GREMLIN Database
TRMFO - Methylenetetrahydrofolate--tRNA-(uracil-5-)-methyltransferase TrmFO
UniProt: P39815 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 435 (417)
Sequences: 3726 (1702)
Seq/√Len: 83.3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
216_E220_E3.8521.00
178_L204_E3.4811.00
418_E425_I3.1881.00
375_E416_R2.9781.00
209_A260_Y2.9411.00
153_E328_F2.7731.00
125_E146_Q2.7701.00
222_F251_E2.7541.00
355_V382_A2.7161.00
4_Q117_T2.6941.00
71_E97_V2.6831.00
110_V118_V2.6321.00
28_Q115_N2.6191.00
213_P216_E2.5981.00
214_L295_L2.5481.00
11_A48_F2.5271.00
293_L302_V2.5071.00
372_F376_T2.4971.00
274_L305_V2.4441.00
321_L330_N2.4181.00
175_K300_E2.3911.00
212_V259_P2.3551.00
293_L304_I2.3491.00
425_I429_Q2.3211.00
418_E428_I2.3191.00
70_K106_V2.2721.00
323_K327_Q2.2641.00
362_K367_E2.2541.00
335_F363_L2.2441.00
172_D175_K2.2371.00
167_E170_S2.2361.00
375_E427_T2.2311.00
171_L275_Y2.2301.00
288_D291_E2.2221.00
317_N320_S2.2061.00
56_S351_A2.1981.00
211_T297_P2.1811.00
176_V265_L2.1581.00
27_I365_L2.1291.00
30_K119_I2.1201.00
332_S363_L2.0831.00
154_D317_N2.0581.00
6_V22_L2.0371.00
355_V378_I2.0351.00
415_E419_Q2.0341.00
146_Q149_E1.9941.00
111_K120_N1.9841.00
171_L176_V1.9731.00
224_E287_G1.9691.00
169_D273_T1.9691.00
154_D321_L1.9551.00
16_S40_T1.9541.00
24_K113_H1.9501.00
29_V116_V1.9161.00
56_S393_F1.9031.00
265_L299_L1.9021.00
105_S108_N1.8961.00
156_L315_F1.8811.00
327_Q363_L1.8661.00
417_N423_R1.8441.00
316_I336_F1.8401.00
74_R85_D1.8331.00
167_E303_E1.8221.00
20_W66_V1.8131.00
326_Y382_A1.8001.00
167_E305_V1.7971.00
168_K173_M1.7961.00
108_N112_N1.7891.00
362_K370_V1.7641.00
190_L427_T1.7331.00
73_M105_S1.7301.00
294_K302_V1.7051.00
355_V372_F1.7031.00
164_P293_L1.6921.00
36_P118_V1.6841.00
113_H116_V1.6721.00
282_T308_G1.6581.00
228_P251_E1.6571.00
229_I240_M1.6411.00
357_G361_A1.6311.00
428_I432_S1.6281.00
128_E286_W1.6131.00
414_K423_R1.5831.00
73_M350_A1.5771.00
42_A97_V1.5761.00
217_F295_L1.5521.00
370_V416_R1.5401.00
27_I361_A1.5371.00
175_K297_P1.5361.00
153_E330_N1.5271.00
107_T111_K1.5190.99
63_A417_N1.5170.99
30_K117_T1.4710.99
145_A149_E1.4660.99
39_Q118_V1.4570.99
144_S155_Y1.4500.99
20_W113_H1.4490.99
82_A109_R1.4470.99
22_L27_I1.4450.99
377_A398_A1.4420.99
220_E291_E1.4380.99
57_L67_G1.4330.99
35_R45_T1.4320.99
173_M275_Y1.4090.99
325_T335_F1.4090.99
265_L275_Y1.4080.99
166_V277_I1.4060.99
172_D301_N1.3910.99
290_K294_K1.3900.99
201_R295_L1.3880.99
69_L190_L1.3860.99
414_K427_T1.3860.99
180_S204_E1.3840.99
7_N30_K1.3810.99
355_V376_T1.3780.99
167_E273_T1.3660.99
48_F118_V1.3640.99
226_C229_I1.3600.99
361_A365_L1.3550.99
164_P302_V1.3380.99
77_D181_R1.3380.99
16_S110_V1.3290.99
35_R38_K1.3270.99
34_M122_E1.3270.99
222_F228_P1.3260.99
110_V116_V1.3210.99
24_K77_D1.3060.98
48_F67_G1.3050.98
172_D300_E1.3040.98
5_T28_Q1.2910.98
205_A208_S1.2890.98
326_Y352_S1.2810.98
74_R105_S1.2800.98
66_V70_K1.2790.98
27_I364_V1.2770.98
145_A148_K1.2620.98
60_N354_L1.2460.98
16_S106_V1.2440.98
231_V234_K1.2440.98
75_A78_S1.2420.98
166_V302_V1.2410.98
148_K155_Y1.2410.98
111_K118_V1.2410.98
290_K304_I1.2340.98
105_S109_R1.2310.98
166_V171_L1.2280.98
351_A381_M1.2230.98
92_G406_L1.2230.98
336_F340_M1.2200.98
125_E149_E1.2170.98
39_Q46_D1.2130.97
25_R362_K1.2120.97
168_K272_G1.2050.97
357_G360_A1.2050.97
32_Y119_I1.2020.97
328_F334_L1.2020.97
70_K105_S1.1940.97
216_E219_K1.1880.97
164_P292_V1.1820.97
32_Y121_E1.1820.97
83_A105_S1.1750.97
210_E285_K1.1740.97
7_N32_Y1.1720.97
168_K275_Y1.1710.97
325_T369_L1.1660.97
22_L360_A1.1570.97
20_W24_K1.1530.97
28_Q117_T1.1470.96
415_E418_E1.1410.96
4_Q30_K1.1400.96
94_A181_R1.1370.96
101_E104_A1.1350.96
134_A137_P1.1220.96
104_A108_N1.1210.96
80_I406_L1.1160.96
22_L29_V1.1150.96
323_K332_S1.1120.96
51_L91_A1.1120.96
60_N88_S1.1110.96
9_I123_V1.1110.96
208_S299_L1.1080.96
99_R268_D1.1070.96
80_I350_A1.0990.95
32_Y123_V1.0980.95
190_L414_K1.0890.95
370_V420_Y1.0840.95
354_L358_I1.0820.95
324_P386_T1.0800.95
252_H257_K1.0770.95
428_I431_I1.0770.95
221_I224_E1.0760.95
73_M109_R1.0740.95
146_Q150_L1.0740.95
36_P120_N1.0730.95
211_T234_K1.0730.95
269_D273_T1.0720.95
94_A97_V1.0710.95
131_T139_T1.0700.95
48_F57_L1.0690.95
178_L206_L1.0670.95
389_N392_N1.0590.94
219_K256_G1.0580.94
100_H271_A1.0570.94
5_T30_K1.0560.94
70_K109_R1.0540.94
131_T141_E1.0480.94
283_H310_M1.0470.94
171_L299_L1.0450.94
292_V295_L1.0410.94
76_L203_H1.0380.94
362_K419_Q1.0340.94
190_L423_R1.0330.94
176_V208_S1.0320.94
162_A309_V1.0300.94
55_N91_A1.0200.93
5_T27_I1.0190.93
71_E74_R1.0160.93
280_F296_I1.0140.93
343_V349_S1.0070.93
71_E94_A1.0050.93
203_H270_A1.0050.93
92_G278_V1.0020.93
66_V347_V0.9970.92
6_V27_I0.9950.92
35_R40_T0.9910.92
122_E142_S0.9910.92
124_T142_S0.9880.92
37_V120_N0.9870.92
158_F315_F0.9870.92
374_Q383_H0.9860.92
425_I428_I0.9850.92
74_R101_E0.9800.92
414_K431_I0.9790.92
171_L265_L0.9790.92
23_A113_H0.9780.92
66_V106_V0.9760.92
126_I133_I0.9760.92
142_S145_A0.9740.92
36_P107_T0.9700.91
175_K298_G0.9700.91
218_E246_K0.9700.91
426_E430_T0.9640.91
380_S398_A0.9620.91
207_T262_V0.9600.91
333_D363_L0.9570.91
60_N350_A0.9560.91
269_D272_G0.9550.91
213_P291_E0.9540.91
25_R365_L0.9470.90
135_T139_T0.9460.90
362_K365_L0.9450.90
424_A427_T0.9440.90
71_E75_A0.9430.90
252_H256_G0.9390.90
47_K103_A0.9350.90
87_C101_E0.9330.90
58_R66_V0.9320.90
280_F292_V0.9250.89
265_L277_I0.9240.89
24_K66_V0.9230.89
290_K303_E0.9220.89
155_Y316_I0.9220.89
223_F226_C0.9200.89
429_Q432_S0.9140.89
164_P308_G0.9130.89
290_K307_Y0.9070.88
181_R202_F0.9040.88
316_I321_L0.9030.88
49_A106_V0.9030.88
286_W307_Y0.9010.88
87_C105_S0.9010.88
304_I307_Y0.9010.88
20_W110_V0.9000.88
31_L110_V0.9000.88
192_C430_T0.8920.88
34_M38_K0.8880.87
51_L394_Q0.8820.87
80_I92_G0.8730.86
76_L270_A0.8670.86
294_K303_E0.8670.86
64_N424_A0.8650.86
169_D303_E0.8640.86
82_A86_E0.8630.86
122_E140_S0.8610.86
66_V69_L0.8560.85
398_A404_K0.8550.85
86_E105_S0.8550.85
256_G260_Y0.8550.85
83_A106_V0.8540.85
191_N194_M0.8530.85
59_S93_G0.8510.85
100_H104_A0.8440.84
11_A31_L0.8440.84
23_A116_V0.8430.84
20_W79_A0.8420.84
22_L364_V0.8420.84
19_A116_V0.8410.84
335_F369_L0.8400.84
48_F71_E0.8400.84
224_E288_D0.8370.84
8_V22_L0.8350.84
107_T305_V0.8340.84
25_R420_Y0.8280.83
78_S394_Q0.8260.83
25_R358_I0.8240.83
25_R361_A0.8210.83
35_R39_Q0.8120.82
416_R419_Q0.8100.82
52_V55_N0.8080.82
141_E144_S0.8070.82
361_A364_V0.8050.82
16_S70_K0.7990.81
38_K41_P0.7950.81
177_Y251_E0.7940.81
328_F332_S0.7930.81
20_W109_R0.7860.80
66_V109_R0.7840.80
58_R92_G0.7830.80
99_R277_I0.7820.80
173_M190_L0.7810.80
212_V219_K0.7800.80
356_A360_A0.7800.80
178_L275_Y0.7800.80
51_L78_S0.7780.79
405_E408_V0.7770.79
351_A378_I0.7740.79
256_G259_P0.7730.79
211_T215_K0.7710.79
36_P111_K0.7690.79
263_V280_F0.7690.79
150_L330_N0.7640.78
325_T362_K0.7630.78
168_K178_L0.7610.78
29_V113_H0.7570.77
423_R431_I0.7570.77
315_F394_Q0.7560.77
168_K273_T0.7540.77
224_E235_R0.7520.77
228_P248_V0.7520.77
412_N415_E0.7510.77
38_K137_P0.7480.77
280_F293_L0.7480.77
109_R112_N0.7470.77
377_A403_L0.7460.76
287_G291_E0.7410.76
74_R97_V0.7400.76
43_H51_L0.7380.76
34_M140_S0.7360.75
325_T359_N0.7350.75
286_W309_V0.7340.75
141_E145_A0.7320.75
418_E423_R0.7310.75
335_F364_V0.7290.75
176_V298_G0.7290.75
411_K415_E0.7260.74
36_P305_V0.7240.74
150_L331_R0.7240.74
296_I299_L0.7230.74
410_I414_K0.7200.74
106_V110_V0.7180.74
77_D82_A0.7180.74
40_T45_T0.7140.73
78_S92_G0.7140.73
21_Q25_R0.7130.73
146_Q331_R0.7110.73
204_E208_S0.7100.73
167_E274_L0.7080.73
56_S381_M0.7080.73
35_R120_N0.7070.73
179_K251_E0.7070.73
263_V277_I0.7050.72
7_N131_T0.7040.72
335_F359_N0.7040.72
77_D202_F0.7030.72
209_A292_V0.7010.72
215_K219_K0.7000.72
408_V412_N0.6960.71
277_I280_F0.6940.71
417_N422_N0.6940.71
290_K293_L0.6920.71
41_P135_T0.6890.71
70_K97_V0.6890.71
316_I328_F0.6870.70
291_E297_P0.6870.70
293_L308_G0.6830.70
283_H309_V0.6830.70
51_L90_P0.6820.70
43_H394_Q0.6800.70
144_S148_K0.6790.69
120_N274_L0.6780.69
27_I115_N0.6770.69
176_V299_L0.6760.69
294_K304_I0.6750.69
417_N425_I0.6730.69
52_V393_F0.6720.69
26_G115_N0.6720.69
101_E105_S0.6710.69
166_V299_L0.6700.68
358_I422_N0.6700.68
159_Y221_I0.6690.68
251_E258_R0.6690.68
359_N371_I0.6680.68
291_E295_L0.6680.68
117_T303_E0.6670.68
286_W290_K0.6660.68
101_E270_A0.6650.68
51_L92_G0.6640.68
147_L336_F0.6640.68
213_P295_L0.6630.68
328_F331_R0.6610.67
224_E227_M0.6600.67
6_V364_V0.6590.67
9_I32_Y0.6590.67
36_P110_V0.6560.67
358_I362_K0.6560.67
81_I347_V0.6550.67
22_L26_G0.6550.67
227_M310_M0.6540.67
378_I382_A0.6530.66
68_V421_A0.6530.66
163_A268_D0.6520.66
328_F336_F0.6520.66
343_V352_S0.6520.66
331_R334_L0.6490.66
41_P99_R0.6490.66
171_L190_L0.6490.66
205_A295_L0.6480.66
47_K104_A0.6470.66
327_Q333_D0.6460.66
426_E429_Q0.6460.66
365_L419_Q0.6440.65
75_A429_Q0.6430.65
226_C231_V0.6400.65
8_V358_I0.6370.65
51_L278_V0.6350.64
127_P133_I0.6350.64
25_R422_N0.6330.64
41_P103_A0.6320.64
129_G231_V0.6320.64
351_A393_F0.6290.64
240_M245_M0.6280.63
62_L421_A0.6270.63
73_M354_L0.6260.63
24_K115_N0.6250.63
411_K431_I0.6250.63
79_A110_V0.6240.63
227_M230_E0.6220.63
176_V297_P0.6210.63
208_S263_V0.6210.63
90_P406_L0.6210.63
335_F362_K0.6200.62
224_E291_E0.6200.62
154_D304_I0.6190.62
23_A115_N0.6190.62
214_L217_F0.6160.62
358_I370_V0.6150.62
154_D330_N0.6120.61
357_G362_K0.6120.61
153_E320_S0.6120.61
203_H241_L0.6120.61
58_R348_E0.6110.61
205_A210_E0.6110.61
180_S183_D0.6110.61
227_M235_R0.6100.61
69_L109_R0.6100.61
368_E419_Q0.6090.61
157_Y221_I0.6090.61
43_H278_V0.6080.61
18_A132_I0.6080.61
60_N85_D0.6080.61
34_M137_P0.6080.61
170_S303_E0.6070.61
43_H92_G0.6050.61
134_A311_H0.6050.61
41_P51_L0.6050.61
11_A107_T0.6050.61
78_S94_A0.6030.60
252_H258_R0.6030.60
123_V146_Q0.6020.60
273_T305_V0.6020.60
415_E431_I0.6010.60
80_I83_A0.6010.60
58_R406_L0.6000.60
130_P360_A0.6000.60
64_N69_L0.6000.60
156_L314_T0.5990.60
232_M235_R0.5990.60
115_N301_N0.5990.60
229_I251_E0.5980.60
201_R204_E0.5950.59
76_L378_I0.5950.59
39_Q45_T0.5950.59
213_P297_P0.5940.59
173_M206_L0.5930.59
122_E137_P0.5920.59
398_A403_L0.5920.59
83_A90_P0.5920.59
55_N393_F0.5910.59
209_A284_L0.5900.59
153_E316_I0.5900.59
376_T380_S0.5890.59
292_V296_I0.5890.59
372_F375_E0.5880.58
355_V370_V0.5880.58
119_I303_E0.5870.58
246_K282_T0.5860.58
221_I288_D0.5850.58
212_V216_E0.5830.58
235_R311_H0.5820.58
140_S144_S0.5810.58
321_L328_F0.5810.58
418_E431_I0.5810.58
367_E419_Q0.5800.57
278_V394_Q0.5780.57
418_E424_A0.5780.57
94_A189_Y0.5750.57
414_K417_N0.5750.57
52_V344_E0.5730.56
415_E428_I0.5720.56
383_H389_N0.5710.56
193_P199_F0.5700.56
385_I390_Q0.5700.56
19_A23_A0.5700.56
16_S35_R0.5690.56
159_Y220_E0.5690.56
60_N67_G0.5690.56
51_L55_N0.5690.56
417_N420_Y0.5650.55
75_A185_G0.5640.55
419_Q422_N0.5640.55
349_S397_N0.5630.55
80_I90_P0.5630.55
80_I106_V0.5630.55
324_P371_I0.5620.55
205_A267_Q0.5620.55
35_R137_P0.5610.55
277_I293_L0.5610.55
43_H78_S0.5600.55
360_A364_V0.5590.55
78_S278_V0.5580.55
22_L28_Q0.5560.54
218_E250_L0.5560.54
85_D88_S0.5550.54
137_P191_N0.5540.54
264_Q282_T0.5540.54
228_P232_M0.5540.54
126_I307_Y0.5530.54
52_V56_S0.5530.54
267_Q272_G0.5520.54
201_R270_A0.5520.54
40_T43_H0.5510.54
91_A394_Q0.5490.53
419_Q423_R0.5490.53
392_N412_N0.5490.53
21_Q24_K0.5470.53
47_K51_L0.5470.53
153_E336_F0.5470.53
341_T352_S0.5470.53
296_I300_E0.5450.53
16_S357_G0.5450.53
362_K420_Y0.5430.53
134_A278_V0.5430.53
177_Y260_Y0.5420.52
137_P315_F0.5420.52
126_I135_T0.5410.52
213_P217_F0.5400.52
335_F358_I0.5400.52
51_L344_E0.5400.52
83_A92_G0.5380.52
24_K82_A0.5380.52
317_N321_L0.5380.52
359_N362_K0.5370.52
274_L306_R0.5360.52
19_A31_L0.5350.51
348_E398_A0.5350.51
226_C230_E0.5350.51
325_T363_L0.5320.51
134_A394_Q0.5310.51
142_S147_L0.5310.51
352_S382_A0.5300.51
336_F394_Q0.5300.51
99_R135_T0.5280.51
190_L426_E0.5270.50
327_Q335_F0.5260.50
82_A105_S0.5250.50
175_K178_L0.5240.50
396_M399_N0.5240.50
79_A179_K0.5220.50
381_M393_F0.5220.50
416_R423_R0.5220.50
58_R286_W0.5200.49
418_E422_N0.5200.49
44_H162_A0.5190.49
114_P174_D0.5180.49
106_V311_H0.5180.49
242_F248_V0.5170.49
272_G275_Y0.5150.49
209_A256_G0.5140.49
61_T162_A0.5140.49
382_A386_T0.5140.49
374_Q391_K0.5130.49
54_S187_A0.5120.48
7_N129_G0.5120.48
41_P137_P0.5110.48
410_I413_K0.5100.48
240_M281_Q0.5100.48
325_T370_V0.5100.48
229_I232_M0.5090.48
348_E397_N0.5080.48
18_A356_A0.5080.48
8_V132_I0.5080.48
58_R347_V0.5070.48
229_I248_V0.5060.48
87_C407_P0.5060.48
383_H387_T0.5050.48
132_I360_A0.5040.47
52_V91_A0.5040.47
78_S185_G0.5030.47
418_E432_S0.5030.47
24_K109_R0.5030.47
106_V109_R0.5030.47
372_F420_Y0.5030.47
188_A191_N0.5010.47
11_A34_M0.5010.47
78_S90_P0.5010.47
159_Y281_Q0.5000.47
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  
3cp8A 2 0.9517 100 0.439 Contact Map
3cesA 2 0.9356 100 0.452 Contact Map
2zxiA 2 0.9563 100 0.48 Contact Map
3g5sA 1 0.9632 100 0.485 Contact Map
3v76A 2 0.7172 100 0.854 Contact Map
3nlcA 1 0.823 99.9 0.855 Contact Map
4cnkA 2 0.754 99.9 0.867 Contact Map
2culA 1 0.4184 99.8 0.886 Contact Map
2i0zA 1 0.7586 99.6 0.912 Contact Map
2gqfA 4 0.7379 99.4 0.921 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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