OPENSEQ.org - NAPD - ECOLI GREMLIN

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NAPD - Protein NapD

UniProt:	P0A9I5	Sequence MHTNWQVCSLVVQAKSERISDISTQLNAFPGCEVAVSDAPSGQLIVVVEAEDSETLIQTIESVRNVEGVLAVSLVYHQQEEQGEETP	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG12143
Length:	87 (85)
Sequences:	188
Seq/Len:	2.21

NAPD
Paralog alert: 0.02 [within 20: 0.00] - ratio of genomes with paralogs

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Scaled Score	Prob
32_C	48_V	2.167	1.00
26_L	32_C	1.794	0.98
10_L	60_I	1.723	0.97
8_C	74_L	1.656	0.96
17_E	28_A	1.656	0.96
27_N	34_V	1.595	0.95
12_V	63_V	1.561	0.94
19_I	36_V	1.423	0.90
13_Q	66_V	1.396	0.88
9_S	49_E	1.382	0.88
58_Q	73_S	1.316	0.84
25_Q	28_A	1.278	0.82
60_I	70_L	1.272	0.81
4_N	26_L	1.267	0.81
15_K	30_P	1.266	0.81
31_G	35_A	1.25	0.80
24_T	40_P	1.248	0.79
35_A	47_V	1.243	0.79
11_V	56_L	1.228	0.78
5_W	50_A	1.217	0.77
30_P	67_E	1.199	0.76
56_L	71_A	1.198	0.75
34_V	48_V	1.188	0.75
6_Q	78_Q	1.169	0.73
7_V	56_L	1.161	0.72
46_V	60_I	1.149	0.71
33_E	47_V	1.133	0.69
1_M	9_S	1.133	0.69
25_Q	67_E	1.118	0.68
48_V	63_V	1.117	0.68
28_A	69_V	1.115	0.68
9_S	63_V	1.087	0.65
42_G	66_V	1.074	0.63
31_G	47_V	1.069	0.63
6_Q	56_L	1.068	0.63
14_A	19_I	1.063	0.62
36_V	45_I	1.057	0.62
57_I	60_I	1.05	0.61
13_Q	73_S	1.047	0.61
47_V	77_H	1.041	0.60
62_S	71_A	1.032	0.59
14_A	31_G	1.029	0.59
13_Q	77_H	1.013	0.57
14_A	58_Q	1.012	0.57
6_Q	32_C	1.011	0.57
11_V	43_Q	1.01	0.56
66_V	72_V	1.009	0.56
40_P	84_E	1.003	0.56
20_S	23_S	1.002	0.56
6_Q	43_Q	1.001	0.55
20_S	28_A	1.001	0.55

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Scaled Score = (raw_score/average(raw_scores)) > 1 are listed. For all 3L/2 predictions, click on one of the links below.

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling

HHsearch Results: GREMLIN results overlayed on top 10 PDB hits:

Legend: Blue filled circles are GREMLIN results (Scaled_score >1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 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	P(%)	HHΔ		Acc
2jsxA	1	0.9885	99.9	0.276	Contact Map	0.296
2zbcA	8	0.908	88.1	0.834	Contact Map	0.398
2djwA	10	0.931	85.8	0.839	Contact Map	0.273
2cviA	2	0.8851	70.4	0.861	Contact Map	0.336
2e1cA	1	0.977	69.6	0.862	Contact Map	0.312
1mw7A	1	0.8161	69.4	0.862	Contact Map	0.145
2ia0A	2	0.9885	69.1	0.862	Contact Map	0.295
4f3qA	1	0.9195	63.8	0.867	Contact Map	0.199
1lfpA	1	0.8966	62.5	0.868	Contact Map	0.203
1konA	1	0.931	62.2	0.868	Contact Map	0.16

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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