OPENSEQ.org - RNK - ECOLI GREMLIN

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RNK - Regulator of nucleoside diphosphate kinase

UniProt:	P0AFW4	Sequence MSRPTIIINDLDAERIDILLEQPAYAGLPIADALNAELDRAQMCSPEEMPHDVVTMNSRVKFRNLSDGEVRVRTLVYPAKMTDSNTQLSVMAPVGAALLGLRVGDSIHWELPGGVATHLEVLELEYQPEAAGDYLL	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG12637
Length:	136 (135)
Sequences:	379
Seq/Len:	2.81

RNK
Paralog alert: 0.04 [within 20: 0.01] - ratio of genomes with paralogs
Cluster includes: GREA GREB RNK

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
56_M	77_Y	3.327	1.00
52_D	102_R	2.407	1.00
13_A	17_D	2.265	1.00
11_L	77_Y	2.022	1.00
103_V	123_E	1.933	0.99
82_T	87_Q	1.903	0.99
62_F	101_L	1.871	0.99
15_R	56_M	1.862	0.99
37_E	40_R	1.808	0.99
61_K	123_E	1.803	0.99
4_P	40_R	1.758	0.99
126_Y	129_E	1.751	0.99
63_R	120_E	1.657	0.98
126_Y	131_A	1.598	0.97
57_N	80_K	1.59	0.97
101_L	105_D	1.58	0.97
8_I	13_A	1.572	0.96
9_N	46_P	1.568	0.96
64_N	117_T	1.552	0.96
54_V	60_V	1.544	0.96
9_N	12_D	1.508	0.95
49_M	55_T	1.472	0.94
6_I	37_E	1.467	0.94
64_N	119_L	1.46	0.94
63_R	122_L	1.435	0.93
15_R	77_Y	1.429	0.93
108_H	118_H	1.337	0.90
37_E	109_W	1.323	0.89
52_D	113_G	1.291	0.87
60_V	92_A	1.287	0.87
73_R	88_L	1.285	0.87
55_T	77_Y	1.274	0.86
71_R	119_L	1.258	0.86
20_L	92_A	1.253	0.85
86_T	105_D	1.22	0.83
126_Y	130_A	1.215	0.83
49_M	124_L	1.209	0.82
59_R	72_V	1.207	0.82
6_I	96_A	1.191	0.81
93_P	97_A	1.187	0.81
10_D	45_S	1.184	0.80
43_M	121_V	1.172	0.80
65_L	120_E	1.16	0.79
55_T	127_Q	1.153	0.78
131_A	135_L	1.148	0.78
9_N	49_M	1.138	0.77
6_I	75_L	1.124	0.75
5_T	48_E	1.122	0.75
127_Q	132_G	1.122	0.75
12_D	15_R	1.118	0.75
2_S	88_L	1.098	0.73
93_P	114_G	1.08	0.71
126_Y	135_L	1.075	0.71
4_P	37_E	1.069	0.70
111_L	117_T	1.064	0.70
11_L	46_P	1.062	0.69
54_V	121_V	1.061	0.69
70_V	113_G	1.049	0.68
64_N	111_L	1.047	0.68
56_M	76_V	1.038	0.67
55_T	128_P	1.035	0.67
14_E	90_V	1.035	0.67
37_E	92_A	1.023	0.65
17_D	20_L	1.023	0.65
64_N	67_D	1.017	0.65
130_A	133_D	1.015	0.64
37_E	107_I	1.012	0.64
61_K	72_V	1.01	0.64
106_S	120_E	1.01	0.64

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
3bmbA	2	1	100	0.26	Contact Map	0.568
2pn0A	4	1	100	0.282	Contact Map	0.569
2p4vA	6	0.9191	99.9	0.463	Contact Map	0.369
1grjA	1	0.9118	99.9	0.466	Contact Map	0.51
2f23A	2	0.8971	99.9	0.468	Contact Map	0.546
1g8fA	1	0.7426	31.7	0.927	Contact Map	0.33
1r6xA	1	0.7426	31.4	0.927	Contact Map	0.368
3gtyX	1	0.8824	22.3	0.932	Contact Map	0.279
2piaA	1	0.5221	18.6	0.935	Contact Map	0.314
1t11A	2	0.9044	18.4	0.935	Contact Map	0.264

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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