TRMJ - ECOLI - GREMLIN Contacts

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TRMJ - tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ

UniProt:	P0AE01	Sequences: MLQNIRIVLVETSHTGNMGSVARAMKTMGLTNLWLVNPLVKPDSQAIALAAGASDVIGNAHIVDTLDEALAGCSLVVGTSARSRTLPWPMLDPRECGLKSVAEAANTPVALVFGRERVGLTNEELQKCHYHVAIAANPEYSSLNLAMAVQVIAYEVRMAWLATQENGEQVEHEETPYPLVDDLERFYGHLEQTLLATGFIRENHPGQVMNKLRRLFTRARPESQELNILRGILASIEQQNKGNKAE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13452
Length:	246 (231)
Sequences:	1787 (1148)
Seq/√Len:	75.5

ECOLI - TRMJ LAST TRMH
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
65_T	68_E	4.855	1.00
67_D	127_K	4.184	1.00
26_K	55_D	3.784	1.00
94_R	158_M	3.643	1.00
132_V	152_I	3.442	1.00
32_N	61_H	3.213	1.00
73_C	110_A	3.135	1.00
20_S	49_L	3.131	1.00
34_W	63_V	2.815	1.00
11_E	115_R	2.773	1.00
78_G	128_C	2.753	1.00
11_E	37_N	2.589	1.00
64_D	68_E	2.530	1.00
66_L	112_V	2.479	1.00
184_E	213_R	2.464	1.00
9_L	145_L	2.439	1.00
7_I	153_A	2.398	1.00
182_D	223_S	2.397	1.00
189_H	230_R	2.226	1.00
32_N	108_P	2.208	1.00
6_R	34_W	2.204	1.00
70_L	76_V	2.149	1.00
115_R	124_E	2.145	1.00
46_A	57_I	2.084	1.00
47_I	58_G	2.062	1.00
113_F	149_V	2.025	1.00
78_G	125_L	1.994	1.00
37_N	64_D	1.978	1.00
34_W	61_H	1.970	1.00
24_A	150_Q	1.947	1.00
111_L	152_I	1.943	1.00
8_V	110_A	1.920	1.00
6_R	32_N	1.855	1.00
178_P	226_L	1.838	1.00
182_D	185_R	1.738	1.00
186_F	216_F	1.731	1.00
185_R	230_R	1.707	1.00
7_I	25_M	1.702	1.00
187_Y	217_T	1.685	1.00
16_G	45_Q	1.674	1.00
193_T	237_E	1.672	1.00
145_L	149_V	1.667	1.00
76_V	112_V	1.650	1.00
196_A	237_E	1.634	1.00
30_L	153_A	1.621	1.00
192_Q	237_E	1.589	0.99
77_V	96_C	1.551	0.99
28_M	150_Q	1.529	0.99
75_L	130_Y	1.494	0.99
81_A	84_R	1.488	0.99
94_R	155_E	1.467	0.99
193_T	236_I	1.466	0.99
121_T	124_E	1.460	0.99
226_L	230_R	1.453	0.99
9_L	149_V	1.426	0.99
194_L	232_I	1.413	0.99
54_S	58_G	1.401	0.99
40_V	43_D	1.396	0.99
10_V	120_L	1.361	0.98
72_G	181_D	1.359	0.98
25_M	30_L	1.357	0.98
21_V	149_V	1.356	0.98
179_L	182_D	1.355	0.98
36_V	69_A	1.344	0.98
186_F	226_L	1.343	0.98
8_V	73_C	1.343	0.98
91_L	130_Y	1.328	0.98
112_V	128_C	1.325	0.98
197_T	236_I	1.307	0.98
215_L	221_P	1.307	0.98
18_M	41_K	1.306	0.98
13_S	117_R	1.303	0.98
197_T	235_S	1.300	0.98
113_F	145_L	1.282	0.98
129_H	180_V	1.275	0.97
66_L	70_L	1.274	0.97
26_K	53_A	1.259	0.97
76_V	180_V	1.253	0.97
157_R	161_L	1.238	0.97
193_T	233_L	1.230	0.97
47_I	54_S	1.215	0.97
176_P	223_S	1.214	0.97
212_L	232_I	1.213	0.97
99_K	130_Y	1.208	0.96
37_N	65_T	1.193	0.96
93_P	152_I	1.192	0.96
7_I	111_L	1.169	0.96
80_S	131_H	1.163	0.96
181_D	185_R	1.163	0.96
74_S	108_P	1.160	0.96
74_S	107_T	1.156	0.95
91_L	99_K	1.150	0.95
35_L	38_P	1.147	0.95
15_T	43_D	1.131	0.95
103_E	220_R	1.119	0.95
195_L	205_P	1.117	0.95
96_C	132_V	1.106	0.94
34_W	72_G	1.104	0.94
16_G	49_L	1.098	0.94
234_A	238_Q	1.098	0.94
186_F	190_L	1.092	0.94
191_E	209_M	1.086	0.94
136_A	140_Y	1.085	0.94
73_C	76_V	1.078	0.93
118_V	121_T	1.066	0.93
77_V	132_V	1.064	0.93
10_V	115_R	1.053	0.93
197_T	232_I	1.049	0.92
70_L	73_C	1.042	0.92
6_R	63_V	1.030	0.92
20_S	27_T	1.029	0.92
235_S	238_Q	1.026	0.92
115_R	121_T	1.025	0.92
4_N	108_P	1.024	0.92
49_L	147_M	1.017	0.91
46_A	60_A	1.000	0.91
72_G	108_P	0.989	0.90
9_L	21_V	0.983	0.90
94_R	159_A	0.968	0.89
31_T	59_N	0.962	0.89
6_R	73_C	0.957	0.89
38_P	62_I	0.955	0.88
221_P	229_L	0.953	0.88
103_E	107_T	0.953	0.88
80_S	88_W	0.943	0.88
28_M	136_A	0.931	0.87
12_T	35_L	0.919	0.86
100_S	112_V	0.914	0.86
219_A	225_E	0.913	0.86
50_A	54_S	0.910	0.86
63_V	68_E	0.897	0.85
194_L	197_T	0.895	0.85
215_L	229_L	0.892	0.85
77_V	130_Y	0.878	0.84
5_I	30_L	0.870	0.83
221_P	226_L	0.870	0.83
21_V	146_A	0.868	0.83
19_G	23_R	0.867	0.83
35_L	219_A	0.861	0.83
81_A	141_S	0.860	0.83
143_L	150_Q	0.851	0.82
14_H	49_L	0.843	0.81
10_V	36_V	0.842	0.81
186_F	229_L	0.834	0.81
101_V	159_A	0.832	0.80
99_K	102_A	0.824	0.80
79_T	152_I	0.823	0.80
223_S	227_N	0.821	0.80
16_G	150_Q	0.820	0.79
184_E	188_G	0.817	0.79
104_A	109_V	0.817	0.79
179_L	183_L	0.805	0.78
27_T	49_L	0.803	0.78
20_S	146_A	0.800	0.78
191_E	195_L	0.798	0.78
81_A	122_N	0.797	0.77
75_L	103_E	0.794	0.77
185_R	189_H	0.793	0.77
76_V	128_C	0.789	0.77
186_F	233_L	0.788	0.77
77_V	99_K	0.787	0.77
187_Y	213_R	0.785	0.76
129_H	183_L	0.785	0.76
201_R	205_P	0.785	0.76
173_E	222_E	0.778	0.76
5_I	156_V	0.776	0.76
216_F	236_I	0.776	0.76
11_E	121_T	0.775	0.75
7_I	30_L	0.773	0.75
17_N	23_R	0.765	0.75
136_A	141_S	0.763	0.74
61_H	68_E	0.760	0.74
6_R	108_P	0.760	0.74
22_A	46_A	0.749	0.73
123_E	126_Q	0.747	0.73
18_M	21_V	0.747	0.73
59_N	165_E	0.744	0.72
207_Q	210_N	0.738	0.72
8_V	63_V	0.735	0.72
93_P	154_Y	0.734	0.71
175_T	222_E	0.728	0.71
99_K	103_E	0.728	0.71
97_G	156_V	0.728	0.71
69_A	72_G	0.727	0.71
126_Q	210_N	0.724	0.70
26_K	56_V	0.721	0.70
214_R	222_E	0.720	0.70
22_A	57_I	0.711	0.69
27_T	150_Q	0.710	0.69
26_K	137_N	0.710	0.69
26_K	31_T	0.708	0.69
42_P	47_I	0.707	0.69
95_E	98_L	0.706	0.69
13_S	142_S	0.704	0.68
26_K	140_Y	0.703	0.68
129_H	217_T	0.696	0.67
95_E	172_H	0.693	0.67
22_A	122_N	0.691	0.67
8_V	69_A	0.689	0.67
118_V	222_E	0.689	0.67
137_N	140_Y	0.687	0.66
82_R	142_S	0.682	0.66
52_G	137_N	0.681	0.66
30_L	146_A	0.681	0.66
92_D	98_L	0.681	0.66
24_A	28_M	0.677	0.65
35_L	62_I	0.676	0.65
136_A	143_L	0.676	0.65
235_S	239_Q	0.672	0.65
57_I	60_A	0.666	0.64
201_R	204_H	0.663	0.64
173_E	176_P	0.663	0.64
71_A	181_D	0.662	0.64
185_R	188_G	0.662	0.64
155_E	158_M	0.662	0.64
188_G	192_Q	0.661	0.63
10_V	73_C	0.660	0.63
15_T	41_K	0.658	0.63
15_T	42_P	0.658	0.63
53_A	140_Y	0.651	0.62
63_V	72_G	0.648	0.62
15_T	18_M	0.648	0.62
59_N	105_A	0.641	0.61
28_M	143_L	0.640	0.61
28_M	157_R	0.639	0.61
76_V	129_H	0.637	0.61
67_D	112_V	0.636	0.60
15_T	47_I	0.633	0.60
45_Q	49_L	0.633	0.60
127_K	184_E	0.632	0.60
98_L	162_A	0.631	0.60
95_E	166_N	0.628	0.59
80_S	127_K	0.627	0.59
201_R	206_G	0.627	0.59
25_M	153_A	0.622	0.59
100_S	111_L	0.621	0.59
31_T	137_N	0.616	0.58
78_G	143_L	0.612	0.58
6_R	61_H	0.608	0.57
25_M	56_V	0.606	0.57
200_I	205_P	0.603	0.56
140_Y	147_M	0.602	0.56
43_D	51_A	0.601	0.56
66_L	127_K	0.601	0.56
87_P	214_R	0.600	0.56
187_Y	209_M	0.599	0.56
155_E	231_G	0.598	0.56
25_M	154_Y	0.598	0.56
82_R	143_L	0.598	0.56
79_T	154_Y	0.594	0.55
176_P	179_L	0.592	0.55
44_S	48_A	0.592	0.55
29_G	137_N	0.591	0.55
52_G	140_Y	0.591	0.55
100_S	156_V	0.589	0.55
27_T	136_A	0.588	0.55
41_K	47_I	0.588	0.55
90_M	131_H	0.586	0.54
94_R	162_A	0.585	0.54
32_N	73_C	0.584	0.54
70_L	180_V	0.584	0.54
4_N	106_N	0.582	0.54
34_W	73_C	0.580	0.54
98_L	102_A	0.580	0.54
233_L	236_I	0.579	0.53
195_L	200_I	0.579	0.53
129_H	213_R	0.578	0.53
93_P	135_A	0.575	0.53
7_I	149_V	0.574	0.53
125_L	133_A	0.572	0.53
190_L	233_L	0.572	0.53
134_I	151_V	0.571	0.52
126_Q	131_H	0.571	0.52
197_T	239_Q	0.569	0.52
180_V	217_T	0.568	0.52
33_L	134_I	0.568	0.52
22_A	81_A	0.568	0.52
68_E	123_E	0.567	0.52
211_K	224_Q	0.566	0.52
64_D	67_D	0.566	0.52
6_R	72_G	0.564	0.52
31_T	56_V	0.563	0.51
28_M	153_A	0.562	0.51
204_H	235_S	0.560	0.51
80_S	125_L	0.558	0.51
101_V	160_W	0.555	0.50
210_N	217_T	0.554	0.50
142_S	145_L	0.553	0.50
187_Y	190_L	0.553	0.50
83_S	87_P	0.553	0.50
27_T	234_A	0.552	0.50
13_S	39_L	0.552	0.50
43_D	48_A	0.551	0.50
32_N	165_E	0.551	0.50
137_N	151_V	0.549	0.50
31_T	139_E	0.548	0.50
21_V	153_A	0.546	0.49
14_H	20_S	0.544	0.49
224_Q	228_I	0.543	0.49
85_T	90_M	0.542	0.49
98_L	101_V	0.541	0.49
195_L	198_G	0.540	0.49
204_H	228_I	0.540	0.49
88_W	131_H	0.539	0.48
11_E	118_V	0.538	0.48
117_R	121_T	0.535	0.48
21_V	27_T	0.535	0.48
183_L	226_L	0.535	0.48
136_A	157_R	0.535	0.48
94_R	98_L	0.534	0.48
201_R	232_I	0.533	0.48
24_A	53_A	0.532	0.48
18_M	72_G	0.532	0.48
204_H	208_V	0.532	0.48
10_V	124_E	0.532	0.48
76_V	110_A	0.531	0.47
199_F	228_I	0.531	0.47
190_L	232_I	0.530	0.47
161_L	164_Q	0.530	0.47
202_E	206_G	0.529	0.47
48_A	51_A	0.528	0.47
123_E	181_D	0.528	0.47
177_Y	220_R	0.524	0.47
96_C	100_S	0.524	0.47
225_E	230_R	0.524	0.47
36_V	63_V	0.520	0.46
188_G	191_E	0.518	0.46
54_S	117_R	0.517	0.46
133_A	136_A	0.516	0.46
8_V	76_V	0.515	0.45
142_S	208_V	0.513	0.45
28_M	55_D	0.513	0.45
58_G	105_A	0.512	0.45
15_T	40_V	0.511	0.45
77_V	111_L	0.511	0.45
20_S	150_Q	0.510	0.45
10_V	123_E	0.510	0.45
20_S	147_M	0.507	0.44
22_A	84_R	0.507	0.44
97_G	226_L	0.507	0.44
93_P	96_C	0.506	0.44
215_L	219_A	0.504	0.44
204_H	207_Q	0.503	0.44
41_K	62_I	0.501	0.44
77_V	100_S	0.500	0.44
84_R	87_P	0.500	0.44

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
4cndA	2	0.6667	100	0.301	Contact Map
3ilkA	2	0.9675	100	0.313	Contact Map
3onpA	2	0.6382	100	0.322	Contact Map
4cngA	2	0.6138	100	0.351	Contact Map
3ic6A	2	0.752	100	0.511	Contact Map
3ktyA	2	0.6545	100	0.557	Contact Map
3dcmX	2	0.6301	100	0.599	Contact Map
1zjrA	2	0.7195	100	0.627	Contact Map
1v2xA	2	0.687	100	0.628	Contact Map
1x7oA	2	0.6179	100	0.643	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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