TRUA - HALSA - GREMLIN Contacts

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TRUA - tRNA pseudouridine synthase A

UniProt:	Q9HNP6	Sequences: MPRRAFRVAYDGRPYHGFQRQPDVSTVAGELFGALRRLDVFDGAKPPGYAAAGRTDAGVSARAQTVAFDAPAWLTPDAFTGALPDPIQVWAHADAPPEFHATHDAVARTYVYYWYAPDSRATDDRAAGALDRLTGTHDFHNLTPNTTNTVRELDATLDRDGAFRVITVRAGGFCRELVRRVVSLVQLVTETGDTDRIDTVLGDEPVAGPDGVPPADPHPLVLHAVAYDGLSFTVDEDAAERARTTFRAARADHHERARVAGHLASI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	266 (221)
Sequences:	5572 (3861)
Seq/√Len:	259.7

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
107_A	226_A	2.963	1.00
140_H	149_T	2.937	1.00
3_R	69_D	2.869	1.00
109_T	169_R	2.678	1.00
132_R	198_D	2.514	1.00
141_N	203_D	2.253	1.00
30_E	33_G	2.184	1.00
16_H	24_V	2.151	1.00
107_A	169_R	2.147	1.00
3_R	67_A	2.145	1.00
20_R	32_F	2.070	1.00
136_T	152_E	2.066	1.00
127_A	131_D	2.044	1.00
25_S	30_E	2.043	1.00
192_G	196_R	2.033	1.00
198_D	202_G	2.032	1.00
109_T	167_T	2.018	1.00
29_G	33_G	1.973	1.00
126_A	189_T	1.912	1.00
113_Y	221_V	1.907	1.00
14_P	86_P	1.902	1.00
111_V	223_H	1.873	1.00
111_V	165_V	1.868	1.00
184_L	197_I	1.802	1.00
111_V	167_T	1.801	1.00
222_L	225_V	1.789	1.00
196_R	199_T	1.788	1.00
76_P	92_H	1.773	1.00
166_I	182_V	1.751	1.00
28_A	32_F	1.741	1.00
128_G	194_T	1.732	1.00
131_D	134_T	1.730	1.00
62_R	223_H	1.710	1.00
168_V	181_V	1.687	1.00
177_L	181_V	1.676	1.00
5_A	93_A	1.674	1.00
155_A	166_I	1.667	1.00
116_A	159_R	1.666	1.00
67_A	101_A	1.626	1.00
6_F	66_V	1.574	1.00
132_R	194_T	1.560	1.00
193_D	196_R	1.557	1.00
18_F	66_V	1.552	1.00
155_A	168_V	1.551	1.00
37_R	82_A	1.538	1.00
154_D	169_R	1.526	1.00
113_Y	163_F	1.526	1.00
119_S	190_E	1.526	1.00
15_Y	25_S	1.525	1.00
15_Y	86_P	1.516	1.00
130_L	155_A	1.477	1.00
36_R	46_P	1.475	1.00
153_L	168_V	1.474	1.00
187_L	191_T	1.464	1.00
109_T	226_A	1.448	1.00
8_V	66_V	1.448	1.00
205_P	209_P	1.445	1.00
25_S	86_P	1.436	1.00
9_A	90_W	1.433	1.00
130_L	185_V	1.431	1.00
20_R	29_G	1.430	1.00
5_A	65_T	1.421	1.00
4_R	70_A	1.378	1.00
122_T	125_R	1.345	1.00
49_Y	66_V	1.340	1.00
113_Y	165_V	1.334	1.00
4_R	92_H	1.331	1.00
158_D	167_T	1.324	1.00
151_R	172_G	1.305	1.00
30_E	87_I	1.300	1.00
184_L	212_V	1.297	1.00
7_R	65_T	1.293	1.00
124_D	127_A	1.290	1.00
133_L	181_V	1.288	1.00
31_L	89_V	1.269	1.00
187_L	192_G	1.258	1.00
18_F	51_A	1.244	1.00
130_L	157_L	1.227	1.00
13_R	60_S	1.215	1.00
127_A	157_L	1.215	1.00
127_A	156_T	1.213	1.00
16_H	57_A	1.212	1.00
176_E	180_R	1.203	1.00
129_A	188_V	1.203	1.00
31_L	66_V	1.199	1.00
20_R	48_G	1.195	1.00
114_W	166_I	1.192	1.00
7_R	91_A	1.164	1.00
106_V	228_D	1.160	1.00
109_T	223_H	1.154	1.00
121_A	126_A	1.152	1.00
10_Y	64_Q	1.149	1.00
143_T	149_T	1.146	1.00
52_A	64_Q	1.142	1.00
205_P	210_D	1.137	1.00
134_T	154_D	1.136	1.00
136_T	171_G	1.134	1.00
169_R	226_A	1.129	1.00
168_V	182_V	1.115	1.00
7_R	63_A	1.114	1.00
123_D	159_R	1.114	1.00
128_G	131_D	1.088	1.00
32_F	49_Y	1.084	1.00
33_G	37_R	1.075	1.00
208_G	212_V	1.070	1.00
71_P	74_L	1.068	1.00
128_G	195_D	1.059	1.00
53_G	64_Q	1.055	1.00
193_D	197_I	1.043	1.00
125_R	194_T	1.037	1.00
123_D	164_R	1.028	1.00
157_L	166_I	1.028	1.00
100_H	103_H	1.023	1.00
125_R	128_G	1.022	1.00
6_F	92_H	1.020	1.00
188_V	197_I	1.019	1.00
109_T	224_A	1.019	1.00
63_A	224_A	1.018	1.00
8_V	31_L	1.015	1.00
6_F	68_F	1.012	1.00
16_H	26_T	1.009	1.00
117_P	162_A	1.003	1.00
72_A	92_H	1.001	1.00
132_R	195_D	1.001	1.00
114_W	186_Q	1.001	1.00
116_A	164_R	1.001	1.00
136_T	150_V	0.997	1.00
129_A	189_T	0.996	1.00
25_S	29_G	0.994	1.00
5_A	95_A	0.991	1.00
200_V	203_D	0.989	1.00
144_P	176_E	0.985	1.00
176_E	214_P	0.981	1.00
95_A	98_E	0.980	1.00
26_T	29_G	0.980	1.00
74_L	78_A	0.979	1.00
141_N	204_E	0.976	1.00
203_D	210_D	0.967	1.00
129_A	194_T	0.961	1.00
180_R	214_P	0.938	1.00
155_A	185_V	0.936	1.00
138_D	149_T	0.931	1.00
168_V	178_V	0.927	1.00
143_T	146_T	0.926	1.00
208_G	211_G	0.924	1.00
79_F	89_V	0.918	1.00
27_V	87_I	0.916	1.00
127_A	159_R	0.914	1.00
35_L	68_F	0.910	1.00
50_A	67_A	0.907	1.00
142_L	200_V	0.907	1.00
5_A	99_F	0.906	1.00
38_L	82_A	0.906	1.00
45_K	70_A	0.905	1.00
125_R	193_D	0.904	1.00
7_R	93_A	0.904	1.00
15_Y	87_I	0.904	1.00
126_A	185_V	0.895	1.00
187_L	190_E	0.893	1.00
38_L	75_T	0.891	1.00
167_T	223_H	0.891	1.00
15_Y	27_V	0.888	1.00
157_L	164_R	0.885	1.00
186_Q	215_A	0.884	1.00
52_A	225_V	0.883	1.00
105_A	225_V	0.883	1.00
94_D	97_P	0.869	1.00
155_A	181_V	0.863	1.00
123_D	127_A	0.861	1.00
108_R	172_G	0.860	1.00
58_G	217_P	0.855	1.00
74_L	77_D	0.854	1.00
156_T	167_T	0.850	0.99
43_G	46_P	0.849	0.99
146_T	175_R	0.844	0.99
72_A	94_D	0.834	0.99
108_R	222_L	0.833	0.99
140_H	143_T	0.829	0.99
192_G	200_V	0.829	0.99
159_R	162_A	0.821	0.99
157_L	185_V	0.814	0.99
43_G	70_A	0.809	0.99
133_L	197_I	0.808	0.99
159_R	164_R	0.802	0.99
183_S	212_V	0.795	0.99
16_H	23_D	0.790	0.99
154_D	167_T	0.788	0.99
144_P	175_R	0.787	0.99
133_L	155_A	0.787	0.99
195_D	199_T	0.786	0.99
124_D	128_G	0.784	0.99
144_P	214_P	0.784	0.99
51_A	66_V	0.783	0.99
70_A	75_T	0.780	0.99
187_L	213_P	0.778	0.99
47_P	68_F	0.775	0.99
67_A	100_H	0.773	0.99
38_L	78_A	0.766	0.99
194_T	197_I	0.765	0.99
36_R	43_G	0.761	0.99
34_A	82_A	0.758	0.99
114_W	182_V	0.757	0.99
199_T	210_D	0.753	0.99
158_D	165_V	0.749	0.99
62_R	221_V	0.748	0.99
80_T	88_Q	0.745	0.99
35_L	79_F	0.742	0.99
8_V	18_F	0.742	0.99
121_A	186_Q	0.740	0.99
127_A	155_A	0.737	0.99
186_Q	190_E	0.732	0.98
138_D	204_E	0.729	0.98
185_V	189_T	0.729	0.98
141_N	205_P	0.726	0.98
52_A	227_Y	0.720	0.98
160_D	165_V	0.713	0.98
50_A	100_H	0.712	0.98
153_L	170_A	0.702	0.98
184_L	211_G	0.699	0.98
195_D	198_D	0.692	0.98
77_D	81_G	0.691	0.98
126_A	157_L	0.690	0.98
15_Y	30_E	0.682	0.98
32_F	48_G	0.681	0.98
31_L	49_Y	0.679	0.98
152_E	171_G	0.678	0.97
52_A	105_A	0.677	0.97
28_A	49_Y	0.677	0.97
30_E	34_A	0.677	0.97
65_T	227_Y	0.675	0.97
180_R	208_G	0.674	0.97
129_A	185_V	0.664	0.97
76_P	91_A	0.663	0.97
63_A	90_W	0.659	0.97
73_W	77_D	0.657	0.97
157_L	168_V	0.657	0.97
101_A	104_D	0.657	0.97
66_V	89_V	0.657	0.97
126_A	130_L	0.650	0.97
137_H	150_V	0.649	0.97
7_R	90_W	0.648	0.97
200_V	212_V	0.648	0.97
53_G	222_L	0.648	0.97
200_V	211_G	0.647	0.97
132_R	197_I	0.646	0.97
114_W	164_R	0.646	0.97
18_F	49_Y	0.643	0.97
116_A	162_A	0.643	0.97
53_G	225_V	0.643	0.97
112_Y	215_A	0.641	0.96
43_G	75_T	0.640	0.96
132_R	188_V	0.640	0.96
199_T	203_D	0.638	0.96
141_N	210_D	0.638	0.96
197_I	201_L	0.629	0.96
60_S	219_P	0.629	0.96
123_D	157_L	0.627	0.96
196_R	200_V	0.626	0.96
35_L	43_G	0.625	0.96
36_R	44_A	0.624	0.96
133_L	153_L	0.621	0.96
140_H	204_E	0.621	0.96
182_V	215_A	0.619	0.96
105_A	108_R	0.612	0.95
180_R	211_G	0.612	0.95
132_R	193_D	0.612	0.95
199_T	202_G	0.611	0.95
108_R	170_A	0.610	0.95
133_L	201_L	0.609	0.95
114_W	121_A	0.606	0.95
113_Y	223_H	0.606	0.95
141_N	211_G	0.606	0.95
115_Y	163_F	0.606	0.95
43_G	47_P	0.605	0.95
211_G	214_P	0.604	0.95
53_G	101_A	0.602	0.95
34_A	79_F	0.602	0.95
50_A	101_A	0.601	0.95
62_R	113_Y	0.596	0.95
24_V	29_G	0.595	0.95
187_L	212_V	0.594	0.95
4_R	94_D	0.591	0.95
121_A	189_T	0.590	0.94
72_A	76_P	0.588	0.94
193_D	199_T	0.587	0.94
137_H	201_L	0.585	0.94
194_T	198_D	0.582	0.94
188_V	196_R	0.582	0.94
80_T	83_L	0.579	0.94
170_A	180_R	0.579	0.94
143_T	174_C	0.576	0.94
53_G	104_D	0.575	0.94
15_Y	83_L	0.575	0.94
171_G	177_L	0.569	0.93
223_H	226_A	0.563	0.93
35_L	75_T	0.563	0.93
8_V	64_Q	0.563	0.93
14_P	25_S	0.561	0.93
84_P	87_I	0.561	0.93
108_R	176_E	0.560	0.93
125_R	188_V	0.558	0.93
75_T	92_H	0.557	0.93
155_A	197_I	0.552	0.92
128_G	132_R	0.550	0.92
106_V	226_A	0.550	0.92
138_D	150_V	0.544	0.92
143_T	175_R	0.540	0.91
188_V	192_G	0.539	0.91
31_L	35_L	0.536	0.91
38_L	79_F	0.536	0.91
13_R	218_H	0.534	0.91
180_R	212_V	0.533	0.91
150_V	172_G	0.528	0.91
6_F	35_L	0.528	0.91
64_Q	225_V	0.527	0.90
30_E	83_L	0.523	0.90
141_N	180_R	0.518	0.90
36_R	47_P	0.516	0.90
170_A	173_F	0.515	0.89
134_T	137_H	0.515	0.89
21_Q	26_T	0.513	0.89
9_A	117_P	0.512	0.89
151_R	171_G	0.512	0.89
78_A	82_A	0.510	0.89
16_H	25_S	0.509	0.89
100_H	227_Y	0.508	0.89
36_R	45_K	0.505	0.88
115_Y	162_A	0.505	0.88
166_I	185_V	0.503	0.88
77_D	82_A	0.502	0.88
184_L	200_V	0.502	0.88
23_D	29_G	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
4j37A	1	0.9211	100	0.094	Contact Map
1dj0A	2	0.8985	100	0.146	Contact Map
1vs3A	2	0.8346	100	0.147	Contact Map
2v9kA	1	0.797	70.4	0.948	Contact Map
4adxG	1	0.2406	9	0.968	Contact Map
4k0jA	3	0.8045	5.9	0.971	Contact Map
2l0cA	1	0.1278	5.7	0.971	Contact Map
4i4oA	2	0.2143	5.3	0.972	Contact Map
4nk6A	2	0.1654	4.9	0.972	Contact Map
4i4m6	1	0.203	4.6	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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