GREMLIN Database
TRUD - Probable tRNA pseudouridine synthase D
UniProt: Q980V2 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 377 (338)
Sequences: 789 (592)
Seq/√Len: 32.2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
188_D191_K6.7951.00
274_L335_A5.4291.00
276_R279_D4.4861.00
183_Y188_D4.4151.00
265_Y312_E4.1731.00
70_A117_F3.9381.00
277_K287_K3.7051.00
213_K217_E3.6671.00
60_L98_V3.3831.00
57_V99_Y3.3471.00
246_S249_L3.2961.00
272_L311_D3.2351.00
178_H268_Y2.9911.00
219_D222_E2.9871.00
60_L70_A2.8661.00
337_M356_E2.8111.00
71_I82_V2.7021.00
83_N99_Y2.6041.00
99_Y125_S2.5571.00
180_I192_A2.4580.99
190_E247_Y2.4510.99
59_L97_L2.3710.99
57_V97_L2.3650.99
277_K286_D2.3150.99
214_L226_S2.2790.99
353_F361_A2.2750.99
290_L305_C2.1380.99
152_I368_I2.1190.98
85_I131_H2.1120.98
240_N249_L2.1060.98
162_P274_L2.1030.98
70_A74_V2.0940.98
182_K312_E2.0780.98
82_V98_V2.0520.98
291_L330_D2.0410.98
222_E225_R2.0320.98
57_V125_S2.0150.98
35_V38_E1.9750.97
297_Y305_C1.9610.97
86_G89_D1.9400.97
223_A238_L1.9330.97
149_I153_E1.9260.97
65_I69_S1.9240.97
151_R370_R1.9150.97
182_K186_R1.8910.97
211_I215_I1.8690.96
33_F37_E1.8610.96
56_A124_F1.8440.96
343_K352_S1.8310.96
276_R280_E1.8260.96
166_G367_E1.8150.96
214_L222_E1.8100.96
183_Y191_K1.8070.96
181_G367_E1.7980.96
305_C332_V1.7920.95
32_G35_V1.7900.95
341_D354_V1.7710.95
140_L369_L1.7280.94
60_L71_I1.7100.94
82_V100_I1.7010.94
315_E318_F1.7000.94
303_D307_E1.6980.94
153_E157_K1.6770.94
183_Y195_L1.6540.93
170_F360_Y1.6390.93
353_F364_L1.6110.92
182_K265_Y1.6090.92
32_G37_E1.5910.92
240_N246_S1.5830.91
204_E212_R1.5650.91
70_A98_V1.5620.91
241_Y247_Y1.5610.91
31_N34_K1.5590.91
135_I354_V1.5480.90
297_Y332_V1.5400.90
137_E352_S1.5330.90
71_I98_V1.5330.90
221_K242_M1.5240.90
138_I192_A1.4990.89
170_F271_N1.4980.89
156_K336_F1.4930.89
276_R307_E1.4690.88
155_I364_L1.4600.88
330_D367_E1.4530.87
166_G181_G1.4510.87
337_M359_M1.4190.86
31_N37_E1.4100.86
177_T181_G1.3850.85
64_G91_N1.3820.85
32_G38_E1.3770.84
269_L312_E1.3690.84
59_L120_K1.3500.83
309_Y319_F1.3440.83
166_G366_R1.3300.82
288_V332_V1.3010.81
161_L337_M1.2970.80
32_G36_I1.2940.80
64_G90_A1.2800.80
89_D96_Q1.2770.79
62_K70_A1.2710.79
161_L364_L1.2600.78
54_K101_P1.2500.78
277_K332_V1.2370.77
60_L119_L1.2360.77
356_E359_M1.2260.77
122_L129_L1.2200.76
227_I238_L1.2140.76
190_E194_Y1.2050.75
141_S164_F1.1970.75
127_K130_N1.1950.75
303_D306_K1.1820.74
233_Q254_S1.1820.74
119_L122_L1.1750.73
281_Y284_L1.1690.73
145_F346_E1.1680.73
178_H264_A1.1680.73
167_Y363_I1.1640.73
209_I351_I1.1580.72
211_I227_I1.1500.72
321_L324_F1.1420.71
162_P278_L1.1360.71
59_L121_F1.1240.70
67_H71_I1.1230.70
280_E300_N1.1190.70
181_G330_D1.1130.69
31_N63_W1.1040.69
176_I212_R1.0990.68
86_G168_Q1.0840.67
89_D168_Q1.0830.67
196_I233_Q1.0810.67
165_I248_Y1.0760.67
180_I213_K1.0740.66
178_H181_G1.0680.66
87_I260_L1.0650.66
67_H170_F1.0570.65
61_T118_I1.0550.65
196_I237_L1.0450.64
226_S235_K1.0390.64
73_E114_S1.0290.63
168_Q360_Y1.0260.63
290_L296_I1.0220.63
204_E208_T1.0180.62
86_G96_Q1.0150.62
86_G360_Y1.0110.62
153_E156_K1.0060.61
206_K210_D0.9960.60
290_L297_Y0.9890.60
138_I345_N0.9870.60
136_F168_Q0.9850.60
184_L192_A0.9830.59
74_V82_V0.9820.59
139_S350_T0.9790.59
254_S305_C0.9770.59
228_P231_F0.9610.58
238_L255_F0.9530.57
166_G177_T0.9420.56
193_F251_L0.9390.56
239_K243_R0.9370.56
260_L315_E0.9360.56
36_I135_I0.9350.56
164_F360_Y0.9330.55
270_F328_L0.9320.55
233_Q261_Y0.9280.55
128_K142_I0.9280.55
263_D277_K0.9230.55
103_N106_Q0.9220.55
86_G169_R0.9210.54
196_I261_Y0.9210.54
236_L254_S0.9150.54
193_F196_I0.9140.54
106_Q124_F0.9100.54
30_P37_E0.9040.53
309_Y315_E0.8990.53
218_G352_S0.8980.53
235_K239_K0.8970.52
172_T175_P0.8960.52
265_Y327_S0.8900.52
181_G366_R0.8900.52
207_E217_E0.8880.52
259_S270_F0.8850.52
106_Q110_E0.8830.51
148_V349_K0.8830.51
145_F209_I0.8810.51
66_D69_S0.8760.51
30_P33_F0.8760.51
99_Y197_L0.8710.50
91_N366_R0.8700.50
148_V155_I0.8640.50
287_K332_V0.8620.50
281_Y344_V0.8620.50
184_L326_I0.8600.49
91_N263_D0.8600.49
33_F38_E0.8570.49
269_L290_L0.8570.49
55_Y128_K0.8570.49
169_R360_Y0.8570.49
33_F39_I0.8480.48
291_L332_V0.8460.48
259_S325_K0.8420.48
178_H330_D0.8410.48
214_L217_E0.8380.48
148_V281_Y0.8370.48
186_R313_G0.8370.48
88_K94_T0.8370.48
228_P234_E0.8330.47
108_L111_K0.8280.47
202_L212_R0.8270.47
223_A227_I0.8240.46
171_G234_E0.8220.46
131_H336_F0.8200.46
209_I213_K0.8160.46
58_F82_V0.8130.46
355_L362_T0.8080.45
177_T360_Y0.8060.45
277_K367_E0.8060.45
214_L219_D0.8040.45
224_V239_K0.8040.45
210_D213_K0.8020.45
224_V291_L0.8020.45
265_Y268_Y0.8010.45
319_F327_S0.8000.45
192_A250_A0.7990.44
294_I336_F0.7980.44
74_V112_Y0.7970.44
57_V123_G0.7920.44
300_N303_D0.7850.43
260_L264_A0.7840.43
292_I320_K0.7840.43
65_I260_L0.7790.43
139_S348_T0.7780.43
213_K245_N0.7780.43
214_L220_F0.7780.43
272_L308_I0.7770.43
141_S339_I0.7770.43
48_K52_K0.7690.42
199_Y208_T0.7640.42
58_F100_I0.7590.41
181_G263_D0.7580.41
368_I372_D0.7570.41
85_I291_L0.7570.41
84_Y262_L0.7570.41
233_Q258_I0.7550.41
31_N35_V0.7540.41
166_G277_K0.7500.41
56_A165_I0.7500.41
160_Y339_I0.7490.40
208_T331_L0.7480.40
228_P235_K0.7480.40
198_T212_R0.7470.40
290_L294_I0.7470.40
193_F262_L0.7460.40
147_I365_L0.7440.40
107_E372_D0.7430.40
214_L223_A0.7420.40
149_I345_N0.7420.40
87_I330_D0.7400.40
257_P273_Y0.7400.40
320_K327_S0.7400.40
59_L123_G0.7390.40
183_Y186_R0.7360.39
266_Q362_T0.7350.39
176_I270_F0.7350.39
65_I87_I0.7340.39
88_K134_N0.7320.39
129_L364_L0.7280.39
63_W93_I0.7260.39
161_L363_I0.7250.39
58_F162_P0.7250.39
184_L189_W0.7240.38
181_G332_V0.7230.38
277_K330_D0.7210.38
192_A251_L0.7210.38
73_E76_K0.7200.38
181_G277_K0.7190.38
189_W248_Y0.7170.38
273_Y304_V0.7170.38
270_F312_E0.7140.38
89_D362_T0.7110.37
41_F45_Q0.7110.37
98_V116_S0.7110.37
160_Y349_K0.7100.37
77_V303_D0.7100.37
208_T212_R0.7100.37
66_D87_I0.7100.37
167_Y172_T0.7100.37
316_R321_L0.7070.37
66_D167_Y0.7050.37
104_E107_E0.7030.37
281_Y354_V0.7030.37
299_N304_V0.7010.37
92_A337_M0.7010.37
171_G261_Y0.7010.37
210_D226_S0.7000.37
65_I196_I0.6990.37
292_I327_S0.6990.37
34_K38_E0.6980.36
165_I329_R0.6980.36
234_E261_Y0.6980.36
269_L358_G0.6960.36
71_I84_Y0.6950.36
34_K37_E0.6940.36
108_L114_S0.6930.36
68_F87_I0.6880.36
191_K195_L0.6880.36
66_D181_G0.6880.36
224_V295_P0.6870.36
112_Y122_L0.6840.35
150_E303_D0.6840.35
61_T120_K0.6820.35
99_Y129_L0.6790.35
205_S208_T0.6780.35
304_V307_E0.6770.35
270_F274_L0.6740.35
306_K310_L0.6710.34
266_Q275_S0.6710.34
141_S349_K0.6710.34
55_Y264_A0.6710.34
36_I149_I0.6710.34
177_T234_E0.6680.34
222_E346_E0.6660.34
240_N253_S0.6640.34
255_F291_L0.6610.34
111_K345_N0.6610.34
266_Q330_D0.6600.34
62_K68_F0.6590.34
135_I308_I0.6590.34
139_S262_L0.6580.33
92_A224_V0.6550.33
56_A106_Q0.6540.33
165_I262_L0.6540.33
292_I329_R0.6520.33
259_S265_Y0.6520.33
138_I365_L0.6510.33
166_G348_T0.6510.33
135_I352_S0.6490.33
165_I207_E0.6490.33
134_N168_Q0.6490.33
60_L117_F0.6490.33
211_I223_A0.6480.33
162_P270_F0.6470.33
166_G330_D0.6460.33
175_P179_L0.6450.33
76_K119_L0.6450.33
55_Y152_I0.6440.32
152_I239_K0.6430.32
88_K136_F0.6400.32
165_I359_M0.6400.32
220_F238_L0.6400.32
92_A174_R0.6400.32
180_I191_K0.6390.32
224_V235_K0.6390.32
259_S361_A0.6370.32
194_Y215_I0.6350.32
133_G366_R0.6340.32
304_V308_I0.6330.32
58_F70_A0.6330.32
285_N298_F0.6310.32
335_A369_L0.6300.31
69_S73_E0.6290.31
91_N277_K0.6280.31
215_I218_G0.6240.31
184_L268_Y0.6240.31
343_K346_E0.6230.31
55_Y148_V0.6230.31
286_D297_Y0.6220.31
167_Y274_L0.6220.31
203_S219_D0.6210.31
137_E350_T0.6170.31
208_T211_I0.6160.30
260_L268_Y0.6160.30
148_V151_R0.6110.30
237_L245_N0.6100.30
263_D271_N0.6090.30
167_Y312_E0.6090.30
245_N255_F0.6080.30
128_K218_G0.6040.30
131_H330_D0.6030.30
83_N101_P0.6030.30
92_A99_Y0.6020.29
187_R249_L0.6010.29
224_V228_P0.5940.29
147_I207_E0.5940.29
307_E311_D0.5920.29
88_K96_Q0.5920.29
291_L370_R0.5910.29
146_D303_D0.5900.29
302_D306_K0.5880.29
87_I257_P0.5860.28
87_I256_I0.5850.28
183_Y254_S0.5840.28
87_I91_N0.5830.28
175_P180_I0.5830.28
277_K291_L0.5830.28
142_I372_D0.5810.28
184_L283_N0.5800.28
87_I266_Q0.5790.28
155_I326_I0.5770.28
168_Q171_G0.5750.28
89_D92_A0.5730.28
152_I351_I0.5710.27
119_L243_R0.5710.27
342_L364_L0.5710.27
255_F258_I0.5710.27
128_K338_N0.5710.27
156_K184_L0.5700.27
31_N45_Q0.5700.27
160_Y282_K0.5690.27
163_A359_M0.5690.27
133_G166_G0.5690.27
102_L187_R0.5690.27
151_R332_V0.5670.27
48_K53_G0.5660.27
109_I372_D0.5660.27
353_F368_I0.5650.27
256_I261_Y0.5640.27
57_V65_I0.5630.27
58_F120_K0.5630.27
104_E253_S0.5620.27
184_L307_E0.5610.27
89_D169_R0.5600.27
75_Q127_K0.5600.27
43_P47_W0.5600.27
120_K123_G0.5580.27
85_I129_L0.5580.27
178_H291_L0.5580.27
66_D72_S0.5570.27
210_D214_L0.5540.26
110_E143_S0.5540.26
77_V190_E0.5530.26
66_D177_T0.5530.26
67_H82_V0.5530.26
55_Y99_Y0.5530.26
192_A368_I0.5520.26
228_P330_D0.5520.26
93_I314_I0.5510.26
273_Y284_L0.5510.26
90_A263_D0.5500.26
106_Q112_Y0.5490.26
109_I336_F0.5490.26
286_D367_E0.5480.26
74_V279_D0.5470.26
82_V357_R0.5450.26
71_I344_V0.5450.26
93_I276_R0.5440.26
147_I310_L0.5440.26
190_E227_I0.5430.26
75_Q79_H0.5430.26
215_I220_F0.5420.26
200_P258_I0.5420.26
141_S163_A0.5400.25
58_F166_G0.5400.25
90_A221_K0.5400.25
355_L360_Y0.5400.25
275_S366_R0.5390.25
88_K362_T0.5380.25
86_G136_F0.5360.25
293_R300_N0.5350.25
98_V300_N0.5350.25
87_I95_S0.5330.25
47_W53_G0.5330.25
88_K168_Q0.5320.25
77_V81_K0.5320.25
265_Y361_A0.5290.25
185_L365_L0.5280.25
277_K281_Y0.5280.25
171_G264_A0.5280.25
227_I308_I0.5270.25
62_K86_G0.5270.25
90_A173_R0.5270.25
85_I330_D0.5260.25
139_S260_L0.5240.24
234_E291_L0.5230.24
184_L288_V0.5230.24
171_G180_I0.5220.24
302_D332_V0.5220.24
167_Y181_G0.5190.24
267_S271_N0.5180.24
87_I263_D0.5180.24
58_F64_G0.5170.24
89_D94_T0.5170.24
55_Y118_I0.5170.24
176_I189_W0.5170.24
152_I342_L0.5170.24
87_I187_R0.5160.24
265_Y270_F0.5160.24
285_N345_N0.5150.24
254_S265_Y0.5150.24
39_I97_L0.5150.24
148_V344_V0.5140.24
316_R319_F0.5140.24
117_F212_R0.5140.24
31_N36_I0.5130.24
240_N244_F0.5120.24
329_R358_G0.5120.24
355_L361_A0.5110.24
330_D362_T0.5110.24
139_S207_E0.5100.24
93_I115_R0.5080.23
150_E154_Q0.5050.23
270_F330_D0.5040.23
77_V162_P0.5040.23
87_I131_H0.5030.23
73_E223_A0.5030.23
154_Q180_I0.5020.23
93_I187_R0.5020.23
57_V162_P0.5010.23
367_E370_R0.5000.23
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 0.9708 100 0.191 Contact Map
1szwA 1 0.748 100 0.388 Contact Map
3mkqB 1 0.4615 20.6 0.975 Contact Map
2hr2A 4 0.366 18.9 0.975 Contact Map
3iegA 1 0.5332 15.1 0.976 Contact Map
2vsyA 1 0.4138 14.4 0.976 Contact Map
4bzjA 2 0.8249 12.2 0.977 Contact Map
2mc5A 1 0.1857 11.1 0.978 Contact Map
4ui9J 2 0.4881 10.1 0.978 Contact Map
2katA 1 0.2785 9.8 0.978 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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