OPENSEQ.org - YRDB - ECOLI GREMLIN

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YRDB - Uncharacterized protein YrdB

UniProt:	P45795	Sequence MNQAIQFPDREEWDENKKCVCFPALVNGMQLTCAISGESLAYRFTGDTPEQWLASFRQHRWDLEEEAENLIQEQSEDDQGWVWLP	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG12839
Length:	85 (85)
Sequences:	110
Seq/Len:	1.29

YRDB
Paralog alert: 0.00 [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
34_A	81_W	1.996	0.97
26_V	31_L	1.762	0.93
73_E	84_L	1.713	0.92
67_A	82_V	1.707	0.92
11_E	61_W	1.706	0.92
18_K	55_S	1.559	0.86
77_D	81_W	1.452	0.80
6_Q	11_E	1.45	0.80
20_V	53_L	1.426	0.78
35_I	79_Q	1.422	0.78
48_T	65_E	1.347	0.73
16_N	36_S	1.254	0.65
26_V	66_E	1.242	0.64
49_P	80_G	1.226	0.62
48_T	51_Q	1.216	0.61
11_E	25_L	1.213	0.61
6_Q	61_W	1.208	0.60
13_W	53_L	1.204	0.60
48_T	53_L	1.172	0.57
63_L	67_A	1.161	0.56
34_A	83_W	1.159	0.56
49_P	79_Q	1.152	0.55
43_R	79_Q	1.149	0.55
4_A	10_R	1.145	0.54
36_S	73_E	1.143	0.54
36_S	42_Y	1.126	0.52
36_S	53_L	1.104	0.50
15_E	50_E	1.102	0.50
35_I	63_L	1.081	0.48
67_A	83_W	1.072	0.47
46_G	76_E	1.071	0.47
8_P	13_W	1.068	0.47
31_L	76_E	1.067	0.47
32_T	81_W	1.066	0.47
24_A	58_Q	1.065	0.46
56_F	60_R	1.061	0.46
5_I	60_R	1.057	0.46
8_P	23_P	1.049	0.45
5_I	56_F	1.048	0.45
15_E	41_A	1.045	0.44
20_V	32_T	1.041	0.44
27_N	30_Q	1.041	0.44
42_Y	72_Q	1.041	0.44
11_E	29_M	1.038	0.44
22_F	56_F	1.026	0.43
19_C	63_L	1.025	0.42
16_N	69_N	1.016	0.42
8_P	11_E	1.008	0.41
40_L	60_R	1.003	0.40

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
2gpiA	1	1	100	0.219	Contact Map	0.29
3f2gA	2	0.8235	20.2	0.917	Contact Map	0.202
4m5dB	1	0.8941	17.4	0.919	Contact Map	0.139
1vq8D	1	0.6706	15	0.922	Contact Map	0.377
3j21E	1	0.6824	11.5	0.926	Contact Map	0.115
2m3vA	1	0.9412	4.4	0.938	Contact Map	0.066
1iq4A	2	0.5647	4.2	0.939	Contact Map	0.08
1mjiA	2	0.5647	3.8	0.941	Contact Map	0.237
1v92A	1	0.5412	3.4	0.942	Contact Map	0.259
4kixF	1	0.5647	3.3	0.942	Contact Map	0.085

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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