OPENSEQ.org - YGCO - ECOLI GREMLIN

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YGCO - Ferredoxin-like protein YgcO

UniProt:	Q46905	Sequence MSVARNLWRVADAPHIVPADSVERQTAERLINACPAGLFSLTPEGNLRIDYRSCLECGTCRLLCDESTLQQWRYPPSGFGITYRFG	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG13122
Length:	86 (84)
Sequences:	217
Seq/Len:	2.58

YGCO
Paralog alert: 0.74 [within 20: 0.00] - ratio of genomes with paralogs
Cluster includes: FIXX YDIT YGCO

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
22_V	25_Q	2.301	1.00
11_A	76_P	1.764	0.98
17_V	71_Q	1.648	0.97
4_A	7_L	1.638	0.97
26_T	62_L	1.573	0.96
53_S	61_R	1.522	0.95
38_L	50_D	1.492	0.94
48_R	55_L	1.438	0.92
8_W	77_S	1.414	0.92
15_H	18_P	1.413	0.92
25_Q	30_L	1.41	0.91
37_G	40_S	1.405	0.91
45_G	61_R	1.391	0.91
40_S	73_R	1.388	0.91
30_L	63_L	1.383	0.90
60_C	72_W	1.366	0.90
30_L	64_C	1.318	0.87
78_G	82_T	1.316	0.87
40_S	59_T	1.302	0.86
14_P	74_Y	1.245	0.83
22_V	30_L	1.239	0.82
33_A	63_L	1.225	0.81
24_R	74_Y	1.214	0.81
11_A	39_F	1.184	0.78
59_T	72_W	1.172	0.77
15_H	80_G	1.158	0.76
36_A	52_R	1.154	0.76
31_I	79_F	1.119	0.73
27_A	30_L	1.103	0.71
4_A	83_Y	1.1	0.71
25_Q	28_E	1.098	0.71
76_P	79_F	1.092	0.70
16_I	62_L	1.088	0.70
31_I	63_L	1.085	0.69
25_Q	85_F	1.081	0.69
36_A	58_G	1.081	0.69
64_C	78_G	1.075	0.68
72_W	80_G	1.073	0.68
8_W	38_L	1.072	0.68
26_T	63_L	1.046	0.65
33_A	37_G	1.037	0.64
23_E	44_E	1.002	0.60

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
2gmhA	2	0.9767	99.5	0.571	Contact Map	0.182
1q16B	1	0.9651	98.3	0.743	Contact Map	0.132
1hfeL	2	0.9651	98	0.759	Contact Map	0.075
2ivfB	1	0.9884	97.9	0.765	Contact Map	0.187
1jb0C	1	0.7791	97.9	0.768	Contact Map	0.156
1xerA	1	0.8372	97.8	0.769	Contact Map	0.18
2vpzB	2	0.9535	97.8	0.77	Contact Map	0.189
3gyxB	6	0.8256	97.8	0.77	Contact Map	0.188
3mm5B	2	0.9419	97.8	0.77	Contact Map	0.266
1kqfB	1	0.9884	97.8	0.771	Contact Map	0.16

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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