TRMD - BACSU - GREMLIN Contacts

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TRMD - tRNA (guanine-N(1)-)-methyltransferase

UniProt:	O31741	Sequences: MKIDFLTLFPEMFEGVLGSSILQKAQEKDAVQFQVVNFREYSDNKHNTVDDYPYGGGAGMVLKPQPVFDAVEDLTSKAAAAPRIILVCPQGERFTQKKAEQLAKEEHLLFICGHYEGYDERIREHLVTDEISIGDFVLTGGELPAMMIADSVVRLLPGVLGKEASHIEDSFSTGLLEHPHYTRPADYKGLKVPETLLSGNHAKIEEWRNKESIRRTYLRRPDLLKDHPLTEQQRKWISEWEKE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	243 (227)
Sequences:	3363 (1867)
Seq/√Len:	123.9

ECOLI - TRMD
BACSU - TRMD

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
200_N	203_K	4.067	1.00
211_E	214_R	3.916	1.00
186_D	191_K	3.315	1.00
120_E	124_E	3.223	1.00
65_Q	69_D	3.153	1.00
94_F	99_A	3.081	1.00
72_E	188_K	2.969	1.00
41_Y	73_D	2.717	1.00
87_V	110_F	2.554	1.00
43_D	69_D	2.475	1.00
37_N	40_E	2.474	1.00
6_L	38_F	2.443	1.00
203_K	206_E	2.433	1.00
133_I	147_M	2.334	1.00
143_L	147_M	2.311	1.00
83_R	105_E	2.267	1.00
125_H	190_L	2.246	1.00
31_V	153_V	2.175	1.00
202_A	205_E	2.103	1.00
98_K	129_D	2.102	1.00
136_F	147_M	2.065	1.00
5_F	149_A	2.053	1.00
98_K	101_Q	2.048	1.00
98_K	131_I	2.040	1.00
94_F	151_S	2.007	1.00
83_R	129_D	1.993	1.00
14_E	18_G	1.919	1.00
186_D	189_G	1.844	1.00
94_F	148_I	1.818	1.00
92_E	129_D	1.817	1.00
191_K	194_E	1.805	1.00
23_Q	27_E	1.800	1.00
68_F	187_Y	1.799	1.00
4_D	36_V	1.798	1.00
224_L	227_H	1.797	1.00
92_E	98_K	1.732	1.00
90_Q	215_R	1.728	1.00
214_R	218_L	1.705	1.00
99_A	151_S	1.696	1.00
52_Y	183_R	1.664	1.00
68_F	126_L	1.660	1.00
101_Q	129_D	1.650	1.00
44_N	48_T	1.642	1.00
133_I	136_F	1.639	1.00
148_I	152_V	1.614	1.00
4_D	34_Q	1.610	1.00
4_D	107_H	1.602	1.00
71_V	126_L	1.599	1.00
68_F	188_K	1.587	1.00
124_E	190_L	1.582	1.00
149_A	153_V	1.577	1.00
139_T	150_D	1.568	1.00
54_Y	185_A	1.531	1.00
100_E	172_S	1.529	1.00
110_F	148_I	1.529	1.00
2_K	32_Q	1.500	1.00
96_Q	155_L	1.482	1.00
209_N	227_H	1.444	1.00
202_A	206_E	1.431	1.00
48_T	63_K	1.418	1.00
82_P	109_L	1.417	1.00
53_P	61_V	1.413	1.00
160_L	166_H	1.410	1.00
54_Y	192_V	1.404	1.00
130_E	219_R	1.397	1.00
166_H	169_D	1.385	1.00
68_F	72_E	1.378	1.00
92_E	95_T	1.367	1.00
44_N	63_K	1.350	1.00
95_T	98_K	1.314	1.00
86_L	111_I	1.313	1.00
38_F	62_L	1.309	1.00
131_I	148_I	1.308	1.00
215_R	219_R	1.308	1.00
11_E	19_S	1.305	1.00
185_A	191_K	1.304	1.00
86_L	118_Y	1.297	1.00
11_E	37_N	1.291	1.00
13_F	146_M	1.288	1.00
16_V	146_M	1.271	1.00
97_K	100_E	1.269	1.00
179_P	211_E	1.261	1.00
67_V	111_I	1.257	1.00
217_Y	224_L	1.237	0.99
87_V	148_I	1.236	0.99
11_E	14_E	1.215	0.99
36_V	41_Y	1.209	0.99
213_I	224_L	1.181	0.99
62_L	118_Y	1.170	0.99
102_L	131_I	1.153	0.99
110_F	145_A	1.131	0.99
3_I	149_A	1.125	0.99
21_I	24_K	1.123	0.99
72_E	126_L	1.123	0.99
81_A	106_E	1.122	0.99
2_K	34_Q	1.121	0.99
206_E	210_K	1.111	0.99
171_F	223_L	1.064	0.98
85_I	102_L	1.062	0.98
164_A	167_I	1.062	0.98
18_G	26_Q	1.049	0.98
214_R	217_Y	1.040	0.98
61_V	180_H	1.034	0.98
30_A	159_V	1.031	0.98
3_I	31_V	1.029	0.98
111_I	122_I	1.022	0.98
217_Y	229_L	1.019	0.98
93_R	171_F	1.006	0.98
133_I	144_P	0.999	0.98
209_N	213_I	0.998	0.98
120_E	123_R	0.995	0.98
173_T	212_S	0.992	0.98
13_F	16_V	0.992	0.98
143_L	150_D	0.991	0.97
6_L	70_A	0.990	0.97
84_I	128_T	0.984	0.97
36_V	70_A	0.982	0.97
71_V	122_I	0.980	0.97
224_L	229_L	0.972	0.97
83_R	128_T	0.965	0.97
8_L	49_V	0.963	0.97
163_E	167_I	0.959	0.97
64_P	68_F	0.957	0.97
185_A	197_L	0.953	0.97
177_E	180_H	0.946	0.97
4_D	109_L	0.944	0.97
112_C	145_A	0.933	0.96
86_L	123_R	0.927	0.96
120_E	215_R	0.909	0.96
125_H	188_K	0.902	0.96
168_E	177_E	0.900	0.96
82_P	107_H	0.899	0.96
3_I	153_V	0.898	0.96
90_Q	120_E	0.897	0.95
12_M	16_V	0.889	0.95
114_H	139_T	0.886	0.95
178_H	208_R	0.882	0.95
200_N	204_I	0.875	0.95
31_V	156_L	0.874	0.95
58_A	168_E	0.869	0.95
99_A	155_L	0.867	0.95
169_D	177_E	0.867	0.95
100_E	155_L	0.864	0.94
40_E	47_N	0.862	0.94
198_S	203_K	0.860	0.94
12_M	146_M	0.859	0.94
26_Q	33_F	0.853	0.94
84_I	127_V	0.848	0.94
67_V	118_Y	0.844	0.94
118_Y	122_I	0.844	0.94
58_A	165_S	0.842	0.94
67_V	122_I	0.841	0.94
207_W	211_E	0.836	0.93
8_L	114_H	0.834	0.93
85_I	131_I	0.824	0.93
44_N	47_N	0.819	0.93
210_K	214_R	0.815	0.93
71_V	109_L	0.812	0.92
30_A	156_L	0.811	0.92
75_T	109_L	0.806	0.92
224_L	228_P	0.806	0.92
96_Q	172_S	0.803	0.92
164_A	168_E	0.802	0.92
92_E	101_Q	0.800	0.92
84_I	109_L	0.800	0.92
58_A	162_K	0.795	0.92
63_K	66_P	0.792	0.91
37_N	47_N	0.792	0.91
4_D	74_L	0.789	0.91
64_P	187_Y	0.784	0.91
68_F	71_V	0.783	0.91
171_F	177_E	0.783	0.91
57_G	208_R	0.774	0.91
5_F	33_F	0.771	0.90
94_F	98_K	0.769	0.90
145_A	149_A	0.769	0.90
153_V	159_V	0.768	0.90
26_Q	31_V	0.767	0.90
209_N	212_S	0.763	0.90
22_L	26_Q	0.762	0.90
144_P	147_M	0.761	0.90
52_Y	58_A	0.761	0.90
88_C	130_E	0.760	0.90
120_E	219_R	0.758	0.90
205_E	209_N	0.750	0.89
75_T	82_P	0.749	0.89
123_R	130_E	0.749	0.89
137_V	169_D	0.743	0.89
69_D	72_E	0.743	0.89
2_K	107_H	0.740	0.88
88_C	123_R	0.740	0.88
42_S	63_K	0.738	0.88
42_S	48_T	0.734	0.88
36_V	74_L	0.733	0.88
111_I	127_V	0.729	0.88
114_H	150_D	0.721	0.87
138_L	144_P	0.720	0.87
22_L	139_T	0.717	0.87
43_D	48_T	0.714	0.87
83_R	108_L	0.705	0.86
166_H	172_S	0.704	0.86
34_Q	77_K	0.703	0.86
169_D	178_H	0.697	0.85
95_T	101_Q	0.687	0.84
17_L	149_A	0.684	0.84
3_I	108_L	0.684	0.84
87_V	145_A	0.679	0.84
80_A	106_E	0.678	0.84
38_F	67_V	0.678	0.84
143_L	146_M	0.677	0.84
217_Y	227_H	0.672	0.83
73_D	76_S	0.666	0.83
213_I	229_L	0.659	0.82
25_A	159_V	0.658	0.82
12_M	143_L	0.658	0.82
5_F	110_F	0.657	0.82
153_V	156_L	0.655	0.82
68_F	125_H	0.654	0.81
68_F	122_I	0.652	0.81
12_M	15_G	0.652	0.81
210_K	217_Y	0.649	0.81
21_I	159_V	0.648	0.81
155_L	172_S	0.646	0.81
38_F	118_Y	0.644	0.80
123_R	215_R	0.642	0.80
98_K	102_L	0.640	0.80
70_A	74_L	0.639	0.80
82_P	105_E	0.638	0.80
139_T	143_L	0.637	0.80
138_L	147_M	0.635	0.80
12_M	150_D	0.635	0.80
17_L	33_F	0.634	0.79
116_E	178_H	0.630	0.79
200_N	206_E	0.630	0.79
168_E	205_E	0.626	0.79
102_L	148_I	0.621	0.78
7_T	36_V	0.621	0.78
17_L	146_M	0.621	0.78
156_L	159_V	0.615	0.77
191_K	197_L	0.615	0.77
94_F	131_I	0.615	0.77
122_I	126_L	0.614	0.77
177_E	212_S	0.613	0.77
63_K	182_T	0.612	0.77
83_R	107_H	0.609	0.77
58_A	164_A	0.609	0.77
105_E	108_L	0.608	0.77
194_E	203_K	0.608	0.77
66_P	69_D	0.607	0.76
90_Q	123_R	0.605	0.76
42_S	66_P	0.605	0.76
73_D	77_K	0.603	0.76
111_I	118_Y	0.598	0.75
68_F	190_L	0.597	0.75
211_E	215_R	0.597	0.75
194_E	197_L	0.596	0.75
5_F	13_F	0.594	0.75
75_T	84_I	0.591	0.75
8_L	62_L	0.590	0.74
168_E	178_H	0.589	0.74
8_L	37_N	0.589	0.74
21_I	139_T	0.589	0.74
18_G	27_E	0.587	0.74
6_L	74_L	0.586	0.74
42_S	65_Q	0.583	0.74
8_L	67_V	0.578	0.73
20_S	52_Y	0.577	0.73
22_L	160_L	0.576	0.73
162_K	166_H	0.576	0.73
71_V	75_T	0.576	0.73
145_A	148_I	0.575	0.73
101_Q	104_K	0.574	0.72
13_F	145_A	0.573	0.72
26_Q	32_Q	0.572	0.72
210_K	227_H	0.572	0.72
90_Q	219_R	0.572	0.72
41_Y	70_A	0.571	0.72
16_V	149_A	0.570	0.72
92_E	97_K	0.563	0.71
87_V	144_P	0.563	0.71
118_Y	123_R	0.560	0.71
205_E	208_R	0.558	0.70
126_L	190_L	0.556	0.70
13_F	35_V	0.554	0.70
214_R	229_L	0.554	0.70
76_S	82_P	0.553	0.70
14_E	35_V	0.552	0.69
67_V	71_V	0.552	0.69
20_S	139_T	0.552	0.69
40_E	73_D	0.550	0.69
9_F	115_Y	0.550	0.69
185_A	200_N	0.550	0.69
110_F	152_V	0.550	0.69
161_G	165_S	0.549	0.69
53_P	180_H	0.549	0.69
90_Q	130_E	0.548	0.69
6_L	109_L	0.548	0.69
71_V	84_I	0.548	0.69
51_D	183_R	0.547	0.69
64_P	71_V	0.547	0.69
186_D	194_E	0.546	0.69
187_Y	190_L	0.546	0.69
42_S	47_N	0.545	0.69
185_A	194_E	0.544	0.68
64_P	122_I	0.543	0.68
90_Q	177_E	0.543	0.68
68_F	114_H	0.539	0.68
209_N	229_L	0.539	0.68
110_F	149_A	0.538	0.68
84_I	111_I	0.538	0.68
94_F	152_V	0.536	0.67
7_T	35_V	0.533	0.67
43_D	47_N	0.532	0.67
33_F	153_V	0.529	0.66
71_V	127_V	0.528	0.66
161_G	166_H	0.528	0.66
125_H	187_Y	0.526	0.66
116_E	180_H	0.523	0.65
20_S	26_Q	0.523	0.65
33_F	149_A	0.521	0.65
74_L	109_L	0.521	0.65
162_K	172_S	0.520	0.65
174_G	227_H	0.520	0.65
20_S	177_E	0.519	0.65
210_K	218_L	0.519	0.65
54_Y	115_Y	0.518	0.65
97_K	104_K	0.518	0.65
36_V	77_K	0.517	0.65
31_V	159_V	0.515	0.64
144_P	148_I	0.515	0.64
61_V	208_R	0.514	0.64
115_Y	192_V	0.513	0.64
16_V	22_L	0.510	0.63
166_H	171_F	0.509	0.63
85_I	98_K	0.506	0.63
41_Y	74_L	0.505	0.63
85_I	129_D	0.503	0.62
48_T	52_Y	0.503	0.62
49_V	62_L	0.502	0.62
32_Q	35_V	0.500	0.62

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
4h3zA	2	1	100	0.013	Contact Map
3ky7A	2	0.93	100	0.017	Contact Map
4yvgA	2	0.9671	100	0.02	Contact Map
1oy5A	2	0.8889	100	0.029	Contact Map
3knuA	2	0.823	100	0.039	Contact Map
3iefA	2	0.9218	100	0.04	Contact Map
3quvA	2	0.8889	100	0.05	Contact Map
1to0A	2	0.6008	88.9	0.954	Contact Map
4fakA	2	0.6255	86.9	0.955	Contact Map
3aiaA	2	0.5432	84.2	0.957	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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