GREMLIN Database
TRMA - tRNA/tmRNA (uracil-C(5))-methyltransferase
UniProt: P23003 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG11022
Length: 366 (347)
Sequences: 5364 (3843)
Seq/√Len: 206.3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
333_L363_L4.1361.00
343_E364_T3.9011.00
13_A16_A3.5251.00
19_V23_Q3.4111.00
202_W205_D3.0411.00
228_L297_F3.0131.00
334_E338_Q2.9831.00
234_R261_Q2.8951.00
81_S112_T2.7541.00
73_R92_I2.7441.00
124_Y152_L2.7371.00
14_Q353_Y2.7231.00
296_I313_V2.6721.00
65_D70_S2.5101.00
206_V344_R2.4831.00
219_C237_A2.4501.00
4_E77_F2.4391.00
20_V24_S2.3581.00
342_V361_V2.3461.00
298_V305_L2.3371.00
265_M270_F2.3001.00
213_D234_R2.2681.00
182_R250_Y2.2501.00
19_V35_E2.2211.00
184_V247_A2.1291.00
203_A322_I2.1261.00
215_L293_C2.1151.00
11_Y15_L2.0701.00
266_A269_E2.0151.00
19_V36_V2.0071.00
43_H82_E1.9581.00
22_L357_M1.9491.00
329_L359_C1.9471.00
239_E245_V1.9441.00
310_E335_T1.9431.00
329_L361_V1.9341.00
201_E205_D1.9291.00
314_Q339_T1.9131.00
87_L118_A1.9031.00
313_V319_I1.9001.00
199_M348_F1.8981.00
180_I254_A1.8941.00
219_C245_V1.8901.00
294_E317_P1.8611.00
250_Y253_A1.8611.00
310_E336_L1.8571.00
58_D96_R1.8011.00
305_L310_E1.7911.00
318_R364_T1.7241.00
204_L231_N1.7011.00
52_I108_I1.6841.00
16_A19_V1.6791.00
257_I260_V1.6711.00
329_L333_L1.6541.00
214_L232_F1.6451.00
22_L347_L1.6391.00
82_E86_Q1.6281.00
307_S311_K1.6271.00
225_S235_V1.6131.00
84_I110_Y1.6061.00
10_Q13_A1.6051.00
83_L112_T1.6021.00
119_V149_N1.5891.00
20_V23_Q1.5831.00
179_M230_R1.5771.00
202_W346_A1.5731.00
197_I201_E1.5731.00
15_L38_R1.5571.00
207_T295_T1.5301.00
242_K246_A1.5191.00
31_D334_E1.5091.00
37_F198_Q1.5051.00
48_A80_A1.4961.00
237_A248_A1.4951.00
37_F348_F1.4931.00
27_A33_V1.4831.00
206_V362_L1.4811.00
46_M193_A1.4721.00
26_M333_L1.4661.00
95_V105_L1.4561.00
53_W71_R1.4501.00
26_M345_L1.4391.00
9_E13_A1.4261.00
341_K364_T1.4251.00
212_G294_E1.4141.00
209_G212_G1.3861.00
211_K233_D1.3781.00
248_A262_I1.3731.00
177_K227_A1.3701.00
55_D58_D1.3701.00
76_S85_N1.3551.00
26_M329_L1.3491.00
109_D121_S1.3471.00
246_A249_Q1.3361.00
179_M226_L1.3181.00
138_A141_D1.3061.00
178_E230_R1.2921.00
43_H78_P1.2861.00
333_L342_V1.2841.00
319_I340_H1.2651.00
16_A20_V1.2601.00
226_L252_I1.2571.00
117_Q148_L1.2541.00
202_W206_V1.2481.00
226_L260_V1.2471.00
44_Y354_T1.2391.00
325_N328_T1.2351.00
343_E362_L1.2331.00
171_R180_I1.2301.00
86_Q146_Q1.2281.00
359_C363_L1.2261.00
90_A143_L1.2231.00
5_H355_H1.2211.00
101_L158_K1.2161.00
137_E141_D1.2141.00
4_E7_P1.2121.00
9_E17_E1.2101.00
203_A320_L1.1901.00
23_Q27_A1.1881.00
252_I262_I1.1811.00
237_A260_V1.1811.00
52_I61_H1.1781.00
83_L86_Q1.1761.00
138_A142_A1.1701.00
149_N170_E1.1661.00
25_M326_P1.1511.00
311_K315_A1.1451.00
237_A262_I1.1431.00
59_L96_R1.1431.00
104_K126_K1.1351.00
319_I336_L1.1321.00
298_V321_Y1.1311.00
37_F346_A1.1241.00
6_L17_E1.1221.00
133_R137_E1.1171.00
151_H185_E1.1141.00
167_Y170_E1.1141.00
15_L36_V1.0991.00
42_S353_Y1.0991.00
213_D236_L1.0961.00
93_A96_R1.0941.00
202_W344_R1.0911.00
242_K264_R1.0901.00
250_Y254_A1.0841.00
317_P340_H1.0831.00
344_R362_L1.0781.00
83_L118_A1.0781.00
202_W360_G1.0781.00
171_R178_E1.0761.00
59_L95_V1.0751.00
75_D89_T1.0701.00
202_W348_F1.0691.00
238_T270_F1.0611.00
51_R71_R1.0541.00
137_E140_R1.0531.00
251_N255_N1.0501.00
120_V147_N1.0491.00
51_R64_F1.0441.00
206_V346_A1.0431.00
41_V353_Y1.0381.00
249_Q253_A1.0381.00
187_S247_A1.0381.00
139_L147_N1.0351.00
80_A84_I1.0301.00
167_Y186_N1.0281.00
87_L90_A1.0281.00
229_A257_I1.0261.00
40_P198_Q1.0251.00
320_L362_L1.0241.00
129_D132_W1.0241.00
198_Q201_E1.0191.00
318_R362_L1.0141.00
3_P77_F1.0131.00
43_H76_S1.0131.00
203_A297_F1.0131.00
217_L309_T1.0111.00
225_S260_V1.0031.00
236_L263_I1.0001.00
198_Q348_F0.9951.00
196_N223_N0.9891.00
208_K318_R0.9881.00
204_L227_A0.9871.00
43_H85_N0.9821.00
207_T320_L0.9811.00
93_A142_A0.9811.00
195_M198_Q0.9801.00
236_L293_C0.9781.00
135_E138_A0.9771.00
187_S244_S0.9701.00
193_A196_N0.9701.00
136_A140_R0.9681.00
182_R254_A0.9681.00
345_L361_V0.9681.00
293_C296_I0.9681.00
317_P364_T0.9611.00
333_L361_V0.9590.99
30_S330_C0.9590.99
179_M257_I0.9580.99
360_G364_T0.9560.99
214_L295_T0.9560.99
232_F259_N0.9530.99
132_W136_A0.9510.99
90_A142_A0.9510.99
83_L146_Q0.9500.99
219_C239_E0.9470.99
199_M350_Q0.9440.99
132_W139_L0.9440.99
127_K166_D0.9440.99
335_T338_Q0.9430.99
191_P350_Q0.9430.99
342_V363_L0.9390.99
246_A250_Y0.9350.99
147_N150_V0.9340.99
266_A270_F0.9330.99
87_L143_L0.9240.99
162_E166_D0.9220.99
245_V264_R0.9180.99
105_L122_L0.9140.99
219_C248_A0.9110.99
179_M229_A0.9110.99
26_M330_C0.9090.99
216_E237_A0.9080.99
195_M350_Q0.9080.99
322_I360_G0.9060.99
35_E347_L0.9040.99
177_K197_I0.9020.99
121_S185_E0.9020.99
64_F68_T0.8990.99
265_M269_E0.8990.99
177_K201_E0.8960.99
311_K335_T0.8940.99
200_L224_F0.8890.99
219_C262_I0.8870.99
204_L230_R0.8830.99
307_S335_T0.8810.99
361_V364_T0.8780.99
18_K349_D0.8750.99
69_K98_N0.8750.99
298_V313_V0.8730.99
143_L146_Q0.8730.99
253_A258_D0.8700.99
320_L360_G0.8690.99
131_E134_Q0.8660.99
134_Q137_E0.8650.99
213_D233_D0.8650.99
359_C364_T0.8530.99
218_Y268_E0.8480.99
306_D310_E0.8470.99
267_A271_T0.8470.99
92_I96_R0.8410.99
342_V345_L0.8380.99
81_S85_N0.8360.99
12_E16_A0.8330.99
191_P329_L0.8330.99
48_A63_I0.8320.99
155_R160_K0.8260.98
112_T118_A0.8240.98
37_F202_W0.8200.98
313_V316_Y0.8200.98
270_F274_M0.8170.98
7_P42_S0.8160.98
104_K125_H0.8150.98
270_F273_A0.8150.98
269_E272_Q0.8120.98
48_A84_I0.8110.98
62_I71_R0.8070.98
169_D180_I0.8060.98
243_P246_A0.8040.98
249_Q261_Q0.8040.98
321_Y329_L0.8040.98
182_R247_A0.8040.98
65_D72_I0.8020.98
199_M360_G0.8010.98
226_L257_I0.8000.98
214_L228_L0.8000.98
323_S328_T0.8000.98
25_M330_C0.8000.98
337_S341_K0.7950.98
240_I266_A0.7940.98
265_M271_T0.7930.98
273_A289_K0.7930.98
7_P77_F0.7890.98
206_V360_G0.7890.98
236_L291_Y0.7890.98
61_H92_I0.7860.98
52_I105_L0.7850.98
46_M189_T0.7810.98
80_A85_N0.7810.98
25_M29_F0.7780.98
205_D344_R0.7780.98
188_F324_C0.7780.98
204_L225_S0.7770.98
139_L143_L0.7770.98
312_M316_Y0.7760.98
245_V249_Q0.7730.98
268_E306_D0.7730.98
11_Y38_R0.7720.98
125_H156_A0.7670.98
194_A197_I0.7640.98
40_P194_A0.7640.98
271_T274_M0.7640.98
97_N103_H0.7620.97
64_F69_K0.7580.97
89_T93_A0.7570.97
314_Q336_L0.7570.97
114_L197_I0.7570.97
314_Q335_T0.7570.97
171_R182_R0.7560.97
24_S27_A0.7530.97
324_C358_E0.7510.97
19_V346_A0.7490.97
13_A17_E0.7490.97
215_L271_T0.7430.97
52_I95_V0.7430.97
183_Q189_T0.7410.97
28_P32_L0.7400.97
97_N100_V0.7390.97
90_A93_A0.7390.97
50_F88_M0.7360.97
225_S262_I0.7330.97
167_Y185_E0.7320.97
124_Y128_L0.7290.97
206_V320_L0.7260.97
134_Q138_A0.7250.97
221_N225_S0.7240.97
335_T339_T0.7230.97
164_D167_Y0.7220.96
11_Y41_V0.7210.96
200_L227_A0.7190.96
139_L142_A0.7190.96
32_L337_S0.7170.96
91_M108_I0.7120.96
7_P79_A0.7110.96
208_K231_N0.7090.96
337_S342_V0.7060.96
229_A235_V0.7030.96
29_F32_L0.7020.96
179_M227_A0.6990.96
214_L235_V0.6990.96
109_D123_L0.6980.96
130_D133_R0.6980.96
204_L228_L0.6950.96
60_Y73_R0.6930.96
54_H57_D0.6920.96
11_Y349_D0.6910.96
55_D60_Y0.6890.95
162_E167_Y0.6890.95
19_V347_L0.6880.95
155_R159_T0.6850.95
81_S84_I0.6850.95
132_W168_I0.6840.95
87_L120_V0.6840.95
184_V187_S0.6810.95
213_D291_Y0.6800.95
275_N316_Y0.6790.95
153_I160_K0.6770.95
309_T313_V0.6760.95
44_Y353_Y0.6750.95
22_L359_C0.6750.95
177_K230_R0.6720.95
35_E346_A0.6720.95
332_N335_T0.6690.95
195_M348_F0.6670.95
126_K156_A0.6630.94
14_Q349_D0.6610.94
17_E21_R0.6600.94
151_H169_D0.6600.94
347_L357_M0.6600.94
224_F297_F0.6590.94
241_A244_S0.6570.94
198_Q202_W0.6570.94
276_G289_K0.6560.94
25_M28_P0.6540.94
122_L126_K0.6520.94
39_S194_A0.6510.94
269_E273_A0.6500.94
75_D92_I0.6490.94
164_D168_I0.6480.94
186_N243_P0.6470.94
357_M363_L0.6450.94
265_M272_Q0.6440.93
122_L150_V0.6430.93
212_G232_F0.6430.93
36_V347_L0.6420.93
160_K303_S0.6420.93
25_M327_E0.6420.93
39_S192_N0.6410.93
211_K232_F0.6390.93
50_F217_L0.6380.93
308_E311_K0.6370.93
351_F358_E0.6360.93
324_C351_F0.6360.93
155_R158_K0.6330.93
268_E272_Q0.6330.93
263_I270_F0.6330.93
94_G135_E0.6330.93
236_L261_Q0.6320.93
50_F61_H0.6310.93
242_K249_Q0.6300.93
47_R200_L0.6280.93
302_R356_H0.6280.93
190_Q324_C0.6260.93
164_D170_E0.6240.92
265_M268_E0.6200.92
263_I274_M0.6200.92
31_D337_S0.6200.92
32_L342_V0.6190.92
3_P7_P0.6190.92
6_L9_E0.6170.92
312_M315_A0.6150.92
267_A270_F0.6150.92
179_M255_N0.6150.92
189_T221_N0.6140.92
2_T77_F0.6140.92
326_P357_M0.6120.92
215_L296_I0.6110.92
305_L335_T0.6090.91
122_L125_H0.6090.91
51_R107_Q0.6080.91
112_T116_N0.6070.91
311_K339_T0.6020.91
103_H106_F0.5960.91
124_Y127_K0.5960.91
140_R150_V0.5950.91
91_M95_V0.5940.90
42_S78_P0.5920.90
87_L110_Y0.5920.90
32_L333_L0.5920.90
181_Y221_N0.5910.90
15_L39_S0.5880.90
238_T267_A0.5870.90
248_A260_V0.5840.90
217_L296_I0.5840.90
237_A245_V0.5830.90
245_V262_I0.5820.90
123_L128_L0.5790.89
295_T320_L0.5790.89
53_W60_Y0.5780.89
111_L189_T0.5780.89
61_H110_Y0.5780.89
126_K129_D0.5770.89
188_F358_E0.5770.89
44_Y192_N0.5760.89
86_Q90_A0.5730.89
199_M322_I0.5730.89
212_G317_P0.5710.89
136_A150_V0.5680.88
275_N312_M0.5660.88
110_Y120_V0.5660.88
29_F331_K0.5630.88
84_I112_T0.5630.88
348_F360_G0.5620.88
163_L167_Y0.5600.88
94_G142_A0.5600.88
149_N153_I0.5600.88
177_K204_L0.5590.88
50_F84_I0.5580.88
36_V39_S0.5580.88
123_L127_K0.5560.87
24_S28_P0.5550.87
119_V123_L0.5550.87
132_W135_E0.5540.87
327_E331_K0.5540.87
302_R324_C0.5530.87
21_R327_E0.5520.87
75_D78_P0.5520.87
98_N103_H0.5520.87
336_L363_L0.5510.87
212_G295_T0.5490.87
181_Y223_N0.5490.87
167_Y171_R0.5490.87
39_S195_M0.5490.87
204_L214_L0.5490.87
163_L168_I0.5440.86
249_Q252_I0.5420.86
113_T117_Q0.5400.86
188_F351_F0.5390.86
267_A309_T0.5370.86
91_M122_L0.5360.85
65_D68_T0.5360.85
247_A250_Y0.5350.85
268_E271_T0.5340.85
90_A138_A0.5340.85
188_F300_P0.5330.85
298_V319_I0.5310.85
272_Q275_N0.5310.85
51_R63_I0.5300.85
29_F334_E0.5300.85
132_W152_L0.5290.85
61_H95_V0.5290.85
50_F74_V0.5280.85
334_E337_S0.5250.84
2_T72_I0.5240.84
252_I260_V0.5230.84
345_L359_C0.5230.84
203_A360_G0.5220.84
357_M362_L0.5200.84
148_L152_L0.5170.83
359_C362_L0.5160.83
311_K314_Q0.5160.83
330_C334_E0.5150.83
196_N200_L0.5150.83
200_L223_N0.5130.83
11_Y39_S0.5120.83
151_H167_Y0.5120.83
28_P31_D0.5110.83
153_I159_T0.5110.83
268_E308_E0.5100.82
353_Y356_H0.5080.82
50_F80_A0.5070.82
144_R147_N0.5060.82
245_V248_A0.5060.82
169_D182_R0.5050.82
179_M221_N0.5050.82
210_S318_R0.5020.82
53_W64_F0.5020.82
104_K124_Y0.5020.82
189_T223_N0.5020.82
208_K212_G0.5010.81
4_E79_A0.5000.81
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  
3bt7A 1 1 100 0.246 Contact Map
2jjqA 1 0.8607 100 0.292 Contact Map
1uwvA 1 0.9208 100 0.293 Contact Map
3vseA 1 0.888 100 0.645 Contact Map
4dmgA 2 0.8689 100 0.65 Contact Map
1wxxA 2 0.8607 100 0.657 Contact Map
2b78A 1 0.877 100 0.677 Contact Map
3c0kA 2 0.8634 100 0.683 Contact Map
2as0A 2 0.8798 100 0.702 Contact Map
3k6rA 1 0.6721 100 0.707 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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