OPENSEQ.org - TRML - ECOLI GREMLIN

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TRML - tRNA (cytidine(34)-2'-O)-methyltransferase

UniProt:	P0AGJ7	Sequence MLNIVLYEPEIPPNTGNIIRLCANTGFRLHIIEPMGFAWDDKRLRRAGLDYHEFTAVTRHHDYRAFLEAENPQRLFALTTKGTPAHSAVSYQDGDYLMFGPETRGLPASILDALPAEQKIRIPMVPDSRSMNLSNAVSVVVYEAWRQLGYPGAVLRD	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG11888
Length:	157 (147)
Sequences:	6104
Seq/Len:	41.52

TRML
Paralog alert: 0.90 [within 20: 0.05] - ratio of genomes with paralogs
Cluster includes: RLMB TRML

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
99_F	133_L	3.196	1.00
5_V	96_Y	3.17	1.00
77_A	116_A	3.152	1.00
78_L	140_V	3.107	1.00
135_N	138_S	2.916	1.00
143_E	146_R	2.692	1.00
62_D	65_A	2.58	1.00
108_A	112_D	2.5	1.00
18_I	137_V	2.455	1.00
99_F	137_V	2.454	1.00
33_E	61_H	1.992	1.00
77_A	106_L	1.905	1.00
4_I	18_I	1.799	1.00
27_F	141_V	1.733	1.00
4_I	141_V	1.711	1.00
25_T	142_Y	1.674	1.00
68_E	113_A	1.67	1.00
76_F	120_I	1.654	1.00
101_P	104_R	1.632	1.00
64_R	113_A	1.629	1.00
7_Y	107_P	1.606	1.00
74_R	118_Q	1.57	1.00
97_L	140_V	1.533	1.00
137_V	141_V	1.525	1.00
48_G	52_H	1.512	1.00
23_A	55_T	1.508	1.00
70_E	96_Y	1.496	1.00
79_T	111_L	1.484	1.00
76_F	118_Q	1.451	1.00
23_A	126_P	1.45	1.00
122_I	136_A	1.417	1.00
22_C	27_F	1.357	0.99
4_I	22_C	1.33	0.99
10_E	103_T	1.329	0.99
71_N	117_E	1.288	0.99
29_L	58_T	1.287	0.99
3_N	28_R	1.259	0.99
51_Y	128_S	1.241	0.98
24_N	124_M	1.234	0.98
28_R	58_T	1.226	0.98
9_P	133_L	1.217	0.98
17_N	47_A	1.213	0.98
74_R	95_D	1.213	0.98
21_L	138_S	1.209	0.98
30_H	60_H	1.208	0.98
143_E	147_Q	1.191	0.98
109_S	112_D	1.187	0.98
76_F	95_D	1.182	0.98
19_I	30_H	1.174	0.98
29_L	56_A	1.173	0.98
67_L	75_L	1.167	0.97
25_T	86_H	1.165	0.97
83_T	121_R	1.153	0.97
79_T	119_K	1.146	0.97
66_F	70_E	1.146	0.97
86_H	91_Y	1.143	0.97
86_H	140_V	1.133	0.97
23_A	54_F	1.131	0.97
120_I	140_V	1.124	0.97
19_I	57_V	1.121	0.97
75_L	98_M	1.116	0.96
8_E	101_P	1.101	0.96
17_N	134_S	1.089	0.96
77_A	111_L	1.083	0.96
45_R	52_H	1.08	0.95
19_I	55_T	1.077	0.95
7_Y	106_L	1.061	0.95
13_P	17_N	1.048	0.94
89_V	120_I	1.048	0.94
97_L	144_A	1.047	0.94
111_L	119_K	1.041	0.94
75_L	96_Y	1.039	0.94
65_A	68_E	1.031	0.94
73_Q	94_G	1.03	0.94
25_T	145_W	1.027	0.94
66_F	96_Y	1.024	0.93
23_A	51_Y	1.018	0.93
7_Y	110_I	1.006	0.93
63_Y	110_I	1.005	0.93

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
1ipaA	1	0.9745	100	0.089	Contact Map	0.775
1gz0A	8	0.9363	100	0.097	Contact Map	0.904
1x7oA	2	0.9873	100	0.108	Contact Map	0.787
3n4jA	1	1	100	0.116	Contact Map	0.738
3nk6A	2	0.9745	100	0.116	Contact Map	0.725
4kgnA	8	0.9809	100	0.119	Contact Map	0.746
2i6dA	1	0.9236	100	0.122	Contact Map	0.81
3l8uA	2	0.9809	100	0.135	Contact Map	0.77
1zjrA	1	0.9809	100	0.155	Contact Map	0.785
1v2xA	1	0.9745	100	0.164	Contact Map	0.761

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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