OPENSEQ.org - YDEI - ECOLI GREMLIN

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YDEI - Uncharacterized protein YdeI

UniProt:	P31130	Sequence MKFQAIVLASFLVMPYALADDQGGLKQDAAPPPPHAIEDGYRGTDDAKKMTVDFAKTMHDGASVSLRGNLISHKGEDRYVFRDKSGEINVVIPAAVFDGREVQPDQMINISGSLDKKSAPAVVRVTHLQK	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG11644
Length:	130 (130)
Sequences:	176
Seq/Len:	1.35

YDEI
Paralog alert: 0.58 [within 20: 0.00] - ratio of genomes with paralogs
Cluster includes: YDEI YGIW

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
67_R	109_N	2.84	1.00
70_L	90_V	2.104	0.98
110_I	123_V	1.875	0.96
60_D	115_D	1.851	0.96
115_D	124_R	1.744	0.93
110_I	128_L	1.691	0.92
104_P	116_K	1.656	0.91
79_Y	92_I	1.64	0.90
114_L	123_V	1.63	0.90
43_G	64_V	1.623	0.90
66_L	70_L	1.494	0.84
23_G	28_D	1.433	0.80
90_V	128_L	1.408	0.78
75_G	78_R	1.405	0.78
92_I	96_V	1.404	0.78
77_D	114_L	1.404	0.78
78_R	89_N	1.377	0.76
16_Y	88_I	1.352	0.74
27_Q	31_P	1.343	0.74
64_V	85_S	1.341	0.73
43_G	117_K	1.31	0.71
9_A	29_A	1.298	0.70
106_Q	130_K	1.282	0.69
84_K	110_I	1.26	0.67
41_Y	97_F	1.25	0.66
36_A	108_I	1.238	0.65
91_V	121_A	1.232	0.64
13_V	52_V	1.231	0.64
61_G	93_P	1.228	0.64
73_H	106_Q	1.223	0.63
90_V	110_I	1.216	0.63
88_I	121_A	1.191	0.60
29_A	88_I	1.187	0.60
77_D	113_S	1.178	0.59
8_L	111_S	1.163	0.57
117_K	121_A	1.158	0.57
15_P	18_L	1.147	0.56
15_P	19_A	1.139	0.55
77_D	80_V	1.139	0.55
56_K	73_H	1.13	0.54
119_A	122_V	1.124	0.54
71_I	91_V	1.123	0.54
72_S	80_V	1.117	0.53
5_A	8_L	1.109	0.52
69_N	107_M	1.095	0.51
66_L	88_I	1.082	0.49
72_S	91_V	1.078	0.49
111_S	118_S	1.077	0.49
70_L	97_F	1.065	0.48
40_G	97_F	1.059	0.47
84_K	124_R	1.052	0.46
39_D	97_F	1.049	0.46
8_L	62_A	1.045	0.46
26_K	32_P	1.039	0.45
5_A	94_A	1.037	0.45
43_G	128_L	1.036	0.45
90_V	93_P	1.033	0.45
86_G	99_G	1.033	0.45
64_V	103_Q	1.018	0.43
43_G	103_Q	1.013	0.43
50_M	110_I	1.012	0.42
40_G	55_A	1.008	0.42
73_H	76_E	1	0.41

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
1nnxA	1	0.8154	100	0.246	Contact Map	0.463
1x54A	1	0.6538	95.7	0.863	Contact Map	0.378
3nemA	2	0.6538	95.3	0.867	Contact Map	0.446
1c0aA	1	0.6462	95.2	0.868	Contact Map	0.399
1wydA	2	0.6538	95.1	0.868	Contact Map	0.419
2xgtA	2	0.6154	95.1	0.869	Contact Map	0.448
4gnxB	2	0.6769	95	0.869	Contact Map	0.463
1n9wA	2	0.6	94.9	0.87	Contact Map	0.447
1l0wA	2	0.6538	94.9	0.87	Contact Map	0.395
3e0eA	1	0.6	94.6	0.872	Contact Map	0.383

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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