OPENSEQ.org - YIDB - ECOLI GREMLIN

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YIDB - Uncharacterized protein YidB

UniProt:	P09996	Sequence MGLFDEVVGAFLKGDAGKYQAILSWVEEQGGIQVLLEKLQSGGLGAILSTWLSNQQGNQSVSGEQLESALGTNAVSDLGQKLGVDTSTASSLLAEQLPKIIDALSPQGEVSPQANNDLLSAGMELLKGKLFR	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG11196
Length:	132 (131)
Sequences:	145
Seq/Len:	1.11

YIDB
Paralog alert: 0.00 [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_L	105_S	3.381	1.00
90_S	94_A	2.403	0.99
39_L	69_A	1.787	0.92
117_D	120_S	1.632	0.86
41_S	45_G	1.616	0.86
70_L	75_V	1.597	0.85
2_G	5_D	1.577	0.84
53_S	84_V	1.505	0.80
122_G	129_K	1.459	0.77
4_F	93_L	1.452	0.76
129_K	132_R	1.437	0.75
42_G	89_A	1.418	0.74
25_W	78_L	1.386	0.71
4_F	59_Q	1.366	0.70
21_A	105_S	1.355	0.69
62_S	89_A	1.331	0.67
7_V	70_L	1.317	0.66
45_G	56_Q	1.313	0.65
39_L	47_I	1.303	0.65
36_L	110_V	1.283	0.63
19_Y	107_Q	1.276	0.62
61_V	69_A	1.276	0.62
36_L	104_L	1.266	0.61
32_I	104_L	1.257	0.60
48_L	64_E	1.249	0.60
80_Q	101_I	1.243	0.59
118_L	129_K	1.236	0.58
123_M	127_K	1.229	0.58
65_Q	102_D	1.212	0.56
81_K	99_K	1.212	0.56
4_F	13_K	1.206	0.56
69_A	113_Q	1.201	0.55
33_Q	48_L	1.201	0.55
25_W	29_Q	1.194	0.55
66_L	75_V	1.192	0.54
22_I	101_I	1.192	0.54
29_Q	70_L	1.173	0.53
119_L	122_G	1.167	0.52
44_L	102_D	1.161	0.51
52_L	94_A	1.156	0.51
26_V	34_V	1.151	0.50
82_L	105_S	1.13	0.48
122_G	127_K	1.124	0.48
48_L	68_S	1.111	0.47
42_G	85_D	1.109	0.46
66_L	95_E	1.103	0.46
124_E	127_K	1.102	0.46
8_V	101_I	1.101	0.46
111_S	114_A	1.083	0.44
119_L	128_G	1.083	0.44
35_L	93_L	1.076	0.43
40_Q	52_L	1.074	0.43
87_S	130_L	1.069	0.43
34_V	105_S	1.068	0.43
125_L	128_G	1.061	0.42
42_G	83_G	1.06	0.42
62_S	110_V	1.06	0.42
121_A	129_K	1.06	0.42
3_L	10_A	1.053	0.41
62_S	73_N	1.052	0.41
29_Q	75_V	1.051	0.41
102_D	105_S	1.039	0.40
72_T	81_K	1.03	0.39
6_E	94_A	1.024	0.39
9_G	119_L	1.015	0.38
65_Q	128_G	1.009	0.37
41_S	53_S	1.008	0.37
19_Y	75_V	1.007	0.37
82_L	102_D	1.006	0.37

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
1z67A	1	1	100	0.068	Contact Map	0.211
3do6A	2	0.4621	21.6	0.926	Contact Map	0.191
2gqbA	1	0.7955	12.8	0.933	Contact Map	0.132
2gloA	1	0.3864	11.6	0.934	Contact Map	0.016
1jkoC	1	0.3636	7.2	0.94	Contact Map	0.078
1tuzA	1	0.5303	5.2	0.944	Contact Map	0.178
1tc3C	1	0.3561	4.7	0.945	Contact Map	0.052
3ctpA	2	0.4545	4.6	0.945	Contact Map	0.25
1rzsA	1	0.4091	4.6	0.945	Contact Map	0.007
3hm8A	4	0.447	4.4	0.946	Contact Map	0

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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