OPENSEQ.org - YBIJ - ECOLI GREMLIN

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YBIJ - Uncharacterized protein YbiJ

UniProt:	P0AAX3	Sequence MKTINTVVAAMALSTLSFGVFAAEPVTASQAQNMNKIGVVSADGASTLDALEAKLAEKAAAAGASGYSITSATNNNKLSGTAVIYK	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG12422
Length:	86 (86)
Sequences:	373
Seq/Len:	4.34

YBIJ
Paralog alert: 0.97 [within 20: 0.48] - ratio of genomes with paralogs
Cluster includes: BHSA MCBA YAHO YBIJ YHCN YJFN YJFY

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
47_T	50_A	2.464	1.00
57_E	61_A	1.981	1.00
64_A	84_I	1.901	1.00
74_N	78_L	1.782	1.00
21_F	25_P	1.762	1.00
42_A	51_L	1.682	0.99
36_K	83_V	1.634	0.99
48_L	80_G	1.569	0.99
56_A	60_A	1.566	0.99
18_F	22_A	1.476	0.98
23_A	26_V	1.391	0.96
53_A	57_E	1.385	0.96
51_L	72_A	1.348	0.95
47_T	54_K	1.347	0.95
1_M	5_N	1.345	0.95
35_N	68_S	1.33	0.95
65_S	86_K	1.328	0.95
4_I	7_V	1.32	0.95
8_V	15_T	1.307	0.94
70_T	81_T	1.292	0.94
24_E	27_T	1.279	0.93
1_M	9_A	1.257	0.93
68_S	83_V	1.241	0.92
7_V	12_A	1.231	0.92
46_S	51_L	1.23	0.92
52_E	69_I	1.223	0.91
56_A	83_V	1.219	0.91
69_I	72_A	1.198	0.90
51_L	78_L	1.196	0.90
16_L	19_G	1.193	0.90
51_L	74_N	1.169	0.89
4_I	8_V	1.155	0.88
71_S	81_T	1.154	0.88
57_E	60_A	1.139	0.87
5_N	11_M	1.134	0.86
49_D	84_I	1.12	0.86
17_S	21_F	1.115	0.85
26_V	31_A	1.082	0.83
31_A	34_M	1.073	0.82
76_N	80_G	1.066	0.81
24_E	28_A	1.04	0.79
14_S	19_G	1.039	0.79
11_M	61_A	1.033	0.79
7_V	11_M	1.022	0.78

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
2nocA	1	0.9884	99.9	0.082	Contact Map	0.428
2jnaA	2	0.9884	99.9	0.091	Contact Map	0.412
2m2jA	1	1	99.8	0.254	Contact Map	0.477
2ma4A	1	0.7442	99.8	0.286	Contact Map	0.458
4evuA	2	0.8023	99.8	0.307	Contact Map	0.582
2qgmA	1	0.8605	17	0.893	Contact Map	0.025
2jynA	1	0.5814	12	0.901	Contact Map	0.241
3b55A	1	0.8605	11.9	0.901	Contact Map	0.03
3sg0A	1	0.8837	11.1	0.902	Contact Map	0.097
4kzkA	1	0.9302	6.5	0.912	Contact Map	0.347

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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