TRUA - ECOLI - GREMLIN Contacts

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TRUA - tRNA pseudouridine synthase A

UniProt:	P07649	Sequences: MSDQQQPPVYKIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQVVHFETTALRKDAAWTLGVNANLPGDIAVRWVKTVPDDFHARFSATARRYRYIIYNHRLRPAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRHGPYVVVDIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLYLVAVDYPDRYDLPKPPMGPLFLAD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10454
Length:	270 (244)
Sequences:	5647 (3998)
Seq/√Len:	255.9

ECOLI - TRUA
BACSU - TRUA
HALSA - TRUA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
162_T	174_P	2.971	1.00
115_A	251_D	2.941	1.00
11_K	73_E	2.892	1.00
117_R	195_K	2.722	1.00
154_C	225_A	2.547	1.00
137_T	212_M	2.331	1.00
38_K	41_K	2.274	1.00
163_S	230_A	2.256	1.00
115_A	195_K	2.204	1.00
24_Y	32_V	2.178	1.00
11_K	71_H	2.162	1.00
158_E	177_N	2.149	1.00
28_R	40_E	2.135	1.00
149_H	153_Q	2.107	1.00
225_A	229_A	2.101	1.00
37_E	41_K	2.066	1.00
219_Q	223_W	2.031	1.00
117_R	193_D	2.026	1.00
33_R	38_K	2.011	1.00
22_K	94_D	1.950	1.00
119_R	248_V	1.899	1.00
223_W	226_E	1.874	1.00
210_S	224_I	1.871	1.00
119_R	191_V	1.869	1.00
150_R	221_E	1.860	1.00
119_R	193_D	1.847	1.00
148_M	215_G	1.834	1.00
84_T	100_V	1.819	1.00
192_V	208_V	1.801	1.00
121_I	246_Y	1.774	1.00
36_Q	40_E	1.761	1.00
153_Q	156_L	1.751	1.00
181_I	192_V	1.749	1.00
203_M	207_I	1.725	1.00
194_I	207_I	1.717	1.00
13_A	101_K	1.712	1.00
247_L	250_V	1.710	1.00
66_T	248_V	1.679	1.00
184_T	193_D	1.641	1.00
71_H	109_A	1.628	1.00
181_I	194_I	1.625	1.00
154_C	221_E	1.594	1.00
220_P	223_W	1.589	1.00
14_L	70_V	1.579	1.00
26_W	70_V	1.568	1.00
180_H	195_K	1.567	1.00
45_Q	90_N	1.564	1.00
96_A	128_R	1.564	1.00
178_V	194_I	1.522	1.00
23_Y	33_R	1.518	1.00
23_Y	94_D	1.513	1.00
152_A	181_I	1.508	1.00
115_A	179_M	1.502	1.00
117_R	251_D	1.498	1.00
19_D	135_G	1.494	1.00
141_E	216_A	1.494	1.00
13_A	69_V	1.487	1.00
44_S	50_P	1.471	1.00
33_R	94_D	1.465	1.00
152_A	211_L	1.454	1.00
28_R	37_E	1.443	1.00
124_N	185_R	1.438	1.00
17_E	98_R	1.432	1.00
213_E	218_N	1.427	1.00
121_I	189_Y	1.426	1.00
16_I	70_V	1.426	1.00
144_D	217_H	1.411	1.00
21_S	134_K	1.401	1.00
12_I	74_T	1.375	1.00
144_D	147_R	1.366	1.00
155_L	207_I	1.344	1.00
12_I	100_V	1.337	1.00
39_L	97_V	1.333	1.00
19_D	134_K	1.317	1.00
53_V	70_V	1.312	1.00
146_E	149_H	1.311	1.00
179_M	197_N	1.307	1.00
121_I	191_V	1.279	1.00
210_S	237_A	1.277	1.00
49_E	75_T	1.273	1.00
213_E	219_Q	1.267	1.00
15_G	69_V	1.267	1.00
38_K	95_I	1.259	1.00
176_R	198_A	1.259	1.00
149_H	182_N	1.257	1.00
149_H	183_V	1.237	1.00
152_A	183_V	1.229	1.00
158_E	197_N	1.226	1.00
28_R	52_T	1.220	1.00
22_K	134_K	1.216	1.00
26_W	55_C	1.215	1.00
24_Y	61_A	1.215	1.00
122_I	192_V	1.209	1.00
21_S	64_H	1.183	1.00
15_G	99_W	1.177	1.00
202_H	206_N	1.173	1.00
129_P	132_L	1.166	1.00
39_L	70_V	1.157	1.00
114_T	253_P	1.156	1.00
129_P	136_V	1.153	1.00
117_R	248_V	1.146	1.00
179_M	195_K	1.144	1.00
147_R	217_H	1.141	1.00
150_R	153_Q	1.135	1.00
18_Y	68_Q	1.130	1.00
151_A	214_V	1.129	1.00
19_D	133_S	1.128	1.00
195_K	251_D	1.128	1.00
194_I	208_V	1.110	1.00
56_A	68_Q	1.099	1.00
156_L	180_H	1.089	1.00
232_D	235_L	1.088	1.00
143_L	148_M	1.086	1.00
165_R	174_P	1.075	1.00
214_V	224_I	1.074	1.00
15_G	67_G	1.072	1.00
137_T	241_K	1.071	1.00
220_P	224_I	1.070	1.00
41_K	45_Q	1.064	1.00
230_A	235_L	1.062	1.00
183_V	192_V	1.057	1.00
123_Y	136_V	1.054	1.00
158_E	175_W	1.048	1.00
137_T	240_A	1.045	1.00
117_R	249_A	1.041	1.00
40_E	53_V	1.039	1.00
147_R	150_R	1.028	1.00
147_R	221_E	1.027	1.00
125_H	188_P	1.023	1.00
227_L	230_A	1.020	1.00
132_L	189_Y	1.020	1.00
33_R	37_E	1.019	1.00
154_C	222_S	1.017	1.00
108_H	111_F	1.012	1.00
17_E	130_A	1.010	1.00
163_S	231_K	1.009	1.00
150_R	222_S	1.008	1.00
145_A	190_V	1.008	1.00
16_I	39_L	1.005	1.00
17_E	129_P	1.003	1.00
202_H	239_T	1.000	1.00
160_D	174_P	0.999	1.00
57_G	68_Q	0.999	1.00
24_Y	34_S	0.998	1.00
67_G	249_A	0.996	1.00
151_A	221_E	0.990	1.00
124_N	190_V	0.989	1.00
14_L	72_F	0.988	1.00
139_F	216_A	0.981	1.00
14_L	100_V	0.978	1.00
13_A	103_V	0.975	1.00
145_A	185_R	0.967	1.00
184_T	191_V	0.967	1.00
151_A	215_G	0.966	1.00
103_V	106_D	0.953	1.00
23_Y	95_I	0.952	1.00
137_T	243_E	0.951	1.00
206_N	239_T	0.947	1.00
80_D	100_V	0.944	1.00
122_I	212_M	0.941	1.00
166_A	202_H	0.936	1.00
181_I	211_L	0.936	1.00
147_R	220_P	0.925	1.00
23_Y	35_V	0.923	1.00
82_A	86_G	0.923	1.00
164_F	227_L	0.920	1.00
148_M	211_L	0.911	1.00
212_M	240_A	0.911	1.00
181_I	207_I	0.908	1.00
46_V	90_N	0.904	1.00
183_V	190_V	0.894	1.00
135_G	246_Y	0.893	1.00
194_I	204_V	0.891	1.00
82_A	85_L	0.891	1.00
13_A	107_F	0.889	1.00
87_V	97_V	0.887	1.00
182_N	193_D	0.886	1.00
54_F	71_H	0.886	1.00
46_V	83_W	0.886	1.00
56_A	250_V	0.878	1.00
102_T	105_D	0.874	1.00
80_D	102_T	0.873	1.00
145_A	149_H	0.870	1.00
136_V	189_Y	0.865	1.00
15_G	101_K	0.863	1.00
34_S	37_E	0.860	1.00
47_A	50_P	0.859	0.99
123_Y	129_P	0.859	0.99
219_Q	227_L	0.859	0.99
193_D	248_V	0.856	0.99
43_L	72_F	0.848	0.99
113_A	250_V	0.848	0.99
35_V	95_I	0.847	0.99
132_L	136_V	0.840	0.99
213_E	216_A	0.838	0.99
226_E	235_L	0.832	0.99
71_H	108_H	0.828	0.99
165_R	168_Q	0.822	0.99
62_G	242_A	0.820	0.99
180_H	193_D	0.808	0.99
183_V	211_L	0.803	0.99
116_R	198_A	0.802	0.99
213_E	238_A	0.800	0.99
209_G	237_A	0.800	0.99
165_R	169_C	0.799	0.99
155_L	181_I	0.792	0.99
51_I	72_F	0.792	0.99
222_S	226_E	0.791	0.99
132_L	135_G	0.790	0.99
49_E	74_T	0.790	0.99
221_E	224_I	0.789	0.99
46_V	86_G	0.786	0.99
55_C	70_V	0.780	0.99
139_F	212_M	0.777	0.99
47_A	74_T	0.775	0.99
143_L	212_M	0.771	0.99
185_R	188_P	0.768	0.99
166_A	201_H	0.768	0.99
168_Q	201_H	0.768	0.99
155_L	224_I	0.765	0.99
56_A	252_Y	0.764	0.99
160_D	231_K	0.762	0.99
210_S	236_A	0.759	0.99
16_I	26_W	0.747	0.99
42_A	90_N	0.742	0.99
146_E	150_R	0.742	0.99
44_S	47_A	0.741	0.99
88_N	96_A	0.740	0.99
122_I	208_V	0.736	0.98
162_T	165_R	0.735	0.98
24_Y	31_E	0.731	0.98
116_R	247_L	0.730	0.98
148_M	183_V	0.726	0.98
74_T	83_W	0.721	0.98
43_L	87_V	0.714	0.98
177_N	197_N	0.714	0.98
66_T	246_Y	0.712	0.98
178_V	196_A	0.712	0.98
131_V	135_G	0.704	0.98
121_I	132_L	0.703	0.98
39_L	53_V	0.703	0.98
211_L	215_G	0.698	0.98
222_S	225_A	0.697	0.98
40_E	52_T	0.693	0.98
166_A	239_T	0.691	0.98
212_M	216_A	0.688	0.98
227_L	236_A	0.688	0.98
149_H	181_I	0.685	0.98
122_I	190_V	0.684	0.98
56_A	113_A	0.683	0.97
151_A	211_L	0.683	0.97
23_Y	38_K	0.683	0.97
84_T	99_W	0.681	0.97
223_W	227_L	0.680	0.97
85_L	89_A	0.679	0.97
57_G	247_L	0.676	0.97
186_H	191_V	0.676	0.97
38_K	42_A	0.674	0.97
148_M	152_A	0.666	0.97
54_F	108_H	0.665	0.97
26_W	53_V	0.661	0.97
178_V	181_I	0.660	0.97
206_N	233_R	0.659	0.97
69_V	252_Y	0.658	0.97
120_Y	240_A	0.657	0.97
47_A	83_W	0.657	0.97
36_Q	53_V	0.653	0.97
70_V	97_V	0.652	0.97
233_R	237_A	0.652	0.97
163_S	232_D	0.648	0.97
226_E	229_A	0.645	0.96
109_A	112_S	0.645	0.96
67_G	98_R	0.643	0.96
145_A	183_V	0.641	0.96
227_L	237_A	0.638	0.96
64_H	244_G	0.635	0.96
183_V	194_I	0.635	0.96
81_A	85_L	0.633	0.96
12_I	102_T	0.631	0.96
154_C	224_I	0.630	0.96
155_L	178_V	0.629	0.96
15_G	98_R	0.626	0.96
206_N	236_A	0.624	0.96
57_G	250_V	0.624	0.96
165_R	171_S	0.623	0.96
213_E	237_A	0.623	0.96
79_K	82_A	0.622	0.96
17_E	131_V	0.621	0.96
226_E	230_A	0.617	0.95
155_L	228_L	0.617	0.95
124_N	139_F	0.617	0.95
124_N	188_P	0.615	0.95
220_P	226_E	0.614	0.95
163_S	235_L	0.613	0.95
159_N	175_W	0.607	0.95
122_I	143_L	0.605	0.95
42_A	87_V	0.604	0.95
123_Y	132_L	0.599	0.95
154_C	220_P	0.598	0.95
113_A	116_R	0.598	0.95
150_R	154_C	0.597	0.95
163_S	236_A	0.595	0.94
185_R	190_V	0.594	0.94
221_E	225_A	0.593	0.94
47_A	51_I	0.592	0.94
44_S	48_N	0.591	0.94
154_C	214_V	0.590	0.94
49_E	76_A	0.589	0.94
121_I	248_V	0.588	0.94
78_R	82_A	0.588	0.94
149_H	185_R	0.587	0.94
208_V	240_A	0.584	0.94
171_S	174_P	0.581	0.94
80_D	84_T	0.578	0.94
32_V	37_E	0.576	0.93
143_L	215_G	0.574	0.93
43_L	47_A	0.574	0.93
134_K	243_E	0.573	0.93
66_T	121_I	0.573	0.93
57_G	112_S	0.569	0.93
160_D	175_W	0.562	0.93
248_V	251_D	0.558	0.92
147_R	214_V	0.557	0.92
83_W	100_V	0.556	0.92
176_R	197_N	0.556	0.92
214_V	223_W	0.556	0.92
162_T	231_K	0.554	0.92
54_F	109_A	0.553	0.92
16_I	68_Q	0.551	0.92
236_A	239_T	0.551	0.92
224_I	228_L	0.548	0.92
24_Y	33_R	0.548	0.92
84_T	127_L	0.546	0.92
116_R	196_A	0.544	0.91
233_R	236_A	0.544	0.91
116_R	202_H	0.544	0.91
196_A	206_N	0.541	0.91
114_T	251_D	0.536	0.91
23_Y	91_L	0.532	0.91
57_G	109_A	0.530	0.90
163_S	227_L	0.528	0.90
12_I	76_A	0.525	0.90
96_A	127_L	0.524	0.90
92_P	95_I	0.524	0.90
28_R	41_K	0.524	0.90
134_K	246_Y	0.524	0.90
39_L	43_L	0.521	0.90
165_R	200_V	0.521	0.90
209_G	238_A	0.520	0.90
135_G	138_H	0.520	0.90
22_K	33_R	0.520	0.90
19_D	94_D	0.520	0.90
159_N	228_L	0.519	0.89
14_L	43_L	0.518	0.89
206_N	237_A	0.518	0.89
76_A	83_W	0.515	0.89
43_L	83_W	0.514	0.89
29_Q	34_S	0.512	0.89
196_A	199_F	0.511	0.89
44_S	51_I	0.509	0.89
46_V	87_V	0.507	0.88
139_F	143_L	0.505	0.88
210_S	214_V	0.504	0.88
192_V	211_L	0.504	0.88
179_M	196_A	0.501	0.88
175_W	198_A	0.500	0.88

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
1dj0A	2	0.9778	100	0.051	Contact Map
1vs3A	2	0.9074	100	0.064	Contact Map
4j37A	1	0.8963	100	0.103	Contact Map
2v9kA	1	0.8074	79.2	0.945	Contact Map
4qanA	1	0.2296	15.8	0.965	Contact Map
2x31A	2	0.3407	8.8	0.969	Contact Map
3da5A	2	0.2222	7.9	0.969	Contact Map
1z2zA	1	0.9296	7.8	0.969	Contact Map
3jywP	1	0.263	5.4	0.972	Contact Map
4kw3A	1	0.4741	4.9	0.972	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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