CYBH - ECOLI - GREMLIN Contacts

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CYBH - Probable Ni/Fe-hydrogenase 1 B-type cytochrome subunit

UniProt:	P0AAM1	Sequences: MQQKSDNVVSHYVFEAPVRIWHWLTVLCMAVLMVTGYFIGKPLPSVSGEATYLFYMGYIRLIHFSAGMVFTVVLLMRIYWAFVGNRYSRELFIVPVWRKSWWQGVWYEIRWYLFLAKRPSADIGHNPIAQAAMFGYFLMSVFMIITGFALYSEHSQYAIFAPFRYVVEFFYWTGGNSMDIHSWHRLGMWLIGAFVIGHVYMALREDIMSDDTVISTMVNGYRSHKFGKISNKERS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10470
Length:	235 (189)
Sequences:	1888 (1371)
Seq/√Len:	99.7

ECOLI - CYBH PHSC FDNI FDOI

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
31_V	66_A	5.113	1.00
12_Y	221_Y	3.442	1.00
142_F	187_G	3.053	1.00
10_S	221_Y	2.980	1.00
139_M	194_F	2.320	1.00
70_F	140_S	2.257	1.00
182_S	185_R	2.247	1.00
33_M	195_V	2.208	1.00
19_R	220_G	2.172	1.00
23_W	26_V	2.155	1.00
206_D	212_T	2.108	1.00
142_F	183_W	2.104	1.00
25_T	73_V	2.078	1.00
79_Y	83_V	2.044	1.00
74_L	140_S	2.039	1.00
21_W	73_V	2.034	1.00
30_A	34_V	2.020	1.00
80_W	84_G	1.899	1.00
74_L	144_I	1.888	1.00
17_P	80_W	1.881	1.00
28_C	70_F	1.881	1.00
71_T	144_I	1.821	1.00
33_M	188_M	1.818	1.00
24_L	73_V	1.756	1.00
95_P	134_F	1.751	1.00
62_I	65_S	1.716	1.00
18_V	80_W	1.675	1.00
26_V	30_A	1.639	1.00
140_S	191_I	1.631	1.00
143_M	187_G	1.621	1.00
32_L	66_A	1.609	1.00
21_W	76_M	1.604	1.00
17_P	76_M	1.602	1.00
106_W	110_R	1.595	1.00
132_A	194_F	1.591	1.00
95_P	130_Q	1.586	1.00
189_W	193_A	1.578	1.00
25_T	70_F	1.572	1.00
150_L	181_H	1.542	1.00
33_M	192_G	1.540	1.00
71_T	148_F	1.528	1.00
199_V	202_A	1.516	1.00
18_V	88_S	1.506	1.00
103_Q	107_Y	1.491	1.00
29_M	191_I	1.486	1.00
95_P	104_G	1.472	1.00
135_G	194_F	1.469	1.00
16_A	20_I	1.459	1.00
212_T	216_T	1.445	1.00
107_Y	110_R	1.441	1.00
215_S	219_N	1.441	1.00
202_A	214_I	1.384	0.99
39_I	42_P	1.363	0.99
85_N	88_S	1.356	0.99
105_V	131_A	1.356	0.99
15_E	80_W	1.334	0.99
32_L	70_F	1.325	0.99
192_G	196_I	1.321	0.99
202_A	205_E	1.296	0.99
40_G	185_R	1.277	0.99
20_I	24_L	1.274	0.99
206_D	215_S	1.260	0.99
195_V	199_V	1.248	0.99
108_E	127_P	1.247	0.99
68_M	72_V	1.229	0.99
133_M	194_F	1.221	0.99
129_A	133_M	1.217	0.99
182_S	186_L	1.214	0.99
181_H	185_R	1.211	0.99
149_A	180_I	1.205	0.99
64_F	156_Q	1.198	0.98
125_H	129_A	1.192	0.98
37_Y	188_M	1.189	0.98
179_D	183_W	1.178	0.98
196_I	200_Y	1.168	0.98
93_I	130_Q	1.168	0.98
29_M	195_V	1.163	0.98
28_C	69_V	1.159	0.98
110_R	116_A	1.149	0.98
14_F	125_H	1.119	0.98
42_P	56_M	1.118	0.98
193_A	197_G	1.103	0.97
178_M	181_H	1.102	0.97
67_G	70_F	1.098	0.97
96_V	104_G	1.089	0.97
151_Y	177_S	1.071	0.97
114_F	117_K	1.068	0.97
26_V	199_V	1.063	0.97
200_Y	204_R	1.060	0.97
41_K	67_G	1.050	0.97
177_S	180_I	1.048	0.96
77_R	81_A	1.047	0.96
178_M	182_S	1.045	0.96
15_E	88_S	1.042	0.96
87_Y	92_F	1.040	0.96
205_E	213_V	1.038	0.96
64_F	68_M	1.038	0.96
111_W	118_R	1.037	0.96
61_L	65_S	1.023	0.96
129_A	213_V	1.018	0.96
32_L	36_G	1.014	0.96
38_F	42_P	1.006	0.96
139_M	190_L	0.996	0.95
23_W	218_V	0.984	0.95
136_Y	190_L	0.979	0.95
176_N	179_D	0.978	0.95
31_V	35_T	0.977	0.95
123_I	222_R	0.976	0.95
108_E	111_W	0.972	0.95
58_Y	62_I	0.952	0.94
74_L	137_F	0.950	0.94
142_F	145_I	0.948	0.94
177_S	181_H	0.927	0.93
132_A	135_G	0.920	0.93
131_A	135_G	0.919	0.93
35_T	66_A	0.919	0.93
21_W	25_T	0.918	0.93
204_R	208_M	0.907	0.92
206_D	209_S	0.901	0.92
104_G	127_P	0.901	0.92
80_W	88_S	0.897	0.92
95_P	105_V	0.895	0.92
109_I	113_L	0.893	0.92
124_G	222_R	0.893	0.92
27_L	31_V	0.892	0.92
64_F	151_Y	0.889	0.92
28_C	31_V	0.889	0.92
187_G	190_L	0.888	0.92
82_F	86_R	0.872	0.91
72_V	75_L	0.869	0.91
35_T	59_I	0.866	0.91
151_Y	181_H	0.863	0.90
33_M	37_Y	0.862	0.90
82_F	106_W	0.852	0.90
199_V	214_I	0.851	0.90
153_E	156_Q	0.847	0.90
43_L	56_M	0.845	0.89
78_I	82_F	0.838	0.89
14_F	77_R	0.834	0.89
65_S	68_M	0.833	0.89
84_G	87_Y	0.826	0.88
9_V	141_V	0.824	0.88
214_I	217_M	0.822	0.88
12_Y	15_E	0.813	0.88
64_F	180_I	0.809	0.87
186_L	190_L	0.806	0.87
122_D	127_P	0.805	0.87
111_W	119_P	0.804	0.87
191_I	195_V	0.803	0.87
111_W	117_K	0.803	0.87
215_S	218_V	0.799	0.87
57_G	181_H	0.798	0.87
107_Y	203_L	0.792	0.86
105_V	128_I	0.785	0.86
28_C	66_A	0.782	0.85
105_V	108_E	0.781	0.85
185_R	189_W	0.781	0.85
36_G	188_M	0.777	0.85
212_T	215_S	0.773	0.85
40_G	45_S	0.771	0.85
167_V	176_N	0.771	0.85
111_W	120_S	0.768	0.84
150_L	177_S	0.767	0.84
147_G	184_H	0.765	0.84
45_S	113_L	0.764	0.84
136_Y	194_F	0.759	0.84
17_P	84_G	0.747	0.83
41_K	45_S	0.746	0.83
29_M	188_M	0.745	0.83
16_A	72_V	0.745	0.83
103_Q	106_W	0.743	0.82
123_I	138_L	0.742	0.82
79_Y	200_Y	0.742	0.82
133_M	202_A	0.741	0.82
213_V	216_T	0.738	0.82
26_V	195_V	0.733	0.82
25_T	67_G	0.733	0.82
82_F	97_W	0.730	0.81
38_F	59_I	0.728	0.81
69_V	73_V	0.727	0.81
33_M	189_W	0.726	0.81
165_Y	168_E	0.723	0.81
15_E	84_G	0.721	0.81
94_V	97_W	0.718	0.80
81_A	93_I	0.718	0.80
128_I	194_F	0.715	0.80
151_Y	154_H	0.715	0.80
107_Y	111_W	0.708	0.79
203_L	207_I	0.700	0.79
151_Y	155_S	0.690	0.78
108_E	213_V	0.689	0.77
151_Y	180_I	0.685	0.77
80_W	219_N	0.676	0.76
38_F	43_L	0.673	0.76
13_V	204_R	0.672	0.76
10_S	223_S	0.672	0.76
215_S	223_S	0.672	0.76
80_W	125_H	0.669	0.75
21_W	74_L	0.667	0.75
39_I	60_R	0.663	0.75
146_T	150_L	0.663	0.75
87_Y	124_G	0.659	0.74
67_G	77_R	0.657	0.74
152_S	180_I	0.644	0.73
14_F	124_G	0.635	0.72
202_A	206_D	0.635	0.72
140_S	190_L	0.632	0.71
32_L	219_N	0.631	0.71
17_P	21_W	0.630	0.71
29_M	33_M	0.622	0.70
148_F	159_I	0.620	0.70
78_I	81_A	0.618	0.69
136_Y	140_S	0.617	0.69
35_T	54_F	0.617	0.69
151_Y	183_W	0.614	0.69
77_R	125_H	0.613	0.69
24_L	69_V	0.611	0.69
84_G	88_S	0.609	0.68
141_V	144_I	0.607	0.68
37_Y	57_G	0.605	0.68
41_K	185_R	0.602	0.67
148_F	167_V	0.602	0.67
132_A	136_Y	0.601	0.67
32_L	65_S	0.601	0.67
19_R	218_V	0.601	0.67
153_E	178_M	0.601	0.67
70_F	74_L	0.600	0.67
19_R	23_W	0.598	0.67
70_F	144_I	0.594	0.66
11_H	224_H	0.593	0.66
30_A	33_M	0.592	0.66
205_E	209_S	0.590	0.66
24_L	107_Y	0.589	0.66
107_Y	131_A	0.589	0.66
110_R	114_F	0.588	0.66
152_S	155_S	0.587	0.66
139_M	143_M	0.583	0.65
136_Y	197_G	0.580	0.65
29_M	139_M	0.577	0.64
138_L	195_V	0.575	0.64
13_V	124_G	0.575	0.64
183_W	186_L	0.574	0.64
136_Y	139_M	0.573	0.64
212_T	223_S	0.573	0.64
75_L	104_G	0.569	0.63
150_L	188_M	0.568	0.63
32_L	67_G	0.566	0.63
81_A	84_G	0.564	0.62
58_Y	65_S	0.564	0.62
37_Y	192_G	0.563	0.62
12_Y	17_P	0.562	0.62
42_P	77_R	0.561	0.62
203_L	214_I	0.560	0.62
60_R	156_Q	0.557	0.61
124_G	129_A	0.554	0.61
64_F	153_E	0.551	0.61
18_V	81_A	0.549	0.60
146_T	184_H	0.547	0.60
166_V	217_M	0.547	0.60
80_W	201_M	0.546	0.60
174_G	178_M	0.545	0.60
71_T	195_V	0.541	0.59
45_S	182_S	0.540	0.59
103_Q	117_K	0.540	0.59
72_V	145_I	0.539	0.59
38_F	44_P	0.539	0.59
111_W	114_F	0.538	0.59
94_V	134_F	0.535	0.58
11_H	192_G	0.535	0.58
60_R	64_F	0.529	0.58
27_L	30_A	0.528	0.57
37_Y	189_W	0.527	0.57
108_E	121_A	0.527	0.57
62_I	167_V	0.526	0.57
36_G	57_G	0.515	0.56
209_S	212_T	0.514	0.55
17_P	72_V	0.513	0.55
106_W	109_I	0.511	0.55
14_F	129_A	0.510	0.55
55_Y	58_Y	0.510	0.55
18_V	84_G	0.507	0.54
106_W	179_D	0.505	0.54
17_P	85_N	0.503	0.54
80_W	85_N	0.500	0.53

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
4gd3A	2	0.7489	100	0.342	Contact Map
1kqfC	3	0.8468	100	0.501	Contact Map
3cx5C	2	0.817	90	0.914	Contact Map
2qjyA	2	0.8383	89.9	0.914	Contact Map
1pp9C	2	0.7745	86.1	0.92	Contact Map
4ogqA	2	0.5787	62.2	0.935	Contact Map
4o6yA	2	0.6383	38.5	0.943	Contact Map
1q16C	2	0.7489	21.5	0.95	Contact Map
4cbcA	3	0.3319	4.8	0.963	Contact Map
3vouA	4	0.5277	4.3	0.964	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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