GREMLIN Database
TRUA - tRNA pseudouridine synthase A
UniProt: Q9HNP6 Sequences:
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

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_A226_A2.9631.00
140_H149_T2.9371.00
3_R69_D2.8691.00
109_T169_R2.6781.00
132_R198_D2.5141.00
141_N203_D2.2531.00
30_E33_G2.1841.00
16_H24_V2.1511.00
107_A169_R2.1471.00
3_R67_A2.1451.00
20_R32_F2.0701.00
136_T152_E2.0661.00
127_A131_D2.0441.00
25_S30_E2.0431.00
192_G196_R2.0331.00
198_D202_G2.0321.00
109_T167_T2.0181.00
29_G33_G1.9731.00
126_A189_T1.9121.00
113_Y221_V1.9071.00
14_P86_P1.9021.00
111_V223_H1.8731.00
111_V165_V1.8681.00
184_L197_I1.8021.00
111_V167_T1.8011.00
222_L225_V1.7891.00
196_R199_T1.7881.00
76_P92_H1.7731.00
166_I182_V1.7511.00
28_A32_F1.7411.00
128_G194_T1.7321.00
131_D134_T1.7301.00
62_R223_H1.7101.00
168_V181_V1.6871.00
177_L181_V1.6761.00
5_A93_A1.6741.00
155_A166_I1.6671.00
116_A159_R1.6661.00
67_A101_A1.6261.00
6_F66_V1.5741.00
132_R194_T1.5601.00
193_D196_R1.5571.00
18_F66_V1.5521.00
155_A168_V1.5511.00
37_R82_A1.5381.00
154_D169_R1.5261.00
113_Y163_F1.5261.00
119_S190_E1.5261.00
15_Y25_S1.5251.00
15_Y86_P1.5161.00
130_L155_A1.4771.00
36_R46_P1.4751.00
153_L168_V1.4741.00
187_L191_T1.4641.00
109_T226_A1.4481.00
8_V66_V1.4481.00
205_P209_P1.4451.00
25_S86_P1.4361.00
9_A90_W1.4331.00
130_L185_V1.4311.00
20_R29_G1.4301.00
5_A65_T1.4211.00
4_R70_A1.3781.00
122_T125_R1.3451.00
49_Y66_V1.3401.00
113_Y165_V1.3341.00
4_R92_H1.3311.00
158_D167_T1.3241.00
151_R172_G1.3051.00
30_E87_I1.3001.00
184_L212_V1.2971.00
7_R65_T1.2931.00
124_D127_A1.2901.00
133_L181_V1.2881.00
31_L89_V1.2691.00
187_L192_G1.2581.00
18_F51_A1.2441.00
130_L157_L1.2271.00
13_R60_S1.2151.00
127_A157_L1.2151.00
127_A156_T1.2131.00
16_H57_A1.2121.00
176_E180_R1.2031.00
129_A188_V1.2031.00
31_L66_V1.1991.00
20_R48_G1.1951.00
114_W166_I1.1921.00
7_R91_A1.1641.00
106_V228_D1.1601.00
109_T223_H1.1541.00
121_A126_A1.1521.00
10_Y64_Q1.1491.00
143_T149_T1.1461.00
52_A64_Q1.1421.00
205_P210_D1.1371.00
134_T154_D1.1361.00
136_T171_G1.1341.00
169_R226_A1.1291.00
168_V182_V1.1151.00
7_R63_A1.1141.00
123_D159_R1.1141.00
128_G131_D1.0881.00
32_F49_Y1.0841.00
33_G37_R1.0751.00
208_G212_V1.0701.00
71_P74_L1.0681.00
128_G195_D1.0591.00
53_G64_Q1.0551.00
193_D197_I1.0431.00
125_R194_T1.0371.00
123_D164_R1.0281.00
157_L166_I1.0281.00
100_H103_H1.0231.00
125_R128_G1.0221.00
6_F92_H1.0201.00
188_V197_I1.0191.00
109_T224_A1.0191.00
63_A224_A1.0181.00
8_V31_L1.0151.00
6_F68_F1.0121.00
16_H26_T1.0091.00
117_P162_A1.0031.00
72_A92_H1.0011.00
132_R195_D1.0011.00
114_W186_Q1.0011.00
116_A164_R1.0011.00
136_T150_V0.9971.00
129_A189_T0.9961.00
25_S29_G0.9941.00
5_A95_A0.9911.00
200_V203_D0.9891.00
144_P176_E0.9851.00
176_E214_P0.9811.00
95_A98_E0.9801.00
26_T29_G0.9801.00
74_L78_A0.9791.00
141_N204_E0.9761.00
203_D210_D0.9671.00
129_A194_T0.9611.00
180_R214_P0.9381.00
155_A185_V0.9361.00
138_D149_T0.9311.00
168_V178_V0.9271.00
143_T146_T0.9261.00
208_G211_G0.9241.00
79_F89_V0.9181.00
27_V87_I0.9161.00
127_A159_R0.9141.00
35_L68_F0.9101.00
50_A67_A0.9071.00
142_L200_V0.9071.00
5_A99_F0.9061.00
38_L82_A0.9061.00
45_K70_A0.9051.00
125_R193_D0.9041.00
7_R93_A0.9041.00
15_Y87_I0.9041.00
126_A185_V0.8951.00
187_L190_E0.8931.00
38_L75_T0.8911.00
167_T223_H0.8911.00
15_Y27_V0.8881.00
157_L164_R0.8851.00
186_Q215_A0.8841.00
52_A225_V0.8831.00
105_A225_V0.8831.00
94_D97_P0.8691.00
155_A181_V0.8631.00
123_D127_A0.8611.00
108_R172_G0.8601.00
58_G217_P0.8551.00
74_L77_D0.8541.00
156_T167_T0.8500.99
43_G46_P0.8490.99
146_T175_R0.8440.99
72_A94_D0.8340.99
108_R222_L0.8330.99
140_H143_T0.8290.99
192_G200_V0.8290.99
159_R162_A0.8210.99
157_L185_V0.8140.99
43_G70_A0.8090.99
133_L197_I0.8080.99
159_R164_R0.8020.99
183_S212_V0.7950.99
16_H23_D0.7900.99
154_D167_T0.7880.99
144_P175_R0.7870.99
133_L155_A0.7870.99
195_D199_T0.7860.99
124_D128_G0.7840.99
144_P214_P0.7840.99
51_A66_V0.7830.99
70_A75_T0.7800.99
187_L213_P0.7780.99
47_P68_F0.7750.99
67_A100_H0.7730.99
38_L78_A0.7660.99
194_T197_I0.7650.99
36_R43_G0.7610.99
34_A82_A0.7580.99
114_W182_V0.7570.99
199_T210_D0.7530.99
158_D165_V0.7490.99
62_R221_V0.7480.99
80_T88_Q0.7450.99
35_L79_F0.7420.99
8_V18_F0.7420.99
121_A186_Q0.7400.99
127_A155_A0.7370.99
186_Q190_E0.7320.98
138_D204_E0.7290.98
185_V189_T0.7290.98
141_N205_P0.7260.98
52_A227_Y0.7200.98
160_D165_V0.7130.98
50_A100_H0.7120.98
153_L170_A0.7020.98
184_L211_G0.6990.98
195_D198_D0.6920.98
77_D81_G0.6910.98
126_A157_L0.6900.98
15_Y30_E0.6820.98
32_F48_G0.6810.98
31_L49_Y0.6790.98
152_E171_G0.6780.97
52_A105_A0.6770.97
28_A49_Y0.6770.97
30_E34_A0.6770.97
65_T227_Y0.6750.97
180_R208_G0.6740.97
129_A185_V0.6640.97
76_P91_A0.6630.97
63_A90_W0.6590.97
73_W77_D0.6570.97
157_L168_V0.6570.97
101_A104_D0.6570.97
66_V89_V0.6570.97
126_A130_L0.6500.97
137_H150_V0.6490.97
7_R90_W0.6480.97
200_V212_V0.6480.97
53_G222_L0.6480.97
200_V211_G0.6470.97
132_R197_I0.6460.97
114_W164_R0.6460.97
18_F49_Y0.6430.97
116_A162_A0.6430.97
53_G225_V0.6430.97
112_Y215_A0.6410.96
43_G75_T0.6400.96
132_R188_V0.6400.96
199_T203_D0.6380.96
141_N210_D0.6380.96
197_I201_L0.6290.96
60_S219_P0.6290.96
123_D157_L0.6270.96
196_R200_V0.6260.96
35_L43_G0.6250.96
36_R44_A0.6240.96
133_L153_L0.6210.96
140_H204_E0.6210.96
182_V215_A0.6190.96
105_A108_R0.6120.95
180_R211_G0.6120.95
132_R193_D0.6120.95
199_T202_G0.6110.95
108_R170_A0.6100.95
133_L201_L0.6090.95
114_W121_A0.6060.95
113_Y223_H0.6060.95
141_N211_G0.6060.95
115_Y163_F0.6060.95
43_G47_P0.6050.95
211_G214_P0.6040.95
53_G101_A0.6020.95
34_A79_F0.6020.95
50_A101_A0.6010.95
62_R113_Y0.5960.95
24_V29_G0.5950.95
187_L212_V0.5940.95
4_R94_D0.5910.95
121_A189_T0.5900.94
72_A76_P0.5880.94
193_D199_T0.5870.94
137_H201_L0.5850.94
194_T198_D0.5820.94
188_V196_R0.5820.94
80_T83_L0.5790.94
170_A180_R0.5790.94
143_T174_C0.5760.94
53_G104_D0.5750.94
15_Y83_L0.5750.94
171_G177_L0.5690.93
223_H226_A0.5630.93
35_L75_T0.5630.93
8_V64_Q0.5630.93
14_P25_S0.5610.93
84_P87_I0.5610.93
108_R176_E0.5600.93
125_R188_V0.5580.93
75_T92_H0.5570.93
155_A197_I0.5520.92
128_G132_R0.5500.92
106_V226_A0.5500.92
138_D150_V0.5440.92
143_T175_R0.5400.91
188_V192_G0.5390.91
31_L35_L0.5360.91
38_L79_F0.5360.91
13_R218_H0.5340.91
180_R212_V0.5330.91
150_V172_G0.5280.91
6_F35_L0.5280.91
64_Q225_V0.5270.90
30_E83_L0.5230.90
141_N180_R0.5180.90
36_R47_P0.5160.90
170_A173_F0.5150.89
134_T137_H0.5150.89
21_Q26_T0.5130.89
9_A117_P0.5120.89
151_R171_G0.5120.89
78_A82_A0.5100.89
16_H25_S0.5090.89
100_H227_Y0.5080.89
36_R45_K0.5050.88
115_Y162_A0.5050.88
166_I185_V0.5030.88
77_D82_A0.5020.88
184_L200_V0.5020.88
23_D29_G0.5000.88
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

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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