OPENSEQ.org - YBII - ECOLI GREMLIN

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YBII - Uncharacterized protein YbiI

UniProt:	P41039	Sequence MASGWANDDAVNEQINSTIEDAIARARGEIPRGESLDECEECGAPIPQARREAIPGVRLCIHCQQEKDLQKPAYTGYNRRGSKDSQLR	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG12421
Length:	88 (88)
Sequences:	213
Seq/Len:	2.42

YBII
Paralog alert: 0.06 [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
48_Q	52_E	2.255	1.00
3_S	7_N	2.236	1.00
38_E	43_G	1.913	0.99
36_L	58_R	1.865	0.99
11_V	15_I	1.758	0.98
48_Q	51_R	1.672	0.97
12_N	16_N	1.633	0.96
9_D	13_E	1.559	0.95
3_S	6_A	1.546	0.95
67_K	70_Q	1.536	0.95
9_D	19_I	1.525	0.94
36_L	40_E	1.479	0.93
3_S	18_T	1.454	0.92
18_T	22_A	1.426	0.91
37_D	43_G	1.39	0.90
36_L	59_L	1.341	0.87
13_E	24_A	1.331	0.87
35_S	57_V	1.296	0.85
67_K	71_K	1.292	0.85
5_W	10_A	1.29	0.84
5_W	53_A	1.281	0.84
17_S	81_G	1.27	0.83
62_H	70_Q	1.257	0.82
43_G	54_I	1.249	0.82
38_E	45_P	1.23	0.80
59_L	67_K	1.216	0.79
22_A	26_A	1.215	0.79
29_E	67_K	1.156	0.74
12_N	19_I	1.143	0.73
27_R	30_I	1.137	0.72
27_R	68_D	1.131	0.72
40_E	58_R	1.113	0.70
27_R	49_A	1.112	0.70
13_E	19_I	1.097	0.69
40_E	61_I	1.091	0.68
16_N	19_I	1.079	0.67
62_H	73_A	1.06	0.65
31_P	36_L	1.049	0.64
7_N	74_Y	1.044	0.63
34_E	54_I	1.04	0.63
18_T	77_Y	1.038	0.62
12_N	28_G	1.03	0.61
31_P	59_L	1.002	0.58

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
2kgoA	1	1	100	0.219	Contact Map	0.217
1tjlA	10	0.8523	99.4	0.618	Contact Map	0.336
4ijjA	3	0.8636	99.3	0.632	Contact Map	0.354
2kq9A	1	0.75	99.2	0.648	Contact Map	0.358
2gviA	1	0.7614	87.5	0.87	Contact Map	0.284
3lvqE	1	0.8409	86.7	0.872	Contact Map	0.343
2crrA	1	0.875	81.8	0.879	Contact Map	0.341
3o47A	2	0.9545	81.3	0.88	Contact Map	0.379
2iqjA	2	0.8295	81.1	0.88	Contact Map	0.38
3jueA	2	0.8636	80.2	0.881	Contact Map	0.362

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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