GREMLIN Database
TRM56 - tRNA (cytidine(56)-2'-O)-methyltransferase
UniProt: Q9HRC8 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 192 (169)
Sequences: 208 (134)
Seq/√Len: 10.3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
22_M138_V3.9020.99
53_D57_R2.9420.93
120_V143_V2.8690.92
94_V128_V2.8600.91
131_T140_G2.6440.88
74_I81_V2.5680.86
23_T40_F2.5440.86
12_Y143_V2.5330.85
29_T33_L2.4480.83
89_E94_V2.4270.83
74_I120_V2.3340.80
73_T108_L2.2010.76
7_V149_F2.1840.75
118_G122_E2.1520.74
56_G97_E2.1460.74
77_W165_V1.8740.63
72_A76_D1.8300.61
109_V144_F1.8170.60
80_V107_V1.8150.60
8_A77_W1.7880.59
12_Y120_V1.7580.58
149_F153_E1.7400.57
20_D138_V1.7340.57
80_V105_E1.7250.56
12_Y139_A1.7240.56
164_R175_V1.7190.56
100_T105_E1.7040.55
39_L73_T1.6980.55
74_I110_V1.6900.55
129_G163_R1.6890.55
17_G20_D1.6580.53
77_W81_V1.6510.53
23_T77_W1.6150.51
70_L120_V1.5750.49
47_A50_T1.5630.49
98_I121_Y1.5520.48
50_T58_F1.5450.48
27_G51_V1.5340.47
9_V36_D1.5330.47
39_L91_L1.4660.44
97_E107_V1.4640.44
117_P120_V1.4600.44
7_V175_V1.4550.44
70_L119_D1.4350.43
131_T153_E1.3850.41
22_M44_A1.3420.39
114_E146_D1.3390.39
129_G165_V1.3130.37
75_E169_E1.3050.37
82_V107_V1.2920.37
109_V165_V1.2850.36
36_D149_F1.2820.36
74_I90_Q1.2740.36
129_G132_N1.2680.36
20_D44_A1.2420.34
95_D144_F1.2290.34
7_V148_L1.2260.34
87_Y172_K1.2170.33
12_Y126_W1.2080.33
14_H44_A1.2060.33
52_R165_V1.1930.32
42_D113_G1.1920.32
78_P123_A1.1590.31
46_Q113_G1.1540.31
30_A143_V1.1510.31
124_A130_V1.1390.30
82_V144_F1.1130.29
16_P23_T1.1110.29
89_E129_G1.1110.29
44_A163_R1.1020.29
155_E165_V1.0820.28
93_S109_V1.0750.28
100_T159_E1.0730.28
58_F78_P1.0510.27
40_F77_W1.0500.27
8_A37_R1.0430.27
90_Q93_S1.0350.26
76_D152_R1.0350.26
27_G114_E1.0270.26
69_E96_D1.0260.26
121_Y168_E1.0200.26
82_V141_L1.0160.26
36_D139_A1.0090.25
54_I74_I1.0080.25
37_R68_T1.0070.25
61_P128_V1.0010.25
56_G162_E1.0010.25
51_V138_V0.9970.25
100_T109_V0.9900.25
27_G38_V0.9870.25
26_V114_E0.9820.24
92_Q126_W0.9820.24
47_A123_A0.9770.24
69_E168_E0.9660.24
14_H79_G0.9660.24
131_T155_E0.9640.24
104_E148_L0.9520.23
36_D132_N0.9520.23
39_L108_L0.9410.23
80_V126_W0.9390.23
71_N109_V0.9370.23
85_T141_L0.9320.23
85_T148_L0.9310.23
13_G113_G0.9310.23
12_Y70_L0.9280.23
37_R65_E0.9240.23
132_N139_A0.9230.22
164_R177_V0.9210.22
41_P57_R0.9190.22
81_V124_A0.9160.22
118_G131_T0.9150.22
58_F70_L0.9140.22
96_D130_V0.9120.22
20_D170_L0.9110.22
54_I71_N0.9090.22
168_E173_H0.9090.22
131_T139_A0.9070.22
26_V111_V0.9020.22
72_A89_E0.8930.22
89_E169_E0.8900.21
73_T155_E0.8880.21
33_L81_V0.8860.21
69_E130_V0.8850.21
26_V138_V0.8770.21
64_V160_N0.8750.21
52_R145_L0.8720.21
13_G135_H0.8670.21
48_A52_R0.8640.21
141_L144_F0.8640.21
92_Q131_T0.8540.20
64_V111_V0.8540.20
82_V85_T0.8530.20
109_V156_Q0.8240.19
74_I161_A0.8220.19
29_T43_N0.8220.19
54_I109_V0.8170.19
85_T144_F0.8120.19
58_F165_V0.8050.19
15_R21_R0.7940.19
15_R18_R0.7940.19
18_R21_R0.7940.19
15_R19_D0.7940.19
45_T97_E0.7900.18
135_H139_A0.7820.18
73_T81_V0.7760.18
33_L173_H0.7670.18
86_M142_A0.7450.17
144_F151_G0.7430.17
27_G147_R0.7320.17
94_V97_E0.7310.17
37_R50_T0.7290.17
12_Y39_L0.7260.17
9_V69_E0.7260.17
115_K146_D0.7240.17
72_A157_G0.7120.16
61_P143_V0.6990.16
40_F91_L0.6970.16
38_V51_V0.6930.16
47_A163_R0.6900.16
7_V43_N0.6870.16
107_V147_R0.6860.16
143_V155_E0.6860.16
49_E52_R0.6850.16
27_G53_D0.6850.16
8_A92_Q0.6840.16
7_V156_Q0.6820.16
37_R92_Q0.6780.16
91_L114_E0.6700.15
148_L153_E0.6700.15
14_H77_W0.6680.15
65_E126_W0.6630.15
112_G137_E0.6620.15
85_T153_E0.6610.15
66_R113_G0.6600.15
17_G44_A0.6590.15
33_L162_E0.6540.15
61_P64_V0.6540.15
169_E175_V0.6540.15
49_E169_E0.6530.15
138_V174_V0.6520.15
12_Y42_D0.6460.15
29_T150_D0.6420.15
75_E123_A0.6390.15
37_R63_D0.6370.15
44_A47_A0.6370.15
99_R150_D0.6340.15
111_V143_V0.6340.15
87_Y151_G0.6320.14
112_G136_S0.6300.14
76_D159_E0.6290.14
44_A79_G0.6270.14
49_E150_D0.6230.14
107_V146_D0.6220.14
32_A62_F0.6220.14
55_T165_V0.6210.14
70_L117_P0.6190.14
63_D166_I0.6040.14
13_G114_E0.6040.14
168_E171_G0.6020.14
123_A163_R0.6010.14
16_P37_R0.6010.14
90_Q129_G0.5970.14
77_W108_L0.5970.14
52_R98_I0.5960.14
53_D105_E0.5940.14
119_D123_A0.5940.14
122_E138_V0.5930.14
40_F81_V0.5910.14
49_E164_R0.5850.13
70_L106_P0.5840.13
51_V55_T0.5840.13
46_Q173_H0.5820.13
20_D40_F0.5770.13
69_E150_D0.5770.13
81_V123_A0.5760.13
38_V120_V0.5730.13
26_V146_D0.5720.13
152_R160_N0.5710.13
69_E119_D0.5660.13
22_M143_V0.5640.13
26_V130_V0.5630.13
71_N100_T0.5630.13
83_H136_S0.5610.13
9_V122_E0.5590.13
7_V108_L0.5570.13
81_V140_G0.5570.13
91_L107_V0.5540.13
75_E95_D0.5510.13
29_T165_V0.5480.13
140_G163_R0.5450.13
44_A158_Y0.5400.12
40_F47_A0.5380.12
37_R54_I0.5330.12
12_Y58_F0.5300.12
65_E73_T0.5290.12
144_F153_E0.5230.12
37_R158_Y0.5210.12
48_A130_V0.5200.12
138_V147_R0.5190.12
20_D140_G0.5180.12
104_E107_V0.5160.12
29_T100_T0.5150.12
23_T165_V0.5140.12
37_R165_V0.5140.12
39_L107_V0.5080.12
40_F54_I0.5070.12
51_V62_F0.5060.12
16_P114_E0.5050.12
91_L151_G0.5010.12
11_R21_R0.5000.12
11_R18_R0.5000.12
11_R15_R0.5000.12
11_R19_D0.5000.12
32_A148_L0.5000.12
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  
2yy8A 2 0.901 100 0.068 Contact Map
2o3aA 2 0.849 100 0.097 Contact Map
1v2xA 2 0.849 97.9 0.905 Contact Map
2ha8A 2 0.7083 97.6 0.91 Contact Map
3dcmX 2 0.7708 97.3 0.916 Contact Map
1zjrA 2 0.8438 97 0.919 Contact Map
4kgnA 2 0.7396 96.7 0.922 Contact Map
1gz0A 2 0.7135 96.6 0.923 Contact Map
3n4jA 2 0.7396 96.2 0.926 Contact Map
3nk6A 2 0.7708 95.7 0.929 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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