OPENSEQ.org - RBSD - ECOLI GREMLIN

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RBSD - D-ribose pyranase

UniProt:	P04982	Sequence MKKGTVLNSDISSVISRLGHTDTLVVCDAGLPIPKSTTRIDMALTQGVPSFMQVLGVVTNEMQVEAAIIAEEIKHHNPQLHETLLTHLEQLQKHQGNTIEIRYTTHEQFKQQTAESQAVIRSGECSPYANIILCAGVTF	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG10817
Length:	139 (139)
Sequences:	670
Seq/Len:	4.82

RBSD
Paralog alert: 0.40 [within 20: 0.00] - ratio of genomes with paralogs
Cluster includes: FUCM RBSD

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
11_I	120_I	4.417	1.00
25_V	116_S	3.881	1.00
14_V	118_A	2.72	1.00
13_S	17_R	2.591	1.00
111_Q	114_A	2.185	1.00
23_T	134_C	1.911	1.00
56_G	87_H	1.894	1.00
23_T	112_Q	1.874	1.00
13_S	38_T	1.859	1.00
10_D	38_T	1.823	1.00
24_L	58_V	1.682	0.99
44_L	54_V	1.67	0.99
33_I	39_R	1.6	0.99
50_S	53_Q	1.577	0.99
18_L	62_M	1.572	0.99
108_Q	111_Q	1.559	0.99
68_I	134_C	1.558	0.99
66_A	102_R	1.489	0.98
81_H	103_Y	1.483	0.98
44_L	48_V	1.471	0.98
80_L	129_A	1.463	0.98
40_I	118_A	1.449	0.98
25_V	31_L	1.423	0.98
2_K	61_E	1.417	0.97
48_V	53_Q	1.413	0.97
23_T	132_I	1.377	0.97
12_S	16_S	1.377	0.97
66_A	134_C	1.364	0.97
21_T	31_L	1.34	0.96
15_I	61_E	1.327	0.96
45_T	57_V	1.32	0.96
9_S	39_R	1.304	0.95
42_M	51_F	1.293	0.95
22_D	117_Q	1.288	0.95
113_T	119_V	1.286	0.95
9_S	12_S	1.278	0.95
25_V	109_F	1.238	0.93
5_T	60_N	1.209	0.92
18_L	135_A	1.207	0.92
26_V	120_I	1.205	0.92
8_N	43_A	1.205	0.92
17_R	39_R	1.197	0.92
82_E	86_T	1.193	0.91
69_I	73_I	1.189	0.91
31_L	109_F	1.183	0.91
24_L	118_A	1.178	0.91
18_L	24_L	1.158	0.90
69_I	103_Y	1.155	0.90
9_S	13_S	1.14	0.89
55_L	133_L	1.131	0.88
18_L	22_D	1.128	0.88
53_Q	90_Q	1.123	0.88
71_E	75_H	1.121	0.88
73_I	77_N	1.119	0.88
53_Q	91_L	1.118	0.87
25_V	132_I	1.112	0.87
10_D	13_S	1.106	0.87
45_T	56_G	1.098	0.86
73_I	103_Y	1.096	0.86
82_E	85_L	1.067	0.84
29_A	129_A	1.058	0.83
30_G	121_R	1.054	0.83
29_A	47_G	1.049	0.83
64_V	67_A	1.041	0.82
14_V	40_I	1.04	0.82
59_T	64_V	1.027	0.81
32_P	128_Y	1.024	0.80
47_G	65_E	1.022	0.80
68_I	104_T	1.017	0.80

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
3dsaA	15	1	100	0.012	Contact Map	0.801
3p12A	4	0.9496	100	0.037	Contact Map	0.71
1ogdA	5	0.9424	100	0.039	Contact Map	0.652
4a34A	20	0.9784	100	0.093	Contact Map	0.581
2ob5A	1	0.9712	100	0.097	Contact Map	0.514
3mvkA	10	0.9856	100	0.099	Contact Map	0.599
2wcuA	2	0.964	100	0.109	Contact Map	0.598
2wcvA	10	0.964	100	0.114	Contact Map	0.625
1t4aA	2	0.4964	28.6	0.931	Contact Map	0.175
3j31Q	1	0.4029	12.7	0.941	Contact Map	0.001

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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