YODC - BACSU - GREMLIN Contacts

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YODC - Putative NAD(P)H nitroreductase YodC

UniProt:	P81102	Sequences: MTNTLDVLKARASVKEYDTNAPISKEELTELLDLATKAPSAWNLQHWHFTVFHSDESKAELLPVAYNQKQIVESSAVVAILGDLKANENGEEVYAELASQGYITDEIKQTLLGQINGAYQSEQFARDSAFLNASLAAMQLMIAAKAKGYDTCAIGGFNKEQFQKQFDISERYVPVMLISIGKAVKPAHQSNRLPLSKVSTWL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	202 (181)
Sequences:	8928 (6676)
Seq/√Len:	496.2

ECOLI - NFNB NFSA RUTE YDJA
BACSU - YODC MHQN YFKO YDGI NFRA1 NFRA2 YFHC
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
18_D	21_A	4.473	1.00
30_E	147_K	3.804	1.00
24_S	27_E	3.229	1.00
25_K	53_H	3.075	1.00
21_A	182_K	2.813	1.00
25_K	29_T	2.650	1.00
49_F	136_A	2.534	1.00
150_D	183_A	2.341	1.00
31_L	144_A	2.326	1.00
149_Y	182_K	2.256	1.00
33_D	36_T	2.124	1.00
55_D	59_A	2.121	1.00
60_E	165_Q	2.069	1.00
34_L	143_A	2.009	1.00
163_Q	174_P	2.002	1.00
16_E	184_V	1.977	1.00
27_E	149_Y	1.960	1.00
137_A	176_M	1.927	1.00
6_D	10_A	1.901	1.00
27_E	147_K	1.885	1.00
18_D	184_V	1.861	1.00
141_M	151_T	1.859	1.00
10_A	145_K	1.855	1.00
35_A	140_L	1.727	1.00
141_M	153_A	1.716	1.00
57_S	60_E	1.679	1.00
158_N	161_Q	1.657	1.00
161_Q	164_K	1.646	1.00
64_V	161_Q	1.608	1.00
61_L	162_F	1.603	1.00
9_K	37_K	1.582	1.00
144_A	180_I	1.575	1.00
145_K	150_D	1.538	1.00
4_T	7_V	1.530	1.00
141_M	178_I	1.522	1.00
31_L	140_L	1.515	1.00
64_V	165_Q	1.485	1.00
57_S	165_Q	1.469	1.00
54_S	57_S	1.467	1.00
29_T	196_S	1.467	1.00
131_L	134_S	1.448	1.00
62_L	72_V	1.438	1.00
59_A	63_P	1.417	1.00
4_T	8_L	1.403	1.00
193_L	197_K	1.387	1.00
137_A	178_I	1.377	1.00
144_A	151_T	1.370	1.00
31_L	180_I	1.369	1.00
27_E	182_K	1.342	1.00
149_Y	180_I	1.341	1.00
31_L	149_Y	1.334	1.00
195_L	199_S	1.325	1.00
48_H	172_Y	1.319	1.00
5_L	34_L	1.308	1.00
49_F	78_V	1.303	1.00
5_L	9_K	1.301	1.00
34_L	147_K	1.294	1.00
17_Y	179_S	1.294	1.00
69_K	73_E	1.293	1.00
60_E	63_P	1.268	1.00
5_L	30_E	1.263	1.00
22_P	53_H	1.262	1.00
56_E	59_A	1.256	1.00
133_A	175_V	1.240	1.00
32_L	199_S	1.222	1.00
27_E	30_E	1.215	1.00
55_D	58_K	1.203	1.00
81_L	172_Y	1.195	1.00
29_T	33_D	1.176	1.00
36_T	198_V	1.164	1.00
29_T	195_L	1.161	1.00
13_S	152_C	1.155	1.00
151_T	180_I	1.142	1.00
78_V	140_L	1.137	1.00
69_K	72_V	1.137	1.00
5_L	147_K	1.134	1.00
38_A	139_Q	1.116	1.00
135_L	138_M	1.115	1.00
8_L	139_Q	1.107	1.00
59_A	72_V	1.099	1.00
9_K	33_D	1.083	1.00
161_Q	165_Q	1.069	1.00
23_I	149_Y	1.068	1.00
151_T	178_I	1.057	1.00
160_E	164_K	1.056	1.00
4_T	142_I	1.055	1.00
26_E	29_T	1.053	1.00
98_A	101_G	1.041	1.00
152_C	179_S	1.030	1.00
130_F	175_V	1.022	1.00
51_V	199_S	1.014	1.00
6_D	9_K	1.014	1.00
140_L	180_I	1.011	1.00
18_D	182_K	1.000	1.00
126_R	173_V	1.000	1.00
89_N	92_E	0.993	1.00
131_L	155_G	0.988	1.00
51_V	76_A	0.982	1.00
92_E	95_A	0.973	1.00
80_I	140_L	0.963	1.00
33_D	195_L	0.958	1.00
139_Q	142_I	0.955	1.00
153_A	176_M	0.954	1.00
30_E	34_L	0.950	1.00
157_F	177_L	0.947	1.00
32_L	35_A	0.945	1.00
23_I	182_K	0.937	1.00
85_K	88_E	0.935	1.00
95_A	99_S	0.933	1.00
17_Y	152_C	0.930	1.00
117_G	120_Q	0.928	1.00
41_A	128_S	0.910	1.00
56_E	60_E	0.907	1.00
63_P	67_N	0.906	1.00
140_L	178_I	0.906	1.00
30_E	33_D	0.905	1.00
91_E	95_A	0.904	1.00
127_D	130_F	0.900	1.00
49_F	80_I	0.882	1.00
28_L	180_I	0.879	1.00
163_Q	173_V	0.877	1.00
50_T	81_L	0.867	1.00
23_I	26_E	0.862	1.00
31_L	147_K	0.861	1.00
8_L	142_I	0.854	1.00
96_E	100_Q	0.853	1.00
41_A	155_G	0.847	1.00
85_K	89_N	0.844	1.00
59_A	62_L	0.842	1.00
137_A	153_A	0.840	1.00
4_T	146_A	0.837	1.00
24_S	182_K	0.833	1.00
16_E	185_K	0.832	1.00
86_A	90_G	0.829	1.00
194_P	197_K	0.824	1.00
50_T	172_Y	0.819	1.00
94_Y	97_L	0.819	1.00
82_G	129_A	0.812	1.00
74_S	77_V	0.810	1.00
130_F	134_S	0.809	1.00
159_K	174_P	0.807	1.00
70_Q	73_E	0.804	1.00
168_I	172_Y	0.803	1.00
143_A	146_A	0.795	1.00
23_I	27_E	0.790	1.00
132_N	155_G	0.787	1.00
83_D	86_A	0.786	1.00
14_V	187_A	0.785	1.00
88_E	92_E	0.778	1.00
50_T	166_F	0.777	1.00
127_D	131_L	0.774	1.00
60_E	64_V	0.769	1.00
92_E	197_K	0.768	1.00
39_P	151_T	0.765	1.00
94_Y	98_A	0.763	1.00
97_L	100_Q	0.757	1.00
128_S	155_G	0.751	1.00
121_S	124_F	0.749	1.00
93_V	96_E	0.748	1.00
96_E	99_S	0.743	1.00
68_Q	72_V	0.740	1.00
94_Y	99_S	0.739	1.00
47_W	133_A	0.735	1.00
32_L	51_V	0.732	1.00
72_V	75_S	0.722	1.00
162_F	165_Q	0.721	1.00
28_L	32_L	0.720	1.00
28_L	76_A	0.720	1.00
14_V	183_A	0.718	1.00
73_E	76_A	0.718	1.00
16_E	187_A	0.715	1.00
90_G	94_Y	0.710	1.00
40_S	47_W	0.709	1.00
22_P	55_D	0.704	1.00
77_V	179_S	0.699	1.00
84_L	88_E	0.698	1.00
7_V	146_A	0.697	1.00
28_L	51_V	0.695	1.00
130_F	173_V	0.695	1.00
89_N	93_V	0.695	1.00
131_L	176_M	0.695	1.00
52_F	57_S	0.694	1.00
52_F	166_F	0.692	1.00
154_I	179_S	0.686	1.00
183_A	186_P	0.685	1.00
5_L	146_A	0.684	1.00
143_A	147_K	0.683	1.00
95_A	98_A	0.675	1.00
138_M	142_I	0.674	1.00
37_K	189_Q	0.674	1.00
131_L	175_V	0.666	1.00
80_I	137_A	0.664	1.00
87_N	93_V	0.656	1.00
65_A	177_L	0.654	1.00
35_A	49_F	0.653	1.00
163_Q	168_I	0.653	1.00
135_L	139_Q	0.650	1.00
91_E	98_A	0.650	1.00
169_S	172_Y	0.648	1.00
79_A	177_L	0.643	1.00
93_V	97_L	0.642	1.00
159_K	163_Q	0.642	1.00
58_K	62_L	0.642	1.00
26_E	30_E	0.641	1.00
71_I	74_S	0.639	1.00
8_L	146_A	0.638	1.00
67_N	70_Q	0.637	1.00
160_E	163_Q	0.637	1.00
41_A	132_N	0.635	1.00
99_S	102_Y	0.624	1.00
121_S	125_A	0.624	1.00
90_G	95_A	0.622	1.00
9_K	34_L	0.622	1.00
136_A	198_V	0.621	1.00
91_E	100_Q	0.618	1.00
15_K	70_Q	0.618	1.00
162_F	174_P	0.615	1.00
36_T	49_F	0.614	1.00
57_S	166_F	0.612	0.99
31_L	143_A	0.612	0.99
131_L	135_L	0.607	0.99
65_A	71_I	0.605	0.99
61_L	166_F	0.602	0.99
168_I	174_P	0.595	0.99
23_I	28_L	0.590	0.99
62_L	68_Q	0.585	0.99
157_F	162_F	0.581	0.99
65_A	156_G	0.581	0.99
27_E	31_L	0.578	0.99
18_D	185_K	0.571	0.99
193_L	198_V	0.566	0.99
7_V	142_I	0.561	0.99
98_A	102_Y	0.560	0.99
21_A	24_S	0.559	0.99
8_L	34_L	0.559	0.99
70_Q	74_S	0.556	0.99
47_W	136_A	0.556	0.99
52_F	61_L	0.556	0.99
136_A	140_L	0.555	0.99
32_L	198_V	0.553	0.99
80_I	84_L	0.553	0.99
91_E	94_Y	0.552	0.99
31_L	34_L	0.552	0.99
134_S	153_A	0.550	0.99
145_K	183_A	0.550	0.99
68_Q	71_I	0.546	0.99
128_S	132_N	0.545	0.99
18_D	22_P	0.545	0.99
142_I	146_A	0.545	0.99
163_Q	170_E	0.543	0.99
184_V	187_A	0.538	0.99
8_L	37_K	0.536	0.99
83_D	89_N	0.535	0.99
4_T	143_A	0.528	0.99
71_I	75_S	0.526	0.98
93_V	98_A	0.526	0.98
15_K	152_C	0.524	0.98
90_G	93_V	0.520	0.98
89_N	96_E	0.518	0.98
14_V	17_Y	0.516	0.98
137_A	141_M	0.514	0.98
65_A	162_F	0.511	0.98
5_L	33_D	0.511	0.98
62_L	67_N	0.510	0.98
12_A	187_A	0.510	0.98
92_E	97_L	0.509	0.98
87_N	91_E	0.505	0.98
87_N	90_G	0.503	0.98
39_P	139_Q	0.503	0.98
7_V	148_G	0.503	0.98
36_T	47_W	0.502	0.98
123_Q	126_R	0.500	0.98

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
3bemA	2	1	100	0.161	Contact Map
3gagA	4	0.995	100	0.166	Contact Map
3ge6A	2	1	100	0.171	Contact Map
3gbhA	3	1	100	0.184	Contact Map
4qlxA	2	1	100	0.184	Contact Map
3of4A	3	0.9901	100	0.189	Contact Map
2h0uA	2	0.901	100	0.191	Contact Map
2hayA	2	0.995	100	0.193	Contact Map
1noxA	2	0.9703	100	0.196	Contact Map
1zchA	2	0.9059	100	0.197	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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