OPENSEQ.org - RMF - ECOLI GREMLIN

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RMF - Ribosome modulation factor

UniProt:	P0AFW2	Sequence MKRQKRDRLERAHQRGYQAGIAGRSKEMCPYQTLNQRSQWLGGWREAMADRVVMA	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG50004
Length:	55 (55)
Sequences:	84
Seq/Len:	1.53

RMF
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
17_Y	50_D	3.26	1.00
15_R	18_Q	2.714	1.00
46_E	52_V	1.752	0.95
9_L	27_E	1.745	0.95
50_D	55_A	1.702	0.94
15_R	24_R	1.578	0.90
4_Q	19_A	1.535	0.88
52_V	55_A	1.518	0.87
8_R	31_Y	1.509	0.87
46_E	55_A	1.492	0.86
13_H	47_A	1.391	0.80
21_I	50_D	1.38	0.80
21_I	53_V	1.294	0.73
14_Q	35_N	1.292	0.73
17_Y	28_M	1.251	0.70
14_Q	36_Q	1.235	0.68
13_H	46_E	1.229	0.68
15_R	26_K	1.225	0.67
17_Y	55_A	1.166	0.62
20_G	44_W	1.125	0.58
2_K	19_A	1.085	0.53
2_K	41_L	1.08	0.53
13_H	38_S	1.08	0.53
32_Q	47_A	1.071	0.52
24_R	42_G	1.071	0.52
3_R	29_C	1.061	0.51
33_T	52_V	1.057	0.51

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
3v22V	1	1	99.9	0.088	Contact Map	0.031
2jrmA	1	1	99.9	0.129	Contact Map	0.264
1jmuB	3	0.3455	5.2	0.915	Contact Map
2cw1A	1	0.6	3	0.925	Contact Map	0
3qn1B	1	0.6	2.8	0.926	Contact Map	0
1eswA	1	0.9636	2.5	0.928	Contact Map	0.088
1eboA	6	0.8364	2.4	0.928	Contact Map	0.106
3cb6A	1	0.9818	2.2	0.929	Contact Map	0.082
1p6xA	2	0.9818	2.2	0.93	Contact Map	0.115
3e6pL	1	0.3818	2.1	0.93	Contact Map	0.547

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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