GREMLIN Database
TRMY - tRNA (pseudouridine(54)-N(1))-methyltransferase
UniProt: Q9HNR6 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 196 (188)
Sequences: 185 (124)
Seq/√Len: 9.1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
32_L54_L4.8501.00
134_A187_H4.6020.99
64_I69_V3.7210.97
147_S151_D3.5060.96
64_I83_L3.4080.95
172_P186_N3.1830.93
170_V180_A3.0690.92
9_H156_E2.6940.85
42_V179_H2.6840.85
53_F63_R2.6130.83
80_A100_S2.3370.75
73_H79_V2.3280.75
40_L66_A2.2950.74
53_F108_S2.2340.72
35_C181_I2.1450.69
21_D24_G2.0540.65
132_A190_T2.0510.65
98_E115_V2.0210.64
29_L40_L2.0020.63
175_L185_H1.9960.63
125_A157_A1.9710.62
37_S78_N1.9640.61
73_H78_N1.9390.60
22_L80_A1.9250.60
112_F116_L1.9160.59
5_V69_V1.9030.59
121_G143_V1.9010.59
6_V11_A1.8560.57
64_I105_I1.8400.56
145_V168_V1.7650.53
40_L73_H1.7630.53
35_C41_F1.7060.50
31_V82_L1.6990.50
72_M79_V1.6740.49
66_A126_L1.6060.46
37_S178_D1.5890.45
11_A56_L1.5820.45
1_M4_F1.5490.44
147_S152_F1.5200.42
86_A149_H1.4800.41
37_S41_F1.4670.40
53_F61_T1.4570.40
51_E65_D1.4180.38
50_V113_E1.4110.38
62_V123_V1.3710.36
152_F156_E1.3500.35
31_V134_A1.3430.35
33_C179_H1.3370.35
36_V138_P1.3270.34
84_K102_S1.2540.32
147_S180_A1.2430.31
35_C179_H1.2310.31
108_S115_V1.2250.30
137_D155_A1.2180.30
161_A167_R1.1920.29
122_P133_L1.1880.29
37_S179_H1.1860.29
127_H167_R1.1790.29
26_A29_L1.1760.29
96_H115_V1.1730.29
170_V184_A1.1690.28
31_V57_G1.1560.28
109_K164_S1.1380.27
75_D78_N1.1370.27
98_E108_S1.1310.27
120_S131_D1.1210.27
62_V118_A1.1020.26
5_V62_V1.0960.26
105_I163_A1.0920.26
39_A139_L1.0910.26
5_V55_V1.0890.26
53_F98_E1.0730.25
3_Q143_V1.0710.25
53_F115_V1.0560.25
28_R34_R1.0550.25
30_D34_R1.0550.25
3_Q142_P1.0350.24
9_H153_T1.0300.24
158_S173_T1.0290.24
60_V127_H1.0230.24
23_P84_K1.0190.23
5_V143_V1.0100.23
4_F144_F1.0030.23
25_A124_V1.0020.23
98_E106_H0.9900.23
6_V83_L0.9870.22
31_V159_L0.9760.22
139_L142_P0.9740.22
17_F128_E0.9720.22
158_S161_A0.9680.22
45_G48_D0.9650.22
21_D78_N0.9640.22
19_L24_G0.9640.22
80_A184_A0.9630.22
174_V180_A0.9630.22
75_D156_E0.9590.22
136_V168_V0.9460.21
36_V101_S0.9410.21
46_I115_V0.9370.21
133_L166_H0.9340.21
24_G44_H0.9320.21
34_R74_P0.9210.20
161_A168_V0.9150.20
124_V183_V0.9130.20
26_A124_V0.9080.20
32_L56_L0.9060.20
124_V141_D0.9010.20
37_S42_V0.8990.20
24_G70_Q0.8990.20
153_T156_E0.8980.20
126_L181_I0.8970.20
61_T171_G0.8880.20
113_E120_S0.8830.19
40_L82_L0.8800.19
9_H20_D0.8800.19
13_T149_H0.8760.19
55_V112_F0.8750.19
145_V160_L0.8700.19
14_T70_Q0.8650.19
71_Y81_G0.8650.19
54_L112_F0.8650.19
21_D44_H0.8550.19
59_E152_F0.8540.19
3_Q53_F0.8530.19
2_R185_H0.8490.19
36_V185_H0.8480.18
23_P31_V0.8390.18
185_H188_L0.8370.18
53_F168_V0.8320.18
111_G175_L0.8190.18
37_S79_V0.8160.18
20_D40_L0.8070.17
42_V132_A0.8000.17
96_H186_N0.7980.17
72_M78_N0.7970.17
40_L65_D0.7960.17
22_L48_D0.7930.17
155_A161_A0.7890.17
40_L49_D0.7830.17
8_G127_H0.7790.17
160_L188_L0.7790.17
43_S74_P0.7780.17
38_A179_H0.7770.17
2_R46_I0.7760.17
27_G34_R0.7740.17
128_E174_V0.7700.17
15_P38_A0.7690.16
18_P33_C0.7690.16
62_V105_I0.7640.16
63_R98_E0.7630.16
22_L69_V0.7600.16
121_G173_T0.7590.16
68_A154_A0.7550.16
85_Q155_A0.7550.16
83_L107_V0.7530.16
82_L156_E0.7500.16
40_L79_V0.7470.16
39_A52_V0.7460.16
6_V137_D0.7460.16
28_R74_P0.7460.16
30_D74_P0.7460.16
78_N81_G0.7440.16
60_V109_K0.7440.16
152_F180_A0.7400.16
122_P141_D0.7370.16
134_A190_T0.7220.15
131_D135_A0.7180.15
42_V56_L0.7160.15
116_L159_L0.7160.15
89_A101_S0.7150.15
79_V145_V0.7120.15
105_I118_A0.7090.15
2_R12_P0.7090.15
12_P29_L0.7080.15
86_A177_A0.7040.15
179_H186_N0.7030.15
60_V174_V0.7000.15
36_V123_V0.6990.15
19_L103_P0.6980.15
62_V108_S0.6960.15
36_V39_A0.6940.15
49_D77_R0.6900.15
11_A14_T0.6880.15
27_G30_D0.6850.15
131_D161_A0.6810.14
133_L170_V0.6800.14
20_D185_H0.6790.14
101_S181_I0.6790.14
170_V174_V0.6770.14
141_D178_D0.6760.14
175_L183_V0.6730.14
175_L180_A0.6730.14
68_A113_E0.6730.14
91_T127_H0.6700.14
64_I101_S0.6640.14
20_D114_A0.6620.14
180_A183_V0.6600.14
57_G62_V0.6550.14
28_R75_D0.6540.14
30_D75_D0.6540.14
29_L141_D0.6540.14
153_T162_D0.6540.14
7_L112_F0.6500.14
127_H157_A0.6430.14
187_H190_T0.6420.14
100_S167_R0.6380.14
129_D168_V0.6360.14
86_A107_V0.6350.14
31_V41_F0.6320.13
51_E64_I0.6300.13
2_R188_L0.6280.13
31_V96_H0.6260.13
37_S182_T0.6250.13
9_H150_R0.6250.13
105_I161_A0.6240.13
90_K95_G0.6140.13
79_V82_L0.6120.13
41_F79_V0.6080.13
172_P176_H0.6070.13
2_R160_L0.6050.13
159_L179_H0.6030.13
124_V129_D0.6030.13
80_A145_V0.6010.13
46_I49_D0.6000.13
78_N182_T0.6000.13
5_V150_R0.5980.13
62_V166_H0.5970.13
124_V145_V0.5950.13
56_L111_G0.5900.13
89_A99_A0.5890.13
63_R115_V0.5860.13
127_H174_V0.5830.12
85_Q105_I0.5820.12
13_T41_F0.5800.12
96_H107_V0.5770.12
86_A172_P0.5760.12
22_L34_R0.5750.12
21_D34_R0.5730.12
48_D122_P0.5720.12
35_C177_A0.5690.12
5_V119_V0.5690.12
47_R104_G0.5680.12
78_N136_V0.5680.12
2_R124_V0.5660.12
133_L141_D0.5660.12
38_A156_E0.5640.12
52_V123_V0.5640.12
49_D107_V0.5620.12
86_A103_P0.5600.12
122_P163_A0.5570.12
66_A128_E0.5560.12
130_G146_L0.5560.12
23_P73_H0.5560.12
42_V170_V0.5510.12
108_S184_A0.5490.12
12_P132_A0.5460.12
31_V184_A0.5450.12
70_Q159_L0.5430.12
64_I100_S0.5410.12
98_E125_A0.5400.12
46_I50_V0.5340.12
39_A123_V0.5330.12
23_P108_S0.5310.12
21_D43_S0.5290.11
23_P60_V0.5270.11
74_P80_A0.5260.11
40_L78_N0.5220.11
69_V168_V0.5200.11
21_D77_R0.5200.11
125_A174_V0.5170.11
40_L87_L0.5150.11
16_D140_A0.5140.11
66_A78_N0.5130.11
9_H38_A0.5090.11
124_V153_T0.5070.11
82_L85_Q0.5060.11
8_G149_H0.5060.11
21_D74_P0.5040.11
89_A181_I0.5040.11
11_A29_L0.5020.11
16_D135_A0.5010.11
17_F56_L0.5000.11
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  
2qwvA 2 0.9337 100 0.189 Contact Map
3aiaA 2 0.9694 100 0.37 Contact Map
2qmmA 2 0.9592 100 0.459 Contact Map
3oiiA 2 0.898 93.8 0.929 Contact Map
2egvA 2 0.9031 91.1 0.935 Contact Map
1z85A 2 0.8316 90.9 0.935 Contact Map
3bbdA 2 0.8929 90.5 0.936 Contact Map
4l69A 2 0.9235 87 0.94 Contact Map
1vhyA 2 0.949 86.5 0.94 Contact Map
1vhkA 3 0.9286 86.3 0.94 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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