YDGI - BACSU - GREMLIN Contacts

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YDGI - Putative NAD(P)H nitroreductase YdgI

UniProt:	P96707	Sequences: MIKTNDFMEIMKGRRSIRNYDPAVKISKEEMTEILEEATTAPSSVNAQPWRFLVIDSPEGKEKLAPLASFNQTQVTTSSAVIAVFADMNNADYLEEIYSKAVELGYMPQEVKDRQIAALTAHFEKLPAQVNRETILIDGGLVSMQLMLTARAHGYDTNPIGGYDKENIAETFGLDKERYVPVMLLSIGKAADEGYASYRLPIDTIAEWK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	209 (196)
Sequences:	7957 (5855)
Seq/√Len:	418.2

ECOLI - NFNB NFSA RUTE YDJA
BACSU - YDGI MHQN YODC YFKO 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
21_D	24_V	4.546	1.00
33_E	153_H	3.802	1.00
27_S	30_E	3.073	1.00
28_K	56_D	3.052	1.00
24_V	189_K	2.790	1.00
28_K	32_T	2.729	1.00
52_F	142_V	2.615	1.00
156_D	190_A	2.358	1.00
58_P	62_E	2.328	1.00
34_I	150_A	2.296	1.00
63_K	171_T	2.220	1.00
155_Y	189_K	2.218	1.00
169_A	181_P	2.168	1.00
36_E	39_T	2.065	1.00
143_S	183_M	2.032	1.00
30_E	155_Y	1.994	1.00
147_M	157_T	1.881	1.00
19_N	191_A	1.856	1.00
37_E	149_T	1.810	1.00
147_M	159_P	1.797	1.00
6_D	9_E	1.795	1.00
21_D	191_A	1.751	1.00
164_D	167_N	1.713	1.00
30_E	153_H	1.707	1.00
167_N	170_E	1.689	1.00
9_E	13_G	1.687	1.00
67_L	167_N	1.672	1.00
150_A	187_I	1.670	1.00
38_A	146_L	1.621	1.00
13_G	151_R	1.602	1.00
64_L	168_I	1.598	1.00
65_A	76_T	1.592	1.00
67_L	171_T	1.592	1.00
7_F	10_I	1.578	1.00
151_R	156_D	1.569	1.00
147_M	185_L	1.547	1.00
52_F	82_I	1.530	1.00
58_P	61_K	1.515	1.00
32_T	203_D	1.513	1.00
20_Y	186_S	1.506	1.00
12_K	40_T	1.505	1.00
150_A	157_T	1.484	1.00
60_G	63_K	1.479	1.00
109_Q	113_D	1.474	1.00
62_E	66_P	1.449	1.00
82_I	146_L	1.436	1.00
175_D	178_R	1.433	1.00
202_I	206_A	1.417	1.00
73_T	77_T	1.412	1.00
7_F	11_M	1.412	1.00
34_I	146_L	1.408	1.00
200_L	204_T	1.389	1.00
137_I	140_G	1.382	1.00
57_S	60_G	1.370	1.00
51_R	179_Y	1.358	1.00
34_I	155_Y	1.356	1.00
143_S	185_L	1.343	1.00
85_F	179_Y	1.343	1.00
35_L	206_A	1.331	1.00
113_D	117_A	1.312	1.00
8_M	12_K	1.308	1.00
30_E	189_K	1.292	1.00
120_T	124_E	1.291	1.00
59_E	62_E	1.288	1.00
16_S	158_N	1.281	1.00
60_G	171_T	1.257	1.00
155_Y	187_I	1.247	1.00
26_I	155_Y	1.241	1.00
63_K	66_P	1.232	1.00
32_T	36_E	1.231	1.00
39_T	205_I	1.228	1.00
139_G	182_V	1.225	1.00
30_E	33_E	1.224	1.00
73_T	76_T	1.215	1.00
8_M	37_E	1.208	1.00
25_K	56_D	1.204	1.00
32_T	202_I	1.202	1.00
62_E	76_T	1.201	1.00
34_I	187_I	1.194	1.00
141_L	144_M	1.184	1.00
37_E	153_H	1.176	1.00
167_N	171_T	1.166	1.00
137_I	161_G	1.166	1.00
11_M	145_Q	1.150	1.00
157_T	187_I	1.149	1.00
8_M	153_H	1.124	1.00
93_Y	96_E	1.117	1.00
166_E	170_E	1.114	1.00
8_M	33_E	1.096	1.00
20_Y	158_N	1.089	1.00
41_A	145_Q	1.067	1.00
12_K	36_E	1.058	1.00
146_L	187_I	1.049	1.00
59_E	63_K	1.047	1.00
146_L	185_L	1.033	1.00
54_V	80_A	1.030	1.00
157_T	185_L	1.022	1.00
52_F	84_V	1.010	1.00
29_E	32_T	1.010	1.00
99_S	103_E	1.008	1.00
158_N	186_S	1.003	1.00
84_V	146_L	0.997	1.00
133_E	136_L	0.996	1.00
21_D	189_K	0.985	1.00
174_L	177_E	0.985	1.00
31_M	187_I	0.981	1.00
17_I	194_G	0.978	1.00
26_I	30_E	0.976	1.00
26_I	189_K	0.954	1.00
27_S	189_K	0.951	1.00
54_V	206_A	0.949	1.00
36_E	202_I	0.945	1.00
34_I	153_H	0.939	1.00
117_A	120_T	0.938	1.00
132_R	180_V	0.935	1.00
118_A	121_A	0.933	1.00
53_L	85_F	0.931	1.00
33_E	37_E	0.930	1.00
145_Q	148_L	0.929	1.00
9_E	12_K	0.928	1.00
117_A	121_A	0.924	1.00
119_L	123_F	0.923	1.00
136_L	182_V	0.915	1.00
7_F	148_L	0.911	1.00
133_E	137_I	0.910	1.00
86_A	135_I	0.909	1.00
96_E	204_T	0.907	1.00
35_L	38_A	0.901	1.00
31_M	80_A	0.896	1.00
143_S	159_P	0.893	1.00
72_Q	76_T	0.890	1.00
7_F	152_A	0.887	1.00
26_I	29_E	0.886	1.00
163_Y	184_L	0.883	1.00
31_M	35_L	0.882	1.00
127_P	130_V	0.879	1.00
6_D	152_A	0.876	1.00
44_S	134_T	0.870	1.00
63_K	67_L	0.864	1.00
96_E	99_S	0.863	1.00
89_N	92_D	0.862	1.00
38_A	52_F	0.861	1.00
19_N	194_G	0.861	1.00
113_D	116_I	0.854	1.00
89_N	93_Y	0.854	1.00
92_D	96_E	0.839	1.00
121_A	125_K	0.839	1.00
72_Q	75_V	0.828	1.00
134_T	161_G	0.827	1.00
19_N	192_D	0.825	1.00
33_E	36_E	0.823	1.00
44_S	161_G	0.823	1.00
75_V	78_S	0.822	1.00
62_E	65_A	0.816	1.00
114_R	118_A	0.812	1.00
78_S	81_V	0.806	1.00
165_K	181_P	0.802	1.00
159_P	183_M	0.801	1.00
74_Q	77_T	0.798	1.00
25_K	58_P	0.795	1.00
53_L	172_F	0.792	1.00
53_L	179_Y	0.792	1.00
95_E	99_S	0.792	1.00
81_V	186_S	0.789	1.00
10_I	152_A	0.787	1.00
169_A	180_V	0.785	1.00
55_I	172_F	0.778	1.00
98_Y	102_V	0.777	1.00
114_R	117_A	0.776	1.00
42_P	157_T	0.765	1.00
110_E	113_D	0.760	1.00
11_M	148_L	0.752	1.00
17_I	190_A	0.744	1.00
190_A	193_E	0.743	1.00
168_I	171_T	0.736	1.00
98_Y	103_E	0.736	1.00
123_F	126_L	0.733	1.00
168_I	181_P	0.730	1.00
174_L	179_Y	0.724	1.00
94_L	98_Y	0.723	1.00
149_T	152_A	0.720	1.00
35_L	54_V	0.720	1.00
43_S	50_W	0.717	1.00
136_L	140_G	0.716	1.00
76_T	79_S	0.715	1.00
65_A	72_Q	0.714	1.00
138_D	161_G	0.711	1.00
18_R	74_Q	0.711	1.00
66_P	71_N	0.704	1.00
39_T	52_F	0.703	1.00
31_M	54_V	0.702	1.00
83_A	184_L	0.700	1.00
144_M	148_L	0.699	1.00
68_A	75_V	0.693	1.00
120_T	123_F	0.687	1.00
141_L	145_Q	0.682	1.00
29_E	33_E	0.676	1.00
84_V	143_S	0.675	1.00
82_I	187_I	0.675	1.00
142_V	205_I	0.674	1.00
201_P	204_T	0.671	1.00
160_I	186_S	0.670	1.00
117_A	123_F	0.669	0.99
115_Q	118_A	0.665	0.99
166_E	169_A	0.665	0.99
50_W	139_G	0.664	0.99
30_E	34_I	0.663	0.99
163_Y	168_I	0.661	0.99
98_Y	101_A	0.660	0.99
175_D	179_Y	0.657	0.99
21_D	192_D	0.656	0.99
127_P	131_N	0.656	0.99
116_I	120_T	0.655	0.99
165_K	169_A	0.654	0.99
87_D	90_N	0.654	0.99
137_I	182_V	0.652	0.99
115_Q	119_L	0.651	0.99
68_A	184_L	0.647	0.99
137_I	183_M	0.647	0.99
74_Q	78_S	0.646	0.99
11_M	152_A	0.639	0.99
136_L	180_V	0.638	0.99
64_L	172_F	0.637	0.99
89_N	178_R	0.632	0.99
118_A	123_F	0.624	0.99
60_G	172_F	0.622	0.99
68_A	168_I	0.622	0.99
34_I	149_T	0.622	0.99
100_K	104_L	0.620	0.99
11_M	37_E	0.616	0.99
97_I	100_K	0.612	0.99
84_V	88_M	0.609	0.99
40_T	196_A	0.606	0.99
77_T	80_A	0.598	0.99
44_S	138_D	0.591	0.99
122_H	125_K	0.590	0.99
10_I	154_G	0.589	0.99
95_E	98_Y	0.586	0.99
146_L	157_T	0.585	0.99
174_L	181_P	0.581	0.99
93_Y	97_I	0.581	0.99
8_M	152_A	0.578	0.99
63_K	167_N	0.577	0.99
169_A	177_E	0.576	0.99
169_A	174_L	0.575	0.98
191_A	194_G	0.573	0.98
113_D	118_A	0.572	0.98
26_I	31_M	0.571	0.98
121_A	124_E	0.569	0.98
97_I	101_A	0.568	0.98
34_I	37_E	0.567	0.98
55_I	60_G	0.567	0.98
75_V	81_V	0.566	0.98
102_V	109_Q	0.565	0.98
87_D	93_Y	0.564	0.98
21_D	25_K	0.560	0.98
116_I	119_L	0.559	0.98
82_I	185_L	0.557	0.98
142_V	146_L	0.556	0.98
134_T	137_I	0.556	0.98
122_H	126_L	0.555	0.98
137_I	141_L	0.553	0.98
52_F	205_I	0.550	0.98
107_M	110_E	0.547	0.98
71_N	74_Q	0.546	0.98
100_K	103_E	0.545	0.98
99_S	102_V	0.544	0.98
55_I	64_L	0.543	0.98
140_G	144_M	0.542	0.98
47_A	134_T	0.542	0.98
27_S	32_T	0.540	0.98
12_K	37_E	0.533	0.98
106_Y	109_Q	0.530	0.97
19_N	193_E	0.529	0.97
119_L	124_E	0.527	0.97
88_M	91_A	0.526	0.97
118_A	122_H	0.524	0.97
83_A	172_F	0.524	0.97
148_L	152_A	0.523	0.97
67_L	168_I	0.522	0.97
42_P	145_Q	0.521	0.97
31_M	56_D	0.521	0.97
129_Q	132_R	0.520	0.97
91_A	131_N	0.517	0.97
10_I	148_L	0.515	0.97
42_P	159_P	0.512	0.97
90_N	93_Y	0.510	0.97
115_Q	122_H	0.509	0.97
52_F	146_L	0.507	0.97
104_L	107_M	0.504	0.97
94_L	97_I	0.502	0.96
146_L	149_T	0.501	0.96
38_A	142_V	0.501	0.96
103_E	108_P	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
3ge6A	2	0.9952	100	0.18	Contact Map
3gbhA	3	1	100	0.184	Contact Map
4qlxA	2	0.9952	100	0.186	Contact Map
3gagA	4	0.9761	100	0.192	Contact Map
3bemA	2	0.9904	100	0.198	Contact Map
3of4A	3	0.9665	100	0.202	Contact Map
1noxA	2	0.9522	100	0.209	Contact Map
2b67A	2	0.9617	100	0.209	Contact Map
2h0uA	2	0.8852	100	0.215	Contact Map
1icrA	2	0.9713	100	0.217	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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