YACO - BACSU - GREMLIN Contacts

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YACO - Putative TrmH family tRNA/rRNA methyltransferase YacO

UniProt:	Q06753	Sequences: MSQQHDYVIGKNAVIETLKSDRKLYKLWMAENTVKGQAQQVIELAKKQGITIQYVPRKKLDQMVTGQHQGVVAQVAAYEYAELDDLYKAAEEKNEQPFFLILDELEDPHNLGSIMRTADAVGAHGIVIPKRRAVGLTTTVAKASTGAIEHIPVARVTNLARTLEEMKERGIWVVGTDASAREDFRNMDGNMPLALVIGSEGKGMGRLVKEKCDFLIKLPMAGKVTSLNASVAAGLLMYEVYRKRNPVGE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	249 (232)
Sequences:	8404 (5769)
Seq/√Len:	378.7

ECOLI - RLMB YFIF TRML TRMH
BACSU - YACO YSGA TRML

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
197_I	229_A	4.114	1.00
175_G	212_C	3.550	1.00
101_I	194_A	3.250	1.00
206_R	210_E	2.926	1.00
231_V	234_G	2.884	1.00
25_Y	76_A	2.818	1.00
176_T	236_L	2.801	1.00
114_I	233_A	2.733	1.00
239_E	242_R	2.592	1.00
175_G	204_M	2.529	1.00
197_I	233_A	2.496	1.00
26_K	53_Q	2.397	1.00
164_E	211_K	2.192	1.00
14_V	73_A	2.098	1.00
177_D	209_K	2.072	1.00
100_L	114_I	2.070	1.00
167_K	213_D	2.032	1.00
174_V	216_I	2.020	1.00
103_D	205_G	1.994	1.00
125_G	152_P	1.931	1.00
23_K	76_A	1.916	1.00
115_M	126_I	1.896	1.00
60_L	72_V	1.815	1.00
119_D	222_G	1.776	1.00
5_H	25_Y	1.772	1.00
121_V	238_Y	1.771	1.00
100_L	237_M	1.737	1.00
98_F	123_A	1.737	1.00
97_P	192_P	1.736	1.00
99_F	125_G	1.725	1.00
233_A	237_M	1.718	1.00
119_D	151_I	1.712	1.00
174_V	193_L	1.711	1.00
144_S	148_I	1.661	1.00
172_W	214_F	1.615	1.00
32_N	57_R	1.571	1.00
141_A	148_I	1.554	1.00
123_A	237_M	1.534	1.00
147_A	224_V	1.533	1.00
120_A	220_M	1.516	1.00
184_F	236_L	1.494	1.00
196_V	204_M	1.486	1.00
174_V	214_F	1.480	1.00
171_I	194_A	1.477	1.00
31_E	54_Y	1.466	1.00
195_L	240_V	1.465	1.00
171_I	192_P	1.464	1.00
195_L	236_L	1.456	1.00
118_A	123_A	1.451	1.00
26_K	74_Q	1.450	1.00
57_R	61_D	1.450	1.00
121_V	184_F	1.449	1.00
100_L	118_A	1.415	1.00
119_D	147_A	1.402	1.00
187_M	216_I	1.395	1.00
95_E	124_H	1.395	1.00
113_S	230_S	1.381	1.00
8_V	17_T	1.364	1.00
163_L	173_V	1.339	1.00
27_L	73_A	1.335	1.00
106_E	201_G	1.325	1.00
178_A	217_K	1.315	1.00
100_L	123_A	1.314	1.00
183_D	186_N	1.304	1.00
165_E	169_R	1.301	1.00
199_S	202_K	1.293	1.00
130_K	157_T	1.291	1.00
158_N	161_R	1.287	1.00
105_L	229_A	1.287	1.00
99_F	171_I	1.285	1.00
182_E	214_F	1.281	1.00
117_T	234_G	1.276	1.00
119_D	150_H	1.275	1.00
209_K	215_L	1.272	1.00
97_P	124_H	1.268	1.00
172_W	213_D	1.266	1.00
177_D	215_L	1.262	1.00
55_V	59_K	1.249	1.00
196_V	208_V	1.248	1.00
55_V	60_L	1.242	1.00
15_I	19_K	1.238	1.00
166_M	194_A	1.235	1.00
164_E	168_E	1.235	1.00
175_G	215_L	1.231	1.00
121_V	235_L	1.230	1.00
119_D	224_V	1.206	1.00
31_E	56_P	1.200	1.00
104_E	131_R	1.197	1.00
101_I	163_L	1.189	1.00
197_I	232_A	1.171	1.00
160_A	211_K	1.168	1.00
221_A	241_Y	1.168	1.00
24_L	73_A	1.166	1.00
180_A	217_K	1.147	1.00
15_I	40_Q	1.141	1.00
121_V	241_Y	1.135	1.00
115_M	153_V	1.134	1.00
127_V	162_T	1.131	1.00
183_D	217_K	1.129	1.00
59_K	62_Q	1.122	1.00
101_I	159_L	1.121	1.00
185_R	242_R	1.117	1.00
99_F	127_V	1.115	1.00
173_V	194_A	1.110	1.00
100_L	197_I	1.103	1.00
27_L	45_A	1.102	1.00
189_G	240_V	1.101	1.00
98_F	124_H	1.099	1.00
82_E	85_D	1.099	1.00
98_F	240_V	1.089	1.00
156_V	162_T	1.088	1.00
118_A	126_I	1.088	1.00
24_L	75_V	1.080	1.00
19_K	44_L	1.073	1.00
111_L	128_I	1.069	1.00
125_G	154_A	1.061	1.00
205_G	208_V	1.056	1.00
22_R	78_Y	1.039	1.00
128_I	153_V	1.036	1.00
16_E	150_H	1.024	1.00
117_T	231_V	1.024	1.00
111_L	133_A	1.020	1.00
196_V	212_C	1.019	1.00
58_K	61_D	1.015	1.00
160_A	164_E	1.008	1.00
30_A	57_R	1.005	1.00
98_F	237_M	1.003	1.00
163_L	208_V	1.000	1.00
14_V	71_V	0.996	1.00
16_E	19_K	0.982	1.00
193_L	240_V	0.970	1.00
115_M	140_V	0.964	1.00
127_V	156_V	0.963	1.00
56_P	59_K	0.963	1.00
164_E	167_K	0.962	1.00
64_V	72_V	0.961	1.00
182_E	186_N	0.960	1.00
117_T	237_M	0.959	1.00
159_L	208_V	0.958	1.00
161_R	164_E	0.952	1.00
109_H	143_A	0.949	1.00
160_A	207_L	0.946	1.00
102_L	114_I	0.944	1.00
189_G	193_L	0.934	1.00
119_D	223_K	0.932	1.00
212_C	215_L	0.929	1.00
30_A	33_T	0.922	1.00
176_T	197_I	0.917	1.00
184_F	189_G	0.914	1.00
22_R	149_E	0.908	1.00
102_L	111_L	0.907	1.00
29_M	54_Y	0.905	1.00
6_D	75_V	0.902	1.00
102_L	197_I	0.892	1.00
8_V	13_A	0.881	1.00
122_G	221_A	0.879	1.00
128_I	132_R	0.877	1.00
117_T	121_V	0.874	1.00
179_S	215_L	0.872	1.00
96_Q	191_M	0.870	1.00
150_H	223_K	0.866	1.00
175_G	209_K	0.862	1.00
216_I	236_L	0.853	1.00
9_I	66_G	0.851	1.00
179_S	209_K	0.850	1.00
103_D	208_V	0.845	1.00
101_I	166_M	0.844	1.00
207_L	210_E	0.843	1.00
165_E	168_E	0.842	1.00
7_Y	72_V	0.842	1.00
29_M	71_V	0.840	1.00
44_L	47_K	0.833	1.00
99_F	166_M	0.830	1.00
20_S	150_H	0.827	1.00
167_K	211_K	0.827	1.00
8_V	75_V	0.823	1.00
103_D	204_M	0.823	1.00
5_H	74_Q	0.822	1.00
157_T	161_R	0.821	1.00
121_V	185_R	0.820	1.00
109_H	113_S	0.818	1.00
65_T	138_T	0.817	1.00
104_E	202_K	0.816	1.00
78_Y	136_L	0.816	1.00
120_A	224_V	0.815	1.00
166_M	171_I	0.814	1.00
29_M	52_I	0.810	1.00
87_Y	169_R	0.809	1.00
12_N	145_T	0.805	1.00
161_R	165_E	0.803	1.00
5_H	76_A	0.799	1.00
84_D	165_E	0.798	1.00
26_K	51_T	0.797	1.00
28_W	63_M	0.790	1.00
15_I	44_L	0.788	1.00
104_E	129_P	0.788	1.00
7_Y	74_Q	0.785	1.00
88_K	169_R	0.782	1.00
172_W	191_M	0.780	1.00
185_R	239_E	0.779	1.00
40_Q	44_L	0.778	1.00
115_M	148_I	0.776	1.00
207_L	211_K	0.774	1.00
101_I	196_V	0.766	1.00
104_E	199_S	0.764	1.00
133_A	137_T	0.754	1.00
17_T	75_V	0.752	1.00
83_L	154_A	0.752	1.00
17_T	149_E	0.746	1.00
55_V	72_V	0.743	1.00
162_T	166_M	0.741	1.00
160_A	208_V	0.740	1.00
30_A	60_L	0.739	1.00
104_E	205_G	0.738	1.00
97_P	171_I	0.736	1.00
141_A	149_E	0.734	1.00
98_F	193_L	0.731	1.00
163_L	211_K	0.728	1.00
111_L	140_V	0.726	1.00
197_I	236_L	0.719	1.00
28_W	55_V	0.719	1.00
185_R	219_P	0.718	1.00
167_K	173_V	0.717	1.00
172_W	193_L	0.717	1.00
44_L	48_Q	0.714	1.00
83_L	86_L	0.714	1.00
176_T	204_M	0.712	1.00
105_L	111_L	0.710	1.00
206_R	209_K	0.709	1.00
121_V	237_M	0.709	1.00
96_Q	124_H	0.706	1.00
179_S	217_K	0.706	1.00
163_L	194_A	0.702	0.99
126_I	151_I	0.701	0.99
204_M	212_C	0.698	0.99
25_Y	51_T	0.693	0.99
86_L	125_G	0.693	0.99
177_D	180_A	0.693	0.99
61_D	67_Q	0.692	0.99
36_G	39_Q	0.691	0.99
173_V	196_V	0.691	0.99
181_R	214_F	0.681	0.99
182_E	187_M	0.677	0.99
105_L	114_I	0.675	0.99
102_L	105_L	0.674	0.99
182_E	217_K	0.673	0.99
39_Q	43_E	0.673	0.99
117_T	233_A	0.668	0.99
114_I	229_A	0.667	0.99
174_V	187_M	0.662	0.99
177_D	217_K	0.661	0.99
28_W	53_Q	0.660	0.99
43_E	46_K	0.659	0.99
9_I	142_K	0.659	0.99
37_Q	40_Q	0.657	0.99
106_E	199_S	0.657	0.99
25_Y	74_Q	0.654	0.99
176_T	195_L	0.650	0.99
181_R	217_K	0.648	0.99
187_M	214_F	0.648	0.99
109_H	139_T	0.646	0.99
60_L	69_Q	0.640	0.99
8_V	24_L	0.639	0.99
218_L	238_Y	0.638	0.99
118_A	237_M	0.638	0.99
63_M	72_V	0.636	0.99
33_T	38_A	0.636	0.99
28_W	74_Q	0.631	0.99
42_I	46_K	0.630	0.99
101_I	127_V	0.629	0.99
120_A	225_T	0.626	0.99
181_R	215_L	0.625	0.99
29_M	34_V	0.624	0.99
124_H	171_I	0.620	0.99
178_A	225_T	0.616	0.99
113_S	231_V	0.616	0.99
17_T	21_D	0.615	0.99
109_H	230_S	0.615	0.99
115_M	147_A	0.611	0.99
185_R	238_Y	0.610	0.99
127_V	166_M	0.609	0.99
83_L	127_V	0.604	0.98
83_L	162_T	0.603	0.98
128_I	135_G	0.602	0.98
19_K	223_K	0.601	0.98
147_A	150_H	0.598	0.98
170_G	192_P	0.596	0.98
6_D	22_R	0.594	0.98
83_L	87_Y	0.593	0.98
60_L	64_V	0.588	0.98
121_V	218_L	0.587	0.98
175_G	196_V	0.583	0.98
81_A	152_P	0.583	0.98
134_V	137_T	0.583	0.98
58_K	62_Q	0.580	0.98
42_I	45_A	0.579	0.98
34_V	54_Y	0.577	0.98
45_A	48_Q	0.577	0.98
86_L	99_F	0.577	0.98
60_L	68_H	0.576	0.98
89_A	152_P	0.575	0.98
40_Q	43_E	0.571	0.98
12_N	15_I	0.571	0.98
185_R	189_G	0.571	0.98
11_K	15_I	0.571	0.98
185_R	241_Y	0.569	0.98
150_H	224_V	0.563	0.98
162_T	165_E	0.562	0.98
61_D	68_H	0.560	0.98
13_A	141_A	0.559	0.97
41_V	45_A	0.557	0.97
204_M	208_V	0.554	0.97
131_R	205_G	0.553	0.97
101_I	129_P	0.551	0.97
30_A	54_Y	0.550	0.97
99_F	194_A	0.549	0.97
106_E	202_K	0.549	0.97
9_I	138_T	0.549	0.97
55_V	63_M	0.545	0.97
64_V	67_Q	0.544	0.97
129_P	159_L	0.541	0.97
43_E	47_K	0.539	0.97
84_D	87_Y	0.536	0.97
235_L	238_Y	0.535	0.97
121_V	221_A	0.534	0.97
172_W	190_N	0.534	0.97
69_Q	107_D	0.530	0.97
11_K	38_A	0.530	0.97
199_S	225_T	0.526	0.96
14_V	27_L	0.525	0.96
141_A	144_S	0.525	0.96
230_S	233_A	0.521	0.96
11_K	37_Q	0.519	0.96
121_V	220_M	0.518	0.96
129_P	208_V	0.516	0.96
174_V	189_G	0.515	0.96
123_A	240_V	0.515	0.96
156_V	161_R	0.514	0.96
6_D	9_I	0.513	0.96
177_D	204_M	0.511	0.96
9_I	72_V	0.511	0.96
180_A	215_L	0.510	0.96
185_R	188_D	0.505	0.95
163_L	167_K	0.504	0.95
188_D	191_M	0.501	0.95
158_N	207_L	0.501	0.95
135_G	155_R	0.500	0.95
104_E	208_V	0.500	0.95

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
3nk6A	2	0.9478	100	0.164	Contact Map
1ipaA	1	0.9357	100	0.169	Contact Map
1gz0A	2	0.9679	100	0.177	Contact Map
1x7oA	2	0.9639	100	0.181	Contact Map
2i6dA	2	0.8996	100	0.21	Contact Map
4kgnA	2	0.6225	100	0.382	Contact Map
3l8uA	2	0.5823	100	0.393	Contact Map
1v2xA	2	0.6908	100	0.396	Contact Map
3n4jA	2	0.6185	100	0.397	Contact Map
1zjrA	2	0.6867	100	0.399	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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