OPENSEQ.org - YBAO - ECOLI GREMLIN

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YBAO - Uncharacterized HTH-type transcriptional regulator YbaO

UniProt:	P0ACJ5	Sequence MLDKIDRKLLALLQQDCTLSLQALAEAVNLTTTPCWKRLKRLEDDGILIGKVALLDPEKIGLGLTAFVLIKTQHHSSEWYCRFVTVVTEMPEVLGFWRMAGEYDYLMRVQVADMKRYDEFYKRLVNSVPGLSDVTSSFAMEQIKYTTSLPIE	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG13218
Length:	152 (150)
Sequences:	5745
Seq/Len:	38.30

YBAO
Paralog alert: 0.82 [within 20: 0.14] - ratio of genomes with paralogs
Cluster includes: ASNC LRP YBAO

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
43_E	51_K	3.645	1.00
12_L	27_A	2.997	1.00
58_E	115_K	2.791	1.00
95_G	108_R	2.764	1.00
102_E	135_T	2.639	1.00
49_I	56_D	2.625	1.00
12_L	19_L	2.334	1.00
112_A	116_R	2.245	1.00
21_L	39_L	2.195	1.00
71_K	133_D	2.117	1.00
9_L	24_L	2.09	1.00
41_R	45_D	2.059	1.00
49_I	54_L	2.038	1.00
6_D	38_R	2.022	1.00
116_R	119_E	1.957	1.00
119_E	123_R	1.945	1.00
67_F	97_W	1.912	1.00
90_M	120_F	1.88	1.00
30_L	34_P	1.868	1.00
40_K	44_D	1.815	1.00
94_L	110_Q	1.8	1.00
65_T	108_R	1.766	1.00
12_L	15_Q	1.764	1.00
73_Q	132_S	1.74	1.00
83_F	87_V	1.658	1.00
22_Q	26_E	1.647	1.00
113_D	116_R	1.638	1.00
19_L	24_L	1.545	1.00
28_V	35_C	1.535	1.00
19_L	27_A	1.533	1.00
13_L	39_L	1.496	1.00
15_Q	27_A	1.487	1.00
16_D	27_A	1.464	1.00
21_L	36_W	1.448	1.00
79_W	82_R	1.446	1.00
23_A	26_E	1.425	1.00
68_V	109_V	1.412	1.00
118_D	141_E	1.394	0.99
23_A	27_A	1.391	0.99
5_I	30_L	1.374	0.99
3_D	38_R	1.361	0.99
142_Q	145_Y	1.36	0.99
18_T	51_K	1.358	0.99
22_Q	32_T	1.356	0.99
81_C	85_T	1.333	0.99
86_V	89_E	1.329	0.99
70_I	107_M	1.317	0.99
97_W	142_Q	1.313	0.99
92_E	124_L	1.31	0.99
31_T	34_P	1.308	0.99
63_G	113_D	1.301	0.99
30_L	35_C	1.297	0.99
12_L	24_L	1.273	0.99
96_F	107_M	1.257	0.99
92_E	116_R	1.239	0.98
8_K	11_A	1.234	0.98
69_L	137_S	1.215	0.98
64_L	114_M	1.186	0.98
67_F	106_L	1.182	0.98
84_V	88_T	1.174	0.98
4_K	8_K	1.17	0.97
5_I	28_V	1.168	0.97
84_V	141_E	1.158	0.97
62_L	112_A	1.152	0.97
40_K	43_E	1.117	0.96
21_L	32_T	1.106	0.96
90_M	124_L	1.105	0.96
5_I	8_K	1.089	0.96
19_L	23_A	1.069	0.95
17_C	53_A	1.069	0.95
69_L	103_Y	1.066	0.95
21_L	25_A	1.063	0.95
18_T	43_E	1.049	0.94
86_V	128_V	1.046	0.94
50_G	54_L	1.04	0.94
82_R	86_V	1.038	0.94
20_S	23_A	1.037	0.94
32_T	36_W	1.03	0.94
8_K	12_L	1.013	0.93
56_D	59_K	1.007	0.93
85_T	88_T	1.007	0.93
71_K	102_E	1.002	0.92

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
2p5vA	8	0.9934	100	0.173	Contact Map	0.868
2e1cA	1	0.9737	100	0.177	Contact Map	0.686
3i4pA	1	0.9868	100	0.184	Contact Map	0.666
2cg4A	2	0.9737	100	0.205	Contact Map	0.608
2ia0A	2	0.9803	100	0.206	Contact Map	0.752
2pn6A	1	0.9803	100	0.219	Contact Map	0.673
2gqqA	4	1	100	0.238	Contact Map	0.824
2cyyA	1	0.9737	100	0.238	Contact Map	0.657
2dbbA	2	0.9539	100	0.252	Contact Map	0.797
2w25A	2	0.9605	100	0.266	Contact Map	0.737

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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