OPENSEQ.org - YBBJ - ECOLI GREMLIN

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YBBJ - Inner membrane protein YbbJ

UniProt:	P0AAS3	Sequence MMELMVVHPHIFWLSLGGLLLAAEMLGGNGYLLWSGVAAVITGLVVWLVPLGWEWQGVMFAILTLLAAWLWWKWLSRRVREQKHSDSHLNQRGQQLIGRRFVLESPLVNGRGHMRVGDSSWPVSASEDLGAGTHVEVIAIEGITLHIRAVSS	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG13257
Length:	152 (147)
Sequences:	1005
Seq/Len:	6.84

YBBJ
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
136_E	148_R	3.479	1.00
23_A	32_L	2.617	1.00
17_G	36_G	2.301	1.00
130_G	133_T	2.249	1.00
14_L	43_G	2.184	1.00
41_I	63_L	2.166	1.00
38_A	42_T	2.151	1.00
38_A	63_L	2.118	1.00
106_P	130_G	1.985	1.00
99_R	117_G	1.963	1.00
21_L	36_G	1.894	1.00
100_R	136_E	1.89	1.00
34_W	71_W	1.887	1.00
100_R	134_H	1.85	1.00
101_F	135_V	1.8	1.00
114_M	145_L	1.752	1.00
37_V	67_A	1.713	1.00
42_T	59_M	1.62	1.00
45_V	59_M	1.566	1.00
104_E	115_R	1.555	0.99
133_T	149_A	1.55	0.99
17_G	43_G	1.522	0.99
113_H	120_S	1.517	0.99
51_L	55_W	1.499	0.99
17_G	40_V	1.474	0.99
64_T	68_A	1.442	0.99
42_T	45_V	1.437	0.99
114_M	123_V	1.405	0.99
101_F	137_V	1.39	0.99
124_S	146_H	1.38	0.99
31_Y	68_A	1.375	0.98
17_G	21_L	1.358	0.98
103_L	123_V	1.325	0.98
101_F	113_H	1.318	0.98
116_V	137_V	1.306	0.98
129_L	133_T	1.3	0.98
101_F	116_V	1.296	0.98
105_S	113_H	1.284	0.97
75_L	78_R	1.28	0.97
45_V	51_L	1.269	0.97
103_L	114_M	1.246	0.97
139_A	146_H	1.229	0.96
135_V	147_I	1.229	0.96
39_A	60_F	1.227	0.96
60_F	64_T	1.205	0.96
138_I	148_R	1.192	0.95
28_G	33_L	1.192	0.95
3_E	6_V	1.182	0.95
28_G	31_Y	1.18	0.95
53_W	57_G	1.173	0.95
105_S	131_A	1.156	0.94
111_R	122_P	1.146	0.94
28_G	32_L	1.139	0.94
4_L	7_V	1.134	0.93
27_G	30_G	1.129	0.93
17_G	20_L	1.128	0.93
106_P	131_A	1.122	0.93
16_L	20_L	1.122	0.93
58_V	65_L	1.121	0.93
125_A	129_L	1.12	0.93
102_V	134_H	1.114	0.93
96_L	116_V	1.11	0.92
38_A	64_T	1.109	0.92
103_L	131_A	1.104	0.92
13_W	60_F	1.1	0.92
112_G	147_I	1.088	0.91
74_W	78_R	1.084	0.91
65_L	69_W	1.081	0.91
38_A	41_I	1.08	0.91
30_G	68_A	1.08	0.91
71_W	74_W	1.078	0.91
22_A	25_M	1.058	0.90
52_G	55_W	1.049	0.89
101_F	147_I	1.046	0.89
2_M	5_M	1.043	0.89
30_G	33_L	1.04	0.89
42_T	60_F	1.039	0.89
141_E	146_H	1.024	0.88
32_L	96_L	1.024	0.88
90_N	118_D	1.013	0.87

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
2k5hA	1	0.6316	99.5	0.582	Contact Map	0.612
3cp0A	1	0.5197	99.4	0.591	Contact Map	0.759
2k14A	1	0.5	99.2	0.64	Contact Map	0.689
2exdA	1	0.4671	99.2	0.642	Contact Map	0.621
2w1tA	1	0.3355	7.1	0.933	Contact Map	0.584
2gcxA	1	0.3224	5.7	0.936	Contact Map	0.43
2k5lA	1	0.3487	4.8	0.938	Contact Map	0.463
1vioA	2	0.4013	4.5	0.939	Contact Map	0.229
4lgtA	2	0.4342	4.4	0.939	Contact Map	0.07
2rddB	1	0.2434	4.2	0.94	Contact Map	0.432

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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