QCRC - BACSU - GREMLIN Contacts

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QCRC - Menaquinol-cytochrome c reductase cytochrome b/c subunit

UniProt:	P46913	Sequences: MHRGKGMKFVGDSRIPAEKKPNIPKDYSEYPGKTEAFWPNFLLKEWMVGAVFLIGFLVLTIVHQPPLERMADPTDTGYIPLPDWYFLFLYQLLKYEYAAGSFTVVGAMIMPGLAFGALLLAPFLDRGTERRPWKRPVAVGMMLLAISAAVFLTWQSVATHDWAKAEEQGKITKEADIDTNAEGYKVFKEQGCISCHGDNLQGGAAGPSLVDSGLKPDEIKKIAVEGKGKMPAGVFKGNDKQLEELAKFISETTAK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	255 (231)
Sequences:	253 (179)
Seq/√Len:	11.8

BACSU - QCRC

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
221_K	225_E	6.412	1.00
215_K	218_E	4.367	1.00
137_V	141_M	4.095	0.99
129_E	134_K	3.896	0.99
19_K	22_N	3.126	0.96
18_E	21_P	3.030	0.96
69_R	75_D	3.028	0.96
160_H	165_A	3.022	0.96
68_E	78_Y	2.919	0.95
182_E	244_E	2.664	0.91
88_F	153_T	2.588	0.90
235_F	241_Q	2.523	0.89
151_F	155_Q	2.437	0.87
92_L	156_S	2.389	0.86
91_Q	95_Y	2.355	0.85
83_D	226_G	2.346	0.85
213_G	250_S	2.318	0.84
61_I	70_M	2.302	0.84
113_L	133_W	2.285	0.83
237_G	242_L	2.200	0.81
112_G	120_L	2.142	0.79
191_G	194_S	2.142	0.79
241_Q	244_E	2.139	0.79
77_G	105_V	2.131	0.79
217_D	220_K	2.081	0.77
187_F	245_L	2.004	0.74
198_D	201_Q	2.000	0.74
110_M	126_R	1.971	0.73
187_F	193_I	1.948	0.72
54_I	155_Q	1.793	0.65
108_M	158_A	1.589	0.56
79_I	156_S	1.583	0.55
194_S	203_G	1.580	0.55
59_L	66_P	1.569	0.55
238_N	241_Q	1.558	0.54
174_E	179_T	1.545	0.53
33_K	151_F	1.545	0.53
103_T	151_F	1.544	0.53
167_E	170_K	1.528	0.53
62_V	156_S	1.519	0.52
191_G	234_V	1.518	0.52
56_F	65_P	1.505	0.51
68_E	249_I	1.504	0.51
80_P	136_P	1.485	0.50
44_K	153_T	1.483	0.50
91_Q	100_G	1.473	0.50
147_S	175_A	1.469	0.50
73_P	87_L	1.438	0.48
161_D	164_K	1.398	0.46
188_K	212_S	1.392	0.46
176_D	243_E	1.385	0.45
185_K	236_K	1.381	0.45
220_K	246_A	1.376	0.45
80_P	135_R	1.368	0.45
177_I	180_N	1.364	0.44
108_M	221_K	1.360	0.44
128_T	223_A	1.352	0.44
154_W	169_G	1.342	0.43
73_P	111_P	1.338	0.43
189_E	223_A	1.336	0.43
183_G	188_K	1.328	0.43
43_L	94_K	1.324	0.42
76_T	190_Q	1.313	0.42
189_E	198_D	1.307	0.42
212_S	249_I	1.302	0.41
56_F	143_L	1.301	0.41
108_M	123_F	1.298	0.41
216_P	250_S	1.293	0.41
219_I	222_I	1.290	0.41
33_K	129_E	1.245	0.39
173_K	212_S	1.241	0.38
137_V	216_P	1.228	0.38
19_K	206_G	1.226	0.38
203_G	207_P	1.224	0.38
212_S	218_E	1.223	0.38
162_W	168_Q	1.222	0.38
71_A	94_K	1.217	0.37
98_A	206_G	1.195	0.36
54_I	146_I	1.184	0.36
76_T	101_S	1.169	0.35
205_A	229_K	1.169	0.35
84_W	122_P	1.148	0.34
130_R	135_R	1.146	0.34
165_A	168_Q	1.131	0.33
71_A	125_D	1.121	0.33
124_L	141_M	1.106	0.32
211_D	248_F	1.103	0.32
187_F	241_Q	1.101	0.32
30_Y	119_L	1.097	0.32
42_L	45_E	1.094	0.32
108_M	214_L	1.088	0.32
33_K	131_R	1.081	0.31
109_I	238_N	1.080	0.31
42_L	46_W	1.080	0.31
205_A	234_V	1.069	0.31
37_F	85_Y	1.045	0.30
37_F	82_P	1.042	0.30
241_Q	247_K	1.036	0.29
109_I	249_I	1.031	0.29
31_P	90_Y	1.026	0.29
25_K	52_F	1.023	0.29
148_A	187_F	1.014	0.28
25_K	36_A	1.013	0.28
214_L	227_K	1.011	0.28
216_P	220_K	1.011	0.28
64_Q	107_A	1.007	0.28
187_F	214_L	1.006	0.28
20_K	217_D	0.993	0.28
41_F	90_Y	0.990	0.28
80_P	83_D	0.984	0.27
220_K	243_E	0.981	0.27
58_V	70_M	0.973	0.27
192_C	230_M	0.970	0.27
196_H	230_M	0.970	0.27
192_C	195_C	0.970	0.27
195_C	230_M	0.970	0.27
192_C	196_H	0.970	0.27
18_E	113_L	0.968	0.27
54_I	128_T	0.954	0.26
188_K	241_Q	0.954	0.26
94_K	106_G	0.945	0.26
113_L	250_S	0.941	0.26
99_A	103_T	0.938	0.25
174_E	189_E	0.932	0.25
165_A	186_V	0.930	0.25
235_F	245_L	0.925	0.25
182_E	186_V	0.924	0.25
56_F	190_Q	0.923	0.25
225_E	243_E	0.920	0.25
194_S	198_D	0.915	0.25
30_Y	241_Q	0.908	0.24
43_L	106_G	0.906	0.24
183_G	248_F	0.906	0.24
181_A	244_E	0.900	0.24
151_F	154_W	0.898	0.24
52_F	169_G	0.897	0.24
105_V	174_E	0.897	0.24
34_T	160_H	0.894	0.24
38_W	81_L	0.893	0.24
109_I	137_V	0.891	0.24
194_S	206_G	0.890	0.24
118_L	138_A	0.881	0.23
70_M	75_D	0.881	0.23
93_L	153_T	0.879	0.23
127_G	208_S	0.870	0.23
80_P	138_A	0.868	0.23
203_G	206_G	0.864	0.23
215_K	250_S	0.862	0.23
216_P	243_E	0.861	0.23
183_G	187_F	0.861	0.23
80_P	202_G	0.860	0.23
217_D	239_D	0.857	0.23
101_S	251_E	0.851	0.22
31_P	106_G	0.851	0.22
83_D	87_L	0.850	0.22
154_W	181_A	0.846	0.22
183_G	210_V	0.842	0.22
187_F	244_E	0.842	0.22
234_V	251_E	0.827	0.22
198_D	215_K	0.826	0.21
129_E	151_F	0.825	0.21
76_T	125_D	0.819	0.21
189_E	232_A	0.818	0.21
109_I	170_K	0.814	0.21
91_Q	109_I	0.813	0.21
18_E	108_M	0.813	0.21
68_E	118_L	0.810	0.21
180_N	186_V	0.809	0.21
94_K	125_D	0.808	0.21
23_I	175_A	0.808	0.21
132_P	233_G	0.802	0.21
39_P	82_P	0.801	0.21
216_P	249_I	0.799	0.21
104_V	137_V	0.797	0.21
178_D	237_G	0.796	0.20
183_G	186_V	0.795	0.20
105_V	109_I	0.793	0.20
78_Y	128_T	0.792	0.20
233_G	237_G	0.788	0.20
146_I	227_K	0.787	0.20
65_P	139_V	0.785	0.20
248_F	252_T	0.782	0.20
51_V	124_L	0.781	0.20
37_F	152_L	0.780	0.20
80_P	130_R	0.778	0.20
85_Y	152_L	0.775	0.20
214_L	222_I	0.768	0.20
18_E	22_N	0.767	0.20
89_L	156_S	0.764	0.19
18_E	186_V	0.764	0.19
50_A	178_D	0.763	0.19
78_Y	155_Q	0.762	0.19
19_K	25_K	0.756	0.19
25_K	34_T	0.746	0.19
31_P	112_G	0.743	0.19
123_F	141_M	0.743	0.19
54_I	251_E	0.741	0.19
191_G	213_G	0.740	0.19
20_K	23_I	0.738	0.19
126_R	205_A	0.738	0.19
25_K	183_G	0.738	0.19
45_E	55_G	0.736	0.19
20_K	70_M	0.734	0.19
104_V	148_A	0.733	0.19
62_V	220_K	0.730	0.18
82_P	93_L	0.726	0.18
186_V	248_F	0.724	0.18
60_T	116_G	0.721	0.18
136_P	202_G	0.718	0.18
128_T	133_W	0.717	0.18
234_V	237_G	0.716	0.18
165_A	191_G	0.716	0.18
121_A	138_A	0.714	0.18
140_G	145_A	0.708	0.18
214_L	229_K	0.707	0.18
25_K	184_Y	0.705	0.18
224_V	244_E	0.704	0.18
146_I	190_Q	0.704	0.18
222_I	226_G	0.702	0.18
187_F	198_D	0.697	0.17
70_M	76_T	0.696	0.17
86_F	153_T	0.686	0.17
163_A	170_K	0.685	0.17
187_F	227_K	0.683	0.17
176_D	180_N	0.680	0.17
208_S	218_E	0.679	0.17
146_I	213_G	0.676	0.17
164_K	176_D	0.673	0.17
203_G	248_F	0.671	0.17
200_L	219_I	0.668	0.17
18_E	89_L	0.666	0.17
40_N	104_V	0.661	0.16
91_Q	107_A	0.661	0.16
157_V	168_Q	0.657	0.16
22_N	54_I	0.656	0.16
102_F	119_L	0.656	0.16
33_K	165_A	0.655	0.16
188_K	191_G	0.655	0.16
126_R	147_S	0.653	0.16
91_Q	94_K	0.652	0.16
20_K	158_A	0.648	0.16
186_V	244_E	0.647	0.16
49_G	53_L	0.647	0.16
190_Q	236_K	0.646	0.16
203_G	211_D	0.646	0.16
71_A	82_P	0.644	0.16
92_L	132_P	0.644	0.16
132_P	237_G	0.642	0.16
106_G	142_M	0.641	0.16
84_W	130_R	0.640	0.16
173_K	190_Q	0.639	0.16
202_G	226_G	0.639	0.16
175_A	217_D	0.637	0.16
39_P	122_P	0.635	0.16
82_P	85_Y	0.633	0.16
210_V	244_E	0.633	0.16
95_Y	111_P	0.632	0.16
19_K	232_A	0.631	0.16
101_S	126_R	0.630	0.16
59_L	63_H	0.627	0.16
165_A	227_K	0.623	0.15
148_A	173_K	0.623	0.15
179_T	189_E	0.622	0.15
126_R	200_L	0.619	0.15
65_P	70_M	0.617	0.15
115_F	193_I	0.615	0.15
21_P	150_V	0.615	0.15
229_K	232_A	0.614	0.15
179_T	242_L	0.613	0.15
175_A	178_D	0.602	0.15
150_V	217_D	0.601	0.15
67_L	130_R	0.595	0.15
178_D	184_Y	0.593	0.15
52_F	180_N	0.591	0.15
126_R	229_K	0.590	0.15
47_M	248_F	0.588	0.15
207_P	231_P	0.588	0.15
146_I	176_D	0.585	0.14
129_E	215_K	0.582	0.14
239_D	242_L	0.577	0.14
134_K	138_A	0.576	0.14
80_P	231_P	0.575	0.14
215_K	221_K	0.574	0.14
56_F	177_I	0.574	0.14
180_N	215_K	0.574	0.14
42_L	48_V	0.574	0.14
87_L	228_G	0.571	0.14
173_K	187_F	0.570	0.14
189_E	241_Q	0.569	0.14
99_A	151_F	0.569	0.14
108_M	147_S	0.567	0.14
37_F	93_L	0.565	0.14
82_P	122_P	0.565	0.14
160_H	169_G	0.562	0.14
72_D	200_L	0.561	0.14
136_P	231_P	0.561	0.14
29_E	68_E	0.558	0.14
58_V	62_V	0.557	0.14
182_E	239_D	0.556	0.14
43_L	56_F	0.556	0.14
167_E	173_K	0.553	0.14
64_Q	72_D	0.553	0.14
221_K	245_L	0.552	0.14
199_N	225_E	0.549	0.14
119_L	159_T	0.547	0.14
18_E	217_D	0.546	0.14
81_L	90_Y	0.546	0.14
55_G	124_L	0.546	0.14
18_E	191_G	0.543	0.13
39_P	84_W	0.542	0.13
71_A	91_Q	0.541	0.13
216_P	247_K	0.541	0.13
71_A	85_Y	0.541	0.13
62_V	99_A	0.537	0.13
179_T	250_S	0.537	0.13
130_R	197_G	0.536	0.13
26_D	36_A	0.536	0.13
92_L	111_P	0.536	0.13
119_L	148_A	0.535	0.13
156_S	161_D	0.534	0.13
18_E	210_V	0.532	0.13
56_F	105_V	0.531	0.13
149_A	180_N	0.530	0.13
240_K	251_E	0.529	0.13
138_A	159_T	0.528	0.13
91_Q	106_G	0.523	0.13
22_N	220_K	0.520	0.13
148_A	214_L	0.520	0.13
133_W	149_A	0.519	0.13
52_F	239_D	0.517	0.13
81_L	105_V	0.517	0.13
120_L	209_L	0.517	0.13
41_F	45_E	0.516	0.13
39_P	85_Y	0.516	0.13
35_E	142_M	0.512	0.13
174_E	180_N	0.510	0.13
233_G	247_K	0.507	0.13
143_L	147_S	0.505	0.13
99_A	247_K	0.504	0.13
65_P	107_A	0.504	0.13
27_Y	30_Y	0.503	0.13
116_G	145_A	0.502	0.13
188_K	251_E	0.502	0.13
146_I	211_D	0.501	0.13
177_I	183_G	0.501	0.13
52_F	183_G	0.500	0.13

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
2qjyA	2	0.7647	99.9	0.747	Contact Map
4ogqB	1	0.6157	99.9	0.752	Contact Map
3cx5C	2	0.698	99.9	0.763	Contact Map
1pp9C	2	0.6784	99.9	0.769	Contact Map
3mk7B	1	0.4784	99.7	0.799	Contact Map
3mk7C	2	0.6157	99.7	0.802	Contact Map
3wfdC	1	0.4627	99.7	0.813	Contact Map
4pwaA	3	0.3098	99.6	0.817	Contact Map
1w2lA	1	0.2941	99.6	0.823	Contact Map
3oa8A	1	0.3255	99.6	0.826	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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