GREMLIN Database
TRML - tRNA (cytidine(34)-2'-O)-methyltransferase
UniProt: P0AGJ7 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG11888
Length: 157 (143)
Sequences: 11976 (7285)
Seq/√Len: 609.2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
99_F133_L3.2221.00
5_V96_Y2.8341.00
135_N138_S2.8181.00
143_E146_R2.5301.00
99_F137_V2.4351.00
108_A112_D2.3701.00
18_I137_V2.1891.00
7_Y107_P1.9631.00
80_T140_V1.9571.00
29_L58_T1.8711.00
79_T106_L1.8611.00
62_D65_A1.8571.00
29_L56_A1.7961.00
33_E61_H1.7761.00
101_P104_R1.7701.00
27_F141_V1.7561.00
25_T142_Y1.7241.00
83_T121_R1.7231.00
84_P118_Q1.6981.00
76_F118_Q1.6751.00
4_I18_I1.6621.00
68_E113_A1.6321.00
81_K111_L1.6311.00
19_I30_H1.5441.00
4_I141_V1.5191.00
48_G52_H1.5191.00
70_E96_Y1.5151.00
23_A126_P1.5071.00
137_V141_V1.4871.00
22_C27_F1.4801.00
89_V120_I1.4701.00
10_E103_T1.4631.00
24_N124_M1.4161.00
97_L140_V1.4151.00
111_L119_K1.3731.00
71_N117_E1.3681.00
33_E59_R1.3601.00
122_I136_A1.3461.00
79_T119_K1.3451.00
97_L144_A1.3321.00
25_T86_H1.3251.00
23_A55_T1.3121.00
86_H140_V1.3111.00
78_L118_Q1.2681.00
23_A54_F1.2421.00
19_I57_V1.2281.00
78_L120_I1.2271.00
51_Y128_S1.2111.00
45_R52_H1.2031.00
9_P133_L1.1911.00
3_N29_L1.1711.00
23_A51_Y1.1691.00
64_R113_A1.1611.00
143_E147_Q1.1591.00
3_N28_R1.1461.00
69_A73_Q1.1461.00
54_F127_D1.1411.00
125_V145_W1.1161.00
86_H91_Y1.1141.00
91_Y144_A1.1041.00
21_L135_N1.1031.00
78_L140_V1.1011.00
17_N134_S1.0991.00
64_R68_E1.0941.00
85_A121_R1.0941.00
66_F70_E1.0901.00
82_G119_K1.0811.00
85_A88_A1.0681.00
28_R56_A1.0661.00
84_P88_A1.0561.00
4_I22_C1.0341.00
81_K119_K1.0341.00
95_D144_A1.0331.00
24_N128_S1.0331.00
84_P89_V1.0291.00
23_A128_S1.0261.00
60_H66_F1.0261.00
63_Y67_L1.0211.00
75_L94_G1.0211.00
31_I60_H1.0161.00
32_I57_V1.0121.00
75_L96_Y1.0101.00
78_L95_D1.0081.00
19_I52_H1.0041.00
13_P17_N1.0031.00
107_P110_I1.0031.00
21_L141_V0.9831.00
7_Y110_I0.9821.00
25_T145_W0.9781.00
63_Y110_I0.9521.00
99_F136_A0.9521.00
21_L138_S0.9471.00
89_V118_Q0.9361.00
8_E35_M0.9251.00
45_R53_E0.9251.00
68_E71_N0.9241.00
120_I140_V0.9241.00
31_I66_F0.9221.00
26_G125_V0.9201.00
8_E101_P0.9131.00
98_M106_L0.9111.00
67_L77_A0.9081.00
6_L18_I0.9051.00
28_R58_T0.8981.00
25_T139_V0.8941.00
15_T32_I0.8911.00
109_S113_A0.8791.00
67_L113_A0.8781.00
71_N113_A0.8721.00
64_R109_S0.8631.00
87_S146_R0.8621.00
76_F117_E0.8611.00
19_I55_T0.8541.00
15_T37_F0.8521.00
8_E104_R0.8461.00
5_V98_M0.8431.00
7_Y106_L0.8361.00
13_P47_A0.8341.00
91_Y95_D0.8331.00
32_I36_G0.8171.00
3_N31_I0.8161.00
68_E72_P0.8131.00
40_D43_R0.8091.00
23_A127_D0.8051.00
67_L110_I0.8051.00
65_A68_E0.8041.00
109_S112_D0.7991.00
91_Y147_Q0.7991.00
38_A43_R0.7961.00
10_E101_P0.7891.00
8_E107_P0.7791.00
34_P61_H0.7721.00
4_I99_F0.7651.00
15_T44_L0.7631.00
4_I27_F0.7531.00
17_N135_N0.7461.00
76_F95_D0.7421.00
131_M139_V0.7401.00
66_F96_Y0.7371.00
61_H65_A0.7371.00
18_I133_L0.7311.00
144_A148_L0.7291.00
25_T141_V0.7281.00
39_W59_R0.7271.00
108_A111_L0.7261.00
134_S138_S0.7191.00
74_R95_D0.7191.00
10_E104_R0.7171.00
77_A96_Y0.7121.00
87_S123_P0.7101.00
27_F144_A0.7091.00
5_V63_Y0.7091.00
21_L137_V0.7061.00
92_Q95_D0.6851.00
40_D44_L0.6851.00
81_K121_R0.6781.00
87_S142_Y0.6761.00
77_A98_M0.6711.00
13_P134_S0.6671.00
139_V142_Y0.6671.00
9_P18_I0.6611.00
98_M110_I0.6591.00
25_T87_S0.6591.00
122_I139_V0.6541.00
3_N96_Y0.6531.00
13_P43_R0.6511.00
69_A72_P0.6501.00
7_Y101_P0.6481.00
70_E75_L0.6471.00
8_E33_E0.6441.00
54_F128_S0.6371.00
79_T111_L0.6361.00
77_A80_T0.6341.00
71_N77_A0.6301.00
60_H69_A0.6251.00
65_A69_A0.6191.00
5_V66_F0.6191.00
24_N131_M0.6131.00
76_F79_T0.6131.00
3_N75_L0.6121.00
99_F140_V0.6121.00
41_D44_L0.6031.00
22_C30_H0.6011.00
18_I99_F0.6001.00
6_L15_T0.5951.00
21_L24_N0.5921.00
39_W57_V0.5901.00
58_T69_A0.5821.00
19_I23_A0.5801.00
90_S147_Q0.5781.00
6_L99_F0.5761.00
87_S145_W0.5761.00
19_I44_L0.5681.00
6_L9_P0.5641.00
125_V128_S0.5611.00
82_G121_R0.5591.00
38_A41_D0.5561.00
92_Q147_Q0.5551.00
37_F41_D0.5510.99
84_P87_S0.5390.99
16_G47_A0.5340.99
25_T122_I0.5330.99
34_P62_D0.5320.99
31_I35_M0.5320.99
78_L89_V0.5220.99
3_N70_E0.5200.99
67_L71_N0.5180.99
76_F93_D0.5100.99
23_A125_V0.5090.99
78_L91_Y0.5070.99
60_H65_A0.5030.99
22_C141_V0.5020.99
5_V67_L0.5010.99
110_I113_A0.5000.99
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  
1ipaA 1 0.9299 100 0.136 Contact Map
1gz0A 2 0.9363 100 0.137 Contact Map
1x7oA 2 0.9682 100 0.151 Contact Map
2i6dA 2 0.9172 100 0.16 Contact Map
3nk6A 2 0.9809 100 0.162 Contact Map
4kgnA 2 0.9682 100 0.169 Contact Map
3n4jA 2 0.9745 100 0.175 Contact Map
4pzkA 2 0.9873 100 0.186 Contact Map
1zjrA 2 0.9809 100 0.188 Contact Map
1v2xA 2 0.9745 100 0.2 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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