YDJA - ECOLI - GREMLIN Contacts

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YDJA - Putative NAD(P)H nitroreductase YdjA

UniProt:	P0ACY1	Sequences: MDALELLINRRSASRLAEPAPTGEQLQNILRAGMRAPDHKSMQPWHFFVIEGEGRERFSAVLEQGAIAAGSDDKAIDKARNAPFRAPLIITVVAKCEENHKVPRWEQEMSAGCAVMAMQMAAVAQGFGGIWRSGALTESPVVREAFGCREQDKIVGFLYLGTPQLKASTSINVPDPTPFVTYF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11134
Length:	183 (160)
Sequences:	13279 (9765)
Seq/√Len:	772.0

ECOLI - YDJA RUTE NFNB NFSA
BACSU - YFHC YODC MHQN YDGI YFKO NFRA1 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
22_T	25_Q	3.557	1.00
28_N	125_Q	3.348	1.00
23_G	51_E	2.770	1.00
47_F	114_A	2.508	1.00
23_G	27_Q	2.478	1.00
48_F	93_V	2.477	1.00
29_I	122_A	2.307	1.00
127_F	162_T	2.162	1.00
9_N	123_V	2.157	1.00
128_G	163_P	2.154	1.00
25_Q	125_Q	2.122	1.00
119_Q	129_G	2.119	1.00
93_V	152_D	2.052	1.00
5_E	9_N	1.954	1.00
31_R	34_M	1.925	1.00
47_F	90_I	1.863	1.00
32_A	121_A	1.829	1.00
25_Q	127_F	1.821	1.00
59_S	84_F	1.761	1.00
57_R	145_A	1.741	1.00
33_G	118_M	1.695	1.00
115_V	156_G	1.685	1.00
19_P	162_T	1.675	1.00
17_A	164_Q	1.671	1.00
15_R	164_Q	1.670	1.00
56_E	84_F	1.634	1.00
90_I	118_M	1.624	1.00
115_V	158_L	1.604	1.00
95_K	151_Q	1.542	1.00
29_I	118_M	1.535	1.00
3_A	7_L	1.501	1.00
109_M	112_G	1.496	1.00
143_R	154_I	1.480	1.00
92_V	115_V	1.475	1.00
25_Q	162_T	1.437	1.00
4_L	28_N	1.431	1.00
3_A	6_L	1.419	1.00
119_Q	131_W	1.407	1.00
113_C	116_M	1.397	1.00
20_A	51_E	1.383	1.00
49_V	88_L	1.379	1.00
93_V	148_C	1.355	1.00
91_T	157_F	1.351	1.00
122_A	160_L	1.350	1.00
51_E	88_L	1.321	1.00
119_Q	158_L	1.315	1.00
138_E	141_V	1.295	1.00
123_V	128_G	1.288	1.00
25_Q	28_N	1.286	1.00
54_G	57_R	1.283	1.00
29_I	160_L	1.277	1.00
127_F	160_L	1.275	1.00
8_I	35_R	1.240	1.00
92_V	118_M	1.239	1.00
61_V	145_A	1.239	1.00
141_V	144_E	1.237	1.00
53_E	56_E	1.230	1.00
91_T	154_I	1.227	1.00
47_F	92_V	1.221	1.00
46_H	152_D	1.212	1.00
27_Q	177_T	1.203	1.00
111_A	155_V	1.202	1.00
174_P	178_P	1.176	1.00
4_L	8_I	1.175	1.00
131_W	156_G	1.174	1.00
29_I	127_F	1.153	1.00
89_I	157_F	1.152	1.00
8_I	31_R	1.150	1.00
61_V	141_V	1.140	1.00
90_I	160_L	1.119	1.00
4_L	32_A	1.115	1.00
92_V	111_A	1.111	1.00
121_A	125_Q	1.105	1.00
56_E	60_A	1.104	1.00
26_L	88_L	1.102	1.00
12_S	130_I	1.079	1.00
5_E	8_I	1.062	1.00
32_A	125_Q	1.058	1.00
129_G	160_L	1.050	1.00
57_R	60_A	1.048	1.00
21_P	127_F	1.047	1.00
96_C	153_K	1.042	1.00
36_A	117_A	1.040	1.00
50_I	91_T	1.033	1.00
30_L	49_V	1.029	1.00
122_A	129_G	1.024	1.00
46_H	95_K	1.023	1.00
58_F	142_V	1.017	1.00
27_Q	31_R	1.016	1.00
141_V	145_A	1.013	1.00
94_A	111_A	1.011	1.00
106_E	133_S	1.007	1.00
16_L	159_Y	1.007	1.00
121_A	124_A	1.003	1.00
116_M	120_M	0.993	1.00
39_H	106_E	0.973	1.00
34_M	179_F	0.970	1.00
129_G	158_L	0.961	1.00
92_V	158_L	0.958	1.00
113_C	131_W	0.957	1.00
4_L	125_Q	0.957	1.00
94_A	107_Q	0.947	1.00
22_T	162_T	0.946	1.00
93_V	154_I	0.941	1.00
24_E	27_Q	0.937	1.00
60_A	64_Q	0.933	1.00
49_V	90_I	0.930	1.00
117_A	120_M	0.929	1.00
140_P	144_E	0.916	1.00
95_K	152_D	0.907	1.00
3_A	124_A	0.906	1.00
30_L	33_G	0.905	1.00
118_M	158_L	0.903	1.00
88_L	160_L	0.897	1.00
48_F	152_D	0.895	1.00
130_I	159_Y	0.879	1.00
132_R	159_Y	0.873	1.00
108_E	155_V	0.867	1.00
27_Q	176_P	0.859	1.00
97_E	151_Q	0.857	1.00
112_G	131_W	0.848	1.00
140_P	143_R	0.848	1.00
4_L	124_A	0.836	1.00
91_T	146_F	0.835	1.00
115_V	131_W	0.834	1.00
21_P	162_T	0.822	1.00
143_R	153_K	0.821	1.00
113_C	117_A	0.819	1.00
118_M	160_L	0.817	1.00
15_R	165_L	0.816	1.00
109_M	133_S	0.813	1.00
18_E	85_R	0.811	1.00
56_E	59_S	0.809	1.00
3_A	120_M	0.808	1.00
38_D	45_W	0.808	1.00
29_I	125_Q	0.803	1.00
142_V	145_A	0.802	1.00
20_A	87_P	0.798	1.00
94_A	155_V	0.793	1.00
7_L	117_A	0.792	1.00
17_A	162_T	0.792	1.00
81_N	84_F	0.786	1.00
81_N	85_R	0.785	1.00
175_D	178_P	0.780	1.00
149_R	152_D	0.771	1.00
19_P	22_T	0.768	1.00
4_L	121_A	0.767	1.00
28_N	32_A	0.762	1.00
28_N	31_R	0.762	1.00
104_R	153_K	0.758	1.00
39_H	133_S	0.752	1.00
7_L	120_M	0.750	1.00
20_A	88_L	0.748	1.00
21_P	87_P	0.741	1.00
21_P	24_E	0.736	1.00
21_P	25_Q	0.731	1.00
139_S	153_K	0.728	1.00
45_W	111_A	0.726	1.00
31_R	176_P	0.724	1.00
148_C	152_D	0.721	1.00
139_S	143_R	0.718	1.00
38_D	43_Q	0.706	1.00
110_S	133_S	0.701	1.00
26_L	160_L	0.694	1.00
82_A	85_R	0.692	1.00
46_H	93_V	0.692	1.00
26_L	30_L	0.688	1.00
108_E	112_G	0.673	1.00
109_M	113_C	0.670	1.00
6_L	124_A	0.669	1.00
89_I	159_Y	0.668	1.00
31_R	35_R	0.661	1.00
139_S	154_I	0.657	1.00
52_G	55_R	0.646	1.00
57_R	61_V	0.638	1.00
86_A	89_I	0.637	1.00
6_L	120_M	0.628	1.00
8_I	28_N	0.628	1.00
30_L	90_I	0.626	1.00
10_R	37_P	0.622	1.00
39_H	110_S	0.621	1.00
79_A	85_R	0.620	1.00
15_R	85_R	0.620	1.00
143_R	148_C	0.610	1.00
48_F	146_F	0.609	1.00
17_A	87_P	0.606	1.00
79_A	82_A	0.596	1.00
96_C	151_Q	0.595	1.00
87_P	162_T	0.593	1.00
120_M	124_A	0.583	1.00
62_L	83_P	0.583	1.00
50_I	55_R	0.580	1.00
137_T	157_F	0.580	1.00
116_M	119_Q	0.578	1.00
24_E	28_N	0.576	1.00
17_A	165_L	0.575	1.00
3_A	121_A	0.575	1.00
64_Q	80_R	0.575	1.00
109_M	131_W	0.569	1.00
26_L	90_I	0.568	1.00
83_P	159_Y	0.568	1.00
34_M	176_P	0.564	1.00
143_R	150_E	0.561	1.00
28_N	121_A	0.559	1.00
123_V	163_P	0.558	1.00
148_C	154_I	0.557	1.00
165_L	168_S	0.553	1.00
33_G	47_F	0.550	1.00
50_I	146_F	0.546	1.00
14_S	130_I	0.541	1.00
16_L	130_I	0.541	1.00
60_A	63_E	0.539	1.00
29_I	33_G	0.536	1.00
16_L	19_P	0.536	1.00
63_E	80_R	0.534	1.00
13_A	128_G	0.533	1.00
14_S	82_A	0.533	1.00
38_D	44_P	0.533	1.00
45_W	114_A	0.530	1.00
115_V	119_Q	0.528	1.00
108_E	153_K	0.528	1.00
33_G	114_A	0.527	1.00
54_G	145_A	0.525	1.00
118_M	129_G	0.524	1.00
101_K	104_R	0.524	1.00
58_F	89_I	0.524	1.00
62_L	157_F	0.520	1.00
37_P	116_M	0.517	1.00
80_R	84_F	0.514	1.00
13_A	163_P	0.513	1.00
43_Q	174_P	0.513	1.00
101_K	105_W	0.511	1.00
163_P	166_K	0.510	1.00
83_P	89_I	0.510	1.00
53_E	57_R	0.509	1.00
46_H	174_P	0.506	1.00
13_A	167_A	0.503	1.00
174_P	179_F	0.503	1.00
26_L	49_V	0.502	1.00
29_I	121_A	0.500	1.00

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
3bm1A	2	0.9727	100	0.152	Contact Map
2b67A	2	0.9071	100	0.156	Contact Map
3bemA	2	0.9071	100	0.161	Contact Map
3gagA	4	0.9016	100	0.165	Contact Map
3of4A	3	0.9071	100	0.165	Contact Map
1icrA	2	0.929	100	0.166	Contact Map
3qdlA	4	0.9071	100	0.167	Contact Map
4qlxA	2	0.9126	100	0.169	Contact Map
3ge6A	2	0.9071	100	0.17	Contact Map
1ywqA	2	0.9945	100	0.171	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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