GREMLIN Database
TRMD - tRNA (guanine-N(1)-)-methyltransferase
UniProt: O31741 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 243 (227)
Sequences: 3363 (1867)
Seq/√Len: 123.9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
200_N203_K4.0671.00
211_E214_R3.9161.00
186_D191_K3.3151.00
120_E124_E3.2231.00
65_Q69_D3.1531.00
94_F99_A3.0811.00
72_E188_K2.9691.00
41_Y73_D2.7171.00
87_V110_F2.5541.00
43_D69_D2.4751.00
37_N40_E2.4741.00
6_L38_F2.4431.00
203_K206_E2.4331.00
133_I147_M2.3341.00
143_L147_M2.3111.00
83_R105_E2.2671.00
125_H190_L2.2461.00
31_V153_V2.1751.00
202_A205_E2.1031.00
98_K129_D2.1021.00
136_F147_M2.0651.00
5_F149_A2.0531.00
98_K101_Q2.0481.00
98_K131_I2.0401.00
94_F151_S2.0071.00
83_R129_D1.9931.00
14_E18_G1.9191.00
186_D189_G1.8441.00
94_F148_I1.8181.00
92_E129_D1.8171.00
191_K194_E1.8051.00
23_Q27_E1.8001.00
68_F187_Y1.7991.00
4_D36_V1.7981.00
224_L227_H1.7971.00
92_E98_K1.7321.00
90_Q215_R1.7281.00
214_R218_L1.7051.00
99_A151_S1.6961.00
52_Y183_R1.6641.00
68_F126_L1.6601.00
101_Q129_D1.6501.00
44_N48_T1.6421.00
133_I136_F1.6391.00
148_I152_V1.6141.00
4_D34_Q1.6101.00
4_D107_H1.6021.00
71_V126_L1.5991.00
68_F188_K1.5871.00
124_E190_L1.5821.00
149_A153_V1.5771.00
139_T150_D1.5681.00
54_Y185_A1.5311.00
100_E172_S1.5291.00
110_F148_I1.5291.00
2_K32_Q1.5001.00
96_Q155_L1.4821.00
209_N227_H1.4441.00
202_A206_E1.4311.00
48_T63_K1.4181.00
82_P109_L1.4171.00
53_P61_V1.4131.00
160_L166_H1.4101.00
54_Y192_V1.4041.00
130_E219_R1.3971.00
166_H169_D1.3851.00
68_F72_E1.3781.00
92_E95_T1.3671.00
44_N63_K1.3501.00
95_T98_K1.3141.00
86_L111_I1.3131.00
38_F62_L1.3091.00
131_I148_I1.3081.00
215_R219_R1.3081.00
11_E19_S1.3051.00
185_A191_K1.3041.00
86_L118_Y1.2971.00
11_E37_N1.2911.00
13_F146_M1.2881.00
16_V146_M1.2711.00
97_K100_E1.2691.00
179_P211_E1.2611.00
67_V111_I1.2571.00
217_Y224_L1.2370.99
87_V148_I1.2360.99
11_E14_E1.2150.99
36_V41_Y1.2090.99
213_I224_L1.1810.99
62_L118_Y1.1700.99
102_L131_I1.1530.99
110_F145_A1.1310.99
3_I149_A1.1250.99
21_I24_K1.1230.99
72_E126_L1.1230.99
81_A106_E1.1220.99
2_K34_Q1.1210.99
206_E210_K1.1110.99
171_F223_L1.0640.98
85_I102_L1.0620.98
164_A167_I1.0620.98
18_G26_Q1.0490.98
214_R217_Y1.0400.98
61_V180_H1.0340.98
30_A159_V1.0310.98
3_I31_V1.0290.98
111_I122_I1.0220.98
217_Y229_L1.0190.98
93_R171_F1.0060.98
133_I144_P0.9990.98
209_N213_I0.9980.98
120_E123_R0.9950.98
173_T212_S0.9920.98
13_F16_V0.9920.98
143_L150_D0.9910.97
6_L70_A0.9900.97
84_I128_T0.9840.97
36_V70_A0.9820.97
71_V122_I0.9800.97
224_L229_L0.9720.97
83_R128_T0.9650.97
8_L49_V0.9630.97
163_E167_I0.9590.97
64_P68_F0.9570.97
185_A197_L0.9530.97
177_E180_H0.9460.97
4_D109_L0.9440.97
112_C145_A0.9330.96
86_L123_R0.9270.96
120_E215_R0.9090.96
125_H188_K0.9020.96
168_E177_E0.9000.96
82_P107_H0.8990.96
3_I153_V0.8980.96
90_Q120_E0.8970.95
12_M16_V0.8890.95
114_H139_T0.8860.95
178_H208_R0.8820.95
200_N204_I0.8750.95
31_V156_L0.8740.95
58_A168_E0.8690.95
99_A155_L0.8670.95
169_D177_E0.8670.95
100_E155_L0.8640.94
40_E47_N0.8620.94
198_S203_K0.8600.94
12_M146_M0.8590.94
26_Q33_F0.8530.94
84_I127_V0.8480.94
67_V118_Y0.8440.94
118_Y122_I0.8440.94
58_A165_S0.8420.94
67_V122_I0.8410.94
207_W211_E0.8360.93
8_L114_H0.8340.93
85_I131_I0.8240.93
44_N47_N0.8190.93
210_K214_R0.8150.93
71_V109_L0.8120.92
30_A156_L0.8110.92
75_T109_L0.8060.92
224_L228_P0.8060.92
96_Q172_S0.8030.92
164_A168_E0.8020.92
92_E101_Q0.8000.92
84_I109_L0.8000.92
58_A162_K0.7950.92
63_K66_P0.7920.91
37_N47_N0.7920.91
4_D74_L0.7890.91
64_P187_Y0.7840.91
68_F71_V0.7830.91
171_F177_E0.7830.91
57_G208_R0.7740.91
5_F33_F0.7710.90
94_F98_K0.7690.90
145_A149_A0.7690.90
153_V159_V0.7680.90
26_Q31_V0.7670.90
209_N212_S0.7630.90
22_L26_Q0.7620.90
144_P147_M0.7610.90
52_Y58_A0.7610.90
88_C130_E0.7600.90
120_E219_R0.7580.90
205_E209_N0.7500.89
75_T82_P0.7490.89
123_R130_E0.7490.89
137_V169_D0.7430.89
69_D72_E0.7430.89
2_K107_H0.7400.88
88_C123_R0.7400.88
42_S63_K0.7380.88
42_S48_T0.7340.88
36_V74_L0.7330.88
111_I127_V0.7290.88
114_H150_D0.7210.87
138_L144_P0.7200.87
22_L139_T0.7170.87
43_D48_T0.7140.87
83_R108_L0.7050.86
166_H172_S0.7040.86
34_Q77_K0.7030.86
169_D178_H0.6970.85
95_T101_Q0.6870.84
17_L149_A0.6840.84
3_I108_L0.6840.84
87_V145_A0.6790.84
80_A106_E0.6780.84
38_F67_V0.6780.84
143_L146_M0.6770.84
217_Y227_H0.6720.83
73_D76_S0.6660.83
213_I229_L0.6590.82
25_A159_V0.6580.82
12_M143_L0.6580.82
5_F110_F0.6570.82
153_V156_L0.6550.82
68_F125_H0.6540.81
68_F122_I0.6520.81
12_M15_G0.6520.81
210_K217_Y0.6490.81
21_I159_V0.6480.81
155_L172_S0.6460.81
38_F118_Y0.6440.80
123_R215_R0.6420.80
98_K102_L0.6400.80
70_A74_L0.6390.80
82_P105_E0.6380.80
139_T143_L0.6370.80
138_L147_M0.6350.80
12_M150_D0.6350.80
17_L33_F0.6340.79
116_E178_H0.6300.79
200_N206_E0.6300.79
168_E205_E0.6260.79
102_L148_I0.6210.78
7_T36_V0.6210.78
17_L146_M0.6210.78
156_L159_V0.6150.77
191_K197_L0.6150.77
94_F131_I0.6150.77
122_I126_L0.6140.77
177_E212_S0.6130.77
63_K182_T0.6120.77
83_R107_H0.6090.77
58_A164_A0.6090.77
105_E108_L0.6080.77
194_E203_K0.6080.77
66_P69_D0.6070.76
90_Q123_R0.6050.76
42_S66_P0.6050.76
73_D77_K0.6030.76
111_I118_Y0.5980.75
68_F190_L0.5970.75
211_E215_R0.5970.75
194_E197_L0.5960.75
5_F13_F0.5940.75
75_T84_I0.5910.75
8_L62_L0.5900.74
168_E178_H0.5890.74
8_L37_N0.5890.74
21_I139_T0.5890.74
18_G27_E0.5870.74
6_L74_L0.5860.74
42_S65_Q0.5830.74
8_L67_V0.5780.73
20_S52_Y0.5770.73
22_L160_L0.5760.73
162_K166_H0.5760.73
71_V75_T0.5760.73
145_A148_I0.5750.73
101_Q104_K0.5740.72
13_F145_A0.5730.72
26_Q32_Q0.5720.72
210_K227_H0.5720.72
90_Q219_R0.5720.72
41_Y70_A0.5710.72
16_V149_A0.5700.72
92_E97_K0.5630.71
87_V144_P0.5630.71
118_Y123_R0.5600.71
205_E208_R0.5580.70
126_L190_L0.5560.70
13_F35_V0.5540.70
214_R229_L0.5540.70
76_S82_P0.5530.70
14_E35_V0.5520.69
67_V71_V0.5520.69
20_S139_T0.5520.69
40_E73_D0.5500.69
9_F115_Y0.5500.69
185_A200_N0.5500.69
110_F152_V0.5500.69
161_G165_S0.5490.69
53_P180_H0.5490.69
90_Q130_E0.5480.69
6_L109_L0.5480.69
71_V84_I0.5480.69
51_D183_R0.5470.69
64_P71_V0.5470.69
186_D194_E0.5460.69
187_Y190_L0.5460.69
42_S47_N0.5450.69
185_A194_E0.5440.68
64_P122_I0.5430.68
90_Q177_E0.5430.68
68_F114_H0.5390.68
209_N229_L0.5390.68
110_F149_A0.5380.68
84_I111_I0.5380.68
94_F152_V0.5360.67
7_T35_V0.5330.67
43_D47_N0.5320.67
33_F153_V0.5290.66
71_V127_V0.5280.66
161_G166_H0.5280.66
125_H187_Y0.5260.66
116_E180_H0.5230.65
20_S26_Q0.5230.65
33_F149_A0.5210.65
74_L109_L0.5210.65
162_K172_S0.5200.65
174_G227_H0.5200.65
20_S177_E0.5190.65
210_K218_L0.5190.65
54_Y115_Y0.5180.65
97_K104_K0.5180.65
36_V77_K0.5170.65
31_V159_V0.5150.64
144_P148_I0.5150.64
61_V208_R0.5140.64
115_Y192_V0.5130.64
16_V22_L0.5100.63
166_H171_F0.5090.63
85_I98_K0.5060.63
41_Y74_L0.5050.63
85_I129_D0.5030.62
48_T52_Y0.5030.62
49_V62_L0.5020.62
32_Q35_V0.5000.62
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  
4h3zA 2 1 100 0.013 Contact Map
3ky7A 2 0.93 100 0.017 Contact Map
4yvgA 2 0.9671 100 0.02 Contact Map
1oy5A 2 0.8889 100 0.029 Contact Map
3knuA 2 0.823 100 0.039 Contact Map
3iefA 2 0.9218 100 0.04 Contact Map
3quvA 2 0.8889 100 0.05 Contact Map
1to0A 2 0.6008 88.9 0.954 Contact Map
4fakA 2 0.6255 86.9 0.955 Contact Map
3aiaA 2 0.5432 84.2 0.957 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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