YNFH - ECOLI - GREMLIN Contacts

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YNFH - Anaerobic dimethyl sulfoxide reductase chain YnfH

UniProt:	P76173	Sequences: MGNGWHEWPLVIFTVLGQCVVGALIVSGIGWFAAKNDADRQRIVRGMFFLWLLMGVGFIASVMHLGSPLRAFNSLNRIGASGLSNEIAAGSIFFAVGGLWWLVAVIGKMPQALGKLWLLFSMALGVIFVWMMTCVYQIDTVPTWHNGYTTLAFFLTVLLSGPILAAAILRAARVTFNTTPFAIISVLALIACAGVIVLQGLSLASIHSSVQQASALVPDYASLQVWRVVLLCAGLGCWLCPLIRRREPHVAGLILGLILILGGEMIGRVLFYGLHMTVGMAIAG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13846
Length:	284 (264)
Sequences:	896 (739)
Seq/√Len:	45.5

ECOLI - YNFH DMSC NRFD
SULSO - Q97V35

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
96_V	124_L	8.624	1.00
20_V	93_F	4.830	1.00
21_V	125_G	4.424	1.00
82_G	85_N	3.968	1.00
234_G	238_W	3.900	1.00
98_G	102_L	3.781	1.00
231_L	235_L	3.666	1.00
67_S	70_R	3.408	1.00
86_E	136_Y	3.065	1.00
61_S	86_E	2.884	1.00
24_L	121_S	2.857	1.00
89_A	131_M	2.676	1.00
78_I	84_S	2.639	1.00
55_G	94_F	2.599	1.00
20_V	50_L	2.560	1.00
14_T	136_Y	2.557	1.00
14_T	86_E	2.441	1.00
19_C	53_L	2.375	1.00
26_V	162_P	2.355	1.00
64_H	86_E	2.335	1.00
54_M	94_F	2.156	1.00
235_L	238_W	2.131	1.00
89_A	127_I	2.108	1.00
86_E	131_M	2.071	0.99
223_L	234_G	2.063	0.99
129_V	157_V	2.061	0.99
28_G	118_L	1.956	0.99
53_L	164_L	1.939	0.99
61_S	136_Y	1.864	0.99
149_T	271_F	1.791	0.98
224_Q	227_R	1.762	0.98
18_Q	132_M	1.744	0.98
13_F	136_Y	1.741	0.98
230_L	235_L	1.716	0.98
197_V	258_I	1.694	0.98
79_G	85_N	1.669	0.98
14_T	61_S	1.664	0.98
23_A	165_A	1.654	0.97
13_F	86_E	1.651	0.97
232_C	236_G	1.639	0.97
51_W	97_G	1.639	0.97
28_G	122_M	1.637	0.97
54_M	128_F	1.632	0.97
70_R	73_N	1.627	0.97
61_S	131_M	1.608	0.97
258_I	262_G	1.601	0.97
64_H	136_Y	1.562	0.96
19_C	164_L	1.556	0.96
19_C	160_S	1.553	0.96
186_V	190_I	1.541	0.96
7_E	13_F	1.521	0.96
71_A	84_S	1.513	0.96
22_G	153_F	1.507	0.96
64_H	85_N	1.505	0.96
18_Q	21_V	1.484	0.95
61_S	83_L	1.470	0.95
163_I	257_L	1.451	0.95
7_E	14_T	1.430	0.94
122_M	127_I	1.421	0.94
82_G	134_C	1.396	0.93
216_L	219_D	1.394	0.93
267_G	272_Y	1.383	0.93
137_Q	150_T	1.381	0.93
117_W	166_A	1.353	0.92
23_A	50_L	1.351	0.92
160_S	164_L	1.348	0.92
152_A	156_T	1.347	0.92
85_N	272_Y	1.319	0.91
223_L	238_W	1.315	0.91
58_F	90_G	1.312	0.91
262_G	265_M	1.298	0.90
21_V	157_V	1.298	0.90
238_W	241_P	1.282	0.90
27_S	164_L	1.257	0.89
227_R	267_G	1.252	0.89
58_F	94_F	1.247	0.89
61_S	64_H	1.240	0.88
61_S	74_S	1.236	0.88
86_E	149_T	1.226	0.88
77_R	80_A	1.223	0.88
11_V	270_L	1.211	0.87
10_L	18_Q	1.211	0.87
120_F	191_A	1.204	0.87
120_F	194_G	1.203	0.87
82_G	135_V	1.198	0.87
102_L	106_I	1.188	0.86
21_V	87_I	1.186	0.86
90_G	128_F	1.184	0.86
229_V	246_R	1.175	0.85
13_F	131_M	1.171	0.85
179_T	183_I	1.170	0.85
13_F	17_G	1.163	0.85
185_S	192_C	1.157	0.85
84_S	268_R	1.157	0.85
74_S	82_G	1.150	0.84
18_Q	267_G	1.141	0.84
12_I	33_A	1.118	0.82
227_R	238_W	1.110	0.82
90_G	132_M	1.100	0.81
73_N	85_N	1.078	0.80
79_G	272_Y	1.075	0.80
99_L	265_M	1.074	0.80
7_E	10_L	1.073	0.80
222_S	226_W	1.066	0.79
14_T	131_M	1.066	0.79
128_F	132_M	1.064	0.79
8_W	19_C	1.063	0.79
31_W	104_A	1.059	0.79
83_L	86_E	1.057	0.79
18_Q	264_E	1.055	0.79
147_G	151_L	1.045	0.78
41_Q	45_R	1.045	0.78
190_I	194_G	1.043	0.78
231_L	234_G	1.035	0.77
238_W	242_L	1.031	0.77
142_P	267_G	1.028	0.77
14_T	271_F	1.022	0.76
14_T	64_H	1.022	0.76
62_V	75_L	1.020	0.76
119_L	123_A	1.015	0.76
64_H	71_A	1.014	0.76
16_L	53_L	1.011	0.76
187_L	190_I	0.998	0.75
56_V	123_A	0.995	0.74
203_L	206_I	0.993	0.74
15_V	264_E	0.992	0.74
56_V	254_I	0.992	0.74
238_W	256_G	0.980	0.73
96_V	121_S	0.979	0.73
10_L	61_S	0.976	0.73
222_S	225_V	0.965	0.72
100_W	118_L	0.964	0.72
80_A	148_Y	0.957	0.71
83_L	143_T	0.956	0.71
86_E	267_G	0.954	0.71
7_E	18_Q	0.953	0.71
264_E	267_G	0.952	0.71
122_M	126_V	0.947	0.71
83_L	131_M	0.942	0.70
234_G	260_I	0.936	0.70
225_V	236_G	0.935	0.70
220_Y	226_W	0.933	0.70
58_F	82_G	0.930	0.69
225_V	229_V	0.928	0.69
57_G	127_I	0.920	0.68
18_Q	153_F	0.915	0.68
12_I	60_A	0.896	0.66
86_E	129_V	0.892	0.66
133_T	150_T	0.888	0.66
183_I	189_L	0.888	0.66
220_Y	224_Q	0.886	0.65
11_V	269_V	0.886	0.65
97_G	100_W	0.886	0.65
156_T	160_S	0.883	0.65
229_V	263_G	0.881	0.65
37_D	255_L	0.877	0.65
17_G	135_V	0.875	0.65
112_A	167_A	0.868	0.64
92_I	121_S	0.863	0.63
196_I	200_G	0.858	0.63
13_F	90_G	0.856	0.63
227_R	264_E	0.855	0.63
101_W	206_I	0.852	0.62
8_W	121_S	0.841	0.61
199_Q	275_H	0.837	0.61
230_L	238_W	0.835	0.61
137_Q	145_H	0.834	0.61
251_A	254_I	0.834	0.61
84_S	203_L	0.828	0.60
24_L	27_S	0.826	0.60
131_M	136_Y	0.825	0.60
220_Y	227_R	0.822	0.60
123_A	251_A	0.819	0.59
152_A	267_G	0.818	0.59
95_A	266_I	0.817	0.59
85_N	132_M	0.814	0.59
26_V	57_G	0.810	0.58
24_L	29_I	0.809	0.58
15_V	156_T	0.805	0.58
171_A	258_I	0.793	0.57
64_H	135_V	0.793	0.57
14_T	143_T	0.791	0.57
245_R	258_I	0.788	0.56
18_Q	50_L	0.787	0.56
47_M	100_W	0.787	0.56
75_L	91_S	0.786	0.56
128_F	140_T	0.785	0.56
83_L	153_F	0.783	0.56
13_F	61_S	0.783	0.56
224_Q	232_C	0.780	0.56
18_Q	84_S	0.778	0.55
99_L	201_L	0.777	0.55
193_A	196_I	0.776	0.55
234_G	256_G	0.774	0.55
66_G	71_A	0.774	0.55
221_A	225_V	0.774	0.55
56_V	116_L	0.773	0.55
74_S	77_R	0.770	0.55
194_G	233_A	0.769	0.55
68_P	71_A	0.767	0.54
156_T	264_E	0.767	0.54
232_C	244_R	0.764	0.54
214_S	219_D	0.762	0.54
16_L	261_L	0.762	0.54
114_G	239_L	0.757	0.53
186_V	194_G	0.755	0.53
169_L	181_F	0.754	0.53
101_W	165_A	0.751	0.53
16_L	65_L	0.741	0.52
183_I	187_L	0.740	0.52
199_Q	203_L	0.737	0.51
62_V	98_G	0.736	0.51
227_R	236_G	0.735	0.51
14_T	138_I	0.735	0.51
16_L	130_W	0.733	0.51
127_I	181_F	0.731	0.51
24_L	28_G	0.730	0.51
45_R	244_R	0.730	0.51
9_P	18_Q	0.729	0.51
125_G	156_T	0.728	0.51
62_V	68_P	0.728	0.51
125_G	157_V	0.726	0.50
74_S	132_M	0.724	0.50
20_V	57_G	0.724	0.50
91_S	125_G	0.724	0.50
66_G	70_R	0.723	0.50
200_G	206_I	0.720	0.50
200_G	204_A	0.718	0.50
16_L	228_V	0.717	0.49
58_F	71_A	0.716	0.49
209_S	214_S	0.710	0.49
269_V	272_Y	0.705	0.48
220_Y	238_W	0.704	0.48
82_G	125_G	0.702	0.48
7_E	132_M	0.700	0.48
34_A	254_I	0.700	0.48
10_L	91_S	0.699	0.48
77_R	82_G	0.696	0.47
230_L	266_I	0.696	0.47
242_L	245_R	0.689	0.47
10_L	13_F	0.688	0.47
50_L	93_F	0.687	0.47
224_Q	228_V	0.686	0.46
7_E	272_Y	0.685	0.46
8_W	164_L	0.682	0.46
224_Q	236_G	0.682	0.46
197_V	233_A	0.680	0.46
190_I	208_S	0.679	0.46
45_R	189_L	0.679	0.46
21_V	153_F	0.675	0.45
158_L	261_L	0.672	0.45
232_C	258_I	0.671	0.45
50_L	120_F	0.668	0.45
31_W	44_V	0.666	0.45
65_L	144_W	0.664	0.44
187_L	204_A	0.663	0.44
54_M	60_A	0.661	0.44
137_Q	272_Y	0.660	0.44
157_V	203_L	0.660	0.44
151_L	259_L	0.659	0.44
86_E	143_T	0.658	0.44
217_V	224_Q	0.658	0.44
270_L	275_H	0.657	0.44
24_L	100_W	0.652	0.43
18_Q	125_G	0.652	0.43
136_Y	161_G	0.651	0.43
210_V	216_L	0.649	0.43
16_L	57_G	0.648	0.43
170_R	191_A	0.648	0.43
59_I	63_M	0.647	0.43
183_I	186_V	0.647	0.43
95_A	151_L	0.646	0.43
65_L	253_L	0.644	0.42
10_L	136_Y	0.638	0.42
61_S	65_L	0.638	0.42
189_L	260_I	0.637	0.42
53_L	77_R	0.636	0.42
121_S	150_T	0.629	0.41
220_Y	223_L	0.629	0.41
25_I	218_P	0.628	0.41
255_L	259_L	0.628	0.41
97_G	257_L	0.626	0.41
13_F	267_G	0.625	0.41
20_V	76_N	0.621	0.40
178_T	256_G	0.620	0.40
73_N	76_N	0.619	0.40
56_V	59_I	0.617	0.40
231_L	238_W	0.613	0.39
18_Q	272_Y	0.613	0.39
18_Q	156_T	0.612	0.39
222_S	262_G	0.611	0.39
92_I	96_V	0.610	0.39
80_A	195_V	0.609	0.39
81_S	144_W	0.607	0.39
26_V	181_F	0.604	0.39
86_E	161_G	0.603	0.39
17_G	67_S	0.603	0.39
50_L	261_L	0.602	0.38
6_H	274_L	0.601	0.38
77_R	140_T	0.600	0.38
80_A	275_H	0.599	0.38
155_L	192_C	0.598	0.38
11_V	209_S	0.598	0.38
54_M	273_G	0.598	0.38
128_F	270_L	0.597	0.38
104_A	121_S	0.595	0.38
135_V	264_E	0.594	0.38
7_E	274_L	0.594	0.38
85_N	134_C	0.590	0.37
92_I	124_L	0.588	0.37
240_C	256_G	0.587	0.37
86_E	128_F	0.587	0.37
45_R	167_A	0.587	0.37
58_F	269_V	0.586	0.37
87_I	132_M	0.585	0.37
9_P	63_M	0.585	0.37
171_A	232_C	0.584	0.37
63_M	130_W	0.582	0.37
18_Q	135_V	0.579	0.36
158_L	183_I	0.578	0.36
74_S	86_E	0.577	0.36
153_F	227_R	0.577	0.36
62_V	90_G	0.576	0.36
87_I	93_F	0.574	0.36
187_L	194_G	0.573	0.36
141_V	275_H	0.573	0.36
255_L	261_L	0.572	0.36
197_V	201_L	0.571	0.36
54_M	152_A	0.571	0.36
10_L	86_E	0.571	0.36
228_V	233_A	0.571	0.36
167_A	171_A	0.570	0.36
56_V	223_L	0.570	0.36
99_L	102_L	0.569	0.35
226_W	251_A	0.567	0.35
227_R	232_C	0.566	0.35
125_G	132_M	0.566	0.35
188_A	252_G	0.566	0.35
116_L	127_I	0.566	0.35
191_A	194_G	0.566	0.35
13_F	153_F	0.563	0.35
259_L	265_M	0.562	0.35
160_S	264_E	0.561	0.35
36_N	124_L	0.561	0.35
234_G	264_E	0.560	0.35
27_S	50_L	0.557	0.34
162_P	166_A	0.557	0.34
134_C	267_G	0.556	0.34
171_A	191_A	0.555	0.34
31_W	121_S	0.554	0.34
198_L	201_L	0.551	0.34
46_G	250_V	0.549	0.34
219_D	225_V	0.548	0.34
80_A	139_D	0.546	0.33
153_F	196_I	0.544	0.33
195_V	199_Q	0.543	0.33
160_S	216_L	0.541	0.33
186_V	258_I	0.540	0.33
71_A	86_E	0.540	0.33
117_W	212_Q	0.540	0.33
83_L	133_T	0.540	0.33
83_L	101_W	0.538	0.33
8_W	94_F	0.536	0.33
24_L	44_V	0.533	0.32
21_V	82_G	0.531	0.32
66_G	271_F	0.529	0.32
181_F	207_H	0.527	0.32
70_R	128_F	0.527	0.32
91_S	98_G	0.525	0.32
18_Q	87_I	0.524	0.32
246_R	251_A	0.523	0.31
209_S	215_A	0.521	0.31
187_L	262_G	0.521	0.31
120_F	254_I	0.521	0.31
210_V	214_S	0.521	0.31
124_L	176_F	0.519	0.31
18_Q	85_N	0.519	0.31
90_G	275_H	0.519	0.31
226_W	239_L	0.518	0.31
230_L	234_G	0.518	0.31
73_N	275_H	0.517	0.31
136_Y	149_T	0.517	0.31
166_A	178_T	0.515	0.31
52_L	56_V	0.514	0.31
20_V	132_M	0.514	0.31
49_F	59_I	0.513	0.31
15_V	160_S	0.510	0.30
155_L	188_A	0.508	0.30
142_P	153_F	0.506	0.30
74_S	85_N	0.505	0.30
29_I	120_F	0.505	0.30
74_S	89_A	0.504	0.30
50_L	185_S	0.502	0.30
29_I	33_A	0.501	0.30
17_G	90_G	0.501	0.30
85_N	136_Y	0.500	0.30

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
2vpzC	2	0.838	100	0.543	Contact Map
4gc0A	1	0.6127	7.4	0.96	Contact Map
1pw4A	1	0.9085	4.3	0.964	Contact Map
3wdoA	1	0.8838	3.9	0.965	Contact Map
1dc1A	2	0.2113	3.7	0.965	Contact Map
3wt9A	1	0.257	3.3	0.966	Contact Map
3ne5A	3	0.3732	2.9	0.967	Contact Map
3am6A	3	0.243	2.6	0.968	Contact Map
3dh4A	3	0.6268	2	0.97	Contact Map
3iynN	3	0	2	0.97	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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