GREMLIN Database
TRUB - Probable tRNA pseudouridine synthase B
UniProt: Q9HPA4 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 301 (241)
Sequences: 3006 (2153)
Seq/√Len: 138.7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
108_Y123_T4.0161.00
106_E123_T3.7321.00
24_D172_R3.4061.00
93_P97_P3.3111.00
23_L34_V3.0611.00
83_V142_R2.8881.00
106_E125_T2.7121.00
81_E142_R2.7051.00
22_N60_C2.6171.00
102_A161_A2.4851.00
239_E244_A2.4491.00
81_E144_R2.4311.00
132_L142_R2.3081.00
27_P58_T2.2961.00
87_E138_Q2.2821.00
92_P95_I2.2681.00
38_I47_A2.2191.00
87_E169_G2.1721.00
99_V158_I2.1451.00
128_D144_R2.1151.00
86_L155_C2.0841.00
130_D142_R2.0311.00
113_K119_R1.9871.00
91_D160_R1.9841.00
117_V122_R1.9791.00
88_L139_V1.9451.00
100_I131_V1.9191.00
86_L141_L1.9061.00
83_V140_L1.8901.00
58_T172_R1.8891.00
95_I98_D1.8731.00
38_I63_V1.8701.00
44_V65_T1.8691.00
110_K121_L1.8441.00
100_I129_L1.8351.00
155_C168_M1.8341.00
103_F161_A1.8121.00
143_I154_L1.8041.00
85_V140_L1.7901.00
159_G166_A1.7821.00
233_A236_A1.7621.00
84_A141_L1.7301.00
86_L139_V1.7241.00
64_L72_A1.7141.00
50_A64_L1.7101.00
85_V138_Q1.6931.00
93_P134_V1.6441.00
79_F144_R1.6411.00
107_I124_R1.6381.00
159_G164_T1.6181.00
23_L190_L1.6021.00
159_G165_N1.6001.00
101_E104_T1.5951.00
133_D140_L1.5901.00
232_I240_V1.5861.00
81_E175_A1.5581.00
188_H191_A1.5391.00
153_K156_H1.5291.00
186_T189_D1.5281.00
97_P131_V1.5161.00
91_D165_N1.4791.00
191_A195_A1.4521.00
32_H39_R1.4331.00
60_C184_L1.4311.00
24_D58_T1.4131.00
22_N184_L1.4091.00
38_I65_T1.4071.00
37_W191_A1.4031.00
144_R175_A1.3951.00
83_V132_L1.3511.00
134_V139_V1.3431.00
100_I141_L1.3401.00
104_T129_L1.3311.00
18_F67_T1.3221.00
138_Q169_G1.3171.00
27_P56_K1.3121.00
212_A215_A1.3081.00
181_D184_L1.3011.00
218_Q222_R1.2921.00
20_V64_L1.2661.00
86_L166_A1.2641.00
85_V169_G1.2591.00
108_Y121_L1.2571.00
37_W40_D1.2551.00
84_A168_M1.2551.00
87_E90_D1.2511.00
97_P104_T1.2501.00
72_A76_L1.2381.00
131_V139_V1.2181.00
128_D142_R1.2031.00
50_A72_A1.1660.99
81_E174_S1.1610.99
85_V170_H1.1580.99
44_V47_A1.1480.99
103_F157_D1.1460.99
67_T70_R1.1380.99
99_V102_A1.1350.99
99_V161_A1.1310.99
127_Y144_R1.1270.99
29_P37_W1.1260.99
56_K168_M1.1100.99
32_H36_A1.1100.99
79_F127_Y1.1060.99
156_H160_R1.1050.99
143_I151_I1.1020.99
221_E270_Y1.0980.99
268_A276_A1.0960.99
179_F222_R1.0800.99
21_V38_I1.0780.99
77_E147_S1.0780.99
239_E242_T1.0620.99
238_H242_T1.0560.99
96_L139_V1.0490.99
104_T128_D1.0490.99
24_D181_D1.0450.99
189_D192_D1.0430.99
180_D183_D1.0270.99
30_S33_Q1.0250.99
172_R181_D1.0230.99
57_V117_V1.0220.99
26_P188_H1.0210.99
94_R98_D1.0170.99
126_V154_L1.0090.98
193_A216_A1.0090.98
125_T146_E1.0050.98
27_P170_H0.9940.98
119_R153_K0.9910.98
175_A180_D0.9770.98
108_Y120_R0.9760.98
127_Y146_E0.9720.98
185_V216_A0.9630.98
93_P133_D0.9610.98
90_D167_H0.9560.98
113_K153_K0.9560.98
21_V42_V0.9560.98
185_V190_L0.9530.98
60_C181_D0.9490.98
129_L141_L0.9470.98
78_G177_T0.9430.98
42_V65_T0.9410.98
47_A65_T0.9330.97
70_R73_P0.9090.97
38_I190_L0.9010.97
145_C149_T0.8940.97
86_L168_M0.8940.97
41_L191_A0.8940.97
194_V213_L0.8890.97
84_A155_C0.8850.96
129_L154_L0.8830.96
232_I236_A0.8790.96
88_L162_L0.8760.96
33_Q37_W0.8670.96
240_V278_C0.8640.96
87_E137_R0.8620.96
47_A63_V0.8590.96
271_T275_T0.8580.96
29_P34_V0.8560.96
97_P130_D0.8550.96
20_V223_A0.8510.96
126_V145_C0.8470.95
84_A129_L0.8470.95
236_A239_E0.8460.95
112_P153_K0.8400.95
132_L140_L0.8250.95
20_V71_I0.8240.95
96_L134_V0.8200.95
140_L170_H0.8160.94
88_L164_T0.8130.94
129_L158_I0.8060.94
83_V174_S0.8050.94
100_I158_I0.8010.94
224_L227_L0.7990.94
240_V269_C0.7980.94
33_Q40_D0.7970.94
32_H35_S0.7900.93
232_I237_A0.7900.93
157_D160_R0.7850.93
131_V134_V0.7820.93
185_V189_D0.7810.93
21_V65_T0.7790.93
219_P222_R0.7790.93
91_D156_H0.7710.93
42_V190_L0.7710.93
104_T107_I0.7690.93
91_D164_T0.7680.93
73_P76_L0.7620.92
228_P265_A0.7620.92
222_R225_T0.7600.92
98_D101_E0.7560.92
274_G278_C0.7510.92
38_I42_V0.7500.92
142_R174_S0.7490.92
24_D186_T0.7470.91
193_A212_A0.7450.91
129_L143_I0.7440.91
35_S47_A0.7440.91
73_P77_E0.7320.91
159_G162_L0.7310.91
85_V139_V0.7300.91
22_N58_T0.7270.90
100_I104_T0.7270.90
62_P176_T0.7240.90
94_R97_P0.7240.90
22_N181_D0.7230.90
235_S239_E0.7210.90
154_L158_I0.7190.90
236_A244_A0.7190.90
271_T277_V0.7190.90
57_V176_T0.7090.89
40_D43_G0.7020.89
139_V158_I0.7010.89
76_L117_V0.7000.89
87_E167_H0.6970.88
29_P187_L0.6970.88
103_F154_L0.6960.88
41_L186_T0.6950.88
135_D140_L0.6940.88
36_A40_D0.6920.88
75_L78_G0.6880.88
119_R156_H0.6870.88
35_S65_T0.6870.88
37_W41_L0.6840.87
88_L166_A0.6830.87
237_A272_A0.6820.87
65_T217_V0.6810.87
58_T170_H0.6790.87
194_V212_A0.6780.87
97_P101_E0.6760.87
267_V270_Y0.6760.87
41_L194_V0.6740.87
220_A223_A0.6740.87
71_I223_A0.6720.87
78_G176_T0.6720.87
71_I224_L0.6710.86
107_I126_V0.6690.86
95_I99_V0.6660.86
247_Y250_G0.6660.86
270_Y278_C0.6570.85
26_P29_P0.6560.85
135_D138_Q0.6550.85
84_A170_H0.6550.85
41_L190_L0.6470.84
183_D218_Q0.6470.84
235_S238_H0.6470.84
96_L162_L0.6460.84
84_A151_I0.6430.84
270_Y276_A0.6430.84
179_F223_A0.6410.84
213_L216_A0.6390.84
252_I255_T0.6330.83
22_N183_D0.6310.83
120_R124_R0.6280.83
229_R268_A0.6280.83
112_P224_L0.6270.83
118_A121_L0.6210.82
91_D167_H0.6210.82
22_N172_R0.6200.82
113_K118_A0.6200.82
134_V137_R0.6200.82
111_P121_L0.6200.82
241_A275_T0.6190.82
175_A178_P0.6170.81
29_P40_D0.6140.81
20_V168_M0.6120.81
64_L147_S0.6120.81
274_G277_V0.6100.81
111_P119_R0.6060.80
231_T271_T0.6050.80
126_V149_T0.6050.80
93_P131_V0.6030.80
21_V190_L0.6030.80
43_G194_V0.6030.80
239_E250_G0.6020.80
38_I41_L0.6020.80
110_K119_R0.6020.80
99_V103_F0.6010.80
126_V143_I0.5990.80
240_V277_V0.5990.80
100_I139_V0.5990.80
229_R274_G0.5970.79
224_L276_A0.5960.79
50_A76_L0.5960.79
86_L167_H0.5960.79
17_S65_T0.5950.79
236_A246_V0.5940.79
271_T274_G0.5920.79
234_D273_G0.5900.79
52_T168_M0.5890.78
155_C159_G0.5880.78
230_L236_A0.5870.78
216_A219_P0.5830.78
60_C176_T0.5830.78
114_K124_R0.5810.78
107_I125_T0.5810.78
21_V216_A0.5800.77
110_K113_K0.5790.77
76_L79_F0.5780.77
264_G269_C0.5750.77
109_Q157_D0.5740.77
267_V273_G0.5720.76
88_L165_N0.5720.76
42_V63_V0.5690.76
147_S168_M0.5690.76
238_H241_A0.5670.76
237_A241_A0.5660.76
41_L187_L0.5620.75
18_F46_K0.5610.75
268_A271_T0.5610.75
32_H44_V0.5600.75
98_D102_A0.5580.75
64_L71_I0.5580.75
156_H159_G0.5570.75
104_T130_D0.5570.75
188_H192_D0.5560.74
18_F66_G0.5550.74
26_P187_L0.5530.74
26_P46_K0.5520.74
124_R146_E0.5520.74
20_V72_A0.5510.74
68_A220_A0.5490.73
44_V66_G0.5480.73
149_T154_L0.5480.73
129_L151_I0.5460.73
234_D237_A0.5390.72
211_D214_R0.5360.72
23_L35_S0.5360.72
234_D238_H0.5350.72
141_L151_I0.5340.71
236_A240_V0.5340.71
221_E268_A0.5340.71
96_L141_L0.5280.71
35_S52_T0.5270.70
32_H47_A0.5260.70
162_L165_N0.5250.70
19_G217_V0.5240.70
265_A268_A0.5230.70
147_S176_T0.5220.70
236_A248_A0.5220.70
40_D191_A0.5210.70
71_I220_A0.5210.70
97_P134_V0.5190.69
99_V162_L0.5190.69
141_L155_C0.5180.69
86_L158_I0.5170.69
186_T190_L0.5150.69
57_V165_N0.5150.69
57_V84_A0.5150.69
36_A39_R0.5140.69
18_F220_A0.5140.69
93_P136_G0.5130.68
185_V193_A0.5120.68
111_P122_R0.5120.68
225_T229_R0.5110.68
119_R154_L0.5100.68
33_Q47_A0.5090.68
237_A271_T0.5080.68
50_A75_L0.5070.68
98_D192_D0.5040.67
124_R149_T0.5030.67
37_W187_L0.5030.67
72_A177_T0.5000.66
26_P186_T0.5000.66
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  
3u28A 1 0.9502 100 0.198 Contact Map
2apoA 1 0.9302 100 0.206 Contact Map
2ausC 1 0.9269 100 0.211 Contact Map
1k8wA 1 0.8904 100 0.213 Contact Map
1r3eA 1 0.8704 100 0.216 Contact Map
1sgvA 1 0.8007 100 0.229 Contact Map
2v9kA 1 0.5714 100 0.717 Contact Map
1kskA 1 0.5781 99.8 0.806 Contact Map
4lgtA 1 0.6213 98.9 0.881 Contact Map
3dh3A 1 0.6047 98.7 0.891 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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