OPENSEQ.org - YBED - ECOLI GREMLIN

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YBED - UPF0250 protein YbeD

UniProt:	P0A8J4	Sequence MKTKLNELLEFPTPFTYKVMGQALPELVDQVVEVVQRHAPGDYTPTVKPSSKGNYHSVSITINATHIEQVETLYEELGKIDIVRMVL	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG11592
Length:	87 (86)
Sequences:	305
Seq/Len:	3.55

YBED
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
16_T	59_S	2.869	1.00
14_P	63_N	2.575	1.00
37_R	76_E	1.945	1.00
11_F	67_I	1.626	0.98
74_Y	78_G	1.574	0.98
15_F	71_E	1.533	0.97
23_A	56_H	1.532	0.97
21_G	27_L	1.513	0.97
61_T	64_A	1.423	0.95
28_V	35_V	1.388	0.95
75_E	79_K	1.386	0.94
49_P	54_N	1.38	0.94
19_V	83_V	1.338	0.93
3_T	7_E	1.328	0.93
67_I	71_E	1.327	0.93
28_V	47_V	1.325	0.93
26_E	30_Q	1.322	0.92
35_V	60_I	1.321	0.92
72_T	76_E	1.311	0.92
9_L	13_T	1.31	0.92
20_M	85_M	1.298	0.92
34_V	83_V	1.281	0.91
47_V	58_V	1.213	0.87
49_P	56_H	1.201	0.87
26_E	82_I	1.186	0.86
19_V	45_P	1.166	0.85
14_P	46_T	1.16	0.84
7_E	67_I	1.159	0.84
32_V	45_P	1.152	0.84
36_Q	41_G	1.146	0.83
37_R	72_T	1.146	0.83
27_L	58_V	1.145	0.83
38_H	72_T	1.131	0.82
48_K	57_S	1.123	0.81
51_S	79_K	1.121	0.81
22_Q	54_N	1.119	0.81
2_K	7_E	1.102	0.80
27_L	56_H	1.097	0.79
39_A	62_I	1.088	0.78
42_D	45_P	1.067	0.77
33_E	37_R	1.063	0.76
40_P	56_H	1.056	0.75
35_V	69_Q	1.055	0.75
27_L	41_G	1.053	0.75
38_H	76_E	1.044	0.74
8_L	74_Y	1.043	0.74
22_Q	84_R	1.041	0.74
46_T	55_Y	1.029	0.73
36_Q	45_P	1.014	0.71
76_E	79_K	1.001	0.70

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
1rwuA	1	1	100	0.151	Contact Map	0.328
2h9zA	1	0.9655	99.9	0.24	Contact Map	0.306
2ko1A	2	0.8736	84.8	0.858	Contact Map	0.422
2f1fA	2	0.8621	84.7	0.858	Contact Map	0.572
2pc6A	4	0.8736	82.5	0.862	Contact Map	0.548
2lvwA	2	0.908	80.8	0.864	Contact Map	0.399
2fgcA	1	0.9885	75.8	0.87	Contact Map	0.454
1y7pA	3	0.8736	60.7	0.883	Contact Map	0.478
1zpvA	3	0.8736	45	0.894	Contact Map	0.4
1u8sA	2	0.8851	17.7	0.914	Contact Map	0.266

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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