GREMLIN Database
TRMD - tRNA (guanine-N(1)-)-methyltransferase
UniProt: P0A873 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG11023
Length: 255 (228)
Sequences: 3381 (1883)
Seq/√Len: 124.7

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_E4.1491.00
211_Q214_G3.9241.00
120_E124_Q3.3881.00
94_L99_V3.3191.00
65_Q69_D3.2801.00
186_V191_E3.2161.00
72_H188_E3.0041.00
41_F73_A2.7901.00
87_L110_L2.6231.00
6_I38_P2.5921.00
37_S40_D2.5371.00
43_H69_D2.4311.00
203_E206_R2.4231.00
143_L147_T2.3671.00
133_I147_T2.3281.00
125_T190_M2.2691.00
83_K105_N2.2331.00
31_L153_S2.1551.00
5_I149_I2.1191.00
94_L151_S2.1031.00
136_Y147_T2.0921.00
202_A205_R2.0901.00
98_G129_E2.0821.00
83_K129_E2.0641.00
98_G101_E2.0481.00
98_G131_W1.9971.00
94_L148_L1.8981.00
186_V189_G1.8221.00
4_G36_W1.7971.00
92_R129_E1.7891.00
68_R187_L1.7861.00
224_L227_L1.7801.00
23_G27_K1.7751.00
14_R18_D1.7701.00
191_E194_P1.7451.00
90_Q215_R1.7261.00
148_L152_V1.7211.00
214_G218_L1.7161.00
44_D48_T1.7111.00
52_R183_R1.6971.00
92_R98_G1.6821.00
99_V151_S1.6671.00
68_R126_E1.6511.00
110_L148_L1.6381.00
101_E129_E1.6321.00
71_I126_E1.6271.00
139_S150_D1.6181.00
4_G34_Q1.6081.00
133_I136_Y1.6021.00
4_G107_K1.5911.00
149_I153_S1.5631.00
209_L227_L1.5551.00
166_A169_D1.5411.00
68_R188_E1.5401.00
54_Y185_E1.5351.00
96_Q155_F1.5141.00
2_W32_S1.4791.00
100_S172_A1.4721.00
53_P61_L1.4511.00
160_L166_A1.4381.00
202_A206_R1.4361.00
48_T63_M1.4271.00
44_D63_M1.4221.00
54_Y192_V1.4111.00
82_A109_I1.4011.00
124_Q190_M1.3991.00
13_F146_M1.3811.00
130_E219_R1.3681.00
92_R95_D1.3671.00
67_L111_V1.3521.00
38_P62_M1.3491.00
86_Y118_I1.3471.00
95_D98_G1.3441.00
68_R72_H1.3421.00
131_W148_L1.3331.00
86_Y111_V1.3271.00
215_R219_R1.3131.00
11_E37_S1.3021.00
62_M118_I1.2961.00
185_E191_E1.2881.00
16_I146_M1.2741.00
11_E19_Y1.2581.00
102_L131_W1.2350.99
217_W224_L1.2260.99
97_A100_S1.2260.99
87_L148_L1.2240.99
179_P211_Q1.2050.99
81_G106_Q1.1970.99
213_L224_L1.1870.99
21_V24_R1.1860.99
36_W41_F1.1730.99
11_E14_R1.1370.99
110_L145_A1.1300.99
206_R210_K1.1280.99
85_I102_L1.1010.99
61_L180_H1.0860.99
171_F223_L1.0820.99
143_L150_D1.0790.99
3_I149_I1.0750.99
2_W34_Q1.0730.99
133_I144_P1.0620.98
214_G217_W1.0560.98
3_I31_L1.0480.98
72_H126_E1.0400.98
84_V128_D1.0220.98
30_L159_V1.0210.98
111_V122_V1.0110.98
36_W70_A1.0090.98
6_I70_A1.0070.98
18_D26_V0.9990.98
173_E212_S0.9970.98
177_D180_H0.9910.98
93_K171_F0.9890.98
164_A167_T0.9880.97
217_W229_L0.9860.97
64_V68_R0.9760.97
83_K128_D0.9710.97
86_Y123_I0.9670.97
71_I122_V0.9660.97
3_I153_S0.9580.97
120_E215_R0.9490.97
118_I122_V0.9460.97
8_L49_V0.9460.97
4_G109_I0.9400.97
114_R139_S0.9400.97
90_Q120_E0.9340.96
168_E177_D0.9220.96
99_V155_F0.9160.96
200_N204_I0.9160.96
209_L213_L0.9110.96
112_C145_A0.9040.96
31_L156_I0.9000.96
224_L229_L0.9000.96
169_D177_D0.8990.96
178_C208_R0.8890.95
163_E167_T0.8850.95
67_L118_I0.8810.95
185_E197_L0.8810.95
82_A107_K0.8770.95
12_M146_M0.8700.95
13_F16_I0.8610.94
85_I131_W0.8590.94
58_P168_E0.8560.94
26_V33_I0.8540.94
207_W211_Q0.8500.94
100_S155_F0.8450.94
171_F177_D0.8430.94
44_D47_R0.8420.94
67_L122_V0.8390.94
198_S203_E0.8350.94
125_T188_E0.8330.93
92_R101_E0.8330.93
96_Q172_A0.8300.93
8_L114_R0.8280.93
30_L156_I0.8260.93
58_P165_S0.8230.93
63_M66_P0.8190.93
84_V127_I0.8180.93
137_V169_D0.8170.93
40_D47_R0.8150.93
4_G74_A0.8090.92
120_E219_R0.8040.92
58_P162_H0.8030.92
22_T26_V0.7980.92
52_R58_P0.7960.92
68_R71_I0.7950.92
5_I33_I0.7870.91
64_V187_L0.7830.91
84_V109_I0.7800.91
37_S47_R0.7790.91
153_S159_V0.7780.91
57_G208_R0.7780.91
169_D178_C0.7770.91
144_P147_T0.7760.91
205_R209_L0.7740.91
120_E123_I0.7740.91
12_M15_A0.7700.90
71_I109_I0.7700.90
12_M16_I0.7700.90
83_K108_L0.7700.90
94_L98_G0.7640.90
42_T48_T0.7600.90
210_K214_G0.7540.90
36_W74_A0.7530.89
164_A168_E0.7510.89
209_L212_S0.7500.89
75_K109_I0.7500.89
224_L228_A0.7490.89
26_V31_L0.7440.89
88_S123_I0.7380.88
69_D72_H0.7360.88
22_T139_S0.7320.88
2_W107_K0.7270.88
42_T63_M0.7260.88
38_P118_I0.7250.88
114_R150_D0.7240.88
111_V127_I0.7190.87
153_S156_I0.7170.87
12_M150_D0.7140.87
139_S143_L0.7020.86
145_A149_I0.7020.86
12_M143_L0.6980.86
155_F172_A0.6950.85
88_S130_E0.6940.85
21_V159_V0.6930.85
138_L144_P0.6920.85
98_G102_L0.6900.85
87_L145_A0.6830.84
17_T149_I0.6810.84
3_I108_L0.6800.84
43_H48_T0.6750.84
116_E178_C0.6750.84
166_A172_A0.6710.83
123_I130_E0.6670.83
217_W227_L0.6630.83
38_P67_L0.6620.82
156_I159_V0.6570.82
75_K82_A0.6560.82
210_K217_W0.6520.81
7_S36_W0.6480.81
143_L146_M0.6460.81
68_R125_T0.6430.81
17_T146_M0.6420.81
105_N108_L0.6390.80
42_T66_P0.6380.80
118_I123_I0.6370.80
95_D101_E0.6360.80
94_L131_W0.6360.80
5_I110_L0.6340.80
5_I13_F0.6340.80
8_L37_S0.6320.79
82_A105_N0.6310.79
200_N206_R0.6310.79
83_K107_K0.6290.79
15_A18_D0.6280.79
122_V126_E0.6280.79
70_A74_A0.6260.79
177_D212_S0.6260.79
168_E205_R0.6230.78
145_A148_L0.6210.78
138_L147_T0.6180.78
26_V32_S0.6180.78
63_M182_T0.6140.77
194_P203_E0.6130.77
68_R122_V0.6130.77
90_Q177_D0.6130.77
8_L62_M0.6100.77
6_I74_A0.6090.77
8_L67_L0.6080.77
191_E197_L0.6070.77
25_A159_V0.6050.76
66_P69_D0.6030.76
110_L152_V0.6000.76
68_R190_M0.5990.76
211_Q215_R0.5950.75
210_K227_L0.5920.75
21_V139_S0.5890.75
22_T160_L0.5880.74
20_G139_S0.5850.74
123_I215_R0.5840.74
102_L148_L0.5830.74
58_P164_A0.5820.74
13_F35_S0.5820.74
17_T33_I0.5790.73
61_L208_R0.5790.73
84_V111_V0.5740.73
168_E178_C0.5730.73
111_V118_I0.5730.73
213_L229_L0.5720.72
87_L144_P0.5710.72
115_Y192_V0.5700.72
9_F115_Y0.5700.72
20_G114_R0.5690.72
194_P197_L0.5690.72
186_V194_P0.5690.72
43_H47_R0.5670.72
18_D27_K0.5660.72
49_V62_M0.5650.71
90_Q219_R0.5640.71
67_L71_I0.5640.71
144_P148_L0.5610.71
41_F70_A0.5610.71
42_T65_Q0.5600.71
16_I149_I0.5570.70
53_P180_H0.5560.70
20_G52_R0.5540.70
7_S35_S0.5520.70
92_R97_A0.5470.69
101_E104_T0.5470.69
54_Y115_Y0.5460.69
71_I75_K0.5460.69
67_L150_D0.5420.68
70_A73_A0.5410.68
185_E194_P0.5390.68
21_V160_L0.5390.68
227_L230_T0.5390.68
68_R114_R0.5380.68
93_K136_Y0.5370.68
20_G177_D0.5370.68
166_A171_F0.5370.68
116_E169_D0.5360.68
73_A76_A0.5350.67
161_G166_A0.5330.67
64_V71_I0.5320.67
20_G26_V0.5320.67
185_E200_N0.5320.67
51_D183_R0.5320.67
162_H172_A0.5300.67
116_E180_H0.5290.67
40_D73_A0.5290.67
209_L229_L0.5290.67
13_F145_A0.5260.66
94_L110_L0.5220.65
14_R35_S0.5210.65
210_K218_L0.5200.65
33_I153_S0.5190.65
20_G23_G0.5190.65
123_I128_D0.5170.65
33_I149_I0.5170.65
187_L190_M0.5170.65
224_L230_T0.5160.65
80_E106_Q0.5160.65
42_T47_R0.5150.64
90_Q130_E0.5150.64
161_G165_S0.5140.64
71_I127_I0.5140.64
16_I22_T0.5140.64
97_A104_T0.5130.64
123_I127_I0.5110.64
6_I109_I0.5100.64
221_P224_L0.5080.63
15_A146_M0.5080.63
76_A82_A0.5080.63
31_L159_V0.5080.63
126_E190_M0.5060.63
116_E177_D0.5050.63
67_L126_E0.5040.63
75_K128_D0.5040.63
17_T23_G0.5020.63
162_H166_A0.5020.63
205_R208_R0.5010.62
102_L171_F0.5000.62
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 0.9647 100 0.04 Contact Map
3ky7A 2 0.8941 100 0.042 Contact Map
4yvgA 2 0.9333 100 0.047 Contact Map
1oy5A 2 0.8471 100 0.059 Contact Map
3knuA 2 0.7843 100 0.063 Contact Map
3iefA 2 0.8784 100 0.064 Contact Map
3quvA 2 0.8471 100 0.074 Contact Map
1to0A 2 0.5647 88.8 0.955 Contact Map
3aiaA 2 0.5176 88.5 0.956 Contact Map
4fakA 2 0.5882 87.4 0.956 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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