OPENSEQ.org - YBHB - ECOLI GREMLIN

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YBHB - UPF0098 protein YbhB

UniProt:	P12994	Sequence MKLISNDLRDGDKLPHRHVFNGMGYDGDNISPHLAWDDVPAGTKSFVVTCYDPDAPTGSGWWHWVVVNLPADTRVLPQGFGSGLVAMPDGVLQTRTDFGKTGYDGAAPPKGETHRYIFTVHALDIERIDVDEGASGAMVGFNVHFHSLASASITAMFS	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG11238
Length:	158 (158)
Sequences:	1167
Seq/Len:	7.39

YBHB
Paralog alert: 0.28 [within 20: 0.02] - ratio of genomes with paralogs
Cluster includes: YBCL YBHB

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
124_D	146_H	5.438	1.00
25_Y	107_A	3.92	1.00
39_V	46_F	3.688	1.00
68_N	129_D	3.144	1.00
48_V	120_V	3.097	1.00
98_F	104_D	2.467	1.00
6_N	33_H	2.458	1.00
50_C	118_F	2.415	1.00
17_R	78_Q	2.354	1.00
1_M	151_A	2.297	1.00
7_D	78_Q	2.227	1.00
13_K	156_M	2.187	1.00
46_F	71_A	2.176	1.00
7_D	33_H	2.131	1.00
8_L	155_A	2.055	1.00
117_I	154_T	1.979	1.00
3_L	120_V	1.967	1.00
47_V	139_V	1.917	1.00
31_S	76_L	1.916	1.00
44_K	126_E	1.89	1.00
14_L	106_A	1.89	1.00
36_W	76_L	1.829	1.00
123_L	143_V	1.799	1.00
29_N	105_G	1.762	1.00
119_T	152_S	1.72	1.00
9_R	12_D	1.717	1.00
5_S	34_L	1.608	1.00
35_A	75_V	1.594	1.00
94_T	139_V	1.559	1.00
139_V	143_V	1.506	0.99
54_D	115_R	1.499	0.99
33_H	75_V	1.488	0.99
18_H	78_Q	1.485	0.99
39_V	74_R	1.472	0.99
3_L	151_A	1.461	0.99
8_L	15_P	1.456	0.99
14_L	155_A	1.423	0.99
5_S	153_I	1.41	0.99
143_V	147_S	1.381	0.99
67_V	94_T	1.356	0.99
67_V	139_V	1.331	0.98
17_R	28_D	1.321	0.98
13_K	158_S	1.311	0.98
40_P	122_A	1.303	0.98
66_V	91_V	1.277	0.98
52_D	63_H	1.269	0.97
1_M	38_D	1.255	0.97
68_N	127_R	1.22	0.97
40_P	43_T	1.21	0.96
68_N	92_L	1.186	0.96
103_Y	106_A	1.183	0.96
119_T	150_S	1.182	0.96
81_G	93_Q	1.173	0.95
67_V	134_A	1.169	0.95
113_T	158_S	1.152	0.95
142_N	145_F	1.15	0.95
88_P	91_V	1.146	0.95
43_T	46_F	1.139	0.94
1_M	39_V	1.139	0.94
46_F	74_R	1.121	0.94
120_V	151_A	1.117	0.94
39_V	43_T	1.105	0.93
3_L	34_L	1.082	0.92
2_K	37_D	1.071	0.92
65_V	94_T	1.07	0.92
94_T	136_G	1.063	0.91
31_S	80_F	1.05	0.91
30_I	79_G	1.035	0.90
117_I	152_S	1.031	0.90
17_R	30_I	1.022	0.89
47_V	143_V	1.016	0.89
18_H	33_H	1.015	0.89
20_F	104_D	1.012	0.88
121_H	147_S	1.011	0.88
93_Q	102_G	1.009	0.88
63_H	114_H	1.008	0.88
14_L	118_F	1.003	0.88

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
1fjjA	1	1	100	0.089	Contact Map	0.888
1fuxA	2	1	100	0.103	Contact Map	0.828
4begA	2	0.9937	100	0.121	Contact Map	0.814
3n08A	2	0.9114	100	0.151	Contact Map	0.817
2evvA	4	0.943	100	0.212	Contact Map	0.758
1wpxB	1	0.981	100	0.5	Contact Map	0.292
2jyzA	1	0.8228	99.9	0.535	Contact Map	0.25
2gzqA	1	0.8481	99.9	0.549	Contact Map	0.463
3axyA	4	0.7911	99.9	0.555	Contact Map	0.348
1wkoA	2	0.8481	99.9	0.563	Contact Map	0.319

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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