GREMLIN Database
TRML - Putative tRNA (cytidine(34)-2'-O)-methyltransferase
UniProt: O31590 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 160 (146)
Sequences: 12017 (7263)
Seq/√Len: 601.1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
106_F139_L3.3421.00
9_V103_F2.9181.00
141_N144_A2.9091.00
83_T122_M2.6751.00
149_E152_R2.5501.00
106_F143_A2.5181.00
115_K119_Q2.4591.00
22_I143_A2.2851.00
11_Y114_P2.0491.00
66_S69_E1.8951.00
84_K146_L1.8801.00
37_R65_D1.8441.00
72_E121_N1.8421.00
108_R111_S1.8341.00
33_L62_V1.8051.00
33_L60_N1.7981.00
29_T148_Y1.7821.00
31_T147_V1.7531.00
87_Q127_R1.7051.00
8_V147_V1.6921.00
8_V22_I1.6631.00
88_Q124_R1.6531.00
80_F124_R1.6481.00
85_F118_I1.6251.00
83_T113_L1.6181.00
52_G56_W1.5601.00
27_A132_E1.5571.00
23_A34_H1.5481.00
143_A147_V1.5231.00
88_Q92_S1.5141.00
14_E110_T1.4941.00
74_Y103_F1.4941.00
104_F146_L1.4941.00
26_C31_T1.4771.00
7_H33_L1.4421.00
28_A130_M1.4381.00
104_F150_A1.4101.00
37_R63_Y1.3881.00
93_F126_L1.3851.00
118_I125_C1.3591.00
128_L142_T1.3451.00
27_A59_V1.3441.00
83_T125_C1.2901.00
55_Y134_V1.2681.00
75_K123_D1.2591.00
23_A61_V1.2481.00
90_H95_Y1.2431.00
27_A58_F1.2361.00
82_I146_L1.2291.00
49_K56_W1.2291.00
29_T90_H1.2281.00
13_P139_L1.2171.00
88_Q93_F1.1991.00
82_I126_L1.1951.00
27_A55_Y1.1861.00
6_L31_T1.1641.00
70_L74_Y1.1401.00
82_I124_R1.1391.00
73_A77_G1.1311.00
68_E72_E1.1261.00
25_T141_N1.1231.00
58_F133_H1.1211.00
89_P127_R1.1191.00
149_E153_Q1.1181.00
90_H146_L1.1151.00
21_N140_S1.1051.00
68_E121_N1.0861.00
32_T60_N1.0851.00
8_V26_C1.0761.00
89_P92_S1.0681.00
27_A134_V1.0661.00
5_A32_T1.0491.00
28_A134_V1.0411.00
36_I61_V1.0361.00
114_P117_L1.0321.00
131_T151_L1.0271.00
23_A56_W1.0151.00
86_G125_C1.0071.00
17_A21_N1.0031.00
6_L150_A1.0011.00
67_L71_F1.0011.00
12_Q39_L1.0011.00
72_E76_K0.9811.00
35_L70_L0.9741.00
25_T144_A0.9671.00
11_Y117_L0.9621.00
29_T151_L0.9611.00
67_L117_L0.9541.00
122_M125_C0.9471.00
79_F103_F0.9341.00
30_N131_T0.9271.00
106_F142_T0.9251.00
105_V113_L0.9241.00
25_T147_V0.9241.00
95_Y150_A0.9201.00
29_T145_I0.9201.00
126_L146_L0.9191.00
9_V105_V0.9171.00
72_E75_K0.9161.00
10_L22_I0.9141.00
19_T36_I0.9091.00
49_K57_E0.9031.00
85_F125_C0.8921.00
32_T62_V0.8821.00
95_Y99_D0.8781.00
12_Q108_R0.8771.00
71_F81_F0.8621.00
17_A51_A0.8561.00
68_E116_D0.8551.00
12_Q111_S0.8521.00
11_Y113_L0.8471.00
19_T41_F0.8461.00
23_A59_V0.8441.00
27_A133_H0.8421.00
7_H35_L0.8411.00
8_V106_F0.8361.00
35_L64_H0.8311.00
93_F124_R0.8271.00
42_S47_M0.8221.00
36_I40_G0.8201.00
8_V31_T0.8011.00
81_F84_K0.7871.00
116_D119_Q0.7781.00
75_K121_N0.7771.00
29_T147_V0.7651.00
14_E108_R0.7651.00
64_H70_L0.7631.00
71_F121_N0.7601.00
38_P65_D0.7591.00
80_F123_D0.7581.00
71_F117_L0.7551.00
19_T48_L0.7511.00
21_N141_N0.7501.00
69_E72_E0.7491.00
44_D47_M0.7461.00
12_Q114_P0.7451.00
7_H32_T0.7411.00
91_T152_R0.7391.00
43_T63_Y0.7361.00
6_L32_T0.7341.00
22_I139_L0.7291.00
150_A154_Q0.7291.00
44_D48_L0.7251.00
9_V67_L0.7191.00
95_Y153_Q0.7161.00
140_S144_A0.7161.00
14_E111_S0.7151.00
116_D121_N0.7141.00
5_A98_L0.7121.00
121_N124_R0.7071.00
83_T118_I0.7001.00
96_T99_D0.6981.00
70_L103_F0.6961.00
81_F122_M0.6941.00
65_D69_E0.6931.00
78_K81_F0.6881.00
115_K118_I0.6871.00
73_A76_K0.6831.00
80_F83_T0.6801.00
69_E73_A0.6761.00
78_K83_T0.6751.00
137_L145_I0.6741.00
81_F103_F0.6741.00
128_L145_I0.6681.00
145_I148_Y0.6671.00
85_F127_R0.6471.00
26_C34_H0.6461.00
105_V117_L0.6451.00
11_Y108_R0.6431.00
17_A140_S0.6421.00
7_H103_F0.6411.00
13_P22_I0.6371.00
10_L19_T0.6351.00
31_T150_A0.6321.00
106_F146_L0.6311.00
17_A47_M0.6291.00
96_T153_Q0.6221.00
25_T143_A0.6221.00
6_L147_V0.6181.00
113_L122_M0.6121.00
7_H79_F0.6051.00
45_D48_L0.5991.00
9_V70_L0.5951.00
12_Q37_R0.5911.00
58_F134_V0.5861.00
91_T129_P0.5821.00
91_T148_Y0.5771.00
81_F105_V0.5741.00
25_T28_A0.5721.00
28_A137_L0.5721.00
70_L73_A0.5721.00
78_K99_D0.5711.00
94_D153_Q0.5701.00
74_Y79_F0.5651.00
42_S45_D0.5641.00
35_L39_L0.5611.00
23_A48_L0.5601.00
23_A27_A0.5591.00
71_F75_K0.5510.99
41_F45_D0.5470.99
78_K84_K0.5450.99
62_V73_A0.5450.99
81_F121_N0.5430.99
10_L13_P0.5420.99
38_P66_S0.5380.99
9_V37_R0.5330.99
22_I106_F0.5310.99
34_H64_H0.5210.99
53_L110_T0.5150.99
29_T91_T0.5120.99
29_T128_L0.5120.99
43_T61_V0.5100.99
88_Q91_T0.5100.99
82_I99_D0.5100.99
10_L106_F0.5070.99
77_G81_F0.5060.99
75_K81_F0.5050.99
25_T29_T0.5020.99
131_T134_V0.5000.99
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  
1gz0A 2 0.9437 100 0.122 Contact Map
1ipaA 1 0.9375 100 0.128 Contact Map
1x7oA 2 0.975 100 0.138 Contact Map
2i6dA 2 0.9437 100 0.142 Contact Map
3nk6A 2 0.9625 100 0.147 Contact Map
1zjrA 2 0.9688 100 0.17 Contact Map
4kgnA 2 0.9625 100 0.17 Contact Map
4pzkA 2 0.9688 100 0.17 Contact Map
3n4jA 2 0.9563 100 0.178 Contact Map
1v2xA 2 0.9625 100 0.182 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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