NFNB - ECOLI - GREMLIN Contacts

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NFNB - Oxygen-insensitive NAD(P)H nitroreductase

UniProt:	P38489	Sequences: MDIISVALKRHSTKAFDASKKLTPEQAEQIKTLLQYSPSSTNSQPWHFIVASTEEGKARVAKSAAGNYVFNERKMLDASHVVVFCAKTAMDDVWLKLVVDQEDADGRFATPEAKAANDKGRKFFADMHRKDLHDDAEWMAKQVYLNVGNFLLGVAALGLDAVPIEGFDAAILDAEFGLKEKGYTSLVVVPVGHHSVEDFNATLPKSRLPQNITLTEV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG20151
Length:	217 (198)
Sequences:	7049 (5454)
Seq/√Len:	387.6

ECOLI - NFNB RUTE NFSA YDJA
BACSU - MHQN YODC YFKO YDGI NFRA1 YFHC NFRA2
HALSA - Q9HQZ4
SULSO - Q97VQ3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
17_D	20_K	4.548	1.00
29_Q	157_L	4.039	1.00
24_P	52_S	3.101	1.00
24_P	28_E	2.907	1.00
23_T	26_Q	2.802	1.00
20_K	193_H	2.766	1.00
48_F	146_N	2.642	1.00
160_D	194_H	2.472	1.00
30_I	154_V	2.428	1.00
173_D	185_S	2.386	1.00
54_E	58_A	2.329	1.00
59_R	175_E	2.255	1.00
159_L	193_H	2.253	1.00
32_T	35_Q	2.232	1.00
147_V	187_V	2.065	1.00
26_Q	159_L	1.973	1.00
56_G	59_R	1.938	1.00
15_A	195_S	1.893	1.00
33_L	153_G	1.868	1.00
151_L	163_P	1.835	1.00
26_Q	157_L	1.820	1.00
63_S	171_I	1.802	1.00
8_L	36_Y	1.785	1.00
63_S	175_E	1.770	1.00
210_Q	214_L	1.753	1.00
3_I	6_V	1.667	1.00
155_A	160_D	1.663	1.00
61_A	76_L	1.659	1.00
60_V	172_L	1.651	1.00
154_V	191_V	1.637	1.00
5_S	9_K	1.630	1.00
9_K	155_A	1.607	1.00
208_L	212_I	1.603	1.00
17_D	195_S	1.596	1.00
16_F	190_P	1.585	1.00
34_L	150_F	1.553	1.00
171_I	174_A	1.552	1.00
194_H	197_E	1.550	1.00
30_I	159_L	1.544	1.00
3_I	7_A	1.521	1.00
28_E	211_N	1.521	1.00
151_L	161_A	1.508	1.00
147_V	189_V	1.478	1.00
179_K	182_G	1.456	1.00
47_H	183_Y	1.440	1.00
154_V	161_A	1.430	1.00
73_R	77_D	1.429	1.00
56_G	175_E	1.424	1.00
12_S	162_V	1.423	1.00
110_T	114_K	1.414	1.00
53_T	56_G	1.412	1.00
151_L	189_V	1.404	1.00
30_I	150_F	1.403	1.00
35_Q	213_T	1.399	1.00
58_A	62_K	1.335	1.00
141_K	144_Y	1.326	1.00
30_I	191_V	1.322	1.00
120_G	124_F	1.315	1.00
16_F	162_V	1.312	1.00
159_L	191_V	1.308	1.00
143_V	186_L	1.300	1.00
145_L	148_G	1.283	1.00
168_D	171_I	1.278	1.00
22_L	159_L	1.276	1.00
141_K	165_E	1.264	1.00
7_A	149_N	1.253	1.00
33_L	157_L	1.249	1.00
54_E	57_K	1.244	1.00
4_I	157_L	1.239	1.00
31_K	214_L	1.225	1.00
4_I	8_L	1.209	1.00
97_L	212_I	1.207	1.00
171_I	175_E	1.204	1.00
48_F	82_V	1.203	1.00
59_R	62_K	1.199	1.00
21_K	52_S	1.195	1.00
55_E	58_A	1.193	1.00
103_D	106_G	1.191	1.00
4_I	33_L	1.186	1.00
118_D	121_R	1.177	1.00
114_K	118_D	1.161	1.00
116_A	119_K	1.150	1.00
27_A	191_V	1.146	1.00
26_Q	29_Q	1.144	1.00
73_R	76_L	1.144	1.00
8_L	32_T	1.110	1.00
37_S	149_N	1.104	1.00
98_V	102_E	1.103	1.00
101_Q	105_D	1.096	1.00
117_N	120_G	1.093	1.00
22_L	193_H	1.082	1.00
102_E	105_D	1.077	1.00
150_F	191_V	1.068	1.00
119_K	122_K	1.063	1.00
28_E	210_Q	1.034	1.00
22_L	26_Q	1.033	1.00
89_A	92_D	1.025	1.00
4_I	29_Q	1.025	1.00
28_E	32_T	1.025	1.00
29_Q	33_L	1.008	1.00
161_A	191_V	1.002	1.00
150_F	189_V	1.000	1.00
26_Q	193_H	0.983	1.00
118_D	122_K	0.982	1.00
116_A	120_G	0.975	1.00
136_A	184_T	0.974	1.00
178_L	181_K	0.972	1.00
93_V	97_L	0.970	1.00
78_A	81_V	0.968	1.00
149_N	152_L	0.967	1.00
99_V	102_E	0.963	1.00
34_L	48_F	0.958	1.00
170_A	174_A	0.952	1.00
82_V	150_F	0.952	1.00
98_V	103_D	0.948	1.00
77_D	80_H	0.947	1.00
72_E	76_L	0.945	1.00
99_V	103_D	0.944	1.00
101_Q	104_A	0.937	1.00
25_E	28_E	0.936	1.00
40_S	165_E	0.925	1.00
87_K	93_V	0.920	1.00
3_I	156_A	0.910	1.00
71_N	74_K	0.910	1.00
6_V	156_A	0.908	1.00
98_V	101_Q	0.907	1.00
161_A	189_V	0.906	1.00
15_A	196_V	0.902	1.00
23_T	193_H	0.901	1.00
78_A	82_V	0.898	1.00
30_I	157_L	0.897	1.00
121_R	124_F	0.896	1.00
97_L	100_D	0.894	1.00
5_S	8_L	0.883	1.00
138_W	165_E	0.870	1.00
100_D	104_A	0.867	1.00
31_K	50_V	0.862	1.00
50_V	214_L	0.862	1.00
137_E	141_K	0.858	1.00
31_K	34_L	0.857	1.00
96_K	100_D	0.855	1.00
122_K	125_A	0.847	1.00
118_D	124_F	0.847	1.00
140_A	186_L	0.843	1.00
13_T	198_D	0.843	1.00
115_A	119_K	0.839	1.00
84_F	150_F	0.836	1.00
87_K	90_M	0.832	1.00
58_A	61_A	0.830	1.00
21_K	54_E	0.827	1.00
76_L	79_S	0.814	1.00
146_N	213_T	0.813	1.00
162_V	190_P	0.809	1.00
117_N	121_R	0.808	1.00
29_Q	32_T	0.805	1.00
49_I	183_Y	0.799	1.00
173_D	184_T	0.799	1.00
172_L	175_E	0.795	1.00
32_T	210_Q	0.793	1.00
39_S	46_W	0.791	1.00
137_E	140_A	0.784	1.00
64_A	188_V	0.783	1.00
49_I	176_F	0.782	1.00
40_S	138_W	0.778	1.00
169_A	185_S	0.772	1.00
102_E	106_G	0.768	1.00
55_E	59_R	0.768	1.00
14_K	74_K	0.767	1.00
3_I	152_L	0.763	1.00
59_R	63_S	0.760	1.00
51_A	56_G	0.751	1.00
113_A	116_A	0.748	1.00
131_D	134_D	0.747	1.00
99_V	104_A	0.745	1.00
13_T	194_H	0.745	1.00
58_A	76_L	0.744	1.00
88_T	91_D	0.743	1.00
113_A	120_G	0.741	1.00
121_R	125_A	0.736	1.00
209_P	212_I	0.734	1.00
27_A	50_V	0.730	1.00
85_C	183_Y	0.728	1.00
172_L	185_S	0.727	1.00
27_A	31_K	0.723	1.00
75_M	78_A	0.723	1.00
98_V	106_G	0.722	1.00
150_F	161_A	0.717	1.00
163_P	187_V	0.712	1.00
141_K	186_L	0.708	1.00
153_G	156_A	0.707	1.00
7_A	33_L	0.703	1.00
111_P	114_K	0.700	1.00
100_D	103_D	0.699	1.00
90_M	93_V	0.698	1.00
22_L	25_E	0.697	1.00
114_K	117_N	0.694	0.99
88_T	92_D	0.692	0.99
178_L	183_Y	0.689	0.99
25_E	29_Q	0.680	0.99
178_L	185_S	0.679	0.99
17_D	193_H	0.677	0.99
84_F	88_T	0.676	0.99
194_H	198_D	0.675	0.99
99_V	105_D	0.673	0.99
57_K	61_A	0.660	0.99
117_N	123_F	0.660	0.99
95_L	98_V	0.656	0.99
111_P	115_A	0.656	0.99
95_L	102_E	0.650	0.99
123_F	126_D	0.649	0.99
120_G	123_F	0.648	0.99
140_A	144_Y	0.647	0.99
119_K	123_F	0.644	0.99
164_I	190_P	0.643	0.99
72_E	75_M	0.643	0.99
74_K	77_D	0.643	0.99
27_A	80_H	0.643	0.99
15_A	198_D	0.641	0.99
148_G	152_L	0.639	0.99
145_L	149_N	0.636	0.99
88_T	184_T	0.634	0.99
63_S	172_L	0.631	0.99
119_K	124_F	0.628	0.99
170_A	173_D	0.623	0.99
84_F	87_K	0.622	0.99
103_D	110_T	0.617	0.99
142_Q	165_E	0.612	0.99
48_F	84_F	0.609	0.99
39_S	45_P	0.607	0.99
87_K	91_D	0.605	0.99
169_A	173_D	0.604	0.99
122_K	126_D	0.603	0.99
78_A	83_V	0.603	0.99
81_V	190_P	0.602	0.99
51_A	176_F	0.601	0.99
95_L	99_V	0.600	0.99
46_W	213_T	0.598	0.98
83_V	188_V	0.597	0.98
22_L	27_A	0.595	0.98
61_A	72_E	0.595	0.98
49_I	85_C	0.594	0.98
140_A	184_T	0.591	0.98
4_I	156_A	0.590	0.98
147_V	151_L	0.586	0.98
7_A	156_A	0.584	0.98
113_A	118_D	0.584	0.98
17_D	196_V	0.579	0.98
35_Q	48_F	0.577	0.98
115_A	118_D	0.577	0.98
75_M	81_V	0.577	0.98
113_A	119_K	0.576	0.98
77_D	81_V	0.573	0.98
64_A	75_M	0.568	0.98
31_K	213_T	0.566	0.98
141_K	187_V	0.564	0.98
6_V	158_G	0.564	0.98
50_V	80_H	0.561	0.98
138_W	141_K	0.559	0.98
97_L	101_Q	0.557	0.98
115_A	121_R	0.553	0.98
173_D	178_L	0.551	0.97
64_A	172_L	0.550	0.97
83_V	86_A	0.547	0.97
11_H	204_P	0.545	0.97
23_T	159_L	0.545	0.97
74_K	78_A	0.542	0.97
60_V	176_F	0.542	0.97
30_I	153_G	0.541	0.97
179_K	183_Y	0.539	0.97
46_W	143_V	0.539	0.97
114_K	119_K	0.537	0.97
150_F	153_G	0.534	0.97
80_H	84_F	0.533	0.97
195_S	198_D	0.533	0.97
23_T	28_E	0.532	0.97
103_D	108_F	0.531	0.97
27_A	52_S	0.529	0.97
110_T	113_A	0.529	0.97
75_M	79_S	0.527	0.97
36_Y	204_P	0.526	0.97
30_I	34_L	0.525	0.97
89_A	182_G	0.525	0.97
56_G	176_F	0.523	0.97
40_S	142_Q	0.521	0.96
172_L	188_V	0.519	0.96
12_S	163_P	0.516	0.96
6_V	152_L	0.515	0.96
118_D	123_F	0.515	0.96
7_A	36_Y	0.511	0.96
56_G	60_V	0.509	0.96
79_S	83_V	0.507	0.96
13_T	16_F	0.506	0.96
113_A	122_K	0.503	0.96
89_A	93_V	0.503	0.96
152_L	156_A	0.501	0.96
167_F	188_V	0.500	0.96
30_I	33_L	0.500	0.96

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
3of4A	3	0.9539	100	0.196	Contact Map
1icrA	2	0.9908	100	0.197	Contact Map
3bemA	2	0.9447	100	0.202	Contact Map
3gagA	4	0.9309	100	0.202	Contact Map
3ge6A	2	0.9401	100	0.206	Contact Map
4qlxA	2	0.9447	100	0.207	Contact Map
1vfrA	2	0.9677	100	0.217	Contact Map
3gbhA	3	0.9447	100	0.218	Contact Map
1noxA	2	0.9124	100	0.223	Contact Map
2h0uA	2	0.8571	100	0.225	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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