.684	1.00
267_F	307_I	2.630	1.00
333_Q	337_S	2.621	1.00
181_I	207_A	2.618	1.00
132_V	173_G	2.612	1.00
168_F	222_L	2.592	1.00
202_L	206_R	2.587	1.00
45_E	199_R	2.567	1.00
34_C	177_L	2.549	1.00
24_I	295_S	2.548	1.00
205_K	283_Y	2.445	1.00
47_R	51_N	2.297	1.00
107_R	120_D	2.249	1.00
13_L	17_V	2.213	1.00
32_I	49_V	2.209	1.00
178_G	214_C	2.188	1.00
193_V	366_T	2.169	1.00
92_L	133_V	2.167	1.00
286_R	289_W	2.138	1.00
17_V	21_V	2.115	1.00
186_V	204_T	2.088	1.00
204_T	282_I	2.080	1.00
352_L	355_L	2.060	1.00
131_P	176_S	2.037	1.00
19_L	71_L	2.016	1.00
136_I	173_G	2.005	1.00
8_R	330_T	1.994	1.00
174_L	178_G	1.993	1.00
48_I	365_M	1.978	1.00
341_V	345_I	1.967	1.00
124_V	128_L	1.924	1.00
355_L	359_Y	1.907	1.00
139_G	172_C	1.907	1.00
99_F	122_G	1.890	1.00
216_L	272_F	1.868	1.00
178_G	210_L	1.866	1.00
74_A	339_M	1.859	1.00
160_S	163_Q	1.857	1.00
148_A	158_L	1.838	1.00
118_M	121_A	1.820	1.00
170_L	174_L	1.806	1.00
312_F	325_T	1.805	1.00
143_L	166_T	1.791	1.00
49_V	188_L	1.791	1.00
131_P	180_V	1.791	1.00
10_I	340_L	1.767	1.00
43_D	116_R	1.765	1.00
58_E	105_D	1.759	1.00
126_G	130_P	1.759	1.00
281_A	293_M	1.742	1.00
185_G	204_T	1.713	1.00
121_A	125_I	1.689	1.00
197_H	287_P	1.680	1.00
215_F	301_V	1.642	1.00
215_F	304_T	1.617	1.00
273_F	277_L	1.594	1.00
183_Q	295_S	1.588	1.00
50_I	104_F	1.533	1.00
133_V	165_L	1.516	1.00
93_V	134_F	1.514	1.00
35_L	185_G	1.513	1.00
34_C	128_L	1.511	1.00
275_P	297_M	1.510	1.00
174_L	214_C	1.490	1.00
122_G	126_G	1.475	1.00
201_Q	205_K	1.475	1.00
346_F	349_I	1.464	1.00
85_G	145_V	1.449	1.00
274_C	300_G	1.448	1.00
274_C	293_M	1.448	1.00
32_I	188_L	1.427	1.00
15_I	70_A	1.422	1.00
175_L	214_C	1.422	1.00
270_L	300_G	1.421	1.00
337_S	341_V	1.420	1.00
96_S	129_V	1.404	1.00
28_F	358_Y	1.402	1.00
96_S	126_G	1.400	1.00
142_L	309_L	1.384	1.00
48_I	196_I	1.374	1.00
195_V	198_L	1.362	1.00
81_A	314_M	1.350	1.00
46_R	120_D	1.343	1.00
90_M	137_A	1.342	1.00
179_M	298_Q	1.342	1.00
20_V	299_F	1.341	1.00
189_Q	197_H	1.327	1.00
30_M	131_P	1.327	1.00
277_L	293_M	1.311	0.99
32_I	53_V	1.310	0.99
340_L	344_L	1.308	0.99
86_F	89_A	1.304	0.99
45_E	367_T	1.300	0.99
190_L	288_G	1.296	0.99
77_R	155_V	1.296	0.99
117_K	121_A	1.287	0.99
213_L	217_L	1.281	0.99
208_A	279_V	1.280	0.99
44_D	367_T	1.279	0.99
171_L	221_W	1.277	0.99
8_R	336_L	1.266	0.99
208_A	278_T	1.260	0.99
28_F	56_H	1.256	0.99
140_N	169_P	1.255	0.99
220_Y	224_V	1.251	0.99
133_V	136_I	1.250	0.99
223_W	255_M	1.242	0.99
132_V	136_I	1.241	0.99
221_W	225_G	1.240	0.99
104_F	119_W	1.240	0.99
37_P	124_V	1.239	0.99
33_G	127_S	1.235	0.99
209_L	213_L	1.232	0.99
278_T	293_M	1.228	0.99
11_W	74_A	1.227	0.99
91_I	95_C	1.217	0.99
149_F	155_V	1.210	0.99
179_M	301_V	1.203	0.99
18_I	21_V	1.202	0.99
9_F	327_W	1.193	0.99
118_M	122_G	1.190	0.99
114_R	118_M	1.189	0.99
139_G	218_A	1.177	0.99
258_F	262_P	1.176	0.99
21_V	351_L	1.175	0.99
42_N	45_E	1.174	0.99
264_L	307_I	1.162	0.99
86_F	140_N	1.148	0.99
34_C	124_V	1.146	0.99
28_F	291_F	1.133	0.98
48_I	51_N	1.126	0.98
332_S	335_T	1.124	0.98
71_L	78_V	1.119	0.98
78_V	82_A	1.114	0.98
268_P	304_T	1.112	0.98
182_L	208_A	1.108	0.98
212_M	275_P	1.107	0.98
334_L	338_I	1.106	0.98
186_V	290_G	1.102	0.98
333_Q	336_L	1.099	0.98
316_S	323_S	1.081	0.98
176_S	180_V	1.077	0.98
78_V	313_V	1.076	0.98
334_L	337_S	1.070	0.98
267_F	300_G	1.066	0.98
20_V	302_I	1.056	0.98
201_Q	285_G	1.050	0.98
203_A	206_R	1.048	0.97
164_L	167_P	1.042	0.97
68_G	83_F	1.041	0.97
183_Q	294_A	1.037	0.97
89_A	136_I	1.034	0.97
18_I	66_L	1.032	0.97
262_P	266_I	1.029	0.97
81_A	147_F	1.029	0.97
312_F	316_S	1.023	0.97
56_H	187_W	1.013	0.97
189_Q	201_Q	1.013	0.97
264_L	267_F	1.013	0.97
125_I	129_V	1.010	0.97
86_F	314_M	1.007	0.97
42_N	367_T	1.000	0.97
39_V	200_S	0.998	0.97
110_I	115_W	0.998	0.97
312_F	323_S	0.991	0.96
134_F	180_V	0.991	0.96
256_N	260_E	0.979	0.96
145_V	314_M	0.976	0.96
44_D	48_I	0.974	0.96
157_Y	163_Q	0.966	0.96
36_L	50_I	0.966	0.96
182_L	186_V	0.965	0.96
110_I	113_A	0.961	0.96
17_V	69_G	0.957	0.96
48_I	192_T	0.950	0.96
263_V	307_I	0.943	0.95
345_I	349_I	0.943	0.95
223_W	265_W	0.941	0.95
17_V	347_L	0.938	0.95
39_V	49_V	0.937	0.95
186_V	294_A	0.933	0.95
189_Q	282_I	0.932	0.95
140_N	164_L	0.932	0.95
203_A	207_A	0.926	0.95
129_V	133_V	0.925	0.95
68_G	79_Y	0.922	0.95
212_M	272_F	0.921	0.95
12_W	16_G	0.921	0.95
178_G	207_A	0.920	0.95
136_I	170_L	0.920	0.95
305_A	309_L	0.918	0.95
260_E	264_L	0.917	0.95
48_I	367_T	0.913	0.94
47_R	108_G	0.913	0.94
141_L	314_M	0.912	0.94
288_G	291_F	0.912	0.94
108_G	116_R	0.906	0.94
47_R	50_I	0.900	0.94
59_G	357_S	0.900	0.94
36_L	124_V	0.899	0.94
82_A	145_V	0.897	0.94
270_L	274_C	0.897	0.94
281_A	289_W	0.892	0.94
26_D	30_M	0.890	0.94
195_V	199_R	0.889	0.94
178_G	211_V	0.889	0.94
288_G	292_L	0.885	0.93
138_F	305_A	0.880	0.93
182_L	204_T	0.878	0.93
112_D	118_M	0.878	0.93
277_L	281_A	0.875	0.93
132_V	170_L	0.870	0.93
216_L	220_Y	0.870	0.93
122_G	125_I	0.869	0.93
83_F	90_M	0.864	0.93
276_L	280_M	0.864	0.93
128_L	132_V	0.860	0.92
187_W	362_W	0.860	0.92
34_C	127_S	0.859	0.92
11_W	339_M	0.857	0.92
98_F	330_T	0.856	0.92
14_L	69_G	0.852	0.92
197_H	201_Q	0.851	0.92
114_R	117_K	0.849	0.92
182_L	278_T	0.847	0.92
23_M	354_T	0.846	0.92
212_M	216_L	0.845	0.92
198_L	202_L	0.844	0.92
175_L	215_F	0.837	0.91
331_S	335_T	0.836	0.91
190_L	291_F	0.835	0.91
219_G	268_P	0.835	0.91
202_L	205_K	0.832	0.91
84_S	87_Y	0.830	0.91
101_P	104_F	0.829	0.91
18_I	69_G	0.824	0.91
171_L	217_L	0.823	0.91
121_A	124_V	0.823	0.91
93_V	133_V	0.823	0.91
14_L	17_V	0.816	0.90
89_A	164_L	0.816	0.90
325_T	328_D	0.815	0.90
33_G	131_P	0.806	0.90
267_F	270_L	0.802	0.90
51_N	54_G	0.797	0.89
272_F	276_L	0.794	0.89
96_S	130_P	0.787	0.89
26_D	191_K	0.786	0.89
210_L	213_L	0.781	0.88
292_L	296_L	0.777	0.88
131_P	134_F	0.776	0.88
85_G	89_A	0.774	0.88
356_W	360_K	0.772	0.88
23_M	134_F	0.771	0.88
72_F	79_Y	0.771	0.88
212_M	279_V	0.771	0.88
128_L	131_P	0.767	0.87
28_F	191_K	0.767	0.87
267_F	271_G	0.767	0.87
324_L	328_D	0.765	0.87
219_G	304_T	0.765	0.87
185_G	203_A	0.765	0.87
115_W	118_M	0.764	0.87
147_F	314_M	0.763	0.87
35_L	188_L	0.761	0.87
146_P	163_Q	0.760	0.87
280_M	284_R	0.757	0.87
267_F	304_T	0.756	0.87
297_M	301_V	0.753	0.86
299_F	303_F	0.749	0.86
182_L	294_A	0.748	0.86
113_A	116_R	0.744	0.86
30_M	101_P	0.744	0.86
69_G	347_L	0.733	0.85
252_G	256_N	0.732	0.85
198_L	201_Q	0.731	0.85
49_V	195_V	0.730	0.85
338_I	342_I	0.727	0.84
15_I	342_I	0.720	0.84
19_L	67_A	0.717	0.84
324_L	329_S	0.717	0.84
78_V	81_A	0.714	0.83
323_S	328_D	0.710	0.83
20_V	24_I	0.707	0.83
16_G	306_G	0.707	0.83
52_S	187_W	0.707	0.83
209_L	279_V	0.704	0.83
58_E	353_Y	0.703	0.82
101_P	304_T	0.700	0.82
119_W	122_G	0.699	0.82
258_F	261_S	0.699	0.82
51_N	108_G	0.698	0.82
35_L	181_I	0.697	0.82
192_T	364_R	0.696	0.82
57_W	79_Y	0.690	0.81
24_I	299_F	0.681	0.80
14_L	347_L	0.681	0.80
198_L	285_G	0.681	0.80
45_E	49_V	0.680	0.80
278_T	294_A	0.678	0.80
30_M	97_L	0.676	0.80
259_V	265_W	0.674	0.80
92_L	129_V	0.673	0.80
126_G	131_P	0.672	0.80
197_H	364_R	0.671	0.79
188_L	200_S	0.670	0.79
113_A	117_K	0.668	0.79
12_W	326_L	0.668	0.79
40_A	49_V	0.667	0.79
23_M	180_V	0.664	0.79
14_L	343_V	0.657	0.78
276_L	279_V	0.656	0.78
15_I	78_V	0.656	0.78
68_G	339_M	0.654	0.78
287_P	290_G	0.652	0.77
77_R	329_S	0.652	0.77
70_A	73_A	0.645	0.77
29_D	32_I	0.644	0.77
56_H	357_S	0.643	0.76
125_I	366_T	0.643	0.76
20_V	295_S	0.643	0.76
116_R	120_D	0.642	0.76
182_L	207_A	0.642	0.76
103_A	122_G	0.640	0.76
132_V	174_L	0.640	0.76
278_T	297_M	0.639	0.76
185_G	189_Q	0.639	0.76
352_L	357_S	0.639	0.76
347_L	351_L	0.635	0.76
296_L	300_G	0.635	0.76
186_V	278_T	0.634	0.75
41_R	199_R	0.634	0.75
189_Q	285_G	0.633	0.75
8_R	333_Q	0.632	0.75
354_T	357_S	0.631	0.75
188_L	192_T	0.630	0.75
192_T	291_F	0.628	0.75
88_V	92_L	0.620	0.74
92_L	95_C	0.619	0.74
207_A	210_L	0.619	0.74
313_V	326_L	0.619	0.74
213_L	273_F	0.618	0.74
300_G	307_I	0.618	0.74
38_L	203_A	0.618	0.74
269_L	273_F	0.618	0.74
42_N	195_V	0.616	0.73
53_V	104_F	0.616	0.73
340_L	343_V	0.613	0.73
264_L	268_P	0.613	0.73
52_S	366_T	0.613	0.73
206_R	209_L	0.612	0.73
22_F	30_M	0.612	0.73
179_M	297_M	0.612	0.73
49_V	110_I	0.612	0.73
98_F	103_A	0.611	0.73
15_I	203_A	0.610	0.73
50_I	108_G	0.610	0.73
40_A	45_E	0.606	0.72
17_V	343_V	0.605	0.72
23_M	302_I	0.605	0.72
12_W	80_A	0.605	0.72
271_G	275_P	0.601	0.72
186_V	282_I	0.600	0.71
135_G	173_G	0.599	0.71
174_L	199_R	0.598	0.71
49_V	196_I	0.598	0.71
58_E	61_Q	0.595	0.71
109_K	354_T	0.595	0.71
41_R	45_E	0.594	0.71
93_V	179_M	0.592	0.70
281_A	286_R	0.591	0.70
9_F	310_F	0.590	0.70
66_L	342_I	0.589	0.70
147_F	316_S	0.589	0.70
355_L	362_W	0.589	0.70
138_F	218_A	0.586	0.70
303_F	307_I	0.586	0.70
146_P	159_G	0.585	0.70
165_L	169_P	0.582	0.69
147_F	155_V	0.581	0.69
67_A	71_L	0.580	0.69
211_V	301_V	0.580	0.69
199_R	202_L	0.579	0.69
22_F	361_M	0.579	0.69
90_M	298_Q	0.578	0.69
196_I	200_S	0.577	0.68
201_Q	287_P	0.577	0.68
167_P	221_W	0.576	0.68
142_L	305_A	0.576	0.68
341_V	344_L	0.575	0.68
206_R	210_L	0.574	0.68
310_F	336_L	0.574	0.68
66_L	70_A	0.573	0.68
205_K	208_A	0.573	0.68
340_L	364_R	0.572	0.68
123_L	127_S	0.570	0.68
34_C	96_S	0.568	0.67
140_N	167_P	0.567	0.67
43_D	108_G	0.567	0.67
43_D	120_D	0.566	0.67
51_N	109_K	0.566	0.67
68_G	165_L	0.565	0.67
57_W	100_R	0.564	0.67
18_I	70_A	0.563	0.67
81_A	155_V	0.562	0.66
20_V	303_F	0.561	0.66
9_F	326_L	0.560	0.66
275_P	279_V	0.560	0.66
83_F	87_Y	0.557	0.66
13_L	344_L	0.556	0.66
181_I	203_A	0.555	0.66
18_I	339_M	0.554	0.65
33_G	100_R	0.551	0.65
52_S	64_L	0.551	0.65
101_P	106_Y	0.550	0.65
170_L	323_S	0.550	0.65
186_V	281_A	0.550	0.65
42_N	213_L	0.549	0.65
293_M	296_L	0.549	0.65
261_S	264_L	0.548	0.65
27_G	60_N	0.547	0.64
17_V	65_I	0.546	0.64
264_L	300_G	0.546	0.64
68_G	90_M	0.545	0.64
8_R	327_W	0.545	0.64
287_P	364_R	0.544	0.64
212_M	264_L	0.544	0.64
45_E	48_I	0.543	0.64
113_A	263_V	0.543	0.64
181_I	185_G	0.542	0.64
140_N	166_T	0.536	0.63
14_L	18_I	0.534	0.63
43_D	46_R	0.534	0.63
193_V	368_E	0.533	0.62
49_V	52_S	0.532	0.62
270_L	280_M	0.531	0.62
55_A	343_V	0.530	0.62
278_T	281_A	0.527	0.62
55_A	97_L	0.527	0.62
148_A	156_E	0.526	0.61
277_L	280_M	0.526	0.61
68_G	353_Y	0.525	0.61
22_F	71_L	0.524	0.61
46_R	107_R	0.524	0.61
347_L	352_L	0.524	0.61
202_L	285_G	0.523	0.61
182_L	211_V	0.523	0.61
267_F	303_F	0.522	0.61
26_D	187_W	0.522	0.61
83_F	339_M	0.522	0.61
16_G	302_I	0.521	0.61
37_P	117_K	0.519	0.60
312_F	315_P	0.518	0.60
136_I	162_W	0.518	0.60
164_L	169_P	0.515	0.60
279_V	293_M	0.515	0.60
45_E	195_V	0.514	0.60
205_K	209_L	0.513	0.60
192_T	197_H	0.511	0.59
49_V	170_L	0.511	0.59
37_P	121_A	0.510	0.59
139_G	363_G	0.510	0.59
281_A	285_G	0.510	0.59
88_V	191_K	0.509	0.59
330_T	336_L	0.509	0.59
46_R	116_R	0.508	0.59
274_C	277_L	0.508	0.59
263_V	266_I	0.508	0.59
73_A	172_C	0.508	0.59
44_D	273_F	0.506	0.58
131_P	141_L	0.505	0.58
72_F	356_W	0.505	0.58
54_G	74_A	0.505	0.58
60_N	63_W	0.504	0.58
269_L	283_Y	0.502	0.58
44_D	365_M	0.502	0.58
112_D	115_W	0.502	0.58
54_G	59_G	0.501	0.58
217_L	221_W	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
2mfrA	1	0.1508	37.4	0.969	Contact Map
2m20A	2	0.1217	13.3	0.975	Contact Map
3wdoA	1	0.8148	10.1	0.976	Contact Map
2kncA	1	0.1376	8.5	0.977	Contact Map
3rkoN	1	0.2778	8.2	0.977	Contact Map
2l8sA	1	0.1217	8.1	0.977	Contact Map
3hb3B	1	0.1852	7.3	0.978	Contact Map
2m3eA	1	0.127	6.8	0.978	Contact Map
3rkoM	1	0.2698	6.3	0.978	Contact Map
2mgyA	1	0.4365	5.6	0.979	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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