GREMLIN Database
TRM56 - tRNA (cytidine(56)-2'-O)-methyltransferase
UniProt: Q980M4 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 160 (151)
Sequences: 204 (139)
Seq/√Len: 11.3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
1_M120_V4.2060.99
32_K36_S3.2390.97
102_Y125_I3.1020.96
78_F110_I2.9760.95
113_G122_A2.7780.92
55_V65_I2.7420.92
8_V12_F2.6380.90
55_V102_Y2.6250.90
58_W63_G2.5080.88
73_I78_F2.5040.87
100_G104_H2.2820.82
2_T19_I2.1830.79
54_I90_L2.1500.78
91_I126_F2.1320.77
64_T87_Y2.0330.74
55_V92_I1.9240.69
18_Y54_I1.8840.68
53_S57_E1.8380.66
146_K157_I1.8330.65
131_Y135_E1.8280.65
35_D81_R1.8030.64
111_A145_I1.7620.62
64_T89_L1.7000.59
58_W147_I1.6920.59
84_K87_Y1.6810.58
58_W65_I1.6640.58
99_E102_Y1.6480.57
91_I147_I1.6450.57
26_M29_S1.6430.57
18_Y75_I1.6400.56
29_S37_W1.6290.56
51_G102_Y1.5980.54
2_T58_W1.5930.54
111_A114_N1.5840.54
1_M23_D1.5410.52
56_N151_K1.4980.49
51_G101_W1.4780.48
6_I30_I1.4470.47
8_V22_K1.3880.44
106_A112_I1.3400.42
73_I111_A1.3330.42
66_I89_L1.3160.41
79_Q126_F1.2880.39
31_L147_I1.2680.38
57_E134_R1.2530.38
16_G49_E1.2500.38
52_K91_I1.2490.38
66_I126_F1.2460.37
15_K131_Y1.2350.37
113_G135_E1.2230.36
35_D144_K1.1870.35
96_E128_D1.1860.35
55_V74_N1.1790.34
6_I96_E1.1660.34
59_K105_N1.1480.33
23_D145_I1.1470.33
5_V96_E1.1450.33
71_Y154_K1.1370.33
103_Y150_Q1.1340.32
25_K95_A1.1180.32
37_W51_G1.1080.31
33_V52_K1.0940.31
18_Y90_L1.0920.31
137_Y147_I1.0900.31
69_T130_I1.0750.30
84_K91_I1.0560.29
20_E36_S1.0520.29
76_N108_Y1.0310.28
26_M105_N1.0180.28
37_W59_K1.0120.27
84_K141_E1.0080.27
10_R13_G1.0000.27
15_K121_A0.9850.26
27_V31_L0.9800.26
113_G121_A0.9740.26
19_I58_W0.9730.26
5_V93_V0.9530.25
111_A147_I0.9450.25
117_H121_A0.9400.25
31_L127_L0.9390.25
16_G44_L0.9370.25
82_F103_Y0.9340.25
150_Q155_K0.9320.24
16_G29_S0.9240.24
45_V93_V0.9230.24
16_G46_K0.9200.24
66_I123_L0.9170.24
54_I137_Y0.9120.24
51_G99_E0.9110.24
66_I69_T0.9040.23
50_N150_Q0.9010.23
16_G76_N0.8980.23
93_V123_L0.8960.23
76_N113_G0.8940.23
40_S125_I0.8940.23
100_G113_G0.8930.23
64_T108_Y0.8830.23
23_D26_M0.8820.23
9_A125_I0.8810.23
69_T126_F0.8740.22
64_T85_I0.8730.22
23_D63_G0.8630.22
69_T123_L0.8620.22
85_I108_Y0.8530.22
65_I106_A0.8530.22
96_E114_N0.8420.21
74_N77_D0.8330.21
4_H7_L0.8300.21
113_G137_Y0.8290.21
53_S73_I0.8250.21
30_I34_I0.8240.21
81_R89_L0.8210.21
37_W147_I0.8200.21
70_M124_A0.8180.21
6_I32_K0.8130.20
33_V55_V0.7950.20
78_F81_R0.7920.20
6_I17_V0.7760.19
44_L50_N0.7650.19
25_K155_K0.7650.19
49_E75_I0.7620.19
50_N142_D0.7550.19
30_I120_V0.7490.18
80_D112_I0.7460.18
16_G140_F0.7460.18
50_N80_D0.7340.18
15_K114_N0.7340.18
125_I137_Y0.7330.18
53_S139_E0.7280.18
120_V156_V0.7230.18
123_L126_F0.7150.18
45_V53_S0.7140.17
94_G119_E0.7140.17
16_G77_D0.7060.17
91_I138_M0.7020.17
45_V54_I0.7020.17
111_A121_A0.7020.17
19_I47_E0.7000.17
97_K128_D0.6980.17
94_G118_S0.6960.17
114_N121_A0.6950.17
65_I105_N0.6930.17
12_F65_I0.6930.17
7_L10_R0.6900.17
7_L13_G0.6900.17
71_Y133_G0.6870.17
26_M145_I0.6840.17
50_N112_I0.6800.17
28_K146_K0.6780.17
75_I133_G0.6750.16
129_R156_V0.6730.16
74_N111_A0.6720.16
9_A157_I0.6660.16
45_V142_D0.6620.16
2_T121_A0.6560.16
17_V102_Y0.6550.16
16_G147_I0.6550.16
40_S45_V0.6530.16
5_V112_I0.6500.16
33_V91_I0.6490.16
44_L148_L0.6450.16
122_A145_I0.6450.16
58_W90_L0.6440.16
12_F144_K0.6430.16
28_K31_L0.6380.15
126_F135_E0.6360.15
8_V147_I0.6330.15
83_E132_K0.6250.15
67_H118_S0.6250.15
137_Y144_K0.6190.15
45_V88_P0.6120.15
73_I151_K0.6110.15
65_I122_A0.6070.15
5_V120_V0.6060.15
23_D140_F0.6040.15
28_K132_K0.6040.15
2_T147_I0.6030.15
111_A150_Q0.6030.15
29_S96_E0.6030.15
30_I43_F0.6020.15
7_L14_A0.5980.14
82_F105_N0.5970.14
3_T7_L0.5970.14
12_F125_I0.5890.14
8_V132_K0.5860.14
8_V84_K0.5840.14
46_K108_Y0.5820.14
54_I65_I0.5800.14
47_E95_A0.5790.14
128_D154_K0.5780.14
18_Y89_L0.5780.14
31_L35_D0.5750.14
17_V21_G0.5740.14
5_V128_D0.5730.14
150_Q153_G0.5720.14
1_M122_A0.5710.14
57_E141_E0.5700.14
35_D150_Q0.5670.14
16_G33_V0.5580.14
120_V129_R0.5550.13
71_Y103_Y0.5500.13
46_K54_I0.5480.13
89_L108_Y0.5480.13
98_V119_E0.5470.13
94_G98_V0.5470.13
77_D91_I0.5450.13
6_I21_G0.5390.13
55_V143_A0.5310.13
32_K87_Y0.5300.13
19_I26_M0.5290.13
89_L130_I0.5250.13
126_F133_G0.5250.13
56_N105_N0.5200.13
98_V118_S0.5200.13
12_F103_Y0.5180.13
19_I75_I0.5180.13
78_F83_E0.5160.13
90_L117_H0.5130.13
56_N79_Q0.5120.13
75_I150_Q0.5110.12
75_I131_Y0.5110.12
99_E142_D0.5100.12
63_G126_F0.5100.12
51_G88_P0.5100.12
71_Y92_I0.5050.12
85_I157_I0.5000.12
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  
2yy8A 2 0.9688 100 0.057 Contact Map
2o3aA 2 0.9125 100 0.078 Contact Map
1v2xA 2 0.9187 98.5 0.866 Contact Map
1zjrA 2 0.9313 98.3 0.875 Contact Map
2ha8A 2 0.8063 98.2 0.879 Contact Map
3dcmX 2 0.8438 97.7 0.892 Contact Map
1gz0A 2 0.7875 97.6 0.895 Contact Map
3n4jA 2 0.8313 97.5 0.896 Contact Map
4kgnA 2 0.825 97.4 0.899 Contact Map
3nk6A 2 0.8438 96.9 0.906 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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