OPENSEQ.org - YDIT - ECOLI GREMLIN

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YDIT - Ferredoxin-like protein YdiT

UniProt:	P77714	Sequence MSQNATVNVDIKLGVNKFHVDEGHPHIILAENPDINEFHKLMKACPAGLYKQDDAGNIHFDSAGCLECGTCRVLCGNTILEQWQYPAGTFGIDFRYG	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG13979
Length:	97 (93)
Sequences:	216
Seq/Len:	2.32

YDIT
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
21_D	87_A	1.93	0.99
28_I	82_Q	1.72	0.97
64_G	72_R	1.639	0.96
37_E	73_V	1.618	0.96
41_L	74_L	1.616	0.96
49_L	61_D	1.548	0.94
36_N	41_L	1.544	0.94
36_N	96_Y	1.474	0.92
18_F	88_G	1.453	0.92
14_G	17_K	1.448	0.91
56_G	72_R	1.439	0.91
51_K	84_Q	1.395	0.89
89_T	93_D	1.379	0.88
35_I	85_Y	1.334	0.86
59_H	66_L	1.334	0.86
87_A	90_F	1.319	0.85
41_L	75_C	1.284	0.83
26_H	29_L	1.257	0.81
71_C	83_W	1.254	0.81
25_P	85_Y	1.237	0.80
44_A	74_L	1.232	0.79
21_D	50_Y	1.232	0.79
12_K	64_G	1.23	0.79
32_N	54_D	1.227	0.79
38_F	41_L	1.213	0.78
48_G	51_K	1.196	0.77
80_L	95_R	1.191	0.76
13_L	28_I	1.19	0.76
44_A	48_G	1.173	0.75
8_N	51_K	1.171	0.74
8_N	70_T	1.168	0.74
42_M	90_F	1.167	0.74
51_K	70_T	1.151	0.73
20_V	23_G	1.122	0.70
47_A	63_A	1.12	0.70
16_N	66_L	1.111	0.69
70_T	83_W	1.109	0.69
75_C	89_T	1.107	0.68
27_I	73_V	1.104	0.68
7_V	17_K	1.103	0.68
18_F	49_L	1.101	0.68
34_D	55_A	1.077	0.65
49_L	60_F	1.075	0.65
40_K	76_G	1.073	0.65
11_I	29_L	1.059	0.63
83_W	91_G	1.047	0.62
22_E	54_D	1.031	0.60
15_V	94_F	1.025	0.60
58_I	88_G	1.019	0.59
14_G	94_F	1.018	0.59
37_E	40_K	1.011	0.58
23_G	52_Q	1.003	0.57

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	0.9897	99.5	0.632	Contact Map	0.215
1hfeL	2	0.9588	98.3	0.774	Contact Map	0.089
1q16B	1	0.9691	98	0.791	Contact Map	0.154
1xerA	1	0.8454	97.7	0.804	Contact Map	0.246
2ivfB	1	0.9485	97.7	0.805	Contact Map	0.247
3gyxB	6	0.732	97.7	0.806	Contact Map	0.279
1jb0C	1	0.6907	97.7	0.806	Contact Map	0.208
1jnrB	2	0.7423	97.6	0.807	Contact Map	0.213
3mm5B	2	0.9588	97.6	0.808	Contact Map	0.353
7fd1A	1	0.7113	97.5	0.811	Contact Map	0.285

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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