OPENSEQ.org - RPPH - ECOLI GREMLIN

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RPPH - RNA pyrophosphohydrolase

UniProt:	P0A776	Sequence MIDDDGYRPNVGIVICNRQGQVMWARRFGQHSWQFPQGGINPGESAEQAMYRELFEEVGLSRKDVRILASTRNWLRYKLPKRLVRWDTKPVCIGQKQKWFLLQLVSGDAEINMQTSSTPEFDGWRWVSYWYPVRQVVSFKRDVYRRVMKEFASVVMSLQENTPKPQNASAYRRKRG	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG13091
Length:	176 (156)
Sequences:	526
Seq/Len:	3.37

RPPH
Paralog alert: 0.02 [within 20: 0.01] - 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
7_Y	78_K	3.462	1.00
70_S	98_K	2.98	1.00
66_R	105_V	2.902	1.00
72_R	150_E	2.792	1.00
66_R	103_Q	2.621	1.00
40_I	46_A	2.258	1.00
64_D	110_E	1.995	1.00
14_V	129_Y	1.987	1.00
50_M	102_L	1.963	1.00
47_E	67_I	1.891	1.00
147_V	151_F	1.878	0.99
106_S	110_E	1.836	0.99
76_R	96_K	1.779	0.99
21_Q	128_S	1.724	0.99
71_T	75_L	1.718	0.99
14_V	35_F	1.717	0.99
45_S	48_Q	1.707	0.99
54_L	65_V	1.609	0.98
129_Y	148_M	1.574	0.98
47_E	51_Y	1.543	0.97
23_M	88_T	1.541	0.97
142_D	145_R	1.514	0.97
12_G	99_W	1.483	0.96
15_I	60_L	1.481	0.96
26_R	122_D	1.479	0.96
67_I	102_L	1.47	0.96
47_E	70_S	1.461	0.96
84_V	146_R	1.44	0.95
128_S	131_Y	1.391	0.94
143_V	147_V	1.386	0.94
20_G	103_Q	1.373	0.94
47_E	102_L	1.306	0.91
5_D	9_P	1.285	0.90
46_A	74_W	1.248	0.88
66_R	152_A	1.248	0.88
71_T	151_F	1.243	0.88
55_F	61_S	1.228	0.87
14_V	132_P	1.214	0.87
17_N	21_Q	1.211	0.86
23_M	58_V	1.208	0.86
78_K	93_I	1.204	0.86
74_W	98_K	1.188	0.85
23_M	86_W	1.167	0.83
10_N	25_A	1.166	0.83
40_I	76_R	1.158	0.83
68_L	117_S	1.139	0.81
128_S	149_K	1.138	0.81
79_L	90_P	1.129	0.81
68_L	118_T	1.126	0.80
16_C	21_Q	1.123	0.80
93_I	103_Q	1.121	0.80
24_W	132_P	1.117	0.80
102_L	136_V	1.116	0.80
103_Q	111_I	1.106	0.79
99_W	124_W	1.087	0.77
15_I	23_M	1.086	0.77
99_W	137_V	1.072	0.76
65_V	136_V	1.065	0.75
85_R	132_P	1.056	0.74
107_G	110_E	1.051	0.74
17_N	150_E	1.044	0.73
54_L	58_V	1.038	0.72
8_R	11_V	1.035	0.72
10_N	143_V	1.006	0.69
55_F	113_M	1.004	0.69
130_W	152_A	1.004	0.69

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
2kdvA	1	0.9318	100	0.583	Contact Map	0.602
1f3yA	1	0.8693	100	0.603	Contact Map	0.568
2o1cA	4	0.8125	99.7	0.735	Contact Map	0.462
2qjtB	2	0.8182	99.7	0.738	Contact Map	0.44
4ijxA	2	0.8182	99.7	0.738	Contact Map	0.548
2fvvA	1	0.8807	99.7	0.74	Contact Map	0.478
4dywA	2	0.7443	99.7	0.742	Contact Map	0.472
3fcmA	2	0.875	99.7	0.747	Contact Map	0.571
1ktgA	2	0.7614	99.7	0.748	Contact Map	0.578
3edsA	1	0.7898	99.7	0.749	Contact Map	0.486

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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