OPENSEQ.org - YDDL - ECOLI GREMLIN

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YDDL - Putative uncharacterized protein YddL

UniProt:	P77519	Sequence MKLKIVAVVVTGLLAANVAHAAEVYNKDGNKLDLYGKVTALRYFTDDKRDDGDKTYARLGFKGETQINDQMIGFGHWEYDFKGYNDEANGSRGKNL	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG13783
Length:	96 (96)
Sequences:	263
Seq/Len:	2.74

YDDL
Paralog alert: 0.94 [within 20: 0.08] - 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
55_T	83_G	2.892	1.00
5_I	8_V	2.227	1.00
67_I	71_M	2.174	1.00
85_N	89_N	2.121	1.00
3_L	7_A	1.979	0.99
85_N	91_S	1.876	0.99
24_V	34_L	1.827	0.99
4_K	8_V	1.789	0.99
1_M	6_V	1.665	0.98
38_V	61_F	1.584	0.97
12_G	16_A	1.55	0.96
6_V	11_T	1.486	0.95
40_A	43_Y	1.458	0.94
57_A	81_F	1.449	0.93
35_Y	76_H	1.44	0.93
40_A	55_T	1.435	0.93
3_L	6_V	1.433	0.93
35_Y	96_L	1.427	0.93
43_Y	54_K	1.387	0.91
9_V	18_V	1.336	0.89
3_L	20_H	1.327	0.89
43_Y	52_G	1.303	0.88
3_L	11_T	1.298	0.87
32_L	69_D	1.271	0.86
47_D	50_D	1.25	0.85
81_F	92_R	1.224	0.83
58_R	80_D	1.22	0.83
86_D	89_N	1.208	0.82
7_A	96_L	1.202	0.81
10_V	20_H	1.187	0.80
44_F	84_Y	1.171	0.79
59_L	81_F	1.165	0.78
4_K	7_A	1.164	0.78
45_T	51_D	1.149	0.77
10_V	15_A	1.119	0.74
45_T	84_Y	1.111	0.74
82_K	93_G	1.103	0.73
9_V	15_A	1.094	0.72
11_T	14_L	1.071	0.70
45_T	50_D	1.068	0.69
13_L	16_A	1.053	0.68
4_K	14_L	1.05	0.67
16_A	19_A	1.049	0.67
6_V	10_V	1.042	0.67
41_L	54_K	1.029	0.65
4_K	13_L	1.028	0.65
35_Y	66_Q	1.027	0.65
34_L	57_A	1.023	0.64
2_K	6_V	1.012	0.63
10_V	16_A	1.003	0.62
3_L	13_L	1.003	0.62

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
2j1nA	3	0.7812	99.3	0.672	Contact Map	0.689
1phoA	1	0.7812	99.3	0.674	Contact Map	0.616
2zfgA	1	0.7812	99.2	0.687	Contact Map	0.612
3nsgA	3	0.7812	99.2	0.691	Contact Map	0.68
4auiA	3	0.8646	98.6	0.753	Contact Map	0.254
3vy8X	1	0.8125	97.6	0.813	Contact Map	0.343
2fgqX	1	0.7083	97.5	0.816	Contact Map	0.32
3prnA	1	0.6667	95.4	0.854	Contact Map	0.42
2porA	1	0.6667	93.9	0.865	Contact Map	0.25
3nb3A	3	0.9375	87.7	0.884	Contact Map	0.523

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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