GREMLIN Database
RLMD - 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD
UniProt: P55135 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG11247
Length: 433 (410)
Sequences: 5393 (3816)
Seq/√Len: 188.5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
51_E68_R4.2101.00
398_S429_F3.6621.00
409_A430_S3.6511.00
99_L102_R3.2851.00
105_S109_A3.1001.00
117_S410_R2.9841.00
20_S49_N2.9421.00
75_E99_L2.9161.00
49_N71_S2.8511.00
399_E403_K2.7801.00
277_R280_E2.7671.00
310_S337_T2.7161.00
19_V52_V2.7101.00
304_L361_L2.6801.00
360_V376_I2.6291.00
66_V69_R2.5011.00
166_A196_Q2.4981.00
52_V64_A2.4471.00
100_Q419_H2.3731.00
158_D177_R2.3531.00
376_I384_I2.3381.00
150_K155_D2.2711.00
106_A110_R2.2481.00
81_C87_C2.2431.00
19_V32_A2.2431.00
249_Y255_R2.2341.00
208_T230_L2.2271.00
45_L48_E2.2231.00
289_R310_S2.2231.00
251_S255_R2.2021.00
295_C313_G2.1751.00
408_I427_V2.1681.00
281_W410_R2.1481.00
53_T65_K2.1321.00
81_C90_C2.0921.00
341_E346_D2.0891.00
362_L369_A2.0731.00
278_A387_V2.0201.00
69_R72_D2.0001.00
87_C90_C1.9801.00
257_T326_Q1.9241.00
44_L50_A1.9061.00
21_V44_L1.8901.00
105_S118_E1.8671.00
377_I404_A1.8431.00
259_S323_K1.8341.00
51_E70_L1.8271.00
97_V101_Q1.8251.00
21_V32_A1.8241.00
291_L357_F1.8201.00
241_T246_M1.8131.00
24_L46_P1.8061.00
56_E63_R1.8051.00
143_Q181_G1.7891.00
373_M401_L1.7851.00
373_M400_A1.7851.00
22_N33_R1.7591.00
87_C162_C1.7501.00
21_V41_I1.7481.00
276_A280_E1.7441.00
295_C321_V1.7271.00
108_L423_L1.7211.00
255_R330_L1.7191.00
126_G167_P1.7181.00
105_S119_V1.7181.00
75_E96_S1.7161.00
358_D382_I1.6991.00
315_E321_V1.6901.00
81_C162_C1.6861.00
394_L427_V1.6711.00
326_Q329_R1.6671.00
117_S412_A1.6561.00
90_C162_C1.6501.00
383_R430_S1.6471.00
394_L425_S1.6411.00
80_R125_W1.6361.00
50_A69_R1.6301.00
342_N345_E1.6271.00
274_M414_L1.6211.00
21_V50_A1.6201.00
247_P257_T1.5941.00
394_L398_S1.5751.00
279_L307_Q1.5431.00
168_Q196_Q1.5341.00
369_A373_M1.5281.00
360_V381_P1.5021.00
108_L413_M1.4871.00
301_T311_V1.4851.00
120_I414_L1.4721.00
272_Q276_A1.4681.00
53_T67_V1.4531.00
37_K62_A1.4421.00
172_L202_L1.4411.00
167_P171_A1.4381.00
112_M411_L1.4361.00
216_R220_E1.4331.00
220_E223_S1.4321.00
169_L194_L1.4311.00
20_S71_S1.4281.00
121_A124_P1.4271.00
39_L62_A1.4261.00
318_P322_E1.4191.00
333_L336_V1.4151.00
106_A109_A1.4121.00
102_R105_S1.4121.00
96_S99_L1.4091.00
222_F225_S1.4071.00
290_V308_A1.4011.00
23_D106_A1.3971.00
254_L306_T1.3941.00
277_R412_A1.3931.00
281_W428_L1.3881.00
25_D29_Q1.3841.00
377_I405_G1.3801.00
80_R163_P1.3781.00
313_G324_G1.3691.00
129_R268_A1.3631.00
32_A52_V1.3611.00
287_E309_A1.3601.00
282_L359_K1.3571.00
122_D273_K1.3551.00
25_D31_V1.3391.00
112_M398_S1.3351.00
54_V62_A1.3341.00
221_R225_S1.3331.00
123_V269_G1.3261.00
180_L192_V1.3181.00
39_L54_V1.3141.00
322_E325_Q1.3051.00
44_L66_V1.3011.00
285_Q288_D1.2981.00
120_I273_K1.2771.00
83_H159_V1.2751.00
136_N156_I1.2731.00
288_D358_D1.2691.00
407_T430_S1.2631.00
398_S408_I1.2571.00
55_T65_K1.2561.00
221_R224_H1.2441.00
32_A41_I1.2351.00
138_L143_Q1.2331.00
252_N303_P1.2321.00
161_Q170_E1.2251.00
37_K57_D1.2251.00
49_N70_L1.2241.00
19_V39_L1.2221.00
254_L302_L1.2211.00
219_L223_S1.2201.00
23_D110_R1.2181.00
324_G338_F1.2161.00
409_A428_L1.2141.00
33_R38_T1.2111.00
112_M394_L1.2091.00
29_Q63_R1.1951.00
131_A165_L1.1931.00
284_V288_D1.1911.00
102_R106_A1.1871.00
302_L336_V1.1831.00
201_T245_E1.1791.00
126_G163_P1.1751.00
253_G306_T1.1681.00
302_L328_A1.1661.00
127_Y420_T1.1641.00
95_A99_L1.1591.00
277_R281_W1.1571.00
168_Q171_A1.1521.00
284_V290_V1.1491.00
109_A113_K1.1481.00
77_E96_S1.1481.00
384_I406_Y1.1461.00
249_Y257_T1.1441.00
313_G336_V1.1361.00
23_D33_R1.1251.00
227_G246_M1.1231.00
328_A338_F1.1151.00
23_D31_V1.1111.00
390_N393_T1.1111.00
54_V64_A1.1051.00
313_G338_F1.1041.00
19_V41_I1.0921.00
190_G193_E1.0891.00
381_P406_Y1.0891.00
111_L391_P1.0861.00
45_L95_A1.0851.00
45_L94_H1.0841.00
91_Q421_G1.0731.00
135_L146_M1.0701.00
87_C93_Q1.0671.00
226_E245_E1.0601.00
134_S156_I1.0561.00
218_K223_S1.0561.00
374_Q378_K1.0521.00
301_T336_V1.0491.00
188_H236_S1.0481.00
289_R312_V1.0431.00
144_L180_L1.0421.00
312_V339_Y1.0421.00
79_P93_Q1.0391.00
273_K276_A1.0381.00
57_D62_A1.0281.00
81_C89_G1.0251.00
144_L181_G1.0211.00
86_V150_K1.0201.00
318_P340_H1.0171.00
277_R414_L1.0171.00
95_A103_S1.0171.00
109_A116_V1.0151.00
82_P161_Q1.0141.00
284_V308_A1.0141.00
138_L141_T1.0131.00
380_E431_R1.0081.00
326_Q330_L1.0061.00
308_A335_N1.0061.00
19_V34_H1.0061.00
21_V30_G1.0061.00
425_S429_F1.0010.99
120_I412_A0.9980.99
227_G230_L0.9910.99
410_R428_L0.9800.99
383_R428_L0.9800.99
382_I430_S0.9790.99
172_L175_K0.9790.99
278_A385_V0.9760.99
168_Q202_L0.9720.99
268_A271_N0.9710.99
293_L372_V0.9700.99
178_A181_G0.9700.99
382_I406_Y0.9680.99
295_C338_F0.9640.99
343_L347_V0.9620.99
305_A333_L0.9610.99
277_R410_R0.9580.99
314_V346_D0.9490.99
160_K174_P0.9480.99
384_I401_L0.9460.99
284_V359_K0.9430.99
374_Q400_A0.9420.99
101_Q119_V0.9410.99
294_F344_E0.9410.99
249_Y330_L0.9350.99
273_K414_L0.9310.99
262_D323_K0.9290.99
262_D320_L0.9270.99
198_T251_S0.9260.99
325_Q329_R0.9240.99
126_G161_Q0.9220.99
426_M430_S0.9200.99
252_N272_Q0.9200.99
271_N299_N0.9120.99
398_S427_V0.9090.99
325_Q337_T0.9090.99
112_M395_A0.9070.99
327_N331_N0.9060.99
277_R426_M0.9030.99
116_V413_M0.9030.99
254_L333_L0.9020.99
220_E224_H0.9010.99
84_F94_H0.8970.99
92_Q103_S0.8970.99
183_L190_G0.8960.99
165_L169_L0.8940.99
247_P250_D0.8940.99
321_V340_H0.8930.99
385_V428_L0.8920.99
19_V50_A0.8910.99
349_K353_A0.8850.99
257_T330_L0.8830.99
233_A238_I0.8820.99
201_T249_Y0.8810.99
134_S149_R0.8800.99
290_V359_K0.8780.99
254_L305_A0.8770.99
125_W419_H0.8740.99
135_L192_V0.8730.99
281_W412_A0.8710.99
30_G44_L0.8680.99
199_S251_S0.8680.99
408_I429_F0.8660.99
295_C324_G0.8650.98
229_D241_T0.8630.98
322_E326_Q0.8620.98
362_L386_Y0.8610.98
218_K225_S0.8600.98
279_L303_P0.8600.98
282_L385_V0.8560.98
235_D239_L0.8550.98
212_S215_D0.8520.98
248_W251_S0.8510.98
252_N276_A0.8480.98
203_M227_G0.8480.98
427_V430_S0.8420.98
274_M416_M0.8390.98
81_C84_F0.8370.98
321_V338_F0.8350.98
117_S281_W0.8350.98
385_V426_M0.8330.98
279_L306_T0.8310.98
357_F360_V0.8210.98
227_G232_L0.8210.98
154_S185_A0.8190.98
411_L427_V0.8180.98
104_K415_D0.8180.98
266_V416_M0.8170.98
48_E76_R0.8140.98
124_P419_H0.8140.98
201_T226_E0.8140.98
270_V273_K0.8100.98
275_V300_F0.8100.98
387_V426_M0.8100.98
283_D383_R0.8090.98
126_G170_E0.8040.98
341_E347_V0.8020.98
290_V304_L0.8000.97
131_A169_L0.7970.97
402_L408_I0.7960.97
278_A361_L0.7950.97
388_S393_T0.7930.97
425_S430_S0.7930.97
400_A404_A0.7910.97
42_P151_A0.7910.97
231_Y234_P0.7900.97
115_D410_R0.7890.97
147_G156_I0.7890.97
90_C93_Q0.7880.97
205_L260_P0.7850.97
312_V357_F0.7850.97
246_M250_D0.7810.97
81_C93_Q0.7800.97
209_A234_P0.7780.97
230_L233_A0.7760.97
131_A148_F0.7740.97
41_I52_V0.7740.97
329_R334_Q0.7740.97
48_E73_S0.7720.97
226_E230_L0.7720.97
321_V325_Q0.7700.97
342_N346_D0.7670.97
108_L425_S0.7650.97
344_E370_A0.7640.97
50_A66_V0.7610.97
178_A182_S0.7610.97
81_C88_G0.7560.96
244_G250_D0.7520.96
227_G231_Y0.7520.96
346_D349_K0.7510.96
245_E249_Y0.7500.96
270_V416_M0.7470.96
34_H37_K0.7470.96
339_Y346_D0.7450.96
386_Y394_L0.7450.96
305_A311_V0.7440.96
198_T272_Q0.7440.96
191_H210_P0.7430.96
377_I401_L0.7430.96
172_L204_I0.7420.96
316_G342_N0.7410.96
75_E102_R0.7410.96
292_D313_G0.7410.96
84_F91_Q0.7400.96
177_R181_G0.7400.96
263_F389_C0.7340.96
408_I411_L0.7330.96
58_K61_Y0.7320.96
165_L170_E0.7320.96
79_P162_C0.7310.96
111_L395_A0.7300.96
275_V303_P0.7260.96
219_L225_S0.7230.95
266_V394_L0.7220.95
97_V124_P0.7210.95
312_V337_T0.7210.95
291_L347_V0.7210.95
105_S116_V0.7190.95
216_R219_L0.7180.95
341_E345_E0.7170.95
289_R355_N0.7170.95
31_V38_T0.7150.95
302_L333_L0.7150.95
295_C315_E0.7150.95
402_L407_T0.7140.95
218_K221_R0.7140.95
258_F264_I0.7120.95
289_R309_A0.7100.95
389_C424_E0.7090.95
319_A322_E0.7060.95
257_T323_K0.7060.95
146_M177_R0.7060.95
269_G272_Q0.7020.95
138_L145_Q0.7010.95
233_A237_E0.7000.95
341_E348_T0.6990.95
129_R264_I0.6970.94
120_I277_R0.6970.94
98_D102_R0.6950.94
84_F87_C0.6900.94
250_D264_I0.6890.94
400_A403_K0.6890.94
166_A170_E0.6880.94
71_S74_P0.6870.94
133_L173_L0.6870.94
149_R154_S0.6840.94
51_E67_V0.6840.94
93_Q125_W0.6830.94
290_V311_V0.6810.94
116_V119_V0.6780.94
135_L180_L0.6750.94
79_P84_F0.6740.93
183_L189_L0.6720.93
31_V40_F0.6670.93
24_L95_A0.6670.93
175_K178_A0.6660.93
184_Q187_R0.6630.93
281_W426_M0.6620.93
110_R113_K0.6620.93
279_L301_T0.6610.93
97_V415_D0.6610.93
176_V180_L0.6610.93
105_S412_A0.6610.93
45_L73_S0.6610.93
89_G162_C0.6600.93
377_I400_A0.6590.93
100_Q415_D0.6580.93
118_E413_M0.6570.93
226_E231_Y0.6550.92
188_H209_A0.6550.92
40_F61_Y0.6530.92
191_H209_A0.6530.92
105_S413_M0.6520.92
345_E348_T0.6520.92
301_T338_F0.6520.92
288_D308_A0.6490.92
73_S76_R0.6490.92
274_M426_M0.6480.92
145_Q158_D0.6480.92
150_K157_V0.6480.92
67_V71_S0.6460.92
196_Q200_G0.6450.92
58_K63_R0.6450.92
52_V66_V0.6430.92
279_L304_L0.6430.92
280_E410_R0.6420.92
362_L376_I0.6420.92
254_L303_P0.6420.92
226_E229_D0.6410.92
79_P87_C0.6380.91
24_L103_S0.6360.91
197_A248_W0.6350.91
169_L196_Q0.6340.91
136_N145_Q0.6340.91
370_A373_M0.6330.91
366_R422_H0.6330.91
265_Q389_C0.6330.91
229_D233_A0.6320.91
44_L48_E0.6290.91
283_D307_Q0.6290.91
230_L238_I0.6270.91
374_Q404_A0.6250.91
229_D232_L0.6230.91
217_E220_E0.6230.91
219_L222_F0.6200.90
189_L193_E0.6180.90
34_H52_V0.6170.90
344_E371_G0.6170.90
77_E124_P0.6160.90
83_H86_V0.6160.90
341_E344_E0.6150.90
223_S243_S0.6140.90
55_T63_R0.6130.90
79_P90_C0.6120.90
48_E94_H0.6120.90
174_P178_A0.6110.90
230_L234_P0.6110.90
312_V355_N0.6100.90
230_L235_D0.6100.90
413_M423_L0.6090.89
121_A269_G0.6050.89
29_Q42_P0.6040.89
54_V57_D0.6040.89
423_L428_L0.6000.89
233_A239_L0.5990.89
231_Y238_I0.5990.89
42_P66_V0.5980.89
371_G374_Q0.5980.89
41_I44_L0.5930.88
310_S355_N0.5920.88
318_P325_Q0.5920.88
182_S221_R0.5910.88
270_V414_L0.5910.88
166_A169_L0.5900.88
196_Q202_L0.5900.88
425_S428_L0.5900.88
297_M301_T0.5900.88
389_C417_F0.5890.88
101_Q121_A0.5890.88
263_F424_E0.5890.88
82_P160_K0.5890.88
32_A50_A0.5890.88
372_V376_I0.5880.88
160_K177_R0.5870.88
84_F90_C0.5870.88
39_L52_V0.5850.88
175_K222_F0.5850.88
83_H162_C0.5850.88
22_N32_A0.5840.87
423_L429_F0.5790.87
25_D38_T0.5790.87
58_K62_A0.5780.87
84_F93_Q0.5780.87
119_V413_M0.5780.87
259_S262_D0.5770.87
281_W385_V0.5770.87
359_K385_V0.5750.87
93_Q164_I0.5750.87
417_F424_E0.5740.87
273_K277_R0.5730.86
32_A39_L0.5730.86
228_L231_Y0.5720.86
24_L30_G0.5720.86
103_S107_A0.5710.86
317_V320_L0.5700.86
150_K153_S0.5700.86
80_R419_H0.5680.86
414_L426_M0.5680.86
380_E405_G0.5650.86
175_K225_S0.5650.86
133_L293_L0.5640.86
84_F125_W0.5630.86
261_R319_A0.5630.86
243_S246_M0.5620.85
87_C91_Q0.5620.85
138_L142_Q0.5610.85
43_G66_V0.5610.85
116_V411_L0.5600.85
314_V343_L0.5600.85
288_D382_I0.5590.85
244_G248_W0.5590.85
380_E406_Y0.5580.85
133_L146_M0.5580.85
72_D78_T0.5560.85
244_G251_S0.5560.85
339_Y350_Q0.5550.85
83_H87_C0.5540.85
83_H163_P0.5540.85
287_E308_A0.5540.85
77_E80_R0.5530.85
33_R36_G0.5530.85
347_V372_V0.5520.84
324_G336_V0.5510.84
182_S218_K0.5510.84
236_S239_L0.5500.84
210_P234_P0.5490.84
127_Y419_H0.5490.84
24_L45_L0.5480.84
375_Q378_K0.5480.84
256_L297_M0.5460.84
111_L392_A0.5440.84
300_F361_L0.5430.83
88_G157_V0.5430.83
226_E233_A0.5420.83
234_P237_E0.5370.83
183_L188_H0.5370.83
207_H211_L0.5370.83
345_E349_K0.5360.83
125_W163_P0.5360.83
233_A236_S0.5360.83
83_H90_C0.5350.83
369_A400_A0.5350.83
130_R275_V0.5350.83
194_L204_I0.5340.82
331_N335_N0.5330.82
82_P163_P0.5320.82
350_Q354_K0.5320.82
241_T244_G0.5320.82
217_E221_R0.5320.82
228_L233_A0.5310.82
263_F417_F0.5310.82
238_I367_A0.5300.82
34_H54_V0.5290.82
127_Y266_V0.5290.82
122_D270_V0.5270.82
184_Q189_L0.5260.81
172_L194_L0.5260.81
211_L215_D0.5250.81
274_M387_V0.5230.81
37_K61_Y0.5230.81
88_G162_C0.5210.81
192_V206_R0.5210.81
110_R114_H0.5200.81
99_L103_S0.5200.81
80_R93_Q0.5200.81
216_R223_S0.5200.81
21_V69_R0.5180.81
343_L372_V0.5170.80
108_L411_L0.5150.80
293_L360_V0.5150.80
252_N306_T0.5140.80
252_N279_L0.5130.80
227_G233_A0.5130.80
256_L299_N0.5120.80
81_C91_Q0.5120.80
264_I297_M0.5100.79
397_D400_A0.5100.79
254_L297_M0.5080.79
344_E348_T0.5070.79
205_L208_T0.5060.79
69_R76_R0.5060.79
232_L240_E0.5040.79
39_L55_T0.5030.79
44_L69_R0.5030.79
345_E371_G0.5030.79
271_N275_V0.5030.79
197_A250_D0.5020.78
300_F303_P0.5010.78
93_Q162_C0.5010.78
33_R40_F0.5000.78
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  
1uwvA 1 0.963 100 0.191 Contact Map
2jjqA 1 0.8637 100 0.267 Contact Map
3bt7A 1 0.7875 100 0.446 Contact Map
3vseA 1 0.7483 100 0.71 Contact Map
4dmgA 2 0.7344 100 0.731 Contact Map
1wxxA 2 0.7275 100 0.734 Contact Map
2b78A 1 0.7344 100 0.74 Contact Map
3c0kA 2 0.7252 100 0.758 Contact Map
3k6rA 1 0.5589 100 0.767 Contact Map
3a27A 1 0.4688 100 0.77 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.

Page generated in 0.0118 seconds.