OPENSEQ.org - TADA - ECOLI GREMLIN

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TADA - tRNA-specific adenosine deaminase

UniProt:	P68398	Sequence MSEVEFSHEYWMRHALTLAKRAWDEREVPVGAVLVHNNRVIGEGWNRPIGRHDPTAHAEIMALRQGGLVMQNYRLIDATLYVTLEPCVMCAGAMIHSRIGRVVFGARDAKTGAAGSLMDVLHHPGMNHRVEITEGILADECAALLSDFFRMRRQEIKAQKKAQSSTD	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG11372
Length:	167 (151)
Sequences:	4371
Seq/Len:	28.95

TADA
Paralog alert: 0.74 [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
14_H	43_E	3.868	1.00
105_G	141_C	2.989	1.00
80_L	94_M	2.539	1.00
101_R	131_E	2.525	1.00
92_G	120_V	2.401	1.00
79_T	103_V	2.356	1.00
13_R	137_L	2.347	1.00
77_D	100_G	2.185	1.00
53_D	64_R	2.111	1.00
14_H	17_T	2.081	1.00
18_L	43_E	1.968	1.00
101_R	133_T	1.96	1.00
11_W	35_V	1.939	1.00
13_R	140_E	1.932	1.00
11_W	40_V	1.89	1.00
34_L	62_A	1.86	1.00
104_F	118_M	1.854	1.00
138_A	142_A	1.845	1.00
137_L	140_E	1.835	1.00
150_R	154_Q	1.819	1.00
92_G	96_H	1.808	1.00
47_R	61_M	1.798	1.00
106_A	149_F	1.796	1.00
79_T	101_R	1.762	1.00
32_A	80_L	1.758	1.00
107_R	134_E	1.741	1.00
104_F	107_R	1.73	1.00
21_R	45_W	1.707	1.00
47_R	51_R	1.698	1.00
119_D	123_H	1.674	1.00
18_L	21_R	1.661	1.00
142_A	153_R	1.659	1.00
104_F	134_E	1.629	1.00
35_V	81_Y	1.599	1.00
14_H	40_V	1.566	1.00
119_D	122_H	1.51	1.00
15_A	83_T	1.504	1.00
18_L	45_W	1.498	1.00
94_M	102_V	1.463	1.00
14_H	18_L	1.425	1.00
42_G	65_Q	1.413	1.00
80_L	99_I	1.401	0.99
88_V	120_V	1.391	0.99
8_H	101_R	1.357	0.99
42_G	62_A	1.349	0.99
143_A	147_D	1.33	0.99
88_V	91_A	1.314	0.99
36_H	77_D	1.27	0.99
44_G	61_M	1.267	0.99
147_D	151_M	1.265	0.99
36_H	39_R	1.253	0.99
143_A	146_S	1.25	0.99
142_A	146_S	1.244	0.98
36_H	78_A	1.217	0.98
8_H	133_T	1.202	0.98
149_F	153_R	1.2	0.98
30_V	84_L	1.199	0.98
60_I	93_A	1.195	0.98
36_H	41_I	1.193	0.98
8_H	81_Y	1.186	0.98
56_A	64_R	1.185	0.98
139_D	143_A	1.183	0.98
88_V	116_S	1.158	0.97
76_I	98_R	1.136	0.97
135_G	138_A	1.135	0.97
79_T	100_G	1.134	0.97
20_K	144_L	1.131	0.97
19_A	144_L	1.131	0.97
22_A	45_W	1.124	0.97
84_L	145_L	1.122	0.97
49_I	73_Y	1.108	0.96
133_T	136_I	1.103	0.96
44_G	62_A	1.099	0.96
39_R	69_V	1.095	0.96
17_T	20_K	1.078	0.95
23_W	151_M	1.069	0.95
63_L	93_A	1.063	0.95
20_K	24_D	1.061	0.95
34_L	80_L	1.057	0.95
60_I	64_R	1.053	0.95
95_I	120_V	1.037	0.94
93_A	97_S	1.035	0.94
91_A	95_I	1.013	0.93
106_A	142_A	1.012	0.93
20_K	140_E	1.001	0.92

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
1z3aA	2	1	100	0.166	Contact Map	0.813
2nx8A	1	1	100	0.187	Contact Map	0.717
2b3jA	4	0.9521	100	0.227	Contact Map	0.766
3dh1A	4	0.976	100	0.235	Contact Map	0.763
1wwrA	4	0.9341	100	0.245	Contact Map	0.809
2a8nA	2	0.8623	100	0.261	Contact Map	0.789
2g84A	2	0.982	100	0.288	Contact Map	0.688
3zpgA	1	0.9162	100	0.305	Contact Map	0.71
2b3zA	4	0.9222	100	0.305	Contact Map	0.815
1wkqA	2	0.9341	100	0.307	Contact Map	0.769

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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