TRML - ECOLI - GREMLIN Contacts

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

UniProt:	P0AGJ7	Sequences: MLNIVLYEPEIPPNTGNIIRLCANTGFRLHIIEPMGFAWDDKRLRRAGLDYHEFTAVTRHHDYRAFLEAENPQRLFALTTKGTPAHSAVSYQDGDYLMFGPETRGLPASILDALPAEQKIRIPMVPDSRSMNLSNAVSVVVYEAWRQLGYPGAVLRD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11888
Length:	157 (143)
Sequences:	11976 (7285)
Seq/√Len:	609.2

ECOLI - TRML YFIF RLMB 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
99_F	133_L	3.222	1.00
5_V	96_Y	2.834	1.00
135_N	138_S	2.818	1.00
143_E	146_R	2.530	1.00
99_F	137_V	2.435	1.00
108_A	112_D	2.370	1.00
18_I	137_V	2.189	1.00
7_Y	107_P	1.963	1.00
80_T	140_V	1.957	1.00
29_L	58_T	1.871	1.00
79_T	106_L	1.861	1.00
62_D	65_A	1.857	1.00
29_L	56_A	1.796	1.00
33_E	61_H	1.776	1.00
101_P	104_R	1.770	1.00
27_F	141_V	1.756	1.00
25_T	142_Y	1.724	1.00
83_T	121_R	1.723	1.00
84_P	118_Q	1.698	1.00
76_F	118_Q	1.675	1.00
4_I	18_I	1.662	1.00
68_E	113_A	1.632	1.00
81_K	111_L	1.631	1.00
19_I	30_H	1.544	1.00
4_I	141_V	1.519	1.00
48_G	52_H	1.519	1.00
70_E	96_Y	1.515	1.00
23_A	126_P	1.507	1.00
137_V	141_V	1.487	1.00
22_C	27_F	1.480	1.00
89_V	120_I	1.470	1.00
10_E	103_T	1.463	1.00
24_N	124_M	1.416	1.00
97_L	140_V	1.415	1.00
111_L	119_K	1.373	1.00
71_N	117_E	1.368	1.00
33_E	59_R	1.360	1.00
122_I	136_A	1.346	1.00
79_T	119_K	1.345	1.00
97_L	144_A	1.332	1.00
25_T	86_H	1.325	1.00
23_A	55_T	1.312	1.00
86_H	140_V	1.311	1.00
78_L	118_Q	1.268	1.00
23_A	54_F	1.242	1.00
19_I	57_V	1.228	1.00
78_L	120_I	1.227	1.00
51_Y	128_S	1.211	1.00
45_R	52_H	1.203	1.00
9_P	133_L	1.191	1.00
3_N	29_L	1.171	1.00
23_A	51_Y	1.169	1.00
64_R	113_A	1.161	1.00
143_E	147_Q	1.159	1.00
3_N	28_R	1.146	1.00
69_A	73_Q	1.146	1.00
54_F	127_D	1.141	1.00
125_V	145_W	1.116	1.00
86_H	91_Y	1.114	1.00
91_Y	144_A	1.104	1.00
21_L	135_N	1.103	1.00
78_L	140_V	1.101	1.00
17_N	134_S	1.099	1.00
64_R	68_E	1.094	1.00
85_A	121_R	1.094	1.00
66_F	70_E	1.090	1.00
82_G	119_K	1.081	1.00
85_A	88_A	1.068	1.00
28_R	56_A	1.066	1.00
84_P	88_A	1.056	1.00
4_I	22_C	1.034	1.00
81_K	119_K	1.034	1.00
95_D	144_A	1.033	1.00
24_N	128_S	1.033	1.00
84_P	89_V	1.029	1.00
23_A	128_S	1.026	1.00
60_H	66_F	1.026	1.00
63_Y	67_L	1.021	1.00
75_L	94_G	1.021	1.00
31_I	60_H	1.016	1.00
32_I	57_V	1.012	1.00
75_L	96_Y	1.010	1.00
78_L	95_D	1.008	1.00
19_I	52_H	1.004	1.00
13_P	17_N	1.003	1.00
107_P	110_I	1.003	1.00
21_L	141_V	0.983	1.00
7_Y	110_I	0.982	1.00
25_T	145_W	0.978	1.00
63_Y	110_I	0.952	1.00
99_F	136_A	0.952	1.00
21_L	138_S	0.947	1.00
89_V	118_Q	0.936	1.00
8_E	35_M	0.925	1.00
45_R	53_E	0.925	1.00
68_E	71_N	0.924	1.00
120_I	140_V	0.924	1.00
31_I	66_F	0.922	1.00
26_G	125_V	0.920	1.00
8_E	101_P	0.913	1.00
98_M	106_L	0.911	1.00
67_L	77_A	0.908	1.00
6_L	18_I	0.905	1.00
28_R	58_T	0.898	1.00
25_T	139_V	0.894	1.00
15_T	32_I	0.891	1.00
109_S	113_A	0.879	1.00
67_L	113_A	0.878	1.00
71_N	113_A	0.872	1.00
64_R	109_S	0.863	1.00
87_S	146_R	0.862	1.00
76_F	117_E	0.861	1.00
19_I	55_T	0.854	1.00
15_T	37_F	0.852	1.00
8_E	104_R	0.846	1.00
5_V	98_M	0.843	1.00
7_Y	106_L	0.836	1.00
13_P	47_A	0.834	1.00
91_Y	95_D	0.833	1.00
32_I	36_G	0.817	1.00
3_N	31_I	0.816	1.00
68_E	72_P	0.813	1.00
40_D	43_R	0.809	1.00
23_A	127_D	0.805	1.00
67_L	110_I	0.805	1.00
65_A	68_E	0.804	1.00
109_S	112_D	0.799	1.00
91_Y	147_Q	0.799	1.00
38_A	43_R	0.796	1.00
10_E	101_P	0.789	1.00
8_E	107_P	0.779	1.00
34_P	61_H	0.772	1.00
4_I	99_F	0.765	1.00
15_T	44_L	0.763	1.00
4_I	27_F	0.753	1.00
17_N	135_N	0.746	1.00
76_F	95_D	0.742	1.00
131_M	139_V	0.740	1.00
66_F	96_Y	0.737	1.00
61_H	65_A	0.737	1.00
18_I	133_L	0.731	1.00
144_A	148_L	0.729	1.00
25_T	141_V	0.728	1.00
39_W	59_R	0.727	1.00
108_A	111_L	0.726	1.00
134_S	138_S	0.719	1.00
74_R	95_D	0.719	1.00
10_E	104_R	0.717	1.00
77_A	96_Y	0.712	1.00
87_S	123_P	0.710	1.00
27_F	144_A	0.709	1.00
5_V	63_Y	0.709	1.00
21_L	137_V	0.706	1.00
92_Q	95_D	0.685	1.00
40_D	44_L	0.685	1.00
81_K	121_R	0.678	1.00
87_S	142_Y	0.676	1.00
77_A	98_M	0.671	1.00
13_P	134_S	0.667	1.00
139_V	142_Y	0.667	1.00
9_P	18_I	0.661	1.00
98_M	110_I	0.659	1.00
25_T	87_S	0.659	1.00
122_I	139_V	0.654	1.00
3_N	96_Y	0.653	1.00
13_P	43_R	0.651	1.00
69_A	72_P	0.650	1.00
7_Y	101_P	0.648	1.00
70_E	75_L	0.647	1.00
8_E	33_E	0.644	1.00
54_F	128_S	0.637	1.00
79_T	111_L	0.636	1.00
77_A	80_T	0.634	1.00
71_N	77_A	0.630	1.00
60_H	69_A	0.625	1.00
65_A	69_A	0.619	1.00
5_V	66_F	0.619	1.00
24_N	131_M	0.613	1.00
76_F	79_T	0.613	1.00
3_N	75_L	0.612	1.00
99_F	140_V	0.612	1.00
41_D	44_L	0.603	1.00
22_C	30_H	0.601	1.00
18_I	99_F	0.600	1.00
6_L	15_T	0.595	1.00
21_L	24_N	0.592	1.00
39_W	57_V	0.590	1.00
58_T	69_A	0.582	1.00
19_I	23_A	0.580	1.00
90_S	147_Q	0.578	1.00
6_L	99_F	0.576	1.00
87_S	145_W	0.576	1.00
19_I	44_L	0.568	1.00
6_L	9_P	0.564	1.00
125_V	128_S	0.561	1.00
82_G	121_R	0.559	1.00
38_A	41_D	0.556	1.00
92_Q	147_Q	0.555	1.00
37_F	41_D	0.551	0.99
84_P	87_S	0.539	0.99
16_G	47_A	0.534	0.99
25_T	122_I	0.533	0.99
34_P	62_D	0.532	0.99
31_I	35_M	0.532	0.99
78_L	89_V	0.522	0.99
3_N	70_E	0.520	0.99
67_L	71_N	0.518	0.99
76_F	93_D	0.510	0.99
23_A	125_V	0.509	0.99
78_L	91_Y	0.507	0.99
60_H	65_A	0.503	0.99
22_C	141_V	0.502	0.99
5_V	67_L	0.501	0.99
110_I	113_A	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
1ipaA	1	0.9299	100	0.136	Contact Map
1gz0A	2	0.9363	100	0.137	Contact Map
1x7oA	2	0.9682	100	0.151	Contact Map
2i6dA	2	0.9172	100	0.16	Contact Map
3nk6A	2	0.9809	100	0.162	Contact Map
4kgnA	2	0.9682	100	0.169	Contact Map
3n4jA	2	0.9745	100	0.175	Contact Map
4pzkA	2	0.9873	100	0.186	Contact Map
1zjrA	2	0.9809	100	0.188	Contact Map
1v2xA	2	0.9745	100	0.2	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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