OPENSEQ.org - VSR - ECOLI GREMLIN

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VSR - Very short patch repair protein

UniProt:	P09184	Sequence MADVHDKATRSKNMRAIATRDTAIEKRLASLLTGQGLAFRVQDASLPGRPDFVVDEYRCVIFTHGCFWHHHHCYLFKVPATRTEFWLEKIGKNVERDRRDISRLQELGWRVLIVWECALRGREKLTDEALTERLEEWICGEGASAQIDTQGIHLLA	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG11068
Length:	156 (146)
Sequences:	466
Seq/Len:	3.19

VSR
Paralog alert: 0.05 [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
70_H	90_I	4.672	1.00
5_H	13_N	3.053	1.00
6_D	9_T	2.902	1.00
32_L	52_F	2.457	1.00
13_N	16_A	2.278	1.00
5_H	9_T	2.155	1.00
12_K	16_A	2.017	1.00
33_T	38_A	1.945	1.00
9_T	13_N	1.912	1.00
91_G	95_E	1.755	0.99
99_R	103_R	1.747	0.99
92_K	99_R	1.732	0.99
77_K	90_I	1.731	0.99
53_V	109_W	1.708	0.99
11_S	15_R	1.69	0.98
66_C	73_C	1.649	0.98
30_S	34_G	1.642	0.98
66_C	117_C	1.634	0.98
66_C	79_P	1.616	0.98
64_H	113_I	1.605	0.98
70_H	94_V	1.586	0.97
71_H	117_C	1.557	0.97
29_A	52_F	1.523	0.97
47_P	107_L	1.467	0.95
9_T	12_K	1.439	0.95
64_H	101_I	1.413	0.94
78_V	90_I	1.399	0.94
3_D	10_R	1.387	0.93
54_V	57_Y	1.377	0.93
13_N	17_I	1.365	0.93
12_K	15_R	1.34	0.92
101_I	113_I	1.326	0.91
90_I	94_V	1.322	0.91
59_C	110_R	1.314	0.91
64_H	117_C	1.303	0.90
73_C	79_P	1.303	0.90
76_F	90_I	1.299	0.90
44_A	49_R	1.282	0.89
30_S	39_F	1.277	0.89
37_L	61_I	1.256	0.88
4_V	9_T	1.251	0.88
4_V	13_N	1.249	0.87
70_H	76_F	1.239	0.87
24_I	41_V	1.236	0.87
24_I	65_G	1.23	0.86
54_V	59_C	1.214	0.85
70_H	78_V	1.211	0.85
59_C	137_W	1.198	0.84
66_C	71_H	1.189	0.84
130_L	138_I	1.162	0.82
28_L	31_L	1.157	0.81
70_H	77_K	1.151	0.81
19_T	85_F	1.133	0.80
26_K	30_S	1.116	0.78
3_D	6_D	1.095	0.76
10_R	13_N	1.089	0.76
94_V	98_R	1.079	0.75
30_S	38_A	1.064	0.73
28_L	119_L	1.05	0.72
75_L	82_R	1.048	0.72
10_R	17_I	1.045	0.71
24_I	63_T	1.045	0.71
84_E	88_E	1.044	0.71
21_D	29_A	1.043	0.71
37_L	138_I	1.041	0.71
102_S	105_Q	1.038	0.71
11_S	16_A	1.035	0.70
18_A	116_E	1.033	0.70
66_C	116_E	1.029	0.70
38_A	53_V	1.022	0.69
113_I	117_C	1.021	0.69
59_C	138_I	1.019	0.69
73_C	117_C	1.018	0.68
3_D	8_A	1.01	0.68
29_A	38_A	1.006	0.67
15_R	19_T	1.003	0.67
45_S	113_I	1.002	0.67

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
1cw0A	1	0.9936	100	0.284	Contact Map	0.566
1vsrA	1	0.8718	100	0.376	Contact Map	0.563
3r3pA	2	0.6731	99.8	0.678	Contact Map	0.405
3hrlA	1	0.6474	99.7	0.722	Contact Map	0.476
1ob8A	2	0.7885	24.3	0.951	Contact Map	0.345
2wcwA	4	0.7756	21.9	0.952	Contact Map	0.448
2eo0A	2	0.8077	14.7	0.956	Contact Map	0.345
4e15A	2	0.8269	10.9	0.958	Contact Map	0.276
1tcaA	1	0.6603	10.5	0.959	Contact Map	0.387
1ev7A	2	0.5064	9	0.96	Contact Map	0.384

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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