OPENSEQ.org - YMDF - ECOLI GREMLIN

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YMDF - Uncharacterized protein YmdF

UniProt:	P56614	Sequence MANHRGGSGNFAEDRERASEAGKKGGQHSGGNFKNDPQRASEAGKKGGKSSHGKSDN	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG14358
Length:	57 (56)
Sequences:	72
Seq/Len:	1.29

YMDF
Paralog alert: 0.59 [within 20: 0.01] - ratio of genomes with paralogs
Cluster includes: YCIG YMDF

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
34_K	37_P	3.324	1.00
11_F	21_A	1.804	0.94
19_S	23_K	1.764	0.93
14_D	36_D	1.676	0.91
23_K	39_R	1.482	0.82
14_D	55_S	1.455	0.80
28_H	38_Q	1.418	0.78
5_R	8_S	1.404	0.77
1_M	24_K	1.4	0.77
8_S	13_E	1.399	0.77
4_H	13_E	1.346	0.73
27_Q	45_K	1.337	0.72
50_S	54_K	1.302	0.69
33_F	40_A	1.277	0.67
49_K	54_K	1.269	0.66
3_N	17_R	1.264	0.66
23_K	45_K	1.216	0.61
40_A	48_G	1.171	0.57
12_A	18_A	1.123	0.52
36_D	50_S	1.111	0.51
17_R	39_R	1.097	0.50
9_G	26_G	1.082	0.48
50_S	56_D	1.078	0.48
29_S	35_N	1.055	0.45
33_F	43_A	1.055	0.45
16_E	30_G	1.037	0.44
20_E	42_E	1.021	0.42
29_S	32_N	1.017	0.42
33_F	42_E	1.009	0.41
11_F	18_A	1.002	0.40
2_A	24_K	1.001	0.40

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:

PDB	Chains	Cov	P(%)	HHΔ		Acc
1f15A	3	0.4035	2.7	0.916	Contact Map
1lajA	3	0.3333	1.6	0.926	Contact Map
4dpvZ	1	0.7544	1.1	0.932	Contact Map	0
1mnnA	1	0.3333	0.7	0.943	Contact Map	0
2epgA	2	0.9825	0.5	0.948	Contact Map	0
3k9oB	1	0.4561	0.5	0.949	Contact Map
3p0sA	1	0.9123	0.5	0.949	Contact Map	0
4h03A	1	0.9825	0.5	0.949	Contact Map	0.252
4dwrB	3	0.9825	0.4	0.949	Contact Map	0
2pyxA	2	0.3333	0.4	0.95	Contact Map	0.083

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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