GREMLIN Database
TRUD - Probable tRNA pseudouridine synthase D
UniProt: Q9HSG5 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 434 (405)
Sequences: 695 (522)
Seq/√Len: 25.9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
197_D200_A6.6111.00
285_V394_I5.8351.00
287_E290_A4.3411.00
276_A372_L4.0611.00
40_E44_T4.0141.00
192_A197_D3.8931.00
39_L412_A3.2351.00
187_H279_Y3.1651.00
58_V103_A3.0891.00
333_V337_H2.9731.00
71_F118_A2.9571.00
346_T391_R2.9391.00
61_A102_F2.8811.00
22_G428_K2.8001.00
61_A71_F2.6830.99
103_A126_A2.6590.99
25_G144_V2.5700.99
223_Y232_G2.5640.99
72_A86_V2.5470.99
396_L414_P2.5470.99
351_G389_G2.4510.99
87_R103_A2.4410.99
287_E291_R2.4400.99
256_S259_D2.3840.98
283_R371_D2.3790.98
232_G235_A2.3750.98
189_V201_A2.3300.98
199_E257_F2.2880.98
233_A248_L2.2700.98
222_E226_E2.1970.97
363_E367_G2.1770.97
60_R101_L2.1560.97
229_D232_G2.1280.97
90_G93_D2.0900.96
411_F419_A2.0580.96
58_V126_A2.0360.96
86_V102_F2.0040.95
331_V338_C1.9860.95
288_R301_G1.9760.95
333_V338_C1.9430.95
285_V347_A1.9420.95
15_Y290_A1.9330.94
369_L379_F1.9130.94
333_V336_R1.8930.94
399_D412_A1.8890.94
145_R173_Y1.8510.93
191_L195_R1.8260.93
237_F248_L1.8250.93
86_V104_V1.8230.93
33_D36_V1.8100.92
139_A412_A1.8000.92
251_L257_F1.8000.92
288_R302_D1.7890.92
61_A72_A1.7780.92
72_A102_F1.7640.91
132_F274_H1.7620.91
58_V101_L1.7510.91
90_G177_Q1.7320.90
171_P285_V1.7310.90
280_V350_V1.7210.90
334_M338_C1.7170.90
157_A161_A1.7140.90
65_E95_H1.6790.89
187_H275_A1.6710.89
250_E256_S1.6650.89
250_E259_D1.6620.88
192_A204_A1.6500.88
89_A135_L1.6460.88
223_Y236_E1.6430.88
123_V130_L1.6190.87
311_A314_A1.6170.87
91_T132_F1.6160.87
332_D338_C1.6140.87
179_F282_N1.5890.86
33_D38_E1.5790.86
213_E221_R1.5740.86
331_V335_A1.5600.85
305_W346_T1.5490.85
179_F418_Y1.5480.85
34_F38_E1.5430.84
269_Q281_F1.5390.84
223_Y227_T1.5330.84
55_P105_R1.5250.84
328_D332_D1.5200.83
177_Q418_Y1.5020.83
92_K140_F1.4930.82
71_F102_F1.4920.82
140_F177_Q1.4910.82
163_F422_V1.4880.82
65_E94_R1.4620.81
190_G351_G1.4570.81
350_V365_T1.4540.81
91_T271_L1.4350.80
93_D177_Q1.4300.79
90_G178_R1.4280.79
161_A167_T1.4270.79
375_S378_D1.4240.79
329_S332_D1.4210.79
35_R99_T1.4180.79
347_A359_G1.3960.78
63_L71_F1.3920.78
92_K138_N1.3800.77
92_K98_T1.3760.77
89_A133_G1.3660.76
396_L417_S1.3640.76
236_E245_R1.3620.76
411_F422_V1.3610.76
120_I123_V1.3580.76
90_G418_Y1.3490.75
280_V372_L1.3460.75
60_R122_V1.3430.75
298_P338_C1.3400.75
32_A64_H1.3390.75
26_R29_D1.3320.74
335_A338_C1.3270.74
265_P268_L1.3120.73
145_R398_P1.3110.73
37_R141_E1.3060.73
32_A281_F1.3060.73
283_R368_V1.2980.72
33_D145_R1.2950.72
365_T391_R1.2900.72
175_G190_G1.2880.72
363_E366_R1.2850.72
22_G25_G1.2740.71
331_V337_H1.2710.71
92_K420_T1.2630.70
159_E428_K1.2600.70
25_G427_L1.2450.69
303_V391_R1.2150.67
144_V427_L1.2140.67
161_A166_G1.2140.67
303_V346_T1.2110.67
57_L125_R1.2070.67
357_A391_R1.2020.66
86_V415_S1.2020.66
246_T264_F1.1960.66
138_N177_Q1.1930.66
31_P65_E1.1880.65
96_A183_R1.1870.65
93_D98_T1.1840.65
31_P64_H1.1820.65
336_R339_E1.1790.65
223_Y233_A1.1720.64
205_Y247_M1.1690.64
175_G425_E1.1660.64
357_A365_T1.1610.64
271_L279_Y1.1610.64
244_E272_F1.1560.63
56_W129_G1.1510.63
248_L265_P1.1480.63
27_L144_V1.1440.62
27_L96_A1.1430.62
109_A113_P1.1430.62
16_Y429_P1.1350.62
328_D335_A1.1340.62
74_E78_T1.1270.61
92_K100_Q1.1250.61
66_W70_D1.1240.61
16_Y428_K1.1240.61
280_V368_V1.1150.60
192_A200_A1.1110.60
60_R121_E1.1110.60
130_L133_G1.1070.60
231_T252_A1.1040.60
191_L276_A1.1000.59
332_D336_R1.0970.59
142_I201_A1.0960.59
178_R418_Y1.0920.59
191_L372_L1.0890.59
334_M339_E1.0850.58
350_V354_T1.0820.58
293_L299_V1.0700.57
93_D420_T1.0660.57
143_V408_A1.0660.57
213_E217_S1.0590.56
367_G371_D1.0580.56
347_A365_T1.0530.56
170_T396_L1.0530.56
93_D178_R1.0520.56
68_T72_A1.0410.55
21_D428_K1.0400.55
308_D403_S1.0400.55
224_V228_R1.0390.55
90_G140_F1.0310.54
244_E389_G1.0230.54
298_P333_V1.0160.53
14_A283_R1.0150.53
219_R236_E1.0120.53
133_G137_G1.0110.53
171_P289_M1.0110.53
50_P53_D1.0090.53
142_I247_M1.0090.53
299_V410_E1.0080.53
334_M337_H1.0070.53
141_E410_E1.0060.53
28_R362_G1.0050.52
389_G420_T1.0050.52
220_A224_V1.0040.52
220_A237_F1.0010.52
331_V339_E0.9970.52
13_M421_V0.9920.51
346_T357_A0.9870.51
394_I427_L0.9860.51
28_R38_E0.9810.51
190_G389_G0.9800.51
56_W160_L0.9750.50
92_K419_A0.9750.50
369_L375_S0.9740.50
65_E132_F0.9740.50
49_A54_Y0.9730.50
181_S184_P0.9720.50
23_T159_E0.9720.50
303_V356_F0.9700.50
77_N120_I0.9670.50
27_L113_P0.9660.50
288_R304_V0.9590.49
192_A209_P0.9570.49
187_H271_L0.9550.49
352_T386_D0.9550.49
68_T179_F0.9510.48
63_L98_T0.9450.48
293_L412_A0.9450.48
238_P241_L0.9360.47
199_E203_M0.9350.47
117_N242_R0.9300.47
328_D334_M0.9300.47
234_L249_H0.9270.47
138_N419_A0.9230.46
401_T410_E0.9230.46
22_G427_L0.9180.46
269_Q276_A0.9180.46
92_K177_Q0.9170.46
210_T213_E0.9150.46
294_P298_P0.9140.46
193_I385_F0.9130.46
218_Q222_E0.9120.46
314_A399_D0.9100.45
186_T418_Y0.9060.45
243_Y272_F0.9040.45
243_Y268_L0.9040.45
332_D337_H0.9000.45
133_G190_G0.8970.44
201_A261_V0.8940.44
93_D138_N0.8930.44
115_I123_V0.8890.44
160_L426_F0.8850.44
313_A316_A0.8840.44
345_V395_L0.8830.43
176_Q421_V0.8790.43
37_R139_A0.8780.43
227_T230_W0.8780.43
264_F365_T0.8760.43
209_P222_E0.8750.43
238_P244_E0.8740.43
28_R33_D0.8740.43
205_Y297_E0.8730.43
133_G175_G0.8730.43
138_N420_T0.8720.43
140_F419_A0.8710.43
247_M349_L0.8640.42
202_A363_E0.8620.42
156_V159_E0.8610.42
57_L174_F0.8540.41
332_D339_E0.8520.41
95_H132_F0.8490.41
71_F75_L0.8460.41
234_L238_P0.8450.41
83_R96_A0.8420.41
109_A125_R0.8420.41
347_A391_R0.8420.41
376_R381_L0.8390.40
97_V297_E0.8380.40
277_Q389_G0.8340.40
30_S266_S0.8340.40
90_G278_S0.8330.40
103_A220_A0.8330.40
167_T331_V0.8310.40
95_H274_H0.8290.40
112_V394_I0.8250.39
300_A358_D0.8240.39
91_T277_Q0.8230.39
93_D140_F0.8210.39
351_G391_R0.8200.39
161_A409_F0.8200.39
414_P417_S0.8180.39
63_L68_T0.8160.39
63_L92_K0.8110.38
274_H416_G0.8080.38
27_L354_T0.8070.38
280_V353_D0.8060.38
184_P188_E0.8060.38
271_L375_S0.8030.38
310_D315_V0.7980.37
266_S353_D0.7980.37
179_F186_T0.7970.37
279_Y368_V0.7970.37
301_G425_E0.7970.37
298_P335_A0.7970.37
90_G100_Q0.7960.37
413_L425_E0.7950.37
69_N91_T0.7910.37
327_T330_R0.7900.37
331_V334_M0.7900.37
140_F278_S0.7880.37
298_P340_R0.7820.36
139_A410_E0.7780.36
173_Y294_P0.7770.36
20_S159_E0.7750.36
111_Q115_I0.7740.36
352_T380_D0.7720.36
269_Q384_E0.7720.36
180_G420_T0.7720.36
280_V374_L0.7700.35
352_T388_A0.7700.35
222_E403_S0.7690.35
364_I367_G0.7690.35
133_G288_R0.7660.35
245_R249_H0.7650.35
287_E367_G0.7640.35
379_F386_D0.7590.35
185_V198_W0.7570.35
63_L90_G0.7560.35
110_A159_E0.7560.35
94_R278_S0.7560.35
109_A115_I0.7550.34
388_A416_G0.7550.34
223_Y229_D0.7520.34
311_A316_A0.7510.34
251_L261_V0.7500.34
177_Q278_S0.7490.34
286_S424_R0.7480.34
174_F308_D0.7460.34
154_A161_A0.7430.34
331_V336_R0.7420.34
177_Q420_T0.7400.33
378_D415_S0.7390.33
143_V273_V0.7370.33
265_P351_G0.7360.33
193_I279_Y0.7340.33
163_F225_A0.7340.33
62_T121_E0.7330.33
133_G138_N0.7320.33
137_G190_G0.7300.33
328_D336_R0.7290.33
76_A81_M0.7290.33
19_D189_V0.7270.33
56_W114_E0.7270.33
174_F388_A0.7260.33
297_E411_F0.7220.32
163_F285_V0.7210.32
288_R294_P0.7200.32
140_F275_A0.7190.32
284_I299_V0.7190.32
332_D335_A0.7170.32
63_L93_D0.7170.32
264_F385_F0.7150.32
97_V116_R0.7150.32
171_P185_V0.7140.32
23_T398_P0.7140.32
175_G424_R0.7130.32
248_L252_A0.7120.32
39_L139_A0.7110.32
131_E362_G0.7100.32
190_G425_E0.7070.31
234_L299_V0.7060.31
303_V357_A0.7030.31
161_A399_D0.7020.31
77_N80_G0.7020.31
45_Q48_D0.7010.31
57_L120_I0.7000.31
74_E344_F0.7000.31
187_H277_Q0.7000.31
89_A103_A0.7000.31
294_P383_G0.6980.31
29_D35_R0.6980.31
347_A394_I0.6970.31
353_D388_A0.6970.31
140_F420_T0.6960.31
364_I368_V0.6950.31
358_D361_P0.6940.31
111_Q114_E0.6940.31
59_V65_E0.6930.30
328_D338_C0.6910.30
232_G236_E0.6900.30
277_Q420_T0.6900.30
90_G138_N0.6850.30
346_T365_T0.6850.30
243_Y264_F0.6830.30
23_T407_L0.6820.30
329_S333_V0.6820.30
138_N277_Q0.6820.30
34_F140_F0.6810.30
133_G169_G0.6760.29
93_D419_A0.6760.29
130_L422_V0.6720.29
281_F341_G0.6690.29
291_R360_D0.6670.29
79_V288_R0.6660.29
30_S406_P0.6660.29
14_A39_L0.6640.29
315_V325_R0.6640.29
120_I253_D0.6630.29
276_A386_D0.6620.29
192_A264_F0.6610.29
190_G244_E0.6610.29
344_F395_L0.6600.28
209_P227_T0.6600.28
224_V230_W0.6550.28
76_A94_R0.6550.28
186_T244_E0.6540.28
343_A365_T0.6530.28
265_P298_P0.6520.28
75_L362_G0.6520.28
195_R373_G0.6520.28
98_T138_N0.6500.28
187_H389_G0.6490.28
177_Q186_T0.6480.28
335_A339_E0.6470.28
366_R370_D0.6470.28
57_L123_V0.6470.28
352_T384_E0.6460.28
205_Y272_F0.6450.28
206_L269_Q0.6450.28
380_D386_D0.6410.27
33_D173_Y0.6410.27
75_L86_V0.6400.27
132_F135_L0.6360.27
157_A160_L0.6360.27
218_Q409_F0.6340.27
312_D316_A0.6330.27
16_Y22_G0.6330.27
139_A209_P0.6300.27
93_D96_A0.6290.27
98_T278_S0.6280.27
76_A83_R0.6270.27
284_I364_I0.6260.26
231_T339_E0.6250.26
304_V391_R0.6240.26
108_D275_A0.6230.26
223_Y230_W0.6230.26
186_T190_G0.6220.26
175_G274_H0.6220.26
313_A325_R0.6210.26
151_E298_P0.6210.26
143_V166_G0.6200.26
27_L189_V0.6190.26
49_A106_D0.6190.26
43_D121_E0.6180.26
156_V161_A0.6170.26
90_G420_T0.6170.26
238_P389_G0.6160.26
72_A88_W0.6150.26
288_R391_R0.6150.26
90_G98_T0.6140.26
63_L140_F0.6130.26
206_L247_M0.6120.26
171_P189_V0.6110.26
72_A239_Q0.6110.26
175_G288_R0.6110.26
160_L409_F0.6100.26
185_V221_R0.6090.25
218_Q417_S0.6080.25
281_F372_L0.6080.25
142_I251_L0.6080.25
91_T268_L0.6070.25
304_V311_A0.6050.25
172_N348_P0.6030.25
146_D232_G0.6020.25
68_T92_K0.6020.25
343_A397_R0.6020.25
39_L79_V0.6010.25
186_T274_H0.5990.25
203_M224_V0.5990.25
171_P221_R0.5970.25
82_S261_V0.5930.25
347_A357_A0.5920.25
25_G135_L0.5910.24
367_G370_D0.5910.24
142_I423_L0.5900.24
39_L370_D0.5900.24
20_S188_E0.5900.24
307_A312_D0.5890.24
248_L425_E0.5870.24
155_A160_L0.5870.24
61_A86_V0.5860.24
205_Y243_Y0.5860.24
175_G351_G0.5860.24
276_A419_A0.5860.24
92_K278_S0.5850.24
301_G424_R0.5840.24
80_G124_G0.5830.24
198_W411_F0.5830.24
28_R34_F0.5820.24
234_L244_E0.5810.24
66_W125_R0.5790.24
37_R121_E0.5790.24
177_Q274_H0.5780.24
63_L138_N0.5760.24
117_N337_H0.5750.24
30_S35_R0.5730.24
62_T65_E0.5730.24
16_Y380_D0.5730.24
132_F187_H0.5720.23
140_F277_Q0.5710.23
76_A97_V0.5710.23
211_E304_V0.5710.23
93_D418_Y0.5700.23
300_A337_H0.5700.23
76_A128_R0.5700.23
32_A125_R0.5700.23
203_M225_A0.5680.23
195_R255_G0.5670.23
96_A411_F0.5660.23
221_R279_Y0.5650.23
120_I134_D0.5630.23
44_T193_I0.5620.23
354_T395_L0.5610.23
296_G395_L0.5580.23
360_D363_E0.5570.23
63_L177_Q0.5570.23
91_T196_D0.5560.23
297_E339_E0.5550.23
156_V194_L0.5550.23
170_T422_V0.5540.23
392_R413_L0.5540.23
91_T95_H0.5530.22
219_R403_S0.5530.22
11_V30_S0.5510.22
177_Q271_L0.5500.22
29_D281_F0.5500.22
89_A92_K0.5470.22
185_V343_A0.5460.22
25_G238_P0.5450.22
215_A219_R0.5450.22
199_E254_G0.5430.22
133_G274_H0.5430.22
34_F180_G0.5430.22
15_Y173_Y0.5420.22
16_Y162_A0.5420.22
193_I201_A0.5400.22
95_H277_Q0.5400.22
413_L420_T0.5390.22
34_F92_K0.5380.22
109_A122_V0.5380.22
40_E76_A0.5370.22
244_E274_H0.5370.22
27_L423_L0.5360.22
91_T266_S0.5360.22
244_E278_S0.5360.22
34_F138_N0.5350.22
106_D196_D0.5350.22
80_G146_D0.5350.22
27_L225_A0.5350.22
341_G416_G0.5340.22
167_T309_S0.5320.21
244_E277_Q0.5320.21
43_D57_L0.5310.21
162_A300_A0.5300.21
250_E254_G0.5300.21
264_F357_A0.5290.21
75_L115_I0.5280.21
45_Q273_V0.5270.21
219_R223_Y0.5270.21
176_Q372_L0.5270.21
145_R409_F0.5270.21
30_S260_A0.5250.21
326_V334_M0.5240.21
147_P171_P0.5230.21
180_G244_E0.5220.21
117_N255_G0.5220.21
212_H216_D0.5210.21
329_S334_M0.5210.21
198_W372_L0.5200.21
173_Y286_S0.5190.21
72_A139_A0.5190.21
75_L358_D0.5190.21
185_V281_F0.5180.21
23_T28_R0.5180.21
136_A252_A0.5180.21
166_G395_L0.5180.21
35_R141_E0.5170.21
91_T186_T0.5160.21
219_R222_E0.5160.21
356_F365_T0.5160.21
184_P228_R0.5150.21
189_V200_A0.5140.21
202_A205_Y0.5130.20
105_R163_F0.5130.20
261_V265_P0.5130.20
75_L87_R0.5110.20
251_L303_V0.5090.20
47_A50_P0.5080.20
257_F412_A0.5080.20
177_Q419_A0.5080.20
168_V394_I0.5080.20
209_P212_H0.5080.20
86_V105_R0.5070.20
40_E124_G0.5070.20
310_D326_V0.5050.20
359_G364_I0.5050.20
78_T174_F0.5050.20
78_T281_F0.5040.20
190_G424_R0.5040.20
191_L228_R0.5030.20
303_V347_A0.5030.20
301_G357_A0.5010.20
169_G348_P0.5000.20
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  
1z2zA 1 0.9654 100 0.187 Contact Map
1szwA 1 0.7373 100 0.373 Contact Map
2mc5A 1 0.1659 60.2 0.971 Contact Map
1weyA 1 0.2373 16.4 0.979 Contact Map
2hr2A 4 0.2742 11 0.981 Contact Map
4bjqA 2 0.1774 8.8 0.981 Contact Map
2v9vA 1 0.265 7.3 0.982 Contact Map
1nu0A 1 0.1728 6.9 0.982 Contact Map
3ma5A 1 0.2005 6.3 0.983 Contact Map
3fflA 2 0.2281 5.8 0.983 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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