GREMLIN Database
TRMJ - tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmJ
UniProt: P0AE01 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG13452
Length: 246 (231)
Sequences: 1787 (1148)
Seq/√Len: 75.5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
65_T68_E4.8551.00
67_D127_K4.1841.00
26_K55_D3.7841.00
94_R158_M3.6431.00
132_V152_I3.4421.00
32_N61_H3.2131.00
73_C110_A3.1351.00
20_S49_L3.1311.00
34_W63_V2.8151.00
11_E115_R2.7731.00
78_G128_C2.7531.00
11_E37_N2.5891.00
64_D68_E2.5301.00
66_L112_V2.4791.00
184_E213_R2.4641.00
9_L145_L2.4391.00
7_I153_A2.3981.00
182_D223_S2.3971.00
189_H230_R2.2261.00
32_N108_P2.2081.00
6_R34_W2.2041.00
70_L76_V2.1491.00
115_R124_E2.1451.00
46_A57_I2.0841.00
47_I58_G2.0621.00
113_F149_V2.0251.00
78_G125_L1.9941.00
37_N64_D1.9781.00
34_W61_H1.9701.00
24_A150_Q1.9471.00
111_L152_I1.9431.00
8_V110_A1.9201.00
6_R32_N1.8551.00
178_P226_L1.8381.00
182_D185_R1.7381.00
186_F216_F1.7311.00
185_R230_R1.7071.00
7_I25_M1.7021.00
187_Y217_T1.6851.00
16_G45_Q1.6741.00
193_T237_E1.6721.00
145_L149_V1.6671.00
76_V112_V1.6501.00
196_A237_E1.6341.00
30_L153_A1.6211.00
192_Q237_E1.5890.99
77_V96_C1.5510.99
28_M150_Q1.5290.99
75_L130_Y1.4940.99
81_A84_R1.4880.99
94_R155_E1.4670.99
193_T236_I1.4660.99
121_T124_E1.4600.99
226_L230_R1.4530.99
9_L149_V1.4260.99
194_L232_I1.4130.99
54_S58_G1.4010.99
40_V43_D1.3960.99
10_V120_L1.3610.98
72_G181_D1.3590.98
25_M30_L1.3570.98
21_V149_V1.3560.98
179_L182_D1.3550.98
36_V69_A1.3440.98
186_F226_L1.3430.98
8_V73_C1.3430.98
91_L130_Y1.3280.98
112_V128_C1.3250.98
197_T236_I1.3070.98
215_L221_P1.3070.98
18_M41_K1.3060.98
13_S117_R1.3030.98
197_T235_S1.3000.98
113_F145_L1.2820.98
129_H180_V1.2750.97
66_L70_L1.2740.97
26_K53_A1.2590.97
76_V180_V1.2530.97
157_R161_L1.2380.97
193_T233_L1.2300.97
47_I54_S1.2150.97
176_P223_S1.2140.97
212_L232_I1.2130.97
99_K130_Y1.2080.96
37_N65_T1.1930.96
93_P152_I1.1920.96
7_I111_L1.1690.96
80_S131_H1.1630.96
181_D185_R1.1630.96
74_S108_P1.1600.96
74_S107_T1.1560.95
91_L99_K1.1500.95
35_L38_P1.1470.95
15_T43_D1.1310.95
103_E220_R1.1190.95
195_L205_P1.1170.95
96_C132_V1.1060.94
34_W72_G1.1040.94
16_G49_L1.0980.94
234_A238_Q1.0980.94
186_F190_L1.0920.94
191_E209_M1.0860.94
136_A140_Y1.0850.94
73_C76_V1.0780.93
118_V121_T1.0660.93
77_V132_V1.0640.93
10_V115_R1.0530.93
197_T232_I1.0490.92
70_L73_C1.0420.92
6_R63_V1.0300.92
20_S27_T1.0290.92
235_S238_Q1.0260.92
115_R121_T1.0250.92
4_N108_P1.0240.92
49_L147_M1.0170.91
46_A60_A1.0000.91
72_G108_P0.9890.90
9_L21_V0.9830.90
94_R159_A0.9680.89
31_T59_N0.9620.89
6_R73_C0.9570.89
38_P62_I0.9550.88
221_P229_L0.9530.88
103_E107_T0.9530.88
80_S88_W0.9430.88
28_M136_A0.9310.87
12_T35_L0.9190.86
100_S112_V0.9140.86
219_A225_E0.9130.86
50_A54_S0.9100.86
63_V68_E0.8970.85
194_L197_T0.8950.85
215_L229_L0.8920.85
77_V130_Y0.8780.84
5_I30_L0.8700.83
221_P226_L0.8700.83
21_V146_A0.8680.83
19_G23_R0.8670.83
35_L219_A0.8610.83
81_A141_S0.8600.83
143_L150_Q0.8510.82
14_H49_L0.8430.81
10_V36_V0.8420.81
186_F229_L0.8340.81
101_V159_A0.8320.80
99_K102_A0.8240.80
79_T152_I0.8230.80
223_S227_N0.8210.80
16_G150_Q0.8200.79
184_E188_G0.8170.79
104_A109_V0.8170.79
179_L183_L0.8050.78
27_T49_L0.8030.78
20_S146_A0.8000.78
191_E195_L0.7980.78
81_A122_N0.7970.77
75_L103_E0.7940.77
185_R189_H0.7930.77
76_V128_C0.7890.77
186_F233_L0.7880.77
77_V99_K0.7870.77
187_Y213_R0.7850.76
129_H183_L0.7850.76
201_R205_P0.7850.76
173_E222_E0.7780.76
5_I156_V0.7760.76
216_F236_I0.7760.76
11_E121_T0.7750.75
7_I30_L0.7730.75
17_N23_R0.7650.75
136_A141_S0.7630.74
61_H68_E0.7600.74
6_R108_P0.7600.74
22_A46_A0.7490.73
123_E126_Q0.7470.73
18_M21_V0.7470.73
59_N165_E0.7440.72
207_Q210_N0.7380.72
8_V63_V0.7350.72
93_P154_Y0.7340.71
175_T222_E0.7280.71
99_K103_E0.7280.71
97_G156_V0.7280.71
69_A72_G0.7270.71
126_Q210_N0.7240.70
26_K56_V0.7210.70
214_R222_E0.7200.70
22_A57_I0.7110.69
27_T150_Q0.7100.69
26_K137_N0.7100.69
26_K31_T0.7080.69
42_P47_I0.7070.69
95_E98_L0.7060.69
13_S142_S0.7040.68
26_K140_Y0.7030.68
129_H217_T0.6960.67
95_E172_H0.6930.67
22_A122_N0.6910.67
8_V69_A0.6890.67
118_V222_E0.6890.67
137_N140_Y0.6870.66
82_R142_S0.6820.66
52_G137_N0.6810.66
30_L146_A0.6810.66
92_D98_L0.6810.66
24_A28_M0.6770.65
35_L62_I0.6760.65
136_A143_L0.6760.65
235_S239_Q0.6720.65
57_I60_A0.6660.64
201_R204_H0.6630.64
173_E176_P0.6630.64
71_A181_D0.6620.64
185_R188_G0.6620.64
155_E158_M0.6620.64
188_G192_Q0.6610.63
10_V73_C0.6600.63
15_T41_K0.6580.63
15_T42_P0.6580.63
53_A140_Y0.6510.62
63_V72_G0.6480.62
15_T18_M0.6480.62
59_N105_A0.6410.61
28_M143_L0.6400.61
28_M157_R0.6390.61
76_V129_H0.6370.61
67_D112_V0.6360.60
15_T47_I0.6330.60
45_Q49_L0.6330.60
127_K184_E0.6320.60
98_L162_A0.6310.60
95_E166_N0.6280.59
80_S127_K0.6270.59
201_R206_G0.6270.59
25_M153_A0.6220.59
100_S111_L0.6210.59
31_T137_N0.6160.58
78_G143_L0.6120.58
6_R61_H0.6080.57
25_M56_V0.6060.57
200_I205_P0.6030.56
140_Y147_M0.6020.56
43_D51_A0.6010.56
66_L127_K0.6010.56
87_P214_R0.6000.56
187_Y209_M0.5990.56
155_E231_G0.5980.56
25_M154_Y0.5980.56
82_R143_L0.5980.56
79_T154_Y0.5940.55
176_P179_L0.5920.55
44_S48_A0.5920.55
29_G137_N0.5910.55
52_G140_Y0.5910.55
100_S156_V0.5890.55
27_T136_A0.5880.55
41_K47_I0.5880.55
90_M131_H0.5860.54
94_R162_A0.5850.54
32_N73_C0.5840.54
70_L180_V0.5840.54
4_N106_N0.5820.54
34_W73_C0.5800.54
98_L102_A0.5800.54
233_L236_I0.5790.53
195_L200_I0.5790.53
129_H213_R0.5780.53
93_P135_A0.5750.53
7_I149_V0.5740.53
125_L133_A0.5720.53
190_L233_L0.5720.53
134_I151_V0.5710.52
126_Q131_H0.5710.52
197_T239_Q0.5690.52
180_V217_T0.5680.52
33_L134_I0.5680.52
22_A81_A0.5680.52
68_E123_E0.5670.52
211_K224_Q0.5660.52
64_D67_D0.5660.52
6_R72_G0.5640.52
31_T56_V0.5630.51
28_M153_A0.5620.51
204_H235_S0.5600.51
80_S125_L0.5580.51
101_V160_W0.5550.50
210_N217_T0.5540.50
142_S145_L0.5530.50
187_Y190_L0.5530.50
83_S87_P0.5530.50
27_T234_A0.5520.50
13_S39_L0.5520.50
43_D48_A0.5510.50
32_N165_E0.5510.50
137_N151_V0.5490.50
31_T139_E0.5480.50
21_V153_A0.5460.49
14_H20_S0.5440.49
224_Q228_I0.5430.49
85_T90_M0.5420.49
98_L101_V0.5410.49
195_L198_G0.5400.49
204_H228_I0.5400.49
88_W131_H0.5390.48
11_E118_V0.5380.48
117_R121_T0.5350.48
21_V27_T0.5350.48
183_L226_L0.5350.48
136_A157_R0.5350.48
94_R98_L0.5340.48
201_R232_I0.5330.48
24_A53_A0.5320.48
18_M72_G0.5320.48
204_H208_V0.5320.48
10_V124_E0.5320.48
76_V110_A0.5310.47
199_F228_I0.5310.47
190_L232_I0.5300.47
161_L164_Q0.5300.47
202_E206_G0.5290.47
48_A51_A0.5280.47
123_E181_D0.5280.47
177_Y220_R0.5240.47
96_C100_S0.5240.47
225_E230_R0.5240.47
36_V63_V0.5200.46
188_G191_E0.5180.46
54_S117_R0.5170.46
133_A136_A0.5160.46
8_V76_V0.5150.45
142_S208_V0.5130.45
28_M55_D0.5130.45
58_G105_A0.5120.45
15_T40_V0.5110.45
77_V111_L0.5110.45
20_S150_Q0.5100.45
10_V123_E0.5100.45
20_S147_M0.5070.44
22_A84_R0.5070.44
97_G226_L0.5070.44
93_P96_C0.5060.44
215_L219_A0.5040.44
204_H207_Q0.5030.44
41_K62_I0.5010.44
77_V100_S0.5000.44
84_R87_P0.5000.44
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  
4cndA 2 0.6667 100 0.301 Contact Map
3ilkA 2 0.9675 100 0.313 Contact Map
3onpA 2 0.6382 100 0.322 Contact Map
4cngA 2 0.6138 100 0.351 Contact Map
3ic6A 2 0.752 100 0.511 Contact Map
3ktyA 2 0.6545 100 0.557 Contact Map
3dcmX 2 0.6301 100 0.599 Contact Map
1zjrA 2 0.7195 100 0.627 Contact Map
1v2xA 2 0.687 100 0.628 Contact Map
1x7oA 2 0.6179 100 0.643 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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