OPENSEQ.org - YJDI - ECOLI GREMLIN

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YJDI - Uncharacterized protein YjdI

UniProt:	P0AF59	Sequence MDQALLDGGYRCYTGEKIDVYFNTAICQHSGNCVRGNGKLFNLKRKPWIMPDEVDVATVVKVIDTCPSGALKYRHK	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG12466
Length:	76 (71)
Sequences:	116
Seq/Len:	1.63

YJDI
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
32_N	65_T	2.514	1.00
35_R	55_D	1.947	0.98
36_G	41_F	1.92	0.98
41_F	59_V	1.717	0.95
64_D	73_Y	1.665	0.94
28_Q	63_I	1.572	0.91
40_L	54_V	1.549	0.90
41_F	62_V	1.529	0.89
15_G	51_P	1.514	0.88
60_V	75_H	1.431	0.84
41_F	53_E	1.373	0.81
32_N	35_R	1.365	0.80
49_I	63_I	1.345	0.79
22_F	43_L	1.34	0.78
56_V	60_V	1.327	0.78
15_G	22_F	1.312	0.76
61_K	65_T	1.312	0.76
17_K	68_S	1.283	0.74
40_L	59_V	1.264	0.73
42_N	45_R	1.262	0.72
24_T	37_N	1.259	0.72
46_K	49_I	1.252	0.72
57_A	75_H	1.23	0.70
19_D	76_K	1.225	0.69
15_G	62_V	1.223	0.69
15_G	24_T	1.193	0.66
25_A	49_I	1.097	0.57
36_G	62_V	1.068	0.54
11_R	49_I	1.06	0.53
39_K	58_T	1.055	0.52
39_K	44_K	1.032	0.50
57_A	61_K	1.032	0.50
19_D	37_N	1.031	0.50
17_K	56_V	1.019	0.48
13_Y	29_H	1.019	0.48
18_I	75_H	1.019	0.48
20_V	42_N	1	0.46

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
1daxA	1	0.7895	95.5	0.819	Contact Map	0.264
1rofA	1	0.7632	95.3	0.822	Contact Map	0.49
1dwlA	1	0.7237	95.2	0.823	Contact Map	0.187
1sj1A	2	0.7895	95.2	0.824	Contact Map	0.406
1iqzA	1	0.7895	94.7	0.829	Contact Map	0.254
1f2gA	1	0.7105	94	0.834	Contact Map	0.317
1xerA	1	1	87.3	0.859	Contact Map	0.342
1rgvA	1	0.75	86.1	0.862	Contact Map	0.271
1jnrB	2	0.75	85.4	0.863	Contact Map	0.396
3c8yA	1	1	84.8	0.864	Contact Map	0.262

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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