OPENSEQ.org - RPOZ - ECOLI GREMLIN

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RPOZ - DNA-directed RNA polymerase subunit omega

UniProt:	P0A800	Sequence MARVTVQDAVEKIGNRFDLVLVAARRARQMQVGGKDPLVPEENDKTTVIALREIEEGLINNQILDVRERQEQQEQEAAELQAVTAIAEGRR	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG10899
Length:	91 (89)
Sequences:	194
Seq/Len:	2.18

RPOZ
Paralog alert: 0.00 [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
41_E	49_I	3.493	1.00
38_L	58_L	3.28	1.00
9_A	55_E	1.686	0.97
30_M	59_I	1.626	0.96
30_M	36_D	1.6	0.95
13_I	18_D	1.595	0.95
39_V	49_I	1.545	0.94
13_I	22_V	1.509	0.93
18_D	24_A	1.505	0.92
7_Q	31_Q	1.468	0.91
10_V	14_G	1.434	0.90
9_A	14_G	1.431	0.90
47_T	57_G	1.345	0.85
74_E	80_L	1.29	0.82
35_K	50_A	1.268	0.81
4_V	47_T	1.223	0.77
29_Q	65_D	1.222	0.77
85_A	89_G	1.209	0.76
29_Q	57_G	1.196	0.75
37_P	47_T	1.189	0.74
21_L	59_I	1.158	0.71
15_N	48_V	1.143	0.70
7_Q	11_E	1.112	0.67
76_E	79_E	1.107	0.66
80_L	88_E	1.089	0.65
8_D	83_V	1.085	0.64
82_A	85_A	1.076	0.63
78_A	81_Q	1.073	0.63
10_V	29_Q	1.072	0.63
23_A	55_E	1.068	0.62
22_V	59_I	1.068	0.62
25_R	65_D	1.066	0.62
81_Q	85_A	1.065	0.62
80_L	87_A	1.064	0.62
29_Q	59_I	1.059	0.61
13_I	21_L	1.048	0.60
25_R	47_T	1.04	0.59
30_M	67_R	1.035	0.59
18_D	35_K	1.034	0.59
82_A	87_A	1.034	0.59
14_G	55_E	1.03	0.58
36_D	46_T	1.02	0.57
80_L	89_G	1.017	0.57
18_D	69_R	1.013	0.56
77_A	83_V	1.011	0.56
77_A	85_A	1.004	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
4kn7E	2	1	99.9	0.304	Contact Map	0.246
4ljzE	2	1	99.9	0.304	Contact Map	0.278
2a6hE	2	0.9231	99.8	0.477	Contact Map	0.176
4aybK	1	0.8681	99.7	0.522	Contact Map	0.104
3h0gF	2	0.8791	99.5	0.573	Contact Map	0.127
1qklA	1	0.9121	99.5	0.574	Contact Map	0.259
1twfF	1	0.9121	99.4	0.603	Contact Map	0.205
3nuhB	1	0.4286	8.9	0.931	Contact Map	0.254
3j3br	1	0.5385	5.2	0.938	Contact Map	0.031
4bj1A	1	0.3407	4.4	0.94	Contact Map	0.27

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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