GREMLIN Database
RLMCD - 23S rRNA (uracil-C(5))-methyltransferase RlmCD
UniProt: O31503 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 459 (439)
Sequences: 4480 (3317)
Seq/√Len: 158.3

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
47_Q64_E4.2581.00
424_L455_I3.4011.00
435_R456_K3.3471.00
95_G98_L3.2971.00
101_Q105_K3.0711.00
335_K362_E3.0311.00
122_H436_E2.9461.00
302_K305_E2.9011.00
71_H95_G2.8851.00
221_T248_Q2.8621.00
329_L386_V2.8531.00
45_K67_E2.8291.00
16_T45_K2.8151.00
385_L402_I2.5941.00
48_I60_G2.5931.00
15_V48_I2.5341.00
96_Q445_H2.5101.00
62_L65_L2.4611.00
425_R429_D2.4091.00
170_Q208_Y2.3991.00
162_D181_K2.3861.00
402_I410_V2.3861.00
275_L280_K2.3691.00
273_Y280_K2.3571.00
154_Q159_D2.3061.00
77_C83_C2.3011.00
15_V28_A2.2691.00
275_L278_D2.2581.00
102_K106_D2.2511.00
434_T453_V2.1871.00
314_T335_K2.1771.00
306_Y436_E2.1611.00
101_Q123_P2.1571.00
41_L44_E2.1271.00
49_K61_R2.1001.00
303_A413_V2.0981.00
320_C338_G2.0541.00
83_C86_C2.0521.00
366_G371_V2.0451.00
265_V270_E2.0401.00
77_C86_C2.0371.00
101_Q124_T2.0131.00
282_A351_R1.9791.00
40_A46_A1.9781.00
65_L68_E1.9781.00
387_V394_C1.9641.00
17_F37_V1.9241.00
20_L42_P1.8691.00
403_V430_G1.8691.00
52_R59_F1.8341.00
316_I382_A1.8291.00
320_C346_I1.8201.00
17_F40_A1.8001.00
17_F28_A1.7991.00
340_E346_I1.7981.00
47_Q66_K1.7841.00
367_E370_T1.7831.00
83_C166_C1.7811.00
299_L440_V1.7791.00
284_S348_D1.7791.00
280_K355_L1.7381.00
147_G185_A1.7281.00
399_L427_L1.7271.00
399_L426_V1.7221.00
93_Y97_L1.7181.00
77_C166_C1.7141.00
141_V204_I1.7031.00
271_Y282_A1.6941.00
216_M245_S1.6791.00
17_F46_A1.6741.00
18_E29_K1.6741.00
46_A65_L1.6721.00
301_D305_E1.6681.00
351_R354_E1.6671.00
76_P131_W1.6581.00
383_D408_K1.6581.00
132_N171_S1.6491.00
245_S270_E1.6421.00
396_E400_R1.6301.00
420_L451_C1.6301.00
176_A215_M1.6121.00
71_H92_T1.6091.00
209_G212_T1.6001.00
86_C166_C1.5571.00
394_C399_L1.5571.00
420_L424_L1.5501.00
358_N361_A1.5471.00
113_K425_R1.5451.00
420_L453_V1.5371.00
35_I58_A1.5301.00
304_L332_Q1.5191.00
49_K63_I1.5111.00
33_F58_A1.5101.00
97_L126_G1.5071.00
172_K208_Y1.5041.00
343_P347_E1.5031.00
338_G349_A1.4941.00
125_L440_V1.4921.00
186_N235_D1.4891.00
279_V327_L1.4721.00
247_V265_V1.4721.00
21_T25_A1.4721.00
403_V431_G1.4681.00
171_S175_E1.4511.00
315_V333_A1.4371.00
98_L101_Q1.4341.00
92_T95_G1.4271.00
326_S336_V1.4251.00
297_K301_D1.4191.00
122_H438_Q1.4171.00
142_G160_I1.4081.00
302_K438_Q1.4061.00
125_L298_V1.4031.00
104_V439_P1.3911.00
40_A62_L1.3891.00
19_D102_K1.3851.00
235_D239_Q1.3811.00
173_N206_V1.3801.00
104_V449_V1.3731.00
279_V331_K1.3701.00
313_E383_D1.3681.00
385_L407_P1.3621.00
309_L315_V1.3581.00
21_T27_V1.3551.00
109_E115_D1.3531.00
76_P167_L1.3521.00
197_H254_K1.3461.00
347_E350_K1.3451.00
28_A48_I1.3421.00
244_K269_E1.3411.00
307_A384_T1.3321.00
214_E269_E1.3311.00
50_V58_A1.3291.00
310_Q313_E1.3231.00
28_A37_V1.3211.00
108_L424_L1.3201.00
128_E298_V1.3181.00
237_T267_W1.3181.00
108_L437_V1.3031.00
277_G328_F1.2971.00
179_A240_F1.2941.00
226_F229_K1.2911.00
35_I50_V1.2911.00
79_I163_M1.2901.00
309_L313_E1.2801.00
91_M95_G1.2731.00
205_M218_V1.2721.00
29_K34_P1.2651.00
33_F53_V1.2631.00
184_C201_L1.2601.00
175_E242_H1.2561.00
16_T67_E1.2541.00
327_L361_A1.2511.00
15_V30_V1.2471.00
51_T61_R1.2431.00
273_Y282_A1.2431.00
214_E244_K1.2391.00
236_I243_V1.2381.00
338_G363_F1.2371.00
127_M130_P1.2291.00
121_V124_T1.2271.00
302_K306_Y1.2211.00
234_E238_A1.2091.00
184_C191_A1.1951.00
143_E147_G1.1911.00
19_D106_D1.1861.00
312_E334_K1.1851.00
133_Y446_T1.1851.00
165_A174_D1.1841.00
135_N293_P1.1821.00
451_C455_I1.1821.00
349_A363_F1.1741.00
234_E237_T1.1741.00
435_R454_L1.1701.00
73_T92_T1.1671.00
41_L90_H1.1671.00
179_A239_Q1.1631.00
400_R404_E1.1571.00
158_H194_E1.1551.00
306_Y454_L1.1521.00
132_N167_L1.1521.00
50_V60_G1.1491.00
176_A240_F1.1451.00
141_V150_A1.1431.00
15_V37_V1.1391.00
424_L434_T1.1371.00
247_V285_A1.1341.00
279_V358_N1.1311.00
41_L91_M1.1271.00
19_D29_K1.1261.00
137_A169_Q1.1261.00
263_T286_R1.1251.00
45_K66_K1.1251.00
409_R456_K1.1241.00
25_A59_F1.1201.00
314_T337_Y1.1171.00
200_W223_T1.1071.00
98_L102_K1.1001.00
102_K105_K1.0910.99
338_G361_A1.0880.99
309_L333_A1.0850.99
77_C85_G1.0780.99
232_I235_D1.0780.99
140_P160_I1.0750.99
200_W222_R1.0680.99
15_V35_I1.0670.99
410_V432_Y1.0670.99
172_K175_E1.0640.99
53_V58_A1.0580.99
343_P365_V1.0550.99
282_A355_L1.0540.99
75_A89_Q1.0480.99
318_A398_L1.0450.99
224_S262_E1.0390.99
293_P296_T1.0390.99
108_L420_L1.0330.99
330_A358_N1.0310.99
298_V440_V1.0300.99
287_S348_D1.0270.99
132_N165_A1.0260.99
433_V456_K1.0230.99
121_V439_P1.0230.99
19_D27_V1.0190.99
327_L353_A1.0180.99
83_C89_Q1.0160.99
105_K109_E1.0150.99
125_L438_Q1.0140.99
277_G301_D1.0130.99
436_E454_L1.0120.99
278_D331_K1.0110.99
374_K378_E1.0110.99
320_C363_F1.0110.99
416_N419_T1.0100.99
214_E273_Y1.0100.99
309_L384_T1.0080.99
212_T275_L1.0070.99
333_A360_N1.0040.99
350_K362_E1.0010.99
164_S178_Q0.9990.99
287_S345_A0.9950.99
148_L185_A0.9950.99
211_V275_L0.9910.99
273_Y355_L0.9910.99
396_E426_V0.9910.99
129_D294_E0.9910.99
107_V417_P0.9900.99
148_L184_C0.9860.99
233_I237_T0.9820.99
400_R426_V0.9800.99
302_K452_C0.9750.99
302_K436_E0.9740.99
80_Y90_H0.9730.99
353_A363_F0.9710.99
148_L191_A0.9690.99
303_A411_V0.9690.99
339_V371_V0.9680.99
91_M99_F0.9670.99
87_Q447_N0.9610.99
452_C456_K0.9590.99
382_A385_L0.9550.99
406_K457_L0.9550.99
326_S361_A0.9540.99
26_G40_A0.9530.99
218_V285_A0.9500.99
277_G297_K0.9480.99
193_N196_R0.9420.98
263_T285_A0.9400.98
77_C80_Y0.9340.98
352_N356_N0.9280.98
410_V427_L0.9270.98
15_V46_A0.9260.98
453_V456_K0.9260.98
298_V301_D0.9250.98
337_Y364_A0.9250.98
217_I243_V0.9240.98
97_L124_T0.9230.98
407_P432_Y0.9210.98
253_N261_N0.9150.98
320_C349_A0.9120.98
308_E409_R0.9070.98
351_R355_L0.9070.98
82_Q154_Q0.9060.98
250_I264_N0.9050.98
249_N260_G0.9040.98
172_K242_H0.8990.98
130_P445_H0.8980.98
122_H306_Y0.8970.98
303_A386_V0.8940.98
426_V429_D0.8910.98
88_L99_F0.8910.98
77_C89_Q0.8860.98
426_V430_G0.8860.98
176_A179_A0.8850.98
306_Y438_Q0.8850.98
38_P155_Q0.8850.98
172_K215_M0.8840.98
230_A234_E0.8820.98
182_D185_A0.8790.98
347_E351_R0.8760.98
302_K440_V0.8760.98
105_K121_V0.8750.98
222_R252_P0.8750.98
346_I365_V0.8710.97
319_Y369_E0.8710.97
315_V384_T0.8660.97
101_Q121_V0.8600.97
315_V329_L0.8600.97
424_L453_V0.8600.97
279_V330_A0.8560.97
124_T127_M0.8520.97
235_D238_A0.8510.97
330_A336_V0.8500.97
182_D239_Q0.8490.97
17_F26_G0.8450.97
317_D338_G0.8390.97
314_T334_K0.8390.97
236_I240_F0.8300.97
434_T455_I0.8290.97
131_W445_H0.8260.96
86_C89_Q0.8230.96
112_G421_A0.8220.96
75_A166_C0.8210.96
354_E359_T0.8170.96
187_Y235_D0.8160.96
437_V453_V0.8150.96
77_C84_G0.8150.96
344_E347_E0.8130.96
137_A152_F0.8130.96
350_K354_E0.8110.96
295_Q442_M0.8090.96
78_P165_A0.8090.96
337_Y382_A0.8080.96
75_A80_Y0.8080.96
408_K456_K0.8060.96
150_A181_K0.8050.96
291_V442_M0.8030.96
376_Y405_M0.8030.96
368_A372_I0.8010.96
140_P153_Y0.7980.96
300_Y325_I0.7960.96
247_V263_T0.7920.96
229_K264_N0.7890.95
125_L302_K0.7880.95
232_I236_I0.7840.95
295_Q298_V0.7830.95
44_E72_R0.7830.95
129_D132_N0.7790.95
408_K432_Y0.7780.95
180_V204_I0.7770.95
100_K441_D0.7730.95
201_L219_F0.7700.95
137_A173_N0.7690.95
304_L329_L0.7690.95
44_E69_S0.7690.95
316_I372_I0.7690.95
141_V184_C0.7690.95
291_V420_L0.7670.95
37_V48_I0.7660.95
283_I289_Y0.7650.95
183_I232_I0.7640.95
50_V53_V0.7640.95
85_G166_C0.7630.95
314_T380_I0.7630.95
132_N174_D0.7610.94
406_K431_G0.7600.94
182_D186_N0.7580.94
71_H98_L0.7570.94
288_F415_C0.7560.94
409_R454_L0.7540.94
371_V374_K0.7530.94
434_T437_V0.7520.94
274_D289_Y0.7500.94
123_P439_P0.7490.94
80_Y87_Q0.7490.94
143_E146_G0.7470.94
411_V452_C0.7410.94
80_Y83_C0.7400.94
304_L328_F0.7400.94
231_K235_D0.7400.94
93_Y130_P0.7370.93
326_S363_F0.7370.93
369_E395_D0.7360.93
246_I267_W0.7350.93
27_V34_P0.7350.93
269_E273_Y0.7350.93
89_Q131_W0.7330.93
415_C450_E0.7330.93
299_L442_M0.7320.93
183_I187_Y0.7290.93
120_T436_E0.7290.93
296_T324_T0.7290.93
176_A243_V0.7290.93
44_E90_H0.7290.93
135_N289_Y0.7270.93
192_Y199_G0.7260.93
272_I276_I0.7260.93
114_L428_E0.7250.93
75_A83_C0.7220.93
320_C340_E0.7180.93
249_N263_T0.7150.92
307_A411_V0.7140.92
313_E333_A0.7140.92
341_I367_E0.7120.92
451_C456_K0.7120.92
169_Q173_N0.7090.92
364_A371_V0.7050.92
93_Y126_G0.7040.92
403_V427_L0.7040.92
104_V451_C0.7020.92
219_F222_R0.7020.92
96_Q441_D0.7000.92
337_Y362_E0.7000.92
306_Y452_C0.6970.91
387_V402_I0.6960.91
108_L421_A0.6940.91
304_L326_S0.6890.91
231_K234_E0.6880.91
428_E433_V0.6870.91
47_Q63_I0.6840.91
451_C454_L0.6830.91
190_K200_W0.6830.91
170_Q174_D0.6820.91
30_V48_I0.6810.90
346_I350_K0.6800.90
54_K57_F0.6800.90
107_V421_A0.6790.90
211_V297_K0.6780.90
412_Y420_L0.6770.90
403_V426_V0.6770.90
46_A62_L0.6740.90
337_Y380_I0.6710.90
335_K380_I0.6690.90
141_V201_L0.6690.90
28_A46_A0.6670.90
343_P350_K0.6660.89
169_Q174_D0.6640.89
205_M220_I0.6640.89
127_M292_N0.6610.89
223_T252_P0.6610.89
25_A38_P0.6600.89
194_E256_N0.6580.89
346_I363_F0.6580.89
245_S268_G0.6570.89
233_I246_I0.6550.89
327_L358_N0.6540.89
127_M294_E0.6520.88
124_T439_P0.6490.88
276_I296_T0.6490.88
93_Y441_D0.6490.88
40_A44_E0.6480.88
80_Y86_C0.6470.88
17_F65_L0.6470.88
370_T397_A0.6440.88
312_E333_A0.6440.88
179_A182_D0.6430.88
111_I114_L0.6430.88
341_I346_I0.6420.88
366_G373_P0.6410.88
153_Y158_H0.6390.87
369_E397_A0.6390.87
428_E434_T0.6390.87
107_V111_I0.6380.87
299_L452_C0.6370.87
290_Q415_C0.6370.87
20_L99_F0.6360.87
216_M219_F0.6350.87
315_V336_V0.6350.87
143_E191_A0.6350.87
376_Y401_T0.6340.87
449_V454_L0.6340.87
36_F57_F0.6340.87
295_Q440_V0.6320.87
331_K358_N0.6320.87
240_F243_V0.6310.87
39_N62_L0.6300.87
178_Q182_D0.6290.87
170_Q173_N0.6280.87
298_V302_K0.6250.86
387_V412_Y0.6220.86
219_F223_T0.6210.86
205_M259_F0.6210.86
449_V455_I0.6200.86
63_I67_E0.6200.86
251_N255_T0.6180.86
367_E371_V0.6170.86
415_C443_F0.6170.86
75_A86_C0.6170.86
140_P203_H0.6150.85
413_V452_C0.6150.85
187_Y228_H0.6150.85
110_R114_L0.6120.85
67_E70_P0.6120.85
54_K58_A0.6080.85
281_F324_T0.6070.85
181_K185_A0.6070.85
440_V452_C0.6070.85
153_Y157_S0.6060.85
123_P438_Q0.6040.84
243_V246_I0.6040.84
228_H231_K0.6040.84
244_K272_I0.6040.84
139_V150_A0.6030.84
51_T59_F0.6030.84
144_R149_V0.6030.84
33_F57_F0.6020.84
114_L434_T0.6010.84
35_I48_I0.6000.84
304_L331_K0.5980.84
233_I236_I0.5970.84
443_F450_E0.5960.84
54_K59_F0.5950.84
111_I421_A0.5950.84
208_Y215_M0.5940.83
370_T373_P0.5940.83
248_Q266_I0.5930.83
101_Q438_Q0.5910.83
164_S181_K0.5910.83
322_I326_S0.5900.83
114_L424_L0.5900.83
154_Q161_I0.5890.83
142_G149_V0.5890.83
236_I239_Q0.5880.83
288_F450_E0.5880.83
139_V177_V0.5870.83
286_R344_E0.5860.83
38_P62_L0.5860.83
30_V50_V0.5850.82
233_I267_W0.5850.82
327_L363_F0.5840.82
206_V217_I0.5840.82
27_V36_F0.5840.82
247_V270_E0.5840.82
30_V33_F0.5840.82
395_D399_L0.5830.82
199_G202_R0.5820.82
69_S72_R0.5820.82
313_E408_K0.5810.82
339_V368_A0.5810.82
84_G166_C0.5800.82
386_V413_V0.5800.82
40_A65_L0.5800.82
245_S265_V0.5790.82
209_G272_I0.5790.82
349_A361_A0.5780.82
237_T240_F0.5780.82
276_I297_K0.5770.82
366_G370_T0.5760.82
21_T34_P0.5760.82
289_Y322_I0.5740.81
133_Y291_V0.5710.81
208_Y213_G0.5710.81
80_Y89_Q0.5710.81
272_I275_L0.5700.81
139_V173_N0.5700.81
39_N65_L0.5680.81
48_I62_L0.5670.80
250_I262_E0.5670.80
173_N208_Y0.5660.80
95_G99_F0.5630.80
340_E345_A0.5630.80
218_V249_N0.5620.80
35_I51_T0.5620.80
229_K233_I0.5610.80
277_G304_L0.5600.80
77_C87_Q0.5590.80
176_A206_V0.5590.80
306_Y411_V0.5580.79
84_G161_I0.5580.79
372_I398_L0.5580.79
20_L41_L0.5580.79
139_V318_A0.5570.79
93_Y127_M0.5560.79
127_M295_Q0.5560.79
202_R207_R0.5560.79
307_A409_R0.5550.79
322_I325_I0.5550.79
88_L91_M0.5530.79
366_G372_I0.5530.79
136_K300_Y0.5530.79
133_Y445_H0.5520.79
89_Q166_C0.5500.78
338_G346_I0.5500.78
190_K198_K0.5490.78
76_P445_H0.5480.78
180_V219_F0.5480.78
417_P449_V0.5480.78
288_F443_F0.5470.78
279_V322_I0.5470.78
299_L413_V0.5460.78
41_L69_S0.5450.78
184_C189_V0.5440.78
78_P167_L0.5420.77
212_T274_D0.5390.77
445_H448_H0.5380.77
79_I166_C0.5380.77
368_A398_L0.5370.77
68_E74_D0.5360.77
200_W221_T0.5360.77
37_V46_A0.5360.77
391_R448_H0.5360.77
22_H107_V0.5350.77
325_I386_V0.5350.77
288_F389_P0.5340.76
137_A177_V0.5340.76
370_T374_K0.5330.76
229_K248_Q0.5310.76
220_I225_D0.5290.76
300_Y328_F0.5280.76
411_V454_L0.5280.76
304_L315_V0.5280.76
108_L434_T0.5270.76
216_M220_I0.5270.76
212_T272_I0.5250.75
202_R251_N0.5240.75
389_P415_C0.5240.75
189_V200_W0.5230.75
219_F246_I0.5230.75
414_S419_T0.5230.75
51_T62_L0.5230.75
274_D322_I0.5220.75
149_V162_D0.5220.75
384_T411_V0.5200.75
296_T300_Y0.5200.75
364_A375_W0.5170.74
83_C87_Q0.5160.74
305_E436_E0.5150.74
143_E148_L0.5150.74
18_E28_A0.5140.74
79_I167_L0.5140.74
325_I328_F0.5130.74
289_Y324_T0.5120.73
249_N259_F0.5120.73
38_P51_T0.5110.73
139_V163_M0.5110.73
180_V184_C0.5100.73
313_E384_T0.5090.73
128_E294_E0.5090.73
400_R430_G0.5080.73
106_D109_E0.5080.73
428_E431_G0.5080.73
111_I422_R0.5080.73
276_I289_Y0.5080.73
154_Q157_S0.5080.73
356_N360_N0.5080.73
65_L72_R0.5070.73
29_K32_G0.5070.73
73_T130_P0.5070.73
369_E373_P0.5060.73
183_I236_I0.5060.73
180_V232_I0.5050.72
308_E332_Q0.5050.72
361_A365_V0.5040.72
37_V40_A0.5040.72
347_E365_V0.5030.72
237_T243_V0.5030.72
79_I83_C0.5020.72
300_Y324_T0.5020.72
372_I401_T0.5000.72
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  
2jjqA 1 0.8497 100 0.242 Contact Map
1uwvA 1 0.9041 100 0.252 Contact Map
3bt7A 1 0.7669 100 0.448 Contact Map
3vseA 1 0.7342 100 0.687 Contact Map
4dmgA 2 0.719 100 0.707 Contact Map
2b78A 1 0.7233 100 0.714 Contact Map
1wxxA 2 0.7211 100 0.72 Contact Map
3c0kA 2 0.7298 100 0.726 Contact Map
2as0A 2 0.7364 100 0.754 Contact Map
3a27A 1 0.4423 100 0.764 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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