NRFC - ECOLI - GREMLIN Contacts

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NRFC - Protein NrfC

UniProt:	P0AAK7	Sequences: MTWSRRQFLTGVGVLAAVSGTAGRVVAKTLNINGVRYGMVHDESLCIGCTACMDACREVNKVPEGVSRLTIIRSEPQGEFPDVKYRFFRKSCQHCDHAPCVDVCPTGASFRDAASGIVDVNPDLCVGCQYCIAACPYRVRFIHPVTKTADKCDFCRKTNLQAGKLPACVEACPTKALTFGNLDDPNSEISQLLRQKPTYRYKLALGTKPKLYRVPFKYGEVSQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11946
Length:	223 (180)
Sequences:	2578 (1482)
Seq/√Len:	110.4

ECOLI - NRFC YDHX HYBA FDNH FDOH YNFG DMSB YDHY HYFA HYDN HYCB YSAA YGFS NARY NARH
BACSU - NARH
HALSA - DMSB
SULSO - Q97XX9 Q97V38 Q97V75

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
112_D	115_S	5.680	1.00
59_V	157_K	3.062	1.00
39_M	154_F	2.709	1.00
166_P	169_V	2.707	1.00
109_S	140_R	2.579	1.00
78_G	81_P	2.494	1.00
200_R	203_L	2.293	1.00
101_V	109_S	2.290	1.00
129_Q	142_I	2.277	1.00
68_R	71_I	2.206	1.00
132_I	149_A	2.077	1.00
154_F	211_L	2.008	1.00
40_V	189_I	1.994	1.00
38_G	182_L	1.987	1.00
98_A	111_R	1.959	1.00
169_V	177_L	1.938	1.00
35_V	183_D	1.826	1.00
96_D	210_K	1.817	1.00
112_D	161_Q	1.806	1.00
103_V	130_Y	1.744	1.00
36_R	96_D	1.735	1.00
46_C	52_C	1.733	1.00
35_V	181_N	1.724	1.00
184_D	187_S	1.712	1.00
46_C	172_C	1.685	1.00
200_R	208_K	1.651	1.00
91_S	211_L	1.637	1.00
121_N	124_L	1.636	1.00
46_C	49_C	1.633	1.00
156_R	161_Q	1.610	1.00
55_A	171_A	1.605	1.00
187_S	190_S	1.596	1.00
103_V	134_A	1.582	1.00
186_N	191_Q	1.581	1.00
129_Q	132_I	1.562	1.00
60_N	153_D	1.556	1.00
68_R	150_D	1.528	1.00
41_H	177_L	1.525	1.00
104_C	125_C	1.524	1.00
60_N	157_K	1.522	1.00
178_T	192_L	1.520	1.00
104_C	131_C	1.504	1.00
142_I	149_A	1.497	1.00
49_C	172_C	1.475	1.00
188_E	191_Q	1.474	1.00
49_C	52_C	1.466	1.00
99_P	207_T	1.449	1.00
143_H	150_D	1.439	1.00
159_N	164_K	1.436	1.00
125_C	131_C	1.434	1.00
47_I	174_T	1.430	1.00
68_R	72_I	1.416	1.00
40_V	192_L	1.388	1.00
159_N	170_E	1.372	1.00
109_S	120_V	1.354	1.00
101_V	111_R	1.347	1.00
52_C	172_C	1.331	1.00
178_T	188_E	1.328	1.00
188_E	192_L	1.262	0.99
50_T	53_M	1.252	0.99
112_D	117_I	1.244	0.99
181_N	184_D	1.238	0.99
44_S	196_K	1.236	0.99
89_R	177_L	1.216	0.99
98_A	101_V	1.213	0.99
117_I	160_L	1.204	0.99
193_L	198_T	1.204	0.99
198_T	214_V	1.196	0.99
59_V	159_N	1.192	0.99
110_F	121_N	1.183	0.99
41_H	89_R	1.175	0.99
202_K	205_L	1.166	0.99
191_Q	195_Q	1.160	0.99
193_L	212_Y	1.149	0.99
112_D	119_D	1.138	0.99
36_R	210_K	1.135	0.98
40_V	214_V	1.130	0.98
90_K	201_Y	1.130	0.98
190_S	194_R	1.129	0.98
106_T	109_S	1.119	0.98
69_L	72_I	1.113	0.98
182_L	186_N	1.103	0.98
41_H	211_L	1.095	0.98
91_S	177_L	1.088	0.98
51_A	171_A	1.079	0.98
196_K	214_V	1.063	0.98
44_S	214_V	1.062	0.98
89_R	213_R	1.059	0.98
38_G	185_P	1.034	0.97
97_H	102_D	1.031	0.97
111_R	118_V	1.027	0.97
200_R	205_L	1.026	0.97
144_P	147_K	1.018	0.97
125_C	128_C	1.016	0.97
96_D	208_K	1.014	0.97
78_G	82_D	1.009	0.97
141_F	150_D	1.005	0.97
64_E	67_S	1.000	0.97
164_K	170_E	0.992	0.96
103_V	109_S	0.984	0.96
111_R	210_K	0.983	0.96
143_H	146_T	0.982	0.96
79_E	82_D	0.980	0.96
191_Q	194_R	0.971	0.96
105_P	131_C	0.969	0.96
110_F	119_D	0.964	0.96
71_I	75_E	0.962	0.96
38_G	189_I	0.959	0.96
96_D	111_R	0.956	0.96
200_R	212_Y	0.943	0.95
119_D	153_D	0.938	0.95
105_P	125_C	0.933	0.95
122_P	148_T	0.929	0.95
59_V	167_A	0.913	0.94
104_C	128_C	0.909	0.94
130_Y	133_A	0.908	0.94
128_C	131_C	0.907	0.94
160_L	179_F	0.905	0.94
48_G	71_I	0.885	0.93
41_H	91_S	0.884	0.93
106_T	126_V	0.876	0.93
185_P	190_S	0.869	0.93
142_I	147_K	0.861	0.92
51_A	54_D	0.860	0.92
43_E	89_R	0.857	0.92
189_I	192_L	0.848	0.92
129_Q	144_P	0.847	0.92
69_L	177_L	0.843	0.92
112_D	156_R	0.840	0.91
117_I	154_F	0.839	0.91
76_P	85_Y	0.837	0.91
57_R	62_V	0.835	0.91
120_V	149_A	0.830	0.91
187_S	191_Q	0.827	0.91
69_L	75_E	0.816	0.90
190_S	193_L	0.815	0.90
55_A	167_A	0.808	0.90
37_Y	179_F	0.804	0.90
78_G	83_V	0.804	0.90
97_H	208_K	0.802	0.89
34_G	183_D	0.785	0.88
71_I	74_S	0.782	0.88
142_I	146_T	0.780	0.88
129_Q	149_A	0.779	0.88
99_P	134_A	0.779	0.88
159_N	167_A	0.778	0.88
69_L	73_R	0.772	0.88
144_P	150_D	0.771	0.88
153_D	157_K	0.767	0.87
120_V	140_R	0.765	0.87
70_T	73_R	0.757	0.87
71_I	76_P	0.756	0.87
105_P	126_V	0.752	0.86
140_R	149_A	0.743	0.86
39_M	169_V	0.742	0.85
37_Y	181_N	0.742	0.85
51_A	174_T	0.740	0.85
165_L	169_V	0.738	0.85
180_G	184_D	0.735	0.85
117_I	156_R	0.735	0.85
56_C	152_C	0.734	0.85
72_I	76_P	0.731	0.85
103_V	133_A	0.727	0.84
186_N	190_S	0.727	0.84
106_T	128_C	0.727	0.84
51_A	58_E	0.725	0.84
106_T	124_L	0.721	0.84
62_V	68_R	0.721	0.84
104_C	127_G	0.720	0.84
165_L	170_E	0.720	0.84
192_L	196_K	0.716	0.83
45_L	192_L	0.715	0.83
67_S	70_T	0.714	0.83
108_A	124_L	0.713	0.83
36_R	182_L	0.713	0.83
200_R	210_K	0.709	0.83
61_K	150_D	0.703	0.82
132_I	142_I	0.701	0.82
36_R	183_D	0.697	0.82
175_K	178_T	0.693	0.81
152_C	155_C	0.691	0.81
45_L	175_K	0.686	0.81
56_C	155_C	0.678	0.80
185_P	189_I	0.678	0.80
206_G	209_P	0.675	0.80
166_P	177_L	0.673	0.79
127_G	131_C	0.669	0.79
193_L	197_P	0.667	0.79
119_D	156_R	0.664	0.79
181_N	185_P	0.662	0.78
201_Y	205_L	0.661	0.78
71_I	77_Q	0.657	0.78
91_S	154_F	0.657	0.78
181_N	187_S	0.652	0.77
70_T	77_Q	0.652	0.77
143_H	147_K	0.638	0.76
184_D	189_I	0.637	0.76
37_Y	117_I	0.635	0.75
68_R	73_R	0.633	0.75
48_G	176_A	0.633	0.75
69_L	76_P	0.624	0.74
39_M	211_L	0.620	0.74
122_P	142_I	0.619	0.74
137_Y	209_P	0.617	0.73
163_G	193_L	0.617	0.73
40_V	193_L	0.617	0.73
58_E	171_A	0.616	0.73
93_Q	139_V	0.616	0.73
58_E	170_E	0.614	0.73
106_T	120_V	0.612	0.73
126_V	131_C	0.607	0.72
70_T	90_K	0.606	0.72
38_G	210_K	0.604	0.72
68_R	141_F	0.603	0.72
129_Q	150_D	0.602	0.71
78_G	84_K	0.599	0.71
122_P	146_T	0.597	0.71
77_Q	84_K	0.597	0.71
115_S	161_Q	0.596	0.71
70_T	74_S	0.595	0.71
74_S	77_Q	0.593	0.70
205_L	210_K	0.589	0.70
37_Y	160_L	0.588	0.70
90_K	93_Q	0.584	0.69
47_I	173_P	0.582	0.69
98_A	118_V	0.581	0.69
201_Y	207_T	0.581	0.69
48_G	139_V	0.581	0.69
57_R	85_Y	0.578	0.68
53_M	173_P	0.575	0.68
42_D	214_V	0.575	0.68
200_R	204_A	0.574	0.68
39_M	179_F	0.572	0.68
102_D	130_Y	0.570	0.67
175_K	192_L	0.569	0.67
75_E	78_G	0.569	0.67
40_V	91_S	0.567	0.67
153_D	156_R	0.567	0.67
39_M	89_R	0.564	0.67
69_L	91_S	0.562	0.66
43_E	88_F	0.557	0.66
101_V	105_P	0.557	0.66
93_Q	140_R	0.556	0.65
182_L	190_S	0.554	0.65
118_V	134_A	0.552	0.65
48_G	172_C	0.552	0.65
110_F	124_L	0.548	0.64
137_Y	207_T	0.543	0.64
154_F	160_L	0.537	0.63
45_L	178_T	0.536	0.63
115_S	156_R	0.535	0.63
193_L	196_K	0.527	0.61
140_R	177_L	0.525	0.61
44_S	212_Y	0.522	0.61
126_V	130_Y	0.521	0.60
48_G	52_C	0.518	0.60
138_R	141_F	0.517	0.60
44_S	192_L	0.512	0.59
209_P	213_R	0.512	0.59
98_A	140_R	0.512	0.59
68_R	75_E	0.512	0.59
41_H	213_R	0.511	0.59
80_F	83_V	0.509	0.59
37_Y	115_S	0.509	0.59
132_I	144_P	0.508	0.59
137_Y	180_G	0.507	0.58
106_T	110_F	0.502	0.58
38_G	212_Y	0.500	0.57
192_L	195_Q	0.500	0.57
59_V	170_E	0.500	0.57

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
2ivfB	1	0.8475	100	0.401	Contact Map
1ti6B	2	0.8251	100	0.423	Contact Map
1kqfB	3	0.9372	100	0.453	Contact Map
1h0hB	1	0.8386	100	0.46	Contact Map
2vpzB	2	0.8341	100	0.483	Contact Map
1q16B	2	0.861	100	0.513	Contact Map
4z3xE	2	0.7309	100	0.632	Contact Map
3mm5B	2	0.991	99.8	0.726	Contact Map
1jnrB	1	0.6368	99.5	0.792	Contact Map
3gyxB	1	0.435	99.5	0.797	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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