OPENSEQ.org - YBAA - ECOLI GREMLIN

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YBAA - Uncharacterized protein YbaA

UniProt:	P0AAQ6	Sequence MKYVDGFVVAVPADKKDAYREMAAKAAPLFKEFGALRIVECWASDVPDGKVTDFRMAVKAEENEEVVFSWIEYPSKEVRDAANQKMMSDPRMKEFGESMPFDGKRMIYGGFESIIDE	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG11099
Length:	117 (116)
Sequences:	259
Seq/Len:	2.23

YBAA
Paralog alert: 0.03 [within 20: 0.02] - 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
75_S	78_V	4.465	1.00
37_R	72_E	3.656	1.00
13_A	65_E	2.646	1.00
32_E	91_R	2.459	1.00
5_D	79_R	2.125	1.00
35_A	71_I	1.92	0.99
6_G	68_F	1.85	0.98
44_S	112_E	1.821	0.98
15_K	18_A	1.807	0.98
46_V	52_T	1.743	0.97
78_V	82_A	1.74	0.97
73_Y	82_A	1.545	0.94
73_Y	83_N	1.488	0.92
33_F	81_A	1.482	0.92
84_Q	88_S	1.473	0.92
41_C	54_F	1.435	0.90
33_F	76_K	1.373	0.87
21_E	24_A	1.35	0.86
52_T	58_V	1.341	0.86
9_V	22_M	1.328	0.85
16_K	42_W	1.32	0.84
7_F	40_E	1.298	0.83
49_G	58_V	1.289	0.83
44_S	79_R	1.278	0.82
7_F	104_K	1.238	0.79
8_V	107_I	1.226	0.78
74_P	78_V	1.205	0.76
41_C	83_N	1.197	0.76
17_D	21_E	1.189	0.75
46_V	49_G	1.184	0.74
103_G	107_I	1.179	0.74
14_D	63_N	1.151	0.71
38_I	73_Y	1.139	0.70
52_T	56_M	1.131	0.70
42_W	73_Y	1.108	0.67
9_V	106_M	1.104	0.67
39_V	70_W	1.093	0.66
43_A	65_E	1.093	0.66
42_W	74_P	1.089	0.65
58_V	107_I	1.089	0.65
53_D	56_M	1.081	0.64
49_G	52_T	1.063	0.63
30_F	86_M	1.063	0.63
12_P	15_K	1.038	0.60
10_A	63_N	1.035	0.60
29_L	33_F	1.032	0.59
23_A	115_I	1.013	0.57
70_W	107_I	1.007	0.56
56_M	59_K	1.003	0.56

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
2okqA	2	1	100	-0.003	Contact Map	0.655
2fiuA	2	0.7949	73.3	0.925	Contact Map	0.512
3lo3A	28	0.7521	30.6	0.943	Contact Map	0.5
1vqsA	5	0.8291	22.9	0.946	Contact Map	0.6
3hx9A	2	0.7863	21.4	0.947	Contact Map	0.497
1vqyA	8	0.8291	9.7	0.955	Contact Map	0.655
3hhlA	1	0.8376	8	0.956	Contact Map	0.422
2zbvA	3	0.5897	7.5	0.957	Contact Map	0.21
2j5aA	1	0.7009	4.2	0.962	Contact Map	0.25
3m84A	2	0.3761	4.1	0.962	Contact Map	0.393

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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