FDNI - ECOLI - GREMLIN Contacts

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FDNI - Formate dehydrogenase, nitrate-inducible, cytochrome b556(Fdn) subunit

UniProt:	P0AEK7	Sequences: MSKSKMIVRTKFIDRACHWTVVICFFLVALSGISFFFPTLQWLTQTFGTPQMGRILHPFFGIAIFVALMFMFVRFVHHNIPDKKDIPWLLNIVEVLKGNEHKVADVGKYNAGQKMMFWSIMSMIFVLLVTGVIIWRPYFAQYFPMQVVRYSLLIHAAAGIILIHAILIHMYMAFWVKGSIKGMIEGKVSRRWAKKHHPRWYREIEKAEAKKESEEGI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11229
Length:	217 (186)
Sequences:	2239 (1465)
Seq/√Len:	107.4

ECOLI - FDNI FDOI 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
27_L	60_F	4.118	1.00
8_V	187_K	3.882	1.00
21_V	67_A	3.029	1.00
64_I	124_I	2.891	1.00
65_F	132_V	2.778	1.00
20_T	67_A	2.638	1.00
87_P	90_L	2.636	1.00
15_R	186_G	2.583	1.00
126_V	158_A	2.582	1.00
92_I	96_L	2.569	1.00
12_F	16_A	2.285	1.00
29_A	163_I	2.282	1.00
75_F	78_H	2.171	1.00
6_M	187_K	2.124	1.00
13_I	74_R	1.965	1.00
11_K	14_D	1.959	1.00
61_G	64_I	1.923	1.00
87_P	91_N	1.878	1.00
173_A	180_I	1.852	1.00
109_Y	113_Q	1.811	1.00
29_A	166_I	1.785	1.00
26_F	30_L	1.774	1.00
83_K	87_P	1.770	1.00
94_E	97_K	1.759	1.00
45_Q	49_T	1.759	1.00
8_V	11_K	1.743	1.00
153_L	157_A	1.742	1.00
127_L	158_A	1.733	1.00
14_D	74_R	1.732	1.00
24_C	63_A	1.729	1.00
65_F	128_L	1.728	1.00
139_F	143_F	1.718	1.00
10_T	109_Y	1.710	1.00
46_T	49_T	1.703	1.00
36_F	156_A	1.679	1.00
25_F	162_L	1.670	1.00
140_A	143_F	1.659	1.00
139_F	142_Y	1.657	1.00
130_T	133_I	1.637	1.00
34_S	53_G	1.578	1.00
85_D	114_K	1.555	1.00
91_N	94_E	1.534	1.00
62_I	66_V	1.522	1.00
22_V	170_M	1.515	1.00
134_I	152_L	1.512	1.00
96_L	99_N	1.508	1.00
17_C	70_F	1.500	1.00
126_V	154_I	1.475	1.00
124_I	162_L	1.471	1.00
27_L	56_L	1.459	1.00
108_K	113_Q	1.453	1.00
86_I	90_L	1.441	1.00
54_R	58_P	1.430	1.00
21_V	71_M	1.403	1.00
144_P	147_V	1.390	1.00
95_V	98_G	1.375	1.00
93_V	97_K	1.368	1.00
123_M	158_A	1.359	1.00
94_E	100_E	1.351	1.00
62_I	135_W	1.325	0.99
44_T	48_G	1.306	0.99
19_W	22_V	1.285	0.99
106_V	111_A	1.283	0.99
94_E	99_N	1.280	0.99
25_F	29_A	1.255	0.99
150_Y	154_I	1.250	0.99
181_K	185_E	1.245	0.99
33_I	159_G	1.227	0.99
130_T	154_I	1.213	0.99
81_P	86_I	1.211	0.99
89_L	115_M	1.204	0.99
119_S	165_A	1.191	0.99
68_L	128_L	1.182	0.99
83_K	86_I	1.177	0.99
170_M	173_A	1.175	0.99
92_I	97_K	1.169	0.99
15_R	19_W	1.129	0.98
157_A	161_I	1.125	0.98
20_T	24_C	1.124	0.98
58_P	61_G	1.124	0.98
116_M	119_S	1.122	0.98
23_I	27_L	1.121	0.98
55_I	59_F	1.112	0.98
119_S	123_M	1.108	0.98
24_C	60_F	1.105	0.98
178_G	181_K	1.100	0.98
68_L	124_I	1.074	0.98
35_F	54_R	1.049	0.97
93_V	96_L	1.038	0.97
81_P	85_D	1.033	0.97
149_R	153_L	1.032	0.97
129_V	133_I	1.019	0.97
166_I	170_M	1.018	0.97
63_A	67_A	1.003	0.96
80_I	90_L	1.001	0.96
35_F	38_P	0.992	0.96
90_L	94_E	0.985	0.96
117_F	165_A	0.980	0.96
178_G	188_V	0.973	0.96
17_C	67_A	0.972	0.96
131_G	155_H	0.971	0.96
19_W	183_M	0.956	0.95
89_L	93_V	0.938	0.95
17_C	68_L	0.938	0.95
81_P	84_K	0.933	0.95
133_I	139_F	0.932	0.95
6_M	189_S	0.925	0.94
85_D	88_W	0.925	0.94
72_F	76_V	0.924	0.94
44_T	49_T	0.909	0.94
92_I	172_M	0.902	0.94
94_E	98_G	0.902	0.94
147_V	150_Y	0.897	0.93
49_T	52_M	0.894	0.93
92_I	95_V	0.884	0.93
90_L	93_V	0.879	0.93
43_L	56_L	0.878	0.93
9_R	188_V	0.877	0.93
116_M	165_A	0.868	0.92
116_M	120_I	0.867	0.92
110_N	113_Q	0.867	0.92
37_F	156_A	0.864	0.92
50_P	53_G	0.855	0.92
24_C	28_V	0.854	0.92
60_F	63_A	0.850	0.91
34_S	44_T	0.846	0.91
92_I	98_G	0.845	0.91
163_I	167_L	0.841	0.91
39_T	54_R	0.835	0.91
137_P	140_A	0.820	0.90
161_I	168_I	0.818	0.90
180_I	183_M	0.813	0.89
122_S	166_I	0.812	0.89
76_V	121_M	0.804	0.89
37_F	145_M	0.800	0.89
182_G	188_V	0.792	0.88
150_Y	153_L	0.791	0.88
138_Y	142_Y	0.782	0.88
34_S	38_P	0.781	0.87
29_A	159_G	0.780	0.87
52_M	55_I	0.780	0.87
158_A	162_L	0.777	0.87
16_A	24_C	0.769	0.87
31_S	56_L	0.768	0.87
116_M	168_I	0.768	0.87
89_L	96_L	0.766	0.86
56_L	59_F	0.766	0.86
58_P	135_W	0.763	0.86
38_P	50_P	0.760	0.86
73_V	174_F	0.758	0.86
72_F	121_M	0.758	0.86
52_M	56_L	0.756	0.86
120_I	165_A	0.754	0.86
116_M	123_M	0.749	0.85
95_V	99_N	0.748	0.85
21_V	24_C	0.746	0.85
154_I	158_A	0.738	0.84
31_S	53_G	0.735	0.84
16_A	82_D	0.731	0.84
130_T	155_H	0.731	0.84
81_P	88_W	0.731	0.84
50_P	62_I	0.724	0.83
31_S	136_R	0.722	0.83
33_I	163_I	0.722	0.83
95_V	101_H	0.705	0.82
179_S	182_G	0.702	0.81
20_T	63_A	0.701	0.81
145_M	149_R	0.697	0.81
38_P	54_R	0.696	0.81
120_I	124_I	0.695	0.81
86_I	187_K	0.694	0.81
130_T	151_S	0.693	0.80
112_G	116_M	0.691	0.80
152_L	156_A	0.688	0.80
10_T	181_K	0.682	0.79
10_T	108_K	0.681	0.79
56_L	60_F	0.681	0.79
82_D	107_G	0.680	0.79
105_D	109_Y	0.676	0.79
35_F	53_G	0.676	0.79
166_I	173_A	0.675	0.79
36_F	111_A	0.666	0.78
133_I	151_S	0.665	0.78
113_Q	117_F	0.663	0.77
136_R	151_S	0.661	0.77
69_M	72_F	0.660	0.77
168_I	172_M	0.660	0.77
148_V	152_L	0.658	0.77
123_M	161_I	0.657	0.77
103_V	106_V	0.657	0.77
44_T	47_F	0.656	0.77
89_L	111_A	0.656	0.77
123_M	127_L	0.650	0.76
128_L	132_V	0.649	0.76
72_F	127_L	0.648	0.76
101_H	104_A	0.638	0.75
133_I	184_I	0.637	0.75
147_V	152_L	0.637	0.75
12_F	15_R	0.635	0.74
8_V	15_R	0.635	0.74
40_L	43_L	0.634	0.74
13_I	86_I	0.634	0.74
30_L	153_L	0.629	0.74
136_R	143_F	0.624	0.73
35_F	50_P	0.623	0.73
112_G	173_A	0.621	0.73
178_G	182_G	0.621	0.73
53_G	132_V	0.614	0.72
130_T	175_W	0.611	0.72
27_L	59_F	0.609	0.71
122_S	125_F	0.608	0.71
68_L	166_I	0.607	0.71
13_I	16_A	0.607	0.71
127_L	162_L	0.601	0.70
127_L	159_G	0.600	0.70
14_D	108_K	0.598	0.70
13_I	157_A	0.595	0.70
36_F	135_W	0.594	0.69
88_W	93_V	0.588	0.69
156_A	160_I	0.585	0.68
66_V	129_V	0.581	0.68
48_G	52_M	0.580	0.68
147_V	151_S	0.579	0.67
61_G	132_V	0.577	0.67
53_G	174_F	0.575	0.67
121_M	124_I	0.574	0.67
116_M	162_L	0.572	0.66
9_R	108_K	0.571	0.66
30_L	166_I	0.570	0.66
151_S	160_I	0.569	0.66
51_Q	152_L	0.569	0.66
12_F	77_H	0.566	0.66
17_C	159_G	0.565	0.66
81_P	106_V	0.563	0.65
10_T	113_Q	0.563	0.65
71_M	117_F	0.561	0.65
149_R	164_H	0.560	0.65
9_R	175_W	0.557	0.64
45_Q	164_H	0.557	0.64
98_G	103_V	0.555	0.64
94_E	102_K	0.554	0.64
69_M	86_I	0.553	0.64
40_L	153_L	0.553	0.64
113_Q	181_K	0.551	0.64
57_H	169_H	0.548	0.63
17_C	175_W	0.544	0.63
114_K	168_I	0.544	0.63
27_L	90_L	0.544	0.63
84_K	162_L	0.543	0.63
23_I	26_F	0.541	0.62
154_I	157_A	0.539	0.62
76_V	117_F	0.537	0.62
53_G	129_V	0.537	0.62
24_C	78_H	0.536	0.62
142_Y	157_A	0.536	0.62
42_W	49_T	0.532	0.61
121_M	166_I	0.532	0.61
28_V	61_G	0.525	0.60
42_W	151_S	0.525	0.60
92_I	99_N	0.525	0.60
58_P	152_L	0.524	0.60
150_Y	161_I	0.524	0.60
142_Y	145_M	0.524	0.60
66_V	69_M	0.521	0.59
118_W	126_V	0.518	0.59
24_C	128_L	0.516	0.59
27_L	51_Q	0.515	0.58
134_I	148_V	0.514	0.58
77_H	136_R	0.512	0.58
50_P	71_M	0.508	0.57
37_F	56_L	0.507	0.57
11_K	21_V	0.507	0.57
19_W	182_G	0.507	0.57
68_L	120_I	0.506	0.57
147_V	154_I	0.506	0.57
119_S	161_I	0.505	0.57
187_K	190_R	0.502	0.57
37_F	59_F	0.501	0.56
94_E	101_H	0.500	0.56

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	0.9954	100	0.281	Contact Map
4gd3A	2	0.7097	100	0.498	Contact Map
4ogqA	2	0.8203	89.9	0.909	Contact Map
2qjyA	2	0.8802	89.7	0.91	Contact Map
1pp9C	2	0.9401	87.4	0.913	Contact Map
4o6yA	2	0.7005	81.5	0.919	Contact Map
3cx5C	2	0.9585	81.1	0.92	Contact Map
1q16C	2	0.7327	32.2	0.942	Contact Map
3ayfA	2	0.7373	13.9	0.951	Contact Map
3mk7A	1	0.7558	10.4	0.954	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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