TRML - BACSU - GREMLIN Contacts

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

UniProt:	O31590	Sequences: MNIVALHVVLYQPEIPANTGNIARTCAATNTTLHLIRPLGFSTDDKMLKRAGLDYWEFVNVVYHDSLEELFEAYKKGKFFFITKFGQQPHTSFDYTDLDEDYFFVFGRETSGLPKDLIQNNMDRCLRLPMTEHVRSLNLSNTAAILVYEALRQQNYRDLK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	160 (146)
Sequences:	12017 (7263)
Seq/√Len:	601.1

ECOLI - YFIF RLMB TRML TRMH
BACSU - TRML YACO YSGA

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
106_F	139_L	3.342	1.00
9_V	103_F	2.918	1.00
141_N	144_A	2.909	1.00
83_T	122_M	2.675	1.00
149_E	152_R	2.550	1.00
106_F	143_A	2.518	1.00
115_K	119_Q	2.459	1.00
22_I	143_A	2.285	1.00
11_Y	114_P	2.049	1.00
66_S	69_E	1.895	1.00
84_K	146_L	1.880	1.00
37_R	65_D	1.844	1.00
72_E	121_N	1.842	1.00
108_R	111_S	1.834	1.00
33_L	62_V	1.805	1.00
33_L	60_N	1.798	1.00
29_T	148_Y	1.782	1.00
31_T	147_V	1.753	1.00
87_Q	127_R	1.705	1.00
8_V	147_V	1.692	1.00
8_V	22_I	1.663	1.00
88_Q	124_R	1.653	1.00
80_F	124_R	1.648	1.00
85_F	118_I	1.625	1.00
83_T	113_L	1.618	1.00
52_G	56_W	1.560	1.00
27_A	132_E	1.557	1.00
23_A	34_H	1.548	1.00
143_A	147_V	1.523	1.00
88_Q	92_S	1.514	1.00
14_E	110_T	1.494	1.00
74_Y	103_F	1.494	1.00
104_F	146_L	1.494	1.00
26_C	31_T	1.477	1.00
7_H	33_L	1.442	1.00
28_A	130_M	1.438	1.00
104_F	150_A	1.410	1.00
37_R	63_Y	1.388	1.00
93_F	126_L	1.385	1.00
118_I	125_C	1.359	1.00
128_L	142_T	1.345	1.00
27_A	59_V	1.344	1.00
83_T	125_C	1.290	1.00
55_Y	134_V	1.268	1.00
75_K	123_D	1.259	1.00
23_A	61_V	1.248	1.00
90_H	95_Y	1.243	1.00
27_A	58_F	1.236	1.00
82_I	146_L	1.229	1.00
49_K	56_W	1.229	1.00
29_T	90_H	1.228	1.00
13_P	139_L	1.217	1.00
88_Q	93_F	1.199	1.00
82_I	126_L	1.195	1.00
27_A	55_Y	1.186	1.00
6_L	31_T	1.164	1.00
70_L	74_Y	1.140	1.00
82_I	124_R	1.139	1.00
73_A	77_G	1.131	1.00
68_E	72_E	1.126	1.00
25_T	141_N	1.123	1.00
58_F	133_H	1.121	1.00
89_P	127_R	1.119	1.00
149_E	153_Q	1.118	1.00
90_H	146_L	1.115	1.00
21_N	140_S	1.105	1.00
68_E	121_N	1.086	1.00
32_T	60_N	1.085	1.00
8_V	26_C	1.076	1.00
89_P	92_S	1.068	1.00
27_A	134_V	1.066	1.00
5_A	32_T	1.049	1.00
28_A	134_V	1.041	1.00
36_I	61_V	1.036	1.00
114_P	117_L	1.032	1.00
131_T	151_L	1.027	1.00
23_A	56_W	1.015	1.00
86_G	125_C	1.007	1.00
17_A	21_N	1.003	1.00
6_L	150_A	1.001	1.00
67_L	71_F	1.001	1.00
12_Q	39_L	1.001	1.00
72_E	76_K	0.981	1.00
35_L	70_L	0.974	1.00
25_T	144_A	0.967	1.00
11_Y	117_L	0.962	1.00
29_T	151_L	0.961	1.00
67_L	117_L	0.954	1.00
122_M	125_C	0.947	1.00
79_F	103_F	0.934	1.00
30_N	131_T	0.927	1.00
106_F	142_T	0.925	1.00
105_V	113_L	0.924	1.00
25_T	147_V	0.924	1.00
95_Y	150_A	0.920	1.00
29_T	145_I	0.920	1.00
126_L	146_L	0.919	1.00
9_V	105_V	0.917	1.00
72_E	75_K	0.916	1.00
10_L	22_I	0.914	1.00
19_T	36_I	0.909	1.00
49_K	57_E	0.903	1.00
85_F	125_C	0.892	1.00
32_T	62_V	0.882	1.00
95_Y	99_D	0.878	1.00
12_Q	108_R	0.877	1.00
71_F	81_F	0.862	1.00
17_A	51_A	0.856	1.00
68_E	116_D	0.855	1.00
12_Q	111_S	0.852	1.00
11_Y	113_L	0.847	1.00
19_T	41_F	0.846	1.00
23_A	59_V	0.844	1.00
27_A	133_H	0.842	1.00
7_H	35_L	0.841	1.00
8_V	106_F	0.836	1.00
35_L	64_H	0.831	1.00
93_F	124_R	0.827	1.00
42_S	47_M	0.822	1.00
36_I	40_G	0.820	1.00
8_V	31_T	0.801	1.00
81_F	84_K	0.787	1.00
116_D	119_Q	0.778	1.00
75_K	121_N	0.777	1.00
29_T	147_V	0.765	1.00
14_E	108_R	0.765	1.00
64_H	70_L	0.763	1.00
71_F	121_N	0.760	1.00
38_P	65_D	0.759	1.00
80_F	123_D	0.758	1.00
71_F	117_L	0.755	1.00
19_T	48_L	0.751	1.00
21_N	141_N	0.750	1.00
69_E	72_E	0.749	1.00
44_D	47_M	0.746	1.00
12_Q	114_P	0.745	1.00
7_H	32_T	0.741	1.00
91_T	152_R	0.739	1.00
43_T	63_Y	0.736	1.00
6_L	32_T	0.734	1.00
22_I	139_L	0.729	1.00
150_A	154_Q	0.729	1.00
44_D	48_L	0.725	1.00
9_V	67_L	0.719	1.00
95_Y	153_Q	0.716	1.00
140_S	144_A	0.716	1.00
14_E	111_S	0.715	1.00
116_D	121_N	0.714	1.00
5_A	98_L	0.712	1.00
121_N	124_R	0.707	1.00
83_T	118_I	0.700	1.00
96_T	99_D	0.698	1.00
70_L	103_F	0.696	1.00
81_F	122_M	0.694	1.00
65_D	69_E	0.693	1.00
78_K	81_F	0.688	1.00
115_K	118_I	0.687	1.00
73_A	76_K	0.683	1.00
80_F	83_T	0.680	1.00
69_E	73_A	0.676	1.00
78_K	83_T	0.675	1.00
137_L	145_I	0.674	1.00
81_F	103_F	0.674	1.00
128_L	145_I	0.668	1.00
145_I	148_Y	0.667	1.00
85_F	127_R	0.647	1.00
26_C	34_H	0.646	1.00
105_V	117_L	0.645	1.00
11_Y	108_R	0.643	1.00
17_A	140_S	0.642	1.00
7_H	103_F	0.641	1.00
13_P	22_I	0.637	1.00
10_L	19_T	0.635	1.00
31_T	150_A	0.632	1.00
106_F	146_L	0.631	1.00
17_A	47_M	0.629	1.00
96_T	153_Q	0.622	1.00
25_T	143_A	0.622	1.00
6_L	147_V	0.618	1.00
113_L	122_M	0.612	1.00
7_H	79_F	0.605	1.00
45_D	48_L	0.599	1.00
9_V	70_L	0.595	1.00
12_Q	37_R	0.591	1.00
58_F	134_V	0.586	1.00
91_T	129_P	0.582	1.00
91_T	148_Y	0.577	1.00
81_F	105_V	0.574	1.00
25_T	28_A	0.572	1.00
28_A	137_L	0.572	1.00
70_L	73_A	0.572	1.00
78_K	99_D	0.571	1.00
94_D	153_Q	0.570	1.00
74_Y	79_F	0.565	1.00
42_S	45_D	0.564	1.00
35_L	39_L	0.561	1.00
23_A	48_L	0.560	1.00
23_A	27_A	0.559	1.00
71_F	75_K	0.551	0.99
41_F	45_D	0.547	0.99
78_K	84_K	0.545	0.99
62_V	73_A	0.545	0.99
81_F	121_N	0.543	0.99
10_L	13_P	0.542	0.99
38_P	66_S	0.538	0.99
9_V	37_R	0.533	0.99
22_I	106_F	0.531	0.99
34_H	64_H	0.521	0.99
53_L	110_T	0.515	0.99
29_T	91_T	0.512	0.99
29_T	128_L	0.512	0.99
43_T	61_V	0.510	0.99
88_Q	91_T	0.510	0.99
82_I	99_D	0.510	0.99
10_L	106_F	0.507	0.99
77_G	81_F	0.506	0.99
75_K	81_F	0.505	0.99
25_T	29_T	0.502	0.99
131_T	134_V	0.500	0.99

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) 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	%	HHΔ
1gz0A	2	0.9437	100	0.122	Contact Map
1ipaA	1	0.9375	100	0.128	Contact Map
1x7oA	2	0.975	100	0.138	Contact Map
2i6dA	2	0.9437	100	0.142	Contact Map
3nk6A	2	0.9625	100	0.147	Contact Map
1zjrA	2	0.9688	100	0.17	Contact Map
4kgnA	2	0.9625	100	0.17	Contact Map
4pzkA	2	0.9688	100	0.17	Contact Map
3n4jA	2	0.9563	100	0.178	Contact Map
1v2xA	2	0.9625	100	0.182	Contact Map

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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