CYOA - ECOLI - GREMLIN Contacts

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CYOA - Cytochrome bo(3) ubiquinol oxidase subunit 2

UniProt:	P0ABJ1	Sequences: MRLRKYNKSLGWLSLFAGTVLLSGCNSALLDPKGQIGLEQRSLILTAFGLMLIVVIPAILMAVGFAWKYRASNKDAKYSPNWSHSNKVEAVVWTVPILIIIFLAVLTWKTTHALEPSKPLAHDEKPITIEVVSMDWKWFFIYPEQGIATVNEIAFPANTPVYFKVTSNSVMNSFFIPRLGSQIYAMAGMQTRLHLIANEPGTYDGISASYSGPGFSGMKFKAIATPDRAAFDQWVAKAKQSPNTMSDMAAFEKLAAPSEYNQVEYFSNVKPDLFADVINKFMAHGKSMDMTQPEGEHSAHEGMEGMDMSHAESAH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10178
Length:	315 (254)
Sequences:	2132 (1465)
Seq/√Len:	91.9

ECOLI - CYOA
BACSU - QOX2 COX2
HALSA - Q9HRJ9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
228_R	232_D	5.481	1.00
165_V	185_A	4.057	1.00
226_P	230_A	4.019	1.00
200_P	226_P	3.909	1.00
129_I	153_I	3.775	1.00
159_T	228_R	3.739	1.00
145_Q	231_F	3.579	1.00
155_F	197_A	3.482	1.00
45_L	49_G	3.409	1.00
173_S	182_Q	3.367	1.00
154_A	225_T	3.365	1.00
155_F	222_A	3.085	1.00
157_A	224_A	3.004	1.00
147_I	235_V	2.846	1.00
200_P	224_A	2.681	1.00
130_E	164_K	2.614	1.00
197_A	224_A	2.571	1.00
180_G	195_L	2.412	1.00
202_T	221_K	2.395	1.00
133_S	185_A	2.273	1.00
230_A	233_Q	2.233	1.00
172_N	207_S	2.167	1.00
35_Q	198_N	2.122	1.00
200_P	230_A	2.122	1.00
98_L	102_F	2.122	1.00
126_P	159_T	2.107	1.00
134_M	139_F	2.107	1.00
128_T	162_Y	2.079	1.00
207_S	211_S	2.056	1.00
204_D	221_K	2.055	1.00
173_S	208_A	2.018	1.00
130_E	141_I	1.996	1.00
157_A	200_P	1.979	1.00
172_N	211_S	1.914	1.00
47_A	103_L	1.912	1.00
226_P	229_A	1.905	1.00
109_K	113_A	1.888	1.00
162_Y	192_R	1.882	1.00
127_I	231_F	1.821	1.00
60_L	64_G	1.798	1.00
157_A	228_R	1.798	1.00
163_F	195_L	1.780	1.00
35_Q	196_I	1.779	1.00
134_M	168_N	1.755	1.00
22_L	25_C	1.746	1.00
225_T	230_A	1.707	1.00
63_V	67_W	1.701	1.00
182_Q	209_S	1.670	1.00
132_V	141_I	1.626	1.00
263_V	267_S	1.600	1.00
254_L	258_S	1.597	1.00
176_I	222_A	1.582	1.00
200_P	203_Y	1.575	1.00
161_V	197_A	1.535	1.00
87_K	92_V	1.524	1.00
38_L	198_N	1.512	1.00
33_K	199_E	1.464	1.00
202_T	223_I	1.454	1.00
206_I	219_K	1.453	1.00
253_K	256_A	1.448	0.99
261_N	264_E	1.425	0.99
59_I	63_V	1.416	0.99
152_E	223_I	1.411	0.99
128_T	144_E	1.406	0.99
233_Q	237_K	1.379	0.99
207_S	218_M	1.372	0.99
41_R	45_L	1.361	0.99
17_A	21_L	1.339	0.99
154_A	223_I	1.335	0.99
128_T	164_K	1.330	0.99
205_G	220_F	1.326	0.99
203_Y	224_A	1.314	0.99
42_S	46_T	1.311	0.99
211_S	215_F	1.302	0.99
184_Y	209_S	1.283	0.99
64_G	68_K	1.278	0.99
255_A	259_E	1.274	0.99
115_E	183_I	1.272	0.99
39_E	42_S	1.263	0.99
129_I	145_Q	1.259	0.99
165_V	183_I	1.259	0.99
164_K	190_Q	1.250	0.99
32_P	37_G	1.247	0.98
39_E	113_A	1.229	0.98
251_F	254_L	1.228	0.98
204_D	219_K	1.211	0.98
258_S	262_Q	1.199	0.98
263_V	266_F	1.199	0.98
135_D	170_V	1.182	0.98
140_F	153_I	1.178	0.98
38_L	42_S	1.161	0.98
236_A	239_K	1.160	0.98
258_S	263_V	1.150	0.97
35_Q	39_E	1.147	0.97
151_N	238_A	1.135	0.97
246_S	249_A	1.131	0.97
110_T	113_A	1.131	0.97
255_A	258_S	1.129	0.97
207_S	215_F	1.126	0.97
158_N	228_R	1.122	0.97
145_Q	235_V	1.114	0.97
158_N	198_N	1.109	0.97
89_E	93_W	1.101	0.97
85_S	89_E	1.085	0.96
127_I	159_T	1.082	0.96
217_G	260_Y	1.077	0.96
155_F	224_A	1.042	0.95
105_V	109_K	1.042	0.95
12_W	16_F	1.038	0.95
73_N	76_A	1.034	0.95
175_F	208_A	1.027	0.95
49_G	53_I	1.005	0.94
33_K	178_R	1.001	0.94
126_P	160_P	0.999	0.94
163_F	193_L	0.998	0.94
254_L	257_P	0.992	0.94
46_T	106_L	0.992	0.94
28_A	178_R	0.988	0.94
34_G	179_L	0.976	0.93
238_A	265_Y	0.975	0.93
130_E	166_T	0.971	0.93
179_L	197_A	0.960	0.93
20_V	23_S	0.958	0.93
251_F	255_A	0.953	0.93
237_K	241_S	0.948	0.92
32_P	111_T	0.942	0.92
183_I	193_L	0.939	0.92
38_L	41_R	0.939	0.92
143_P	147_I	0.931	0.92
23_S	27_S	0.927	0.92
250_A	253_K	0.924	0.91
65_F	69_Y	0.922	0.91
238_A	241_S	0.909	0.91
18_G	22_L	0.906	0.91
258_S	266_F	0.903	0.91
19_T	23_S	0.895	0.90
231_F	235_V	0.891	0.90
117_S	191_T	0.888	0.90
108_W	112_H	0.883	0.90
20_V	25_C	0.880	0.89
258_S	261_N	0.876	0.89
131_V	140_F	0.875	0.89
259_E	263_V	0.875	0.89
49_G	52_L	0.873	0.89
232_D	236_A	0.872	0.89
45_L	48_F	0.869	0.89
146_G	239_K	0.858	0.88
155_F	161_V	0.858	0.88
64_G	69_Y	0.848	0.88
124_E	158_N	0.840	0.87
267_S	271_P	0.839	0.87
36_I	40_Q	0.835	0.87
170_V	211_S	0.831	0.86
266_F	269_V	0.830	0.86
74_K	77_K	0.826	0.86
208_A	215_F	0.824	0.86
171_M	187_A	0.807	0.85
13_L	16_F	0.806	0.85
171_M	186_M	0.806	0.85
140_F	220_F	0.805	0.85
135_D	169_S	0.802	0.84
14_S	18_G	0.801	0.84
46_T	50_L	0.800	0.84
211_S	218_M	0.800	0.84
170_V	209_S	0.796	0.84
172_N	215_F	0.793	0.84
179_L	224_A	0.790	0.84
139_F	148_A	0.788	0.83
246_S	250_A	0.784	0.83
182_Q	208_A	0.784	0.83
155_F	179_L	0.779	0.83
102_F	105_V	0.776	0.82
175_F	206_I	0.775	0.82
259_E	262_Q	0.771	0.82
245_M	251_F	0.770	0.82
162_Y	194_H	0.768	0.82
223_I	226_P	0.767	0.82
263_V	271_P	0.764	0.81
39_E	110_T	0.763	0.81
267_S	270_K	0.763	0.81
233_Q	236_A	0.762	0.81
49_G	98_L	0.761	0.81
53_I	57_P	0.760	0.81
70_R	74_K	0.750	0.80
155_F	195_L	0.747	0.80
252_E	259_E	0.742	0.80
44_I	110_T	0.737	0.79
155_F	158_N	0.734	0.79
93_W	96_P	0.733	0.79
35_Q	197_A	0.728	0.78
89_E	96_P	0.727	0.78
258_S	267_S	0.727	0.78
209_S	215_F	0.726	0.78
71_A	76_A	0.722	0.78
32_P	108_W	0.722	0.78
16_F	19_T	0.719	0.77
160_P	196_I	0.719	0.77
186_M	189_M	0.719	0.77
117_S	192_R	0.714	0.77
235_V	239_K	0.711	0.77
169_S	172_N	0.705	0.76
152_E	210_Y	0.704	0.76
259_E	264_E	0.703	0.76
21_L	24_G	0.700	0.76
131_V	173_S	0.698	0.75
94_T	169_S	0.694	0.75
157_A	197_A	0.690	0.74
134_M	186_M	0.690	0.74
40_Q	114_L	0.685	0.74
255_A	260_Y	0.683	0.74
165_V	193_L	0.683	0.74
11_G	14_S	0.682	0.74
22_L	26_N	0.682	0.74
229_A	233_Q	0.681	0.74
236_A	240_Q	0.679	0.73
243_N	246_S	0.678	0.73
94_T	98_L	0.677	0.73
53_I	95_V	0.674	0.73
240_Q	244_T	0.672	0.73
31_D	41_R	0.671	0.72
169_S	207_S	0.670	0.72
40_Q	180_G	0.668	0.72
210_Y	213_P	0.668	0.72
169_S	187_A	0.666	0.72
258_S	269_V	0.666	0.72
198_N	224_A	0.665	0.72
69_Y	89_E	0.664	0.72
140_F	174_F	0.663	0.72
101_I	105_V	0.661	0.71
80_P	140_F	0.661	0.71
173_S	209_S	0.658	0.71
13_L	18_G	0.657	0.71
161_V	222_A	0.657	0.71
117_S	194_H	0.653	0.70
72_S	76_A	0.652	0.70
35_Q	180_G	0.652	0.70
22_L	129_I	0.650	0.70
30_L	34_G	0.650	0.70
167_S	185_A	0.649	0.70
266_F	270_K	0.647	0.70
141_I	167_S	0.644	0.69
124_E	228_R	0.642	0.69
16_F	23_S	0.641	0.69
172_N	209_S	0.641	0.69
229_A	249_A	0.641	0.69
71_A	74_K	0.640	0.69
176_I	182_Q	0.639	0.69
262_Q	266_F	0.636	0.68
133_S	209_S	0.636	0.68
180_G	205_G	0.635	0.68
169_S	182_Q	0.635	0.68
262_Q	267_S	0.634	0.68
88_V	93_W	0.630	0.68
164_K	192_R	0.630	0.68
215_F	218_M	0.628	0.67
79_S	83_S	0.628	0.67
19_T	24_G	0.628	0.67
134_M	137_K	0.627	0.67
132_V	166_T	0.626	0.67
255_A	270_K	0.626	0.67
33_K	155_F	0.624	0.67
50_L	103_L	0.621	0.67
217_G	259_E	0.620	0.66
50_L	53_I	0.616	0.66
91_V	94_T	0.616	0.66
153_I	222_A	0.613	0.66
229_A	232_D	0.612	0.65
237_K	265_Y	0.611	0.65
100_I	140_F	0.602	0.64
42_S	45_L	0.600	0.64
172_N	218_M	0.598	0.64
98_L	101_I	0.595	0.63
131_V	174_F	0.594	0.63
175_F	182_Q	0.591	0.63
55_V	59_I	0.591	0.63
89_E	94_T	0.590	0.63
131_V	163_F	0.589	0.62
23_S	26_N	0.589	0.62
256_A	262_Q	0.587	0.62
37_G	40_Q	0.584	0.62
182_Q	207_S	0.583	0.62
63_V	66_A	0.582	0.62
197_A	222_A	0.582	0.62
16_F	20_V	0.580	0.61
136_W	210_Y	0.579	0.61
137_K	150_V	0.577	0.61
249_A	252_E	0.576	0.61
253_K	267_S	0.573	0.60
20_V	102_F	0.573	0.60
57_P	99_I	0.572	0.60
30_L	178_R	0.572	0.60
31_D	37_G	0.571	0.60
51_M	214_G	0.570	0.60
233_Q	249_A	0.569	0.60
33_K	197_A	0.569	0.60
137_K	214_G	0.568	0.60
34_G	181_S	0.565	0.59
37_G	180_G	0.563	0.59
79_S	84_H	0.563	0.59
52_L	56_I	0.563	0.59
159_T	232_D	0.562	0.59
154_A	170_V	0.559	0.58
167_S	187_A	0.558	0.58
39_E	198_N	0.558	0.58
37_G	181_S	0.558	0.58
88_V	91_V	0.558	0.58
54_V	95_V	0.557	0.58
172_N	182_Q	0.557	0.58
25_C	34_G	0.556	0.58
117_S	190_Q	0.555	0.58
107_T	209_S	0.553	0.58
133_S	211_S	0.553	0.58
50_L	102_F	0.552	0.58
129_I	155_F	0.552	0.58
100_I	174_F	0.552	0.58
178_R	210_Y	0.551	0.57
254_L	266_F	0.547	0.57
136_W	201_G	0.546	0.57
122_H	196_I	0.544	0.56
37_G	111_T	0.543	0.56
35_Q	224_A	0.542	0.56
251_F	257_P	0.542	0.56
129_I	163_F	0.539	0.56
132_V	139_F	0.538	0.56
246_S	252_E	0.537	0.55
25_C	52_L	0.535	0.55
54_V	83_S	0.534	0.55
86_N	92_V	0.534	0.55
65_F	68_K	0.534	0.55
151_N	186_M	0.532	0.55
139_F	231_F	0.532	0.55
260_Y	263_V	0.532	0.55
102_F	107_T	0.531	0.55
50_L	185_A	0.531	0.55
264_E	267_S	0.531	0.55
133_S	264_E	0.530	0.55
100_I	115_E	0.529	0.54
92_V	95_V	0.528	0.54
29_L	40_Q	0.528	0.54
258_S	270_K	0.528	0.54
229_A	253_K	0.526	0.54
138_W	185_A	0.526	0.54
183_I	194_H	0.526	0.54
70_R	73_N	0.524	0.54
241_S	244_T	0.524	0.54
58_A	107_T	0.523	0.54
122_H	160_P	0.521	0.53
54_V	107_T	0.519	0.53
24_G	27_S	0.518	0.53
200_P	229_A	0.518	0.53
99_I	185_A	0.517	0.53
153_I	163_F	0.517	0.53
123_D	128_T	0.516	0.53
265_Y	268_N	0.516	0.53
174_F	220_F	0.516	0.53
65_F	80_P	0.514	0.52
266_F	271_P	0.514	0.52
263_V	269_V	0.513	0.52
137_K	254_L	0.513	0.52
145_Q	239_K	0.511	0.52
154_A	157_A	0.511	0.52
122_H	125_K	0.511	0.52
146_G	232_D	0.510	0.52
84_H	89_E	0.509	0.52
37_G	178_R	0.509	0.52
89_E	140_F	0.508	0.51
184_Y	215_F	0.508	0.51
202_T	233_Q	0.508	0.51
104_A	107_T	0.507	0.51
21_L	124_E	0.507	0.51
35_Q	144_E	0.506	0.51
175_F	181_S	0.506	0.51
133_S	172_N	0.505	0.51
125_K	128_T	0.505	0.51
128_T	145_Q	0.505	0.51
18_G	21_L	0.504	0.51
54_V	231_F	0.503	0.51
87_K	91_V	0.501	0.51
37_G	88_V	0.501	0.51
253_K	257_P	0.500	0.50
171_M	185_A	0.500	0.50

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
1fftB	1	0.8127	100	0.201	Contact Map
2yevB	1	0.8889	100	0.346	Contact Map
3hb3B	1	0.6825	100	0.359	Contact Map
2gsmB	1	0.6889	100	0.393	Contact Map
1v54B	1	0.6476	100	0.43	Contact Map
1cyxA	1	0.4984	100	0.458	Contact Map
4txvB	1	0.4032	100	0.542	Contact Map
3s8fB	1	0.4571	100	0.635	Contact Map
2cuaA	1	0.4032	100	0.727	Contact Map
3sbqA	2	0.6286	99.9	0.751	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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