GREMLIN Database
TRUB - tRNA pseudouridine synthase B
UniProt: P32732 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 309 (276)
Sequences: 3904 (2768)
Seq/√Len: 166.6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
113_E145_M4.0211.00
111_K145_M3.5851.00
78_T85_E3.3891.00
9_H199_I3.2941.00
98_K102_E3.1361.00
8_L19_C2.8651.00
111_K147_T2.8391.00
68_D169_T2.8241.00
66_T169_T2.7821.00
7_L45_V2.6941.00
80_E183_V2.6211.00
127_K131_E2.6111.00
107_S188_K2.6011.00
252_K257_A2.5811.00
41_E83_T2.5201.00
66_T171_T2.5171.00
72_T165_S2.2541.00
23_I32_V2.1551.00
122_V144_R2.1331.00
154_T169_T2.1021.00
97_D100_D2.0821.00
152_A169_T2.0301.00
12_V43_S2.0291.00
104_V185_I2.0271.00
150_D171_T2.0031.00
71_I182_A1.9821.00
72_T196_S1.9741.00
115_I143_K1.9601.00
76_S187_E1.9541.00
246_S249_L1.9531.00
73_L166_F1.9011.00
70_E167_R1.8681.00
23_I48_I1.8441.00
71_I168_F1.7841.00
112_Q146_I1.7691.00
118_M141_R1.7651.00
76_S88_E1.7641.00
68_D167_R1.7621.00
43_S199_I1.7621.00
64_S171_T1.7381.00
182_A195_M1.7301.00
29_T50_V1.7081.00
82_Q194_H1.7071.00
108_L188_K1.6971.00
80_E180_T1.6781.00
70_E165_S1.6731.00
49_C57_V1.6691.00
71_I166_F1.6541.00
105_L151_I1.6471.00
100_D103_K1.6431.00
132_Y137_I1.6241.00
105_L153_L1.5891.00
69_A168_F1.5751.00
170_V181_L1.5721.00
129_L141_R1.5441.00
106_N109_K1.5321.00
186_G193_A1.5301.00
35_T49_C1.5101.00
155_T167_R1.5031.00
102_E153_L1.4891.00
8_L217_L1.4861.00
186_G191_Y1.4821.00
76_S87_V1.4741.00
240_L286_I1.4741.00
186_G192_P1.4701.00
113_E143_K1.4581.00
69_A195_M1.4551.00
75_F89_T1.4431.00
7_L211_C1.4301.00
128_K131_E1.3941.00
66_T202_A1.3861.00
45_V211_C1.3861.00
253_V276_V1.3721.00
9_H43_S1.3721.00
123_K128_K1.3681.00
127_K132_Y1.3521.00
17_H24_R1.3521.00
77_T194_H1.3451.00
171_T202_A1.3451.00
180_T183_V1.3401.00
150_D169_T1.3361.00
105_L168_F1.3321.00
72_T75_F1.3301.00
215_D218_E1.3061.00
12_V41_E1.2941.00
17_H21_M1.2921.00
165_S196_S1.2741.00
22_K218_E1.2721.00
86_T89_T1.2681.00
234_E277_F1.2681.00
213_T216_E1.2671.00
93_N96_I1.2671.00
245_I253_V1.2641.00
118_M129_L1.2491.00
127_K135_A1.2471.00
70_E197_H1.2401.00
104_V107_S1.2341.00
102_E109_K1.2341.00
208_L211_C1.2291.00
76_S192_P1.2231.00
253_V285_A1.2181.00
231_V235_R1.2171.00
5_V49_C1.2171.00
153_L166_F1.2131.00
68_D154_T1.2011.00
218_E222_Q1.1991.00
109_K151_I1.1941.00
278_T282_T1.1921.00
64_S149_E1.1911.00
75_F86_T1.1901.00
57_V61_T1.1841.00
124_V141_R1.1791.00
3_N52_R1.1741.00
41_E195_M1.1601.00
78_T119_Y1.1541.00
275_A283_C1.1541.00
251_K255_N1.1491.00
124_V129_L1.1481.00
276_V287_Y1.1461.00
23_I50_V1.1451.00
170_V178_V1.1411.00
71_I193_A1.1401.00
6_L23_I1.1331.00
22_K25_K1.1311.00
70_E196_S1.1271.00
149_E171_T1.1211.00
252_K255_N1.1111.00
29_T32_V1.0981.00
199_I208_L1.0871.00
225_T228_E1.0831.00
118_M139_V1.0801.00
66_T201_T1.0761.00
27_L50_V1.0690.99
41_E82_Q1.0690.99
108_L184_M1.0630.99
11_P215_D1.0550.99
207_S210_E1.0450.99
104_V188_K1.0430.99
35_T57_V1.0400.99
101_V166_F1.0390.99
202_A207_S1.0290.99
9_H208_L1.0210.99
52_R55_K1.0210.99
78_T83_T1.0170.99
12_V197_H1.0130.99
147_T173_S1.0100.99
216_E219_A1.0050.99
73_L96_I0.9930.99
151_I168_F0.9850.99
118_M138_E0.9820.99
183_V187_E0.9780.99
15_T18_D0.9750.99
14_M22_K0.9680.99
99_A103_K0.9600.99
75_F194_H0.9580.99
62_E174_K0.9520.99
98_K155_T0.9520.99
119_Y133_A0.9490.99
220_Q229_H0.9360.99
68_D201_T0.9280.99
45_V208_L0.9270.99
206_F235_R0.9230.99
254_E282_T0.9210.98
245_I249_L0.9200.98
113_E142_P0.9120.98
241_P272_D0.9030.98
76_S183_V0.9010.98
63_K204_G0.8990.98
151_I170_V0.8940.98
161_G164_A0.8920.98
72_T164_A0.8900.98
151_I181_L0.8870.98
79_T119_Y0.8800.98
5_V236_A0.8750.98
149_E173_S0.8750.98
109_K150_D0.8740.98
130_Y133_A0.8730.98
32_V48_I0.8730.98
124_V142_P0.8650.98
250_A278_T0.8640.98
169_T201_T0.8640.98
5_V56_I0.8570.98
117_P180_T0.8550.98
249_L252_K0.8530.98
14_M19_C0.8510.97
242_K277_F0.8500.97
118_M133_A0.8490.97
9_H213_T0.8490.97
99_A102_E0.8490.97
17_H20_V0.8400.97
103_K106_N0.8280.97
78_T84_G0.8270.97
42_V122_V0.8240.97
69_A151_I0.8190.97
73_L189_L0.8160.97
80_E117_P0.8150.97
212_F217_L0.8120.97
6_L27_L0.8100.97
244_I278_T0.8090.97
221_A226_V0.8030.96
167_R197_H0.8000.96
77_T86_T0.7980.96
232_P235_R0.7950.96
181_L185_I0.7950.96
212_F229_H0.7930.96
90_K192_P0.7910.96
32_V50_V0.7910.96
172_C176_T0.7900.96
108_L181_L0.7870.96
90_K191_Y0.7850.96
12_V83_T0.7820.96
69_A182_A0.7800.96
212_F216_E0.7800.96
20_V32_V0.7790.96
73_L191_Y0.7720.96
132_Y135_A0.7720.96
105_L185_I0.7720.96
27_L217_L0.7710.96
71_I195_M0.7670.95
129_L139_V0.7670.95
23_I217_L0.7660.95
45_V203_S0.7630.95
12_V82_Q0.7620.95
235_R238_N0.7610.95
242_K275_A0.7560.95
141_R180_T0.7560.95
154_T167_R0.7510.95
128_K132_Y0.7510.95
151_I185_I0.7480.95
118_M180_T0.7470.95
220_Q225_T0.7450.95
47_P203_S0.7440.95
18_D22_K0.7440.95
118_M132_Y0.7410.94
55_K58_E0.7390.94
221_A224_G0.7360.94
109_K112_Q0.7350.94
250_A284_L0.7340.94
248_T252_K0.7330.94
63_K203_S0.7330.94
88_E187_E0.7330.94
247_D280_S0.7320.94
90_K187_E0.7320.94
253_V287_Y0.7300.94
78_T87_V0.7300.94
58_E61_T0.7240.94
105_L109_K0.7230.94
148_I181_L0.7230.94
233_I236_A0.7200.94
60_L63_K0.7190.94
22_K26_L0.7180.93
116_P143_K0.7180.93
96_I191_Y0.7160.93
101_V161_G0.7090.93
23_I27_L0.7090.93
79_T84_G0.7030.93
112_Q148_I0.7010.93
234_E275_A0.7010.93
56_I233_I0.6990.93
161_G166_F0.6960.92
237_L240_L0.6950.92
79_T83_T0.6940.92
276_V284_L0.6910.92
50_V230_T0.6900.92
249_L259_L0.6890.92
43_S197_H0.6890.92
245_I250_A0.6880.92
98_K153_L0.6870.92
124_V140_E0.6850.92
7_L210_E0.6810.92
131_E135_A0.6800.91
18_D25_K0.6770.91
26_L218_E0.6770.91
184_M187_E0.6750.91
114_Q184_M0.6740.91
102_E152_A0.6690.91
7_L208_L0.6650.91
25_K28_K0.6650.91
237_L283_C0.6630.90
274_I287_Y0.6620.90
148_I172_C0.6620.90
69_A178_V0.6600.90
7_L43_S0.6590.90
96_I101_V0.6580.90
17_H128_K0.6570.90
251_K254_E0.6560.90
20_V50_V0.6560.90
88_E192_P0.6550.90
129_L132_Y0.6530.90
19_C46_L0.6510.90
119_Y128_K0.6510.90
73_L193_A0.6440.89
248_T251_K0.6420.89
6_L50_V0.6340.88
98_K161_G0.6340.88
92_V191_Y0.6340.88
124_V128_K0.6330.88
77_T87_V0.6280.88
58_E62_E0.6260.88
253_V284_L0.6250.88
243_W249_L0.6230.88
77_T89_T0.6220.87
182_A193_A0.6210.87
250_A279_E0.6200.87
226_V229_H0.6160.87
148_I170_V0.6150.87
250_A254_E0.6140.87
244_I279_E0.6130.87
56_I237_L0.6130.87
76_S191_Y0.6130.87
23_I26_L0.6130.87
70_E166_F0.6130.87
6_L229_H0.6110.87
100_D104_V0.6100.86
26_L217_L0.6080.86
104_V189_L0.6050.86
42_V203_S0.6030.86
202_A205_D0.6020.86
101_V164_A0.6020.86
247_D279_E0.6010.86
56_I236_A0.5980.85
206_F236_A0.5980.85
272_D288_F0.5970.85
210_E231_V0.5970.85
3_N51_G0.5950.85
237_L242_K0.5950.85
109_K152_A0.5930.85
115_I141_R0.5920.85
132_Y139_V0.5900.85
102_E106_N0.5880.84
28_K221_A0.5840.84
19_C214_F0.5840.84
26_L213_T0.5830.84
271_G288_F0.5820.84
128_K139_V0.5820.84
103_K107_S0.5770.83
72_T194_H0.5760.83
166_F185_I0.5740.83
148_I176_T0.5730.83
260_E263_E0.5720.83
141_R183_V0.5710.83
115_I142_P0.5710.83
155_T162_E0.5680.82
278_T284_L0.5680.82
61_T64_S0.5670.82
56_I285_A0.5660.82
277_F283_C0.5650.82
115_I118_M0.5640.82
71_I186_G0.5630.82
83_T194_H0.5620.82
242_K281_G0.5610.82
22_K214_F0.5600.81
249_L257_A0.5600.81
7_L199_I0.5590.81
261_T264_Q0.5590.81
116_P141_R0.5590.81
162_E165_S0.5570.81
137_I141_R0.5560.81
16_S46_L0.5560.81
234_E283_C0.5540.81
21_M25_K0.5530.81
122_V141_R0.5530.81
37_T195_M0.5530.81
40_P130_Y0.5520.80
14_M18_D0.5500.80
29_T55_K0.5500.80
259_L289_P0.5480.80
151_I178_V0.5470.80
11_P14_M0.5460.80
26_L221_A0.5460.80
35_T60_L0.5450.80
80_E186_G0.5440.80
206_F211_C0.5440.80
247_D250_A0.5430.79
288_F291_P0.5420.79
140_E143_K0.5390.79
49_C174_K0.5380.79
244_I281_G0.5370.79
6_L217_L0.5370.79
18_D21_M0.5360.79
27_L48_I0.5350.78
114_Q146_I0.5330.78
117_P133_A0.5330.78
174_K203_S0.5320.78
101_V189_L0.5280.77
244_I277_F0.5280.77
69_A197_H0.5260.77
76_S80_E0.5240.77
183_V186_G0.5240.77
138_E141_R0.5210.77
7_L206_F0.5210.77
142_P146_I0.5200.76
116_P144_R0.5180.76
253_V257_A0.5170.76
17_H57_V0.5170.76
96_I100_D0.5170.76
125_N132_Y0.5160.76
273_R286_I0.5140.76
92_V96_I0.5130.75
146_I176_T0.5120.75
49_C53_A0.5120.75
182_A196_S0.5100.75
11_P214_F0.5090.75
96_I164_A0.5090.75
278_T281_G0.5080.75
176_T181_L0.5080.75
245_I276_V0.5080.75
261_T289_P0.5070.75
259_L287_Y0.5050.74
224_G227_E0.5040.74
8_L20_V0.5020.74
221_A225_T0.5010.74
238_N242_K0.5000.74
14_M214_F0.5000.74
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  
1r3eA 1 0.9417 100 0.106 Contact Map
1sgvA 1 0.8576 100 0.12 Contact Map
1k8wA 1 0.9482 100 0.12 Contact Map
3u28A 1 0.8608 100 0.288 Contact Map
2apoA 1 0.8317 100 0.294 Contact Map
2ausC 1 0.8252 100 0.295 Contact Map
2v9kA 1 0.521 100 0.744 Contact Map
1kskA 1 0.534 99.8 0.81 Contact Map
4lgtA 1 0.5728 99 0.885 Contact Map
3dh3A 1 0.5502 98.7 0.897 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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