FDOI - ECOLI - GREMLIN Contacts

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FDOI - Formate dehydrogenase, cytochrome b556(fdo) subunit

UniProt:	P0AEL0	Sequences: MKRRDTIVRYTAPERINHWITAFCFILAAVSGLGFLFPSFNWLMQIMGTPQLARILHPFVGVVMFASFIIMFFRYWHHNLINRDDIFWAKNIRKIVVNEEVGDTGRYNFGQKCVFWAAIIFLVLLLVSGVIIWRPYFAPAFSIPVIRFALMLHSFAAVALIVVIMVHIYAALWVKGTITAMVEGWVTSAWAKKHHPRWYREVRKTTEKKAE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11856
Length:	211 (183)
Sequences:	2230 (1512)
Seq/√Len:	111.8

ECOLI - FDOI FDNI PHSC CYBH

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
8_V	185_W	3.962	1.00
27_L	60_V	3.917	1.00
87_F	90_K	3.093	1.00
21_T	67_S	2.953	1.00
65_F	130_V	2.806	1.00
20_I	67_S	2.626	1.00
15_R	184_G	2.440	1.00
94_K	97_V	2.421	1.00
124_L	156_A	2.406	1.00
29_A	161_I	2.240	1.00
64_M	122_L	2.180	1.00
12_A	16_I	2.115	1.00
46_I	49_T	2.077	1.00
6_T	185_W	2.063	1.00
47_M	50_P	2.046	1.00
93_R	97_V	2.028	1.00
45_Q	50_P	2.006	1.00
11_T	14_E	1.974	1.00
61_G	64_M	1.950	1.00
107_Y	111_Q	1.897	1.00
118_A	159_A	1.819	1.00
29_A	164_I	1.794	1.00
86_I	90_K	1.776	1.00
26_I	30_V	1.768	1.00
8_V	11_T	1.753	1.00
87_F	91_N	1.731	1.00
125_L	156_A	1.716	1.00
34_G	53_A	1.710	1.00
25_F	160_L	1.708	1.00
65_F	126_L	1.702	1.00
88_W	91_N	1.668	1.00
24_C	63_V	1.667	1.00
92_I	95_I	1.664	1.00
171_A	178_I	1.631	1.00
36_L	154_S	1.624	1.00
10_Y	107_Y	1.583	1.00
117_A	121_F	1.549	1.00
106_R	111_Q	1.527	1.00
21_T	71_M	1.514	1.00
45_Q	49_T	1.501	1.00
151_M	155_F	1.494	1.00
128_S	152_L	1.484	1.00
22_A	168_I	1.469	1.00
128_S	131_I	1.465	1.00
17_N	70_I	1.459	1.00
85_D	112_K	1.458	1.00
68_F	126_L	1.414	1.00
132_I	150_L	1.413	1.00
62_V	66_A	1.404	1.00
92_I	96_V	1.403	1.00
168_I	171_A	1.382	1.00
83_R	87_F	1.375	1.00
118_A	122_L	1.361	1.00
25_F	29_A	1.350	1.00
54_R	58_P	1.334	1.00
124_L	152_L	1.298	0.99
142_S	145_V	1.272	0.99
19_W	22_A	1.260	0.99
44_M	47_M	1.252	0.99
94_K	101_V	1.251	0.99
120_I	123_V	1.236	0.99
43_L	46_I	1.233	0.99
45_Q	48_G	1.231	0.99
90_K	93_R	1.219	0.99
115_F	163_V	1.219	0.99
33_L	157_A	1.215	0.99
62_V	133_W	1.214	0.99
44_M	49_T	1.213	0.99
118_A	163_V	1.196	0.99
152_L	156_A	1.196	0.99
55_I	59_F	1.195	0.99
46_I	50_P	1.160	0.99
44_M	50_P	1.159	0.99
27_L	56_L	1.157	0.99
147_R	151_M	1.156	0.99
83_R	86_I	1.149	0.99
15_R	19_W	1.140	0.99
72_F	76_W	1.113	0.98
42_W	45_Q	1.113	0.98
104_T	109_F	1.109	0.98
58_P	61_G	1.109	0.98
114_V	117_A	1.077	0.98
91_N	94_K	1.076	0.98
81_I	86_I	1.074	0.98
17_N	67_S	1.069	0.98
155_F	159_A	1.068	0.98
75_Y	78_H	1.066	0.98
23_F	27_L	1.066	0.98
108_N	111_Q	1.063	0.98
24_C	60_V	1.056	0.98
81_I	85_D	1.046	0.98
52_L	56_L	1.046	0.98
176_G	179_T	1.034	0.97
38_P	54_R	1.026	0.97
85_D	88_W	1.018	0.97
180_A	186_V	1.016	0.97
35_F	54_R	1.002	0.97
19_W	181_M	1.001	0.97
9_R	186_V	0.994	0.97
74_R	79_N	0.994	0.97
178_I	181_M	0.993	0.97
76_W	80_L	0.990	0.97
17_N	68_F	0.987	0.96
179_T	183_E	0.977	0.96
74_R	78_H	0.964	0.96
20_I	24_C	0.963	0.96
31_S	134_R	0.961	0.96
63_V	67_S	0.961	0.96
143_I	147_R	0.953	0.96
148_F	152_L	0.934	0.95
117_A	163_V	0.932	0.95
42_W	48_G	0.925	0.95
156_A	160_L	0.922	0.95
43_L	49_T	0.914	0.95
84_D	87_F	0.903	0.94
176_G	186_V	0.902	0.94
127_V	131_I	0.899	0.94
24_C	28_A	0.885	0.94
92_I	97_V	0.879	0.93
114_V	163_V	0.861	0.93
129_G	153_H	0.854	0.92
20_I	63_V	0.851	0.92
119_I	123_V	0.849	0.92
128_S	141_F	0.843	0.92
31_S	56_L	0.843	0.92
6_T	187_T	0.842	0.92
101_V	104_T	0.840	0.92
99_E	102_G	0.834	0.91
114_V	118_A	0.833	0.91
122_L	156_A	0.824	0.91
164_I	168_I	0.821	0.91
94_K	102_G	0.816	0.91
44_M	48_G	0.810	0.90
98_N	102_G	0.808	0.90
10_Y	179_T	0.806	0.90
58_P	133_W	0.806	0.90
16_I	24_C	0.801	0.90
110_G	114_V	0.794	0.89
164_I	171_A	0.792	0.89
75_Y	79_N	0.791	0.89
37_F	59_F	0.789	0.89
9_R	106_R	0.776	0.88
40_F	151_M	0.775	0.88
31_S	53_A	0.773	0.88
80_L	90_K	0.773	0.88
68_F	164_I	0.763	0.87
118_A	123_V	0.761	0.87
10_Y	106_R	0.761	0.87
170_A	177_T	0.759	0.87
29_A	157_A	0.757	0.87
56_L	60_V	0.756	0.87
25_F	122_L	0.756	0.87
72_F	120_I	0.754	0.87
136_Y	139_P	0.754	0.87
91_N	95_I	0.753	0.87
134_R	149_A	0.751	0.86
51_Q	150_L	0.750	0.86
158_V	162_V	0.748	0.86
70_I	73_F	0.745	0.86
21_T	24_C	0.742	0.86
148_F	151_M	0.738	0.86
177_T	180_A	0.736	0.85
176_G	180_A	0.733	0.85
33_L	161_I	0.729	0.85
24_C	126_L	0.724	0.84
159_A	166_V	0.723	0.84
16_I	82_N	0.721	0.84
52_L	55_I	0.715	0.84
101_V	170_A	0.715	0.84
36_L	133_W	0.714	0.84
60_V	63_V	0.712	0.83
145_V	148_F	0.709	0.83
12_A	15_R	0.708	0.83
161_I	165_M	0.707	0.83
162_V	166_V	0.705	0.83
89_A	113_C	0.701	0.82
42_W	47_M	0.699	0.82
14_E	106_R	0.698	0.82
56_L	59_F	0.693	0.82
62_V	130_V	0.688	0.81
150_L	154_S	0.687	0.81
125_L	160_L	0.683	0.81
34_G	39_S	0.683	0.81
89_A	109_F	0.674	0.80
111_Q	115_F	0.671	0.80
111_Q	179_T	0.670	0.80
145_V	150_L	0.668	0.79
117_A	159_A	0.667	0.79
104_T	174_V	0.666	0.79
154_S	158_V	0.663	0.79
8_V	15_R	0.663	0.79
103_D	107_Y	0.659	0.78
22_A	26_I	0.656	0.78
82_N	85_D	0.653	0.78
128_S	153_H	0.650	0.77
175_K	179_T	0.649	0.77
37_F	165_M	0.647	0.77
11_T	21_T	0.646	0.77
128_S	149_A	0.645	0.77
114_V	160_L	0.643	0.77
93_R	98_N	0.641	0.77
10_Y	111_Q	0.637	0.76
146_I	150_L	0.632	0.76
34_G	44_M	0.631	0.75
9_R	85_D	0.623	0.74
131_I	149_A	0.622	0.74
56_L	117_A	0.622	0.74
35_F	53_A	0.621	0.74
72_F	119_I	0.621	0.74
119_I	164_I	0.618	0.74
42_W	49_T	0.618	0.74
20_I	66_A	0.613	0.73
166_V	170_A	0.607	0.73
36_L	109_F	0.606	0.72
145_V	152_L	0.605	0.72
12_A	140_A	0.604	0.72
103_D	168_I	0.602	0.72
27_L	51_Q	0.600	0.72
37_F	154_S	0.595	0.71
69_I	72_F	0.594	0.71
79_N	119_I	0.591	0.71
23_F	26_I	0.587	0.70
38_P	58_P	0.583	0.70
145_V	149_A	0.582	0.69
38_P	132_I	0.578	0.69
81_I	84_D	0.577	0.69
57_H	167_H	0.572	0.68
26_I	164_I	0.569	0.68
111_Q	143_I	0.569	0.68
17_N	124_L	0.569	0.68
16_I	74_R	0.569	0.68
110_G	171_A	0.567	0.67
71_M	115_F	0.563	0.67
166_V	180_A	0.563	0.67
35_F	150_L	0.557	0.66
43_L	50_P	0.555	0.66
66_A	127_V	0.551	0.65
58_P	150_L	0.551	0.65
81_I	104_T	0.551	0.65
37_F	40_F	0.549	0.65
54_R	169_Y	0.548	0.65
13_P	155_F	0.547	0.65
37_F	56_L	0.545	0.64
53_A	71_M	0.544	0.64
91_N	117_A	0.543	0.64
53_A	130_V	0.541	0.64
76_W	115_F	0.540	0.64
154_S	157_A	0.535	0.63
31_S	58_P	0.534	0.63
53_A	127_V	0.530	0.62
94_K	98_N	0.529	0.62
87_F	96_V	0.528	0.62
10_Y	177_T	0.527	0.62
176_G	187_T	0.525	0.62
148_F	159_A	0.522	0.61
21_T	119_I	0.521	0.61
28_A	62_V	0.519	0.61
115_F	173_W	0.518	0.61
148_F	164_I	0.517	0.60
17_N	157_A	0.516	0.60
81_I	109_F	0.516	0.60
90_K	113_C	0.515	0.60
161_I	183_E	0.514	0.60
30_V	151_M	0.514	0.60
71_M	119_I	0.511	0.59
66_A	189_A	0.510	0.59
93_R	96_V	0.509	0.59
76_W	82_N	0.503	0.58
60_V	64_M	0.503	0.58
8_V	14_E	0.503	0.58
38_P	52_L	0.502	0.58
26_I	60_V	0.502	0.58
141_F	144_P	0.501	0.58
80_L	139_P	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
1kqfC	3	0.9953	100	0.28	Contact Map
4gd3A	2	0.7109	100	0.515	Contact Map
4ogqA	2	0.8199	91.7	0.903	Contact Map
2qjyA	2	0.9194	91.4	0.904	Contact Map
1pp9C	2	0.9526	90	0.907	Contact Map
3cx5C	2	0.981	86.1	0.913	Contact Map
4o6yA	2	0.7156	80.6	0.919	Contact Map
1q16C	2	0.7536	47.9	0.935	Contact Map
4ytpC	1	0.5261	23.5	0.945	Contact Map
3s8fA	1	0.6919	15.9	0.949	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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