GREMLIN Database
TRUD - tRNA pseudouridine synthase D
UniProt: Q57261 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG13109
Length: 349 (328)
Sequences: 1441 (1045)
Seq/√Len: 57.7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
209_E212_K4.6831.00
18_G135_L4.2541.00
49_L110_Q3.9231.00
49_L86_E3.8011.00
76_A126_L3.4851.00
18_G338_I3.3321.00
207_V301_M3.2681.00
145_E149_I3.1471.00
25_E51_N3.0101.00
256_T298_R3.0051.00
58_V109_C2.8901.00
19_L137_E2.8851.00
275_E298_R2.8791.00
47_R113_E2.8651.00
156_V333_V2.8501.00
207_V257_A2.7241.00
32_D323_W2.6471.00
59_A89_L2.6301.00
26_D136_R2.5281.00
74_S90_C2.4521.00
53_C57_F2.4481.00
257_A301_M2.3931.00
205_Q281_A2.3761.00
156_V303_L2.3741.00
52_G82_H2.2411.00
206_I258_A2.2371.00
20_L334_V2.2291.00
59_A73_V2.2251.00
30_V130_A2.2151.00
68_I91_A2.2151.00
132_T321_R2.1931.00
134_V319_E2.1681.00
149_I153_V2.1421.00
178_W181_T2.1021.00
303_L325_P2.0981.00
148_L310_W2.0961.00
309_S321_R2.0741.00
225_L253_L2.0551.00
40_E118_K2.0201.00
313_W319_E2.0061.00
133_L334_V2.0051.00
76_A128_G1.9911.00
225_L236_A1.9851.00
209_E213_K1.9711.00
198_A282_E1.9441.00
310_W318_V1.9261.00
15_Q339_N1.9101.00
90_C117_H1.8841.00
134_V317_T1.8671.00
148_L337_L1.8310.99
47_R88_W1.8200.99
254_M302_L1.8130.99
312_W318_V1.8000.99
307_Q323_W1.7940.99
30_V86_E1.7890.99
273_A277_A1.7870.99
28_V132_T1.7630.99
226_Q256_T1.7610.99
73_V89_L1.7540.99
38_D118_K1.7270.99
149_I152_C1.7270.99
72_E92_R1.7130.99
45_L90_C1.7130.99
48_I89_L1.7110.99
58_V89_L1.6840.99
322_F330_A1.6790.99
270_E273_A1.6740.99
246_R250_D1.6320.99
130_A323_W1.6210.99
314_D317_T1.6130.99
209_E277_A1.6040.99
141_R312_W1.6030.99
47_R86_E1.5930.99
262_S293_K1.5860.98
73_V91_A1.5740.98
172_L175_A1.5740.98
210_R223_D1.5730.98
42_E92_R1.5680.98
303_L328_S1.5650.98
173_Q201_A1.5560.98
305_P308_L1.5550.98
126_L329_F1.5490.98
227_L252_E1.5400.98
272_L276_Q1.5380.98
256_T275_E1.4630.97
45_L117_H1.4410.97
132_T319_E1.4410.97
30_V132_T1.4380.97
77_G80_D1.4280.97
78_Q123_L1.4160.97
48_I58_V1.4050.97
58_V62_L1.3840.96
262_S290_V1.3840.96
311_N319_E1.3610.96
69_H72_E1.3330.96
210_R222_G1.3280.95
325_P328_S1.3160.95
45_L88_W1.3040.95
49_L112_L1.2810.94
20_L135_L1.2610.94
157_P207_V1.2590.94
51_N84_V1.2550.94
257_A275_E1.2510.94
219_V245_Q1.2480.94
76_A125_A1.2420.94
43_H90_C1.2310.93
24_P51_N1.2250.93
57_F61_A1.2150.93
202_L282_E1.2140.93
92_R95_G1.1780.92
43_H120_K1.1720.91
25_E84_V1.1720.91
234_F247_R1.1640.91
308_L333_V1.1620.91
274_F277_A1.1620.91
245_Q249_N1.1470.90
13_K147_R1.1350.90
19_L22_A1.1330.90
77_G163_Q1.1300.90
251_K254_M1.1240.90
213_K274_F1.1150.89
28_V86_E1.1100.89
303_L333_V1.1020.89
255_I302_L1.0990.88
175_A198_A1.0970.88
273_A276_Q1.0960.88
80_D163_Q1.0940.88
221_D238_T1.0910.88
260_P296_A1.0890.88
46_V91_A1.0830.88
145_E310_W1.0820.88
165_F204_N1.0790.88
261_G296_A1.0770.87
32_D130_A1.0740.87
201_A205_Q1.0720.87
230_R252_E1.0680.87
257_A298_R1.0510.86
320_I334_V1.0450.86
134_V313_W1.0360.85
95_G116_R1.0340.85
26_D29_V1.0270.85
244_L248_V1.0260.85
141_R145_E1.0230.85
237_T240_E1.0210.84
227_L232_S1.0040.83
77_G164_R0.9940.83
35_F125_A0.9890.83
21_K83_A0.9880.82
44_I116_R0.9850.82
154_K217_N0.9850.82
65_F104_F0.9830.82
145_E148_L0.9810.82
182_N186_R0.9770.82
205_Q278_A0.9720.81
148_L312_W0.9710.81
80_D331_T0.9590.81
279_V285_L0.9580.80
267_T275_E0.9550.80
33_L126_L0.9510.80
98_M101_L0.9460.80
48_I111_V0.9390.79
44_I101_L0.9380.79
76_A124_G0.9360.79
128_G329_F0.9350.79
246_R249_N0.9350.79
27_F31_E0.9320.79
63_A68_I0.9240.78
205_Q282_E0.9230.78
79_K331_T0.9180.78
133_L154_K0.9170.77
229_G300_A0.9130.77
214_A220_V0.9090.77
65_F101_L0.9040.76
147_R339_N0.9040.76
243_E247_R0.9030.76
227_L244_L0.9000.76
140_N143_D0.8890.75
284_E287_A0.8860.75
137_E316_V0.8850.75
53_C108_G0.8830.75
54_N57_F0.8800.74
179_A288_L0.8790.74
135_L338_I0.8780.74
16_G143_D0.8740.74
48_I59_A0.8730.74
21_K170_S0.8720.74
90_C109_C0.8690.74
181_T197_A0.8690.74
221_D270_E0.8680.73
177_R182_N0.8580.73
148_L308_L0.8570.73
131_F163_Q0.8560.72
290_V293_K0.8530.72
22_A136_R0.8510.72
61_A106_L0.8510.72
142_D153_V0.8450.71
261_G298_R0.8450.71
126_L326_A0.8440.71
136_R159_Y0.8420.71
18_G138_V0.8410.71
146_Q150_D0.8390.71
50_K85_T0.8380.71
78_Q193_F0.8360.71
47_R112_L0.8330.70
24_P52_G0.8320.70
245_Q248_V0.8280.70
208_A336_E0.8280.70
55_T59_A0.8250.70
44_I160_F0.8220.69
26_D31_E0.8220.69
121_L124_G0.8210.69
194_W197_A0.8210.69
79_K129_N0.8200.69
37_P45_L0.8200.69
213_K270_E0.8190.69
79_K131_F0.8170.69
219_V225_L0.8130.69
294_V297_A0.8110.68
170_S175_A0.8110.68
32_D128_G0.8030.68
208_A335_R0.8020.67
145_E312_W0.8020.67
178_W182_N0.7970.67
202_L260_P0.7960.67
30_V47_R0.7950.67
79_K85_T0.7950.67
50_K58_V0.7930.67
111_V114_Y0.7910.66
62_L73_V0.7880.66
161_G210_R0.7840.66
196_S327_G0.7830.66
323_W328_S0.7810.65
283_T287_A0.7770.65
191_R291_R0.7760.65
75_F122_R0.7760.65
150_D154_K0.7710.64
37_P40_E0.7700.64
224_A266_G0.7690.64
151_I333_V0.7690.64
322_F333_V0.7640.64
15_Q18_G0.7640.64
333_V337_L0.7630.64
50_K55_T0.7620.63
232_S252_E0.7590.63
178_W185_V0.7560.63
55_T165_F0.7550.63
238_T245_Q0.7530.63
216_V254_M0.7520.62
277_A280_A0.7500.62
219_V255_I0.7500.62
96_K100_D0.7500.62
53_C81_K0.7480.62
221_D243_E0.7480.62
35_F117_H0.7450.62
50_K79_K0.7420.61
51_N110_Q0.7380.61
44_I65_F0.7380.61
207_V216_V0.7370.61
167_I170_S0.7350.61
181_T188_R0.7300.60
217_N248_V0.7290.60
96_K116_R0.7280.60
262_S295_E0.7260.60
274_F278_A0.7240.60
247_R253_L0.7230.59
218_Q249_N0.7210.59
174_G194_W0.7210.59
80_D164_R0.7200.59
206_I278_A0.7180.59
144_V318_V0.7170.59
216_V255_I0.7170.59
79_K163_Q0.7150.59
183_T194_W0.7140.58
163_Q331_T0.7130.58
44_I96_K0.7110.58
51_N91_A0.7070.58
39_G42_E0.7070.58
199_R296_A0.7060.58
229_G252_E0.6990.57
35_F39_G0.6990.57
121_L333_V0.6990.57
138_V318_V0.6970.57
117_H120_K0.6970.57
79_K330_A0.6940.56
163_Q329_F0.6930.56
56_R78_Q0.6920.56
263_G289_L0.6900.56
52_G81_K0.6890.56
32_D201_A0.6870.56
161_G332_S0.6860.55
124_G210_R0.6860.55
129_N163_Q0.6850.55
38_D337_L0.6830.55
129_N330_A0.6800.55
206_I257_A0.6780.55
76_A191_R0.6750.54
68_I72_E0.6740.54
53_C106_L0.6720.54
80_D129_N0.6710.54
89_L108_G0.6710.54
221_D269_R0.6690.54
78_Q82_H0.6690.54
99_P102_S0.6680.53
170_S174_G0.6670.53
239_E245_Q0.6670.53
267_T296_A0.6670.53
171_N178_W0.6640.53
332_S335_R0.6640.53
200_S204_N0.6620.53
83_A156_V0.6610.53
243_E250_D0.6580.52
260_P279_V0.6580.52
264_E296_A0.6560.52
242_A246_R0.6560.52
59_A75_F0.6550.52
222_G261_G0.6550.52
95_G197_A0.6540.52
157_P203_F0.6530.52
23_N134_V0.6500.51
179_A182_N0.6500.51
28_V110_Q0.6490.51
77_G329_F0.6490.51
224_A298_R0.6490.51
238_T242_A0.6480.51
244_L247_R0.6460.51
243_E246_R0.6460.51
75_F89_L0.6450.51
217_N302_L0.6400.50
219_V248_V0.6400.50
77_G331_T0.6400.50
21_K312_W0.6390.50
131_F330_A0.6390.50
22_A64_K0.6390.50
63_A81_K0.6380.50
144_V337_L0.6380.50
44_I114_Y0.6370.50
263_G296_A0.6360.50
53_C58_V0.6350.50
210_R298_R0.6330.50
159_Y208_A0.6300.49
61_A64_K0.6300.49
196_S199_R0.6300.49
66_L73_V0.6270.49
46_V116_R0.6270.49
143_D147_R0.6270.49
192_S196_S0.6260.49
68_I71_R0.6260.49
162_A320_I0.6240.49
80_D85_T0.6230.49
216_V301_M0.6230.49
37_P117_H0.6230.49
80_D131_F0.6220.48
308_L318_V0.6190.48
130_A321_R0.6190.48
83_A303_L0.6170.48
187_D190_K0.6160.48
174_G177_R0.6160.48
58_V90_C0.6160.48
186_R267_T0.6150.48
228_A254_M0.6130.47
74_S92_R0.6130.47
157_P211_L0.6130.47
148_L152_C0.6120.47
57_F60_D0.6110.47
123_L196_S0.6090.47
215_D255_I0.6090.47
227_L247_R0.6090.47
83_A168_G0.6080.47
144_V147_R0.6070.47
216_V302_L0.6030.46
235_V238_T0.6030.46
287_A290_V0.6030.46
129_N331_T0.6020.46
138_V312_W0.6010.46
77_G131_F0.6000.46
19_L23_N0.5970.46
33_L41_G0.5960.46
260_P267_T0.5940.45
128_G323_W0.5900.45
214_A217_N0.5900.45
220_V223_D0.5870.45
80_D83_A0.5860.44
227_L230_R0.5840.44
15_Q338_I0.5830.44
21_K308_L0.5820.44
329_F332_S0.5820.44
45_L126_L0.5800.44
50_K80_D0.5800.44
28_V180_Q0.5790.44
210_R261_G0.5790.44
260_P263_G0.5790.44
54_N190_K0.5780.44
86_E110_Q0.5780.44
183_T187_D0.5760.43
118_K189_N0.5740.43
161_G336_E0.5740.43
48_I332_S0.5730.43
193_F235_V0.5730.43
161_G335_R0.5710.43
239_E242_A0.5710.43
88_W113_E0.5690.43
247_R252_E0.5680.43
50_K131_F0.5680.43
267_T298_R0.5670.42
306_Q323_W0.5670.42
211_L301_M0.5670.42
223_D256_T0.5670.42
159_Y215_D0.5640.42
207_V255_I0.5640.42
197_A212_K0.5620.42
264_E267_T0.5620.42
54_N303_L0.5620.42
167_I173_Q0.5600.42
130_A309_S0.5590.42
124_G155_G0.5580.41
67_K72_E0.5570.41
132_T202_L0.5570.41
51_N134_V0.5570.41
142_D146_Q0.5560.41
67_K193_F0.5550.41
162_A332_S0.5540.41
93_V99_P0.5530.41
41_G55_T0.5520.41
95_G99_P0.5510.41
238_T244_L0.5510.41
320_I333_V0.5510.41
283_T288_L0.5510.41
21_K64_K0.5510.41
243_E253_L0.5500.41
80_D330_A0.5500.41
76_A121_L0.5500.41
61_A109_C0.5480.40
106_L109_C0.5460.40
124_G261_G0.5460.40
23_N321_R0.5440.40
26_D159_Y0.5430.40
224_A244_L0.5430.40
27_F131_F0.5430.40
263_G294_V0.5420.40
152_C211_L0.5410.40
64_K148_L0.5400.40
279_V286_Q0.5370.39
260_P286_Q0.5370.39
81_K200_S0.5350.39
206_I220_V0.5320.39
67_K115_A0.5310.39
95_G185_V0.5300.38
50_K77_G0.5300.38
54_N82_H0.5300.38
195_L292_E0.5290.38
260_P290_V0.5290.38
202_L278_A0.5270.38
285_L290_V0.5270.38
182_N185_V0.5260.38
205_Q209_E0.5260.38
22_A305_P0.5260.38
170_S173_Q0.5260.38
188_R290_V0.5240.38
52_G123_L0.5240.38
23_N315_D0.5230.38
202_L263_G0.5230.38
119_R125_A0.5220.38
80_D87_Q0.5220.38
86_E130_A0.5220.38
287_A291_R0.5220.38
119_R134_V0.5210.38
245_Q251_K0.5190.37
46_V58_V0.5180.37
79_K87_Q0.5170.37
57_F81_K0.5170.37
211_L217_N0.5160.37
206_I271_A0.5150.37
224_A256_T0.5150.37
93_V116_R0.5140.37
138_V144_V0.5140.37
239_E307_Q0.5120.37
153_V221_D0.5120.37
62_L98_M0.5120.37
262_S296_A0.5110.37
79_K164_R0.5080.36
328_S332_S0.5080.36
50_K129_N0.5060.36
42_E247_R0.5060.36
55_T75_F0.5050.36
189_N193_F0.5050.36
33_L88_W0.5040.36
132_T268_Q0.5030.36
36_E40_E0.5030.36
25_E300_A0.5030.36
60_D189_N0.5020.36
56_R60_D0.5010.35
176_Q179_A0.5000.35
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  
1szwA 1 0.9484 100 0.134 Contact Map
1z2zA 1 0.9799 100 0.137 Contact Map
3mgjA 2 0.2464 15.9 0.974 Contact Map
2h80A 1 0.2206 6.5 0.978 Contact Map
4xmmB 1 0.2407 5.6 0.979 Contact Map
2x4iA 2 0.3037 5.5 0.979 Contact Map
2xdhA 1 0.2665 5.4 0.979 Contact Map
4jrbA 1 0.3983 5.2 0.979 Contact Map
2oqkA 1 0.1891 4.8 0.979 Contact Map
3g0tA 2 0.3037 4.6 0.979 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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