GREMLIN Database
MIAB - tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase
UniProt: O31778 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 509 (429)
Sequences: 7175 (4167)
Seq/√Len: 201.2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
253_A293_I3.7451.00
332_S379_Q3.5761.00
333_S346_E3.5161.00
215_V249_V3.4271.00
332_S382_E3.3951.00
448_E486_R3.2361.00
391_E437_K3.2131.00
289_R317_G3.1061.00
308_D354_K3.0841.00
446_V486_R3.0831.00
490_Q500_E3.0431.00
349_M389_E2.9711.00
334_E379_Q2.9541.00
488_K500_E2.9201.00
312_E358_A2.9001.00
451_V474_F2.8761.00
422_E426_R2.6491.00
384_L430_L2.6331.00
287_E290_K2.6071.00
388_R433_E2.5171.00
334_E338_L2.4551.00
385_S389_E2.4461.00
446_V488_K2.4161.00
286_D316_K2.3411.00
249_V260_I2.2641.00
349_M390_V2.2631.00
249_V288_L2.1941.00
419_V422_E2.1861.00
72_T82_T2.1831.00
355_I362_A2.1831.00
324_I362_A2.1621.00
247_Q250_R2.1531.00
174_R177_E2.1351.00
388_R430_L2.1101.00
350_E353_R2.1041.00
258_K294_P2.0791.00
402_P414_N2.0431.00
312_E316_K2.0051.00
67_K95_E1.9961.00
322_D467_E1.9891.00
385_S388_R1.9871.00
377_D419_V1.9861.00
380_F426_R1.9821.00
315_A358_A1.9741.00
250_R254_S1.9721.00
416_P419_V1.9621.00
448_E484_I1.9451.00
345_R382_E1.9321.00
289_R319_N1.9321.00
399_I424_L1.9091.00
353_R389_E1.9071.00
480_A483_K1.8941.00
345_R349_M1.8911.00
443_E492_A1.8681.00
384_L426_R1.8661.00
253_A291_I1.8491.00
294_P448_E1.8401.00
92_L180_S1.8221.00
242_P287_E1.8131.00
289_R318_G1.7891.00
381_E385_S1.7871.00
154_N158_K1.7761.00
436_A440_K1.7691.00
353_R357_E1.7581.00
99_S102_D1.7441.00
328_V386_L1.7391.00
391_E434_I1.7181.00
438_K441_E1.7121.00
347_R350_E1.7011.00
330_S383_T1.6871.00
417_M420_K1.6731.00
448_E467_E1.6681.00
402_P409_A1.6591.00
381_E426_R1.6411.00
70_I82_T1.6261.00
449_V464_G1.6251.00
344_D347_R1.6041.00
451_V485_V1.5881.00
335_V338_L1.5791.00
346_E350_E1.5781.00
224_F236_K1.5781.00
345_R385_S1.5721.00
472_V489_I1.5651.00
286_D317_G1.5631.00
280_G283_D1.5621.00
376_T379_Q1.5591.00
333_S345_R1.5571.00
286_D313_V1.5501.00
322_D361_N1.5481.00
442_Y447_V1.5481.00
377_D381_E1.5451.00
68_F96_A1.5311.00
280_G309_R1.5261.00
313_V317_G1.5161.00
393_D438_K1.5131.00
141_G165_M1.5111.00
132_K164_D1.5051.00
147_S166_I1.5011.00
379_Q382_E1.4911.00
311_I355_I1.4761.00
112_A233_T1.4431.00
324_I355_I1.3961.00
107_L141_G1.3861.00
130_A133_K1.3851.00
85_M143_C1.3801.00
289_R313_V1.3761.00
260_I293_I1.3761.00
241_R244_D1.3751.00
226_T372_F1.3721.00
345_R386_L1.3661.00
487_V499_G1.3651.00
251_R255_E1.3611.00
461_I475_K1.3561.00
247_Q251_R1.3551.00
382_E385_S1.3391.00
226_T340_A1.3341.00
421_K425_Q1.3341.00
368_I387_Y1.3161.00
240_R248_E1.3141.00
282_G313_V1.3091.00
285_M320_L1.3071.00
308_D312_E1.3041.00
338_L379_Q1.3011.00
286_D309_R1.2951.00
277_M280_G1.2931.00
425_Q429_A1.2921.00
246_I250_R1.2901.00
246_I287_E1.2901.00
361_N445_K1.2781.00
314_L320_L1.2781.00
338_L411_M1.2761.00
391_E438_K1.2731.00
171_N174_R1.2631.00
440_K443_E1.2561.00
224_F232_Y1.2551.00
491_Q498_D1.2481.00
283_D309_R1.2471.00
387_Y427_L1.2471.00
407_P410_K1.2331.00
430_L434_I1.2321.00
417_M421_K1.2311.00
313_V320_L1.2251.00
442_Y445_K1.2191.00
240_R244_D1.2171.00
397_T424_L1.2171.00
378_E382_E1.2071.00
112_A118_E1.2061.00
67_K102_D1.2051.00
125_L142_V1.1841.00
338_L372_F1.1831.00
110_T142_V1.1821.00
251_R254_S1.1791.00
288_L296_I1.1741.00
377_D426_R1.1741.00
399_I417_M1.1731.00
359_M362_A1.1701.00
485_V501_M1.1691.00
271_G274_F1.1561.00
429_A433_E1.1511.00
283_D287_E1.1481.00
489_I497_L1.1471.00
350_E354_K1.1451.00
431_V434_I1.1441.00
399_I421_K1.1431.00
317_G320_L1.1431.00
462_L476_G1.1381.00
338_L374_N1.1331.00
70_I107_L1.1321.00
229_I233_T1.1291.00
354_K357_E1.1251.00
165_M182_A1.1251.00
340_A407_P1.1241.00
67_K97_T1.1231.00
296_I319_N1.1191.00
292_D319_N1.1041.00
381_E384_L1.1021.00
148_Q168_G1.1021.00
447_V489_I1.0961.00
352_V364_L1.0961.00
447_V466_T1.0871.00
314_L359_M1.0851.00
378_E381_E1.0841.00
115_E119_N1.0831.00
290_K317_G1.0821.00
333_S344_D1.0821.00
119_N123_G1.0801.00
370_V380_F1.0791.00
143_C167_F1.0721.00
181_E186_K1.0721.00
89_F179_L1.0651.00
165_M178_L1.0631.00
351_L354_K1.0631.00
311_I358_A1.0581.00
222_D236_K1.0541.00
440_K492_A1.0491.00
242_P246_I1.0451.00
387_Y395_A1.0441.00
71_R124_E1.0441.00
240_R245_I1.0421.00
323_H469_S1.0411.00
397_T428_N1.0391.00
139_I182_A1.0391.00
289_R320_L1.0341.00
167_F178_L1.0321.00
267_V298_F1.0301.00
135_N138_L1.0271.00
368_I395_A1.0251.00
391_E441_E1.0241.00
309_R312_E1.0211.00
106_I138_L1.0191.00
226_T407_P1.0171.00
258_K484_I1.0171.00
465_Y471_L1.0161.00
215_V245_I1.0121.00
414_N420_K1.0121.00
281_L310_L1.0091.00
374_N413_D1.0081.00
229_I232_Y1.0071.00
433_E437_K1.0051.00
380_F427_L0.9971.00
366_T392_F0.9961.00
352_V390_V0.9941.00
356_K391_E0.9931.00
315_A359_M0.9881.00
395_A431_V0.9861.00
333_S382_E0.9851.00
439_M470_K0.9801.00
250_R292_D0.9801.00
311_I359_M0.9781.00
130_A134_N0.9761.00
454_E462_L0.9751.00
155_R158_K0.9741.00
443_E491_Q0.9731.00
430_L433_E0.9731.00
149_E233_T0.9721.00
244_D247_Q0.9630.99
126_G129_K0.9620.99
370_V424_L0.9600.99
436_A492_A0.9600.99
361_N441_E0.9580.99
69_Y100_V0.9440.99
285_M317_G0.9410.99
156_I163_V0.9400.99
163_V166_I0.9400.99
314_L324_I0.9380.99
213_G252_L0.9360.99
70_I86_A0.9350.99
68_F94_Y0.9350.99
218_M237_E0.9350.99
258_K483_K0.9350.99
384_L388_R0.9340.99
110_T121_V0.9330.99
139_I183_Y0.9300.99
472_V499_G0.9260.99
366_T395_A0.9250.99
354_K358_A0.9230.99
387_Y392_F0.9190.99
108_L125_L0.9170.99
279_Y287_E0.9130.99
68_F86_A0.9090.99
377_D422_E0.9080.99
332_S335_V0.9040.99
451_V464_G0.9030.99
424_L428_N0.9000.99
279_Y283_D0.8990.99
436_A439_M0.8920.99
86_A96_A0.8880.99
215_V260_I0.8850.99
151_S154_N0.8790.99
294_P484_I0.8750.99
347_R351_L0.8750.99
338_L413_D0.8730.99
473_N496_S0.8730.99
392_F395_A0.8700.99
243_E247_Q0.8700.99
462_L479_E0.8700.99
252_L257_Y0.8700.99
372_F411_M0.8690.99
453_G463_A0.8690.99
250_R287_E0.8680.99
275_E279_Y0.8640.99
489_I499_G0.8630.99
282_G309_R0.8600.99
335_V379_Q0.8590.99
72_T109_N0.8510.99
180_S184_L0.8500.99
142_V163_V0.8490.99
177_E181_E0.8480.99
289_R296_I0.8480.99
431_V435_S0.8470.99
334_E382_E0.8470.99
374_N414_N0.8460.99
429_A432_N0.8450.99
66_R183_Y0.8420.99
68_F90_M0.8410.99
435_S439_M0.8410.99
311_I354_K0.8400.99
285_M310_L0.8390.99
97_T103_A0.8390.99
253_A292_D0.8340.98
363_S468_K0.8340.98
282_G307_D0.8330.98
434_I438_K0.8330.98
322_D359_M0.8320.98
211_I452_E0.8320.98
242_P270_Y0.8310.98
479_E483_K0.8310.98
139_I165_M0.8300.98
426_R430_L0.8300.98
365_T394_S0.8290.98
449_V487_V0.8280.98
169_T172_I0.8270.98
450_L484_I0.8270.98
77_M265_Q0.8260.98
250_R291_I0.8250.98
227_Y343_Y0.8240.98
324_I364_L0.8230.98
237_E269_A0.8220.98
73_Y121_V0.8220.98
293_I319_N0.8220.98
466_T472_V0.8210.98
106_I137_D0.8200.98
409_A414_N0.8190.98
222_D272_K0.8180.98
493_K498_D0.8160.98
94_Y105_V0.8160.98
323_H365_T0.8150.98
105_V139_I0.8150.98
73_Y124_E0.8140.98
331_G382_E0.8140.98
348_Y392_F0.8120.98
223_K266_N0.8120.98
432_N495_W0.8100.98
451_V462_L0.8100.98
213_G257_Y0.8090.98
181_E185_S0.8090.98
328_V368_I0.8090.98
386_L390_V0.8060.98
368_I427_L0.8030.98
454_E478_K0.8010.98
105_V141_G0.7990.98
118_E150_E0.7980.98
249_V291_I0.7980.98
294_P319_N0.7950.98
349_M353_R0.7950.98
150_E155_R0.7920.98
286_D290_K0.7890.98
215_V252_L0.7860.98
387_Y434_I0.7850.98
182_A185_S0.7820.98
476_G480_A0.7820.98
92_L177_E0.7810.98
139_I179_L0.7800.98
475_K500_E0.7800.98
476_G479_E0.7780.98
243_E275_E0.7730.97
346_E349_M0.7700.97
224_F340_A0.7690.97
411_M414_N0.7690.97
69_Y97_T0.7680.97
474_F487_V0.7640.97
442_Y468_K0.7610.97
370_V427_L0.7610.97
388_R434_I0.7600.97
312_E315_A0.7590.97
129_K140_L0.7580.97
298_F314_L0.7570.97
328_V348_Y0.7560.97
131_L138_L0.7550.97
282_G310_L0.7540.97
434_I437_K0.7530.97
307_D310_L0.7520.97
275_E280_G0.7520.97
106_I131_L0.7510.97
306_F351_L0.7490.97
69_Y103_A0.7480.97
295_R321_L0.7480.97
239_S273_D0.7460.97
384_L427_L0.7450.97
246_I288_L0.7450.97
276_D279_Y0.7440.97
283_D286_D0.7440.97
86_A90_M0.7440.97
449_V472_V0.7430.97
381_E388_R0.7430.97
370_V420_K0.7410.97
88_I176_P0.7400.97
331_G348_Y0.7390.97
363_S393_D0.7370.97
232_Y407_P0.7340.97
129_K133_K0.7330.97
380_F384_L0.7330.97
442_Y470_K0.7320.97
218_M264_G0.7310.96
100_V106_I0.7300.96
451_V487_V0.7300.96
85_M175_L0.7290.96
97_T102_D0.7270.96
383_T427_L0.7250.96
437_K440_K0.7220.96
402_P420_K0.7220.96
148_Q151_S0.7220.96
308_D311_I0.7190.96
141_G167_F0.7190.96
66_R94_Y0.7150.96
80_H216_N0.7070.96
269_A304_R0.7030.96
232_Y405_G0.7030.96
306_F310_L0.7020.96
395_A434_I0.7010.96
291_I319_N0.7000.96
83_E87_G0.7000.96
76_Q468_K0.7000.96
212_K261_T0.7000.96
428_N431_V0.6990.95
393_D470_K0.6960.95
182_A186_K0.6950.95
92_L176_P0.6950.95
455_S460_D0.6940.95
82_T86_A0.6930.95
116_N119_N0.6910.95
89_F107_L0.6890.95
432_N494_T0.6880.95
76_Q263_L0.6880.95
243_E287_E0.6860.95
304_R342_K0.6860.95
199_V204_P0.6860.95
246_I291_I0.6840.95
454_E459_P0.6820.95
490_Q499_G0.6820.95
438_K442_Y0.6800.95
69_Y106_I0.6780.95
295_R484_I0.6780.95
94_Y180_S0.6760.95
461_I473_N0.6740.95
191_E194_S0.6730.94
308_D358_A0.6730.94
436_A494_T0.6700.94
269_A305_D0.6680.94
226_T338_L0.6680.94
335_V372_F0.6670.94
223_K269_A0.6660.94
215_V262_L0.6660.94
324_I359_M0.6650.94
214_W261_T0.6640.94
334_E378_E0.6620.94
426_R429_A0.6620.94
455_S473_N0.6610.94
266_N305_D0.6610.94
349_M386_L0.6600.94
113_I229_I0.6600.94
81_D219_Y0.6560.94
387_Y431_V0.6560.94
321_L467_E0.6550.94
116_N401_S0.6550.94
293_I484_I0.6550.94
415_V420_K0.6510.93
82_T109_N0.6510.93
449_V499_G0.6480.93
253_A296_I0.6480.93
155_R159_K0.6460.93
285_M289_R0.6460.93
268_N301_S0.6440.93
331_G383_T0.6440.93
441_E445_K0.6420.93
87_G91_A0.6390.93
404_E409_A0.6390.93
90_M96_A0.6370.93
293_I296_I0.6370.93
216_N219_Y0.6350.93
72_T79_E0.6310.92
276_D283_D0.6300.92
372_F408_A0.6300.92
90_M95_E0.6280.92
282_G286_D0.6270.92
287_E291_I0.6240.92
442_Y446_V0.6240.92
474_F501_M0.6230.92
242_P279_Y0.6220.92
73_Y108_L0.6220.92
474_F485_V0.6200.92
268_N327_P0.6200.92
383_T387_Y0.6190.92
247_Q254_S0.6180.92
331_G345_R0.6180.92
245_I284_L0.6180.92
370_V399_I0.6170.91
394_S435_S0.6150.91
281_L298_F0.6130.91
281_L285_M0.6130.91
77_M80_H0.6120.91
377_D423_R0.6110.91
487_V490_Q0.6100.91
334_E376_T0.6100.91
242_P283_D0.6090.91
68_F89_F0.6070.91
440_K491_Q0.6070.91
418_R422_E0.6060.91
380_F387_Y0.6060.91
399_I420_K0.6050.91
201_E204_P0.6040.91
69_Y98_N0.6030.91
108_L121_V0.6030.91
253_A319_N0.6030.91
99_S131_L0.6030.91
480_A501_M0.6020.90
439_M492_A0.6000.90
464_G474_F0.5980.90
446_V499_G0.5980.90
334_E374_N0.5980.90
112_A149_E0.5970.90
215_V240_R0.5970.90
456_K460_D0.5970.90
421_K424_L0.5970.90
253_A257_Y0.5960.90
157_L166_I0.5950.90
387_Y430_L0.5940.90
199_V202_N0.5910.90
120_K123_G0.5900.90
334_E337_K0.5890.90
129_K132_K0.5880.89
381_E422_E0.5880.89
195_K198_D0.5870.89
154_N157_L0.5860.89
387_Y391_E0.5840.89
288_L291_I0.5840.89
462_L481_I0.5840.89
132_K137_D0.5830.89
285_M288_L0.5820.89
183_Y186_K0.5820.89
175_L179_L0.5810.89
397_T427_L0.5800.89
160_H163_V0.5800.89
316_K319_N0.5770.89
397_T431_V0.5770.89
260_I288_L0.5760.88
174_R191_E0.5760.88
331_G386_L0.5750.88
490_Q498_D0.5740.88
71_R108_L0.5710.88
400_Y411_M0.5710.88
478_K483_K0.5700.88
200_I204_P0.5660.88
131_L135_N0.5660.88
308_D351_L0.5650.88
207_R255_E0.5640.87
274_F279_Y0.5640.87
368_I383_T0.5630.87
123_G126_G0.5630.87
328_V392_F0.5620.87
69_Y99_S0.5620.87
461_I498_D0.5620.87
462_L477_P0.5620.87
333_S350_E0.5610.87
176_P179_L0.5610.87
201_E244_D0.5590.87
388_R391_E0.5590.87
227_Y340_A0.5570.87
88_I91_A0.5560.87
209_G257_Y0.5560.87
200_I203_L0.5550.87
217_I284_L0.5540.86
202_N244_D0.5540.86
132_K138_L0.5530.86
223_K342_K0.5520.86
116_N120_K0.5520.86
268_N305_D0.5510.86
422_E425_Q0.5500.86
217_I267_V0.5480.86
443_E446_V0.5470.86
438_K470_K0.5470.86
439_M497_L0.5460.86
132_K162_F0.5450.86
223_K233_T0.5450.86
110_T125_L0.5450.86
470_K497_L0.5450.86
172_I176_P0.5440.86
131_L137_D0.5440.86
262_L288_L0.5430.85
139_I164_D0.5420.85
242_P284_L0.5420.85
248_E252_L0.5420.85
217_I245_I0.5410.85
300_T323_H0.5410.85
223_K304_R0.5390.85
97_T100_V0.5380.85
223_K340_A0.5370.85
353_R390_V0.5350.85
443_E489_I0.5350.85
132_K140_L0.5350.85
226_T304_R0.5330.84
107_L165_M0.5310.84
285_M296_I0.5310.84
126_G160_H0.5310.84
326_L340_A0.5300.84
246_I284_L0.5290.84
269_A326_L0.5280.84
301_S324_I0.5270.84
463_A471_L0.5260.84
122_F126_G0.5260.84
298_F301_S0.5250.83
87_G204_P0.5250.83
428_N435_S0.5250.83
384_L422_E0.5240.83
118_E149_E0.5240.83
211_I450_L0.5230.83
492_A497_L0.5230.83
199_V203_L0.5230.83
462_L480_A0.5230.83
242_P277_M0.5230.83
361_N468_K0.5220.83
454_E460_D0.5220.83
343_Y348_Y0.5160.82
272_K277_M0.5150.82
222_D237_E0.5150.82
300_T328_V0.5140.82
269_A327_P0.5140.82
435_S494_T0.5140.82
180_S183_Y0.5140.82
377_D384_L0.5130.82
313_V316_K0.5130.82
266_N281_L0.5130.82
211_I257_Y0.5110.82
190_V193_W0.5110.82
454_E476_G0.5100.82
312_E354_K0.5100.82
419_V423_R0.5100.82
464_G484_I0.5100.82
301_S326_L0.5100.82
309_R313_V0.5090.82
267_V299_T0.5080.81
291_I296_I0.5080.81
84_V88_I0.5060.81
212_K452_E0.5060.81
325_H367_D0.5050.81
402_P406_T0.5050.81
425_Q428_N0.5040.81
167_F175_L0.5040.81
464_G485_V0.5030.81
407_P411_M0.5020.81
223_K305_D0.5020.81
68_F82_T0.5020.81
224_F407_P0.5010.81
473_N498_D0.5000.80
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  
4jc0A 1 0.8212 100 0.419 Contact Map
2qgqA 1 0.5226 100 0.602 Contact Map
1oltA 1 0.6424 100 0.796 Contact Map
4u0oB 1 0.5206 99.9 0.843 Contact Map
4wcxA 1 0.666 99.9 0.861 Contact Map
2yx0A 1 0.5776 99.9 0.862 Contact Map
3iixA 1 0.6149 99.9 0.868 Contact Map
2z2uA 1 0.4951 99.8 0.872 Contact Map
3t7vA 1 0.6228 99.8 0.872 Contact Map
3c8fA 1 0.4519 99.8 0.872 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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