TRMH - ECOLI - GREMLIN Contacts

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TRMH - tRNA (guanosine(18)-2'-O)-methyltransferase

UniProt:	P0AGJ2	Sequences: MNPTRYARICEMLARRQPDLTVCMEQVHKPHNVSAIIRTADAVGVHEVHAVWPGSRMRTMASAAAGSNSWVQVKTHRTIGDAVAHLKGQGMQILATHLSDNAVDFREIDYTRPTCILMGQEKTGITQEALALADQDIIIPMIGMVQSLNVSVASALILYEAQRQRQNAGMYLRENSMLPEAEQQRLLFEGGYPVLAKVAKRKGLPYPHVNQQGEIEADADWWATMQAAG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10967
Length:	229 (178)
Sequences:	1896 (1265)
Seq/√Len:	94.8

ECOLI - TRMH TRMJ LAST YFIF RLMB TRML
BACSU - TRML YACO YSGA
HALSA - Q9HQ36
SULSO - Q7LXK8

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
78_T	81_D	5.216	1.00
47_E	74_K	4.261	1.00
80_G	132_L	4.054	1.00
49_H	76_H	3.620	1.00
137_I	157_I	3.561	1.00
41_D	69_S	3.358	1.00
35_A	63_A	3.279	1.00
95_A	133_A	3.057	1.00
23_C	115_C	2.868	1.00
86_L	115_C	2.652	1.00
116_I	157_I	2.645	1.00
22_V	158_L	2.588	1.00
26_Q	52_W	2.415	1.00
77_R	81_D	2.316	1.00
26_Q	120_Q	2.308	1.00
49_H	74_K	2.199	1.00
47_E	113_P	2.144	1.00
118_M	154_S	2.117	1.00
22_V	40_A	2.068	1.00
94_L	135_Q	2.041	1.00
24_M	150_V	1.968	1.00
83_V	93_I	1.932	1.00
21_T	49_H	1.902	1.00
64_A	68_N	1.870	1.00
118_M	150_V	1.785	1.00
183_Q	186_L	1.784	1.00
120_Q	129_A	1.760	1.00
40_A	45_V	1.703	1.00
92_Q	135_Q	1.687	1.00
150_V	154_S	1.679	1.00
39_T	155_A	1.674	1.00
36_I	154_S	1.650	1.00
79_I	117_L	1.590	1.00
45_V	158_L	1.539	1.00
162_Q	166_Q	1.515	1.00
52_W	77_R	1.427	1.00
187_L	191_G	1.385	0.99
94_L	137_I	1.362	0.99
87_K	113_P	1.362	0.99
24_M	154_S	1.355	0.99
37_I	48_V	1.345	0.99
103_V	106_R	1.337	0.99
105_F	108_I	1.317	0.99
31_H	59_T	1.309	0.99
93_I	117_L	1.305	0.99
22_V	116_I	1.299	0.99
79_I	83_V	1.293	0.99
21_T	47_E	1.293	0.99
43_V	155_A	1.285	0.99
160_E	163_R	1.279	0.99
36_I	150_V	1.268	0.99
19_D	113_P	1.234	0.99
120_Q	126_T	1.203	0.98
128_E	131_A	1.197	0.98
189_E	193_P	1.180	0.98
31_H	155_A	1.173	0.98
97_H	136_D	1.171	0.98
107_E	110_Y	1.171	0.98
46_H	72_Q	1.165	0.98
134_D	181_A	1.160	0.98
103_V	107_E	1.128	0.97
51_V	82_A	1.122	0.97
106_R	110_Y	1.119	0.97
30_P	56_R	1.117	0.97
117_L	133_A	1.107	0.97
35_A	42_A	1.103	0.97
126_T	129_A	1.095	0.97
180_E	183_Q	1.092	0.97
25_E	125_I	1.091	0.97
98_L	146_Q	1.083	0.97
179_P	182_E	1.065	0.96
21_T	76_H	1.058	0.96
182_E	186_L	1.058	0.96
63_A	152_V	1.053	0.96
20_L	45_V	1.039	0.96
106_R	109_D	1.037	0.96
134_D	184_Q	1.036	0.96
23_C	86_L	1.035	0.96
188_F	195_L	1.035	0.96
96_T	157_I	1.034	0.96
58_R	61_A	1.032	0.96
61_A	68_N	1.015	0.95
92_Q	112_R	1.008	0.95
28_H	122_K	1.007	0.95
85_H	182_E	1.006	0.95
186_L	190_G	1.003	0.95
79_I	129_A	1.000	0.95
104_D	109_D	0.986	0.94
35_A	151_S	0.985	0.94
22_V	45_V	0.970	0.94
28_H	147_S	0.958	0.93
47_E	72_Q	0.946	0.93
64_A	67_S	0.946	0.93
92_Q	114_T	0.937	0.93
186_L	189_E	0.934	0.93
25_E	129_A	0.931	0.92
195_L	198_V	0.927	0.92
87_K	112_R	0.924	0.92
83_V	86_L	0.920	0.92
141_M	145_V	0.915	0.92
23_C	82_A	0.914	0.92
26_Q	53_P	0.913	0.92
185_R	189_E	0.908	0.91
62_S	65_A	0.895	0.91
20_L	161_A	0.885	0.90
21_T	86_L	0.879	0.90
104_D	107_E	0.876	0.90
130_L	136_D	0.874	0.90
30_P	57_M	0.873	0.90
25_E	120_Q	0.867	0.89
52_W	75_T	0.864	0.89
142_I	145_V	0.857	0.89
60_M	71_V	0.851	0.89
42_A	145_V	0.845	0.88
56_R	61_A	0.844	0.88
95_A	125_I	0.844	0.88
43_V	148_L	0.840	0.88
192_Y	196_A	0.837	0.88
37_I	127_Q	0.833	0.87
165_R	171_Y	0.829	0.87
86_L	93_I	0.823	0.87
57_M	60_M	0.819	0.87
105_F	110_Y	0.815	0.86
41_D	67_S	0.810	0.86
41_D	70_W	0.807	0.86
30_P	33_V	0.790	0.85
95_A	130_L	0.789	0.84
141_M	146_Q	0.787	0.84
116_I	161_A	0.784	0.84
160_E	164_Q	0.782	0.84
49_H	85_H	0.782	0.84
179_P	184_Q	0.780	0.84
37_I	71_V	0.773	0.83
123_T	126_T	0.772	0.83
66_G	145_V	0.771	0.83
59_T	63_A	0.770	0.83
29_K	155_A	0.768	0.83
195_L	199_A	0.756	0.82
148_L	156_L	0.749	0.81
20_L	114_T	0.748	0.81
50_A	53_P	0.747	0.81
49_H	86_L	0.747	0.81
190_G	194_V	0.742	0.81
29_K	63_A	0.742	0.81
100_D	138_I	0.740	0.80
25_E	86_L	0.735	0.80
95_A	134_D	0.726	0.79
22_V	118_M	0.725	0.79
100_D	104_D	0.723	0.79
126_T	178_L	0.723	0.79
52_W	78_T	0.718	0.78
34_S	125_I	0.717	0.78
41_D	145_V	0.716	0.78
33_V	53_P	0.714	0.78
93_I	96_T	0.713	0.78
42_A	63_A	0.710	0.78
117_L	129_A	0.708	0.77
98_L	101_N	0.704	0.77
25_E	122_K	0.698	0.76
43_V	141_M	0.692	0.76
103_V	110_Y	0.692	0.76
25_E	51_V	0.690	0.76
145_V	152_V	0.680	0.75
65_A	68_N	0.677	0.74
95_A	98_L	0.673	0.74
36_I	66_G	0.672	0.74
170_M	177_M	0.672	0.74
53_P	75_T	0.669	0.73
35_A	155_A	0.666	0.73
35_A	152_V	0.659	0.72
70_W	143_G	0.657	0.72
179_P	187_L	0.657	0.72
37_I	125_I	0.655	0.72
174_E	178_L	0.646	0.71
170_M	174_E	0.645	0.71
98_L	127_Q	0.643	0.70
180_E	186_L	0.642	0.70
43_V	162_Q	0.641	0.70
23_C	76_H	0.636	0.70
40_A	158_L	0.635	0.70
33_V	36_I	0.634	0.69
112_R	176_S	0.634	0.69
36_I	151_S	0.633	0.69
29_K	66_G	0.632	0.69
191_G	194_V	0.630	0.69
181_A	185_R	0.628	0.69
102_A	131_A	0.627	0.69
67_S	145_V	0.619	0.68
93_I	181_A	0.618	0.67
32_N	38_R	0.617	0.67
139_I	156_L	0.613	0.67
95_A	117_L	0.613	0.67
19_D	109_D	0.611	0.67
57_M	65_A	0.611	0.67
39_T	152_V	0.605	0.66
168_A	171_Y	0.602	0.65
169_G	174_E	0.602	0.65
96_T	156_L	0.601	0.65
51_V	79_I	0.600	0.65
121_E	124_G	0.598	0.65
127_Q	131_A	0.597	0.65
141_M	162_Q	0.590	0.64
37_I	73_V	0.588	0.64
184_Q	188_F	0.587	0.63
117_L	153_A	0.583	0.63
174_E	177_M	0.580	0.63
48_V	71_V	0.579	0.62
24_M	36_I	0.578	0.62
60_M	67_S	0.577	0.62
77_R	80_G	0.576	0.62
110_Y	137_I	0.576	0.62
28_H	120_Q	0.574	0.62
165_R	177_M	0.572	0.61
28_H	43_V	0.571	0.61
194_V	198_V	0.570	0.61
188_F	191_G	0.568	0.61
51_V	129_A	0.567	0.61
42_A	141_M	0.565	0.61
29_K	35_A	0.565	0.61
47_E	86_L	0.565	0.61
92_Q	134_D	0.560	0.60
42_A	155_A	0.556	0.59
31_H	63_A	0.556	0.59
29_K	56_R	0.556	0.59
113_P	180_E	0.556	0.59
48_V	53_P	0.554	0.59
25_E	126_T	0.553	0.59
28_H	54_G	0.552	0.59
93_I	134_D	0.552	0.59
197_K	200_K	0.549	0.58
60_M	63_A	0.547	0.58
85_H	127_Q	0.547	0.58
60_M	73_V	0.547	0.58
100_D	136_D	0.547	0.58
179_P	186_L	0.546	0.58
40_A	48_V	0.544	0.58
22_V	154_S	0.542	0.57
40_A	73_V	0.541	0.57
110_Y	165_R	0.541	0.57
84_A	182_E	0.541	0.57
194_V	197_K	0.540	0.57
97_H	102_A	0.534	0.56
92_Q	95_A	0.533	0.56
76_H	81_D	0.532	0.56
130_L	138_I	0.530	0.56
100_D	107_E	0.529	0.56
184_Q	195_L	0.529	0.56
40_A	70_W	0.527	0.55
96_T	159_Y	0.525	0.55
86_L	134_D	0.524	0.55
31_H	152_V	0.521	0.54
131_A	136_D	0.520	0.54
159_Y	163_R	0.519	0.54
41_D	139_I	0.517	0.54
31_H	43_V	0.517	0.54
41_D	46_H	0.516	0.54
94_L	114_T	0.511	0.53
132_L	185_R	0.510	0.53
23_C	83_V	0.509	0.53
74_K	77_R	0.508	0.53
96_T	150_V	0.505	0.52
173_R	177_M	0.505	0.52
185_R	188_F	0.504	0.52
189_E	192_Y	0.504	0.52
169_G	172_L	0.503	0.52
103_V	198_V	0.502	0.52
151_S	164_Q	0.500	0.52

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
1v2xA	2	0.821	100	0.32	Contact Map
1zjrA	2	0.8515	100	0.331	Contact Map
4cndA	2	0.6769	100	0.347	Contact Map
3onpA	2	0.6245	100	0.355	Contact Map
3ilkA	2	0.9127	100	0.358	Contact Map
4cngA	2	0.6245	100	0.379	Contact Map
3ic6A	2	0.7817	100	0.4	Contact Map
1gz0A	2	0.7205	100	0.42	Contact Map
1x7oA	2	0.7336	100	0.421	Contact Map
2ha8A	2	0.6856	100	0.426	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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