OPENSEQ.org - YBEY - ECOLI GREMLIN

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YBEY - Endoribonuclease YbeY

UniProt:	P0A898	Sequence MSQVILDLQLACEDNSGLPEESQFQTWLNAVIPQFQEESEVTIRVVDTAESHSLNLTYRGKDKPTNVLSFPFEVPPGMEMSLLGDLVICRQVVEKEAQEQGKPLEAHWAHMVVHGSLHLLGYDHIEDDEAEEMEALETEIMLALGYEDPYIAEKE	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG13655
Length:	155 (147)
Sequences:	1623
Seq/Len:	11.04

YBEY
Paralog alert: 0.01 [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
52_H	62_D	3.55	1.00
48_T	89_C	3.125	1.00
134_E	137_E	2.738	1.00
52_H	63_K	2.425	1.00
138_T	148_D	2.423	1.00
48_T	92_V	2.401	1.00
56_L	62_D	2.36	1.00
48_T	95_K	2.291	1.00
45_V	90_R	2.265	1.00
53_S	57_T	2.227	1.00
24_F	43_I	2.226	1.00
66_N	96_E	2.215	1.00
54_L	68_L	1.981	1.00
66_N	107_H	1.896	1.00
52_H	56_L	1.831	1.00
35_F	136_L	1.813	1.00
67_V	86_L	1.745	1.00
93_V	108_W	1.717	1.00
92_V	95_K	1.711	1.00
89_C	92_V	1.71	1.00
106_A	146_Y	1.692	1.00
96_E	107_H	1.689	1.00
46_V	50_E	1.678	1.00
48_T	91_Q	1.677	1.00
28_L	116_S	1.65	1.00
93_V	111_M	1.637	1.00
52_H	64_P	1.624	1.00
44_R	87_V	1.6	1.00
136_L	139_E	1.556	1.00
71_P	115_G	1.487	1.00
50_E	53_S	1.459	1.00
88_I	93_V	1.449	1.00
109_A	146_Y	1.424	1.00
44_R	50_E	1.416	1.00
51_S	64_P	1.396	0.99
55_N	59_R	1.392	0.99
28_L	32_I	1.391	0.99
46_V	51_S	1.389	0.99
95_K	99_E	1.381	0.99
130_A	134_E	1.372	0.99
96_E	102_K	1.364	0.99
30_A	143_A	1.363	0.99
84_G	119_L	1.337	0.99
46_V	87_V	1.325	0.99
110_H	130_A	1.318	0.99
126_E	129_E	1.317	0.99
88_I	112_V	1.31	0.99
110_H	137_E	1.294	0.99
83_L	120_L	1.289	0.99
34_Q	143_A	1.176	0.98
113_V	140_I	1.175	0.98
71_P	74_V	1.145	0.97
24_F	112_V	1.143	0.97
54_L	87_V	1.124	0.97
104_L	108_W	1.116	0.96
110_H	134_E	1.101	0.96
107_H	110_H	1.073	0.95
69_S	84_G	1.071	0.95
102_K	107_H	1.064	0.95
27_W	109_A	1.054	0.95
59_R	68_L	1.052	0.95
125_I	129_E	1.034	0.94
122_Y	132_E	1.033	0.94
94_E	98_Q	1.032	0.94
51_S	86_L	1.028	0.94
61_K	68_L	1.024	0.93
93_V	104_L	1.016	0.93
90_R	94_E	1.011	0.93
28_L	43_I	1.007	0.93
34_Q	139_E	1.007	0.93
103_P	106_A	1.006	0.93
130_A	137_E	1.006	0.93
66_N	110_H	1.004	0.93
32_I	116_S	1	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
1xaxA	1	0.9935	100	0.057	Contact Map	0.442
1xm5A	4	1	100	0.058	Contact Map	0.842
1oz9A	1	0.9355	100	0.154	Contact Map	0.75
1tviA	1	0.9548	100	0.171	Contact Map	0.439
3ayuA	1	0.9226	75.5	0.908	Contact Map	0.297
1hv5A	6	0.9161	72.3	0.91	Contact Map	0.285
3ma2D	2	0.9419	66.5	0.914	Contact Map	0.298
3ba0A	1	0.9161	65.5	0.914	Contact Map	0.236
1cgeA	1	0.9161	65.5	0.914	Contact Map	0.268
4h1qA	2	0.8774	64.2	0.915	Contact Map	0.305

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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