GREMLIN Database
YWBD - Putative ribosomal RNA large subunit methyltransferase YwbD
UniProt: P39587 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
Length: 396 (379)
Sequences: 2374 (1540)
Seq/√Len: 79.1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
219_A296_L4.1701.00
297_I329_T4.0061.00
51_A65_T4.0031.00
53_G63_G3.7971.00
80_L146_E3.4811.00
253_N257_A3.1881.00
123_Y153_A3.1531.00
223_T245_K3.1411.00
189_I240_L3.1231.00
247_T294_F3.1071.00
192_A261_E2.9141.00
83_L105_F2.8881.00
245_K274_D2.7971.00
235_S248_S2.7531.00
247_T276_K2.6491.00
35_E57_L2.6161.00
223_T292_L2.5821.00
183_I190_Q2.4531.00
191_Y237_A2.3891.00
117_I124_L2.3281.00
223_T330_A2.2941.00
278_M283_Y2.2241.00
145_D174_K2.1961.00
229_S248_S2.1881.00
353_I391_V2.1751.00
305_A314_A2.1661.00
119_Y122_G2.1501.00
185_Q190_Q2.1481.00
100_T121_D2.1291.00
40_D52_R2.1271.00
183_I192_A2.1141.00
181_P261_E2.0791.00
283_Y287_A2.0761.00
293_R330_A2.0671.00
338_S390_V2.0201.00
295_D330_A2.0181.00
49_F52_R2.0101.00
287_A294_F2.0091.00
76_Q142_S2.0061.00
261_E264_S1.9741.00
122_G152_K1.9661.00
52_R67_T1.9651.00
249_V283_Y1.9641.00
224_V298_I1.9501.00
186_E211_R1.9411.00
223_T244_E1.9221.00
227_T280_V1.9111.00
322_L337_A1.8491.00
143_A147_M1.7891.00
259_T275_I1.7781.00
213_A368_E1.7731.00
382_F385_G1.7671.00
54_Y130_S1.7651.00
278_M286_Y1.7621.00
102_F119_Y1.7611.00
43_S48_E1.7541.00
232_G259_T1.7321.00
189_I237_A1.7221.00
72_E81_S1.7081.00
253_N277_V1.7071.00
240_L268_L1.6981.00
256_L277_V1.6701.00
239_A268_L1.6701.00
319_K359_E1.6551.00
297_I325_T1.6491.00
187_N212_K1.6341.00
92_K222_K1.6131.00
83_L147_M1.6101.00
190_Q265_V1.6081.00
80_L84_T1.6061.00
283_Y294_F1.6021.00
26_L62_V1.5881.00
214_I296_L1.5871.00
183_I265_V1.5871.00
315_A352_F1.5470.99
326_I357_F1.5390.99
191_Y236_V1.5350.99
76_Q146_E1.5270.99
115_V133_I1.5210.99
11_A15_K1.5180.99
221_G244_E1.5110.99
17_G68_R1.5060.99
323_K359_E1.5010.99
194_D197_E1.4890.99
105_F112_V1.4880.99
257_A260_I1.4790.99
155_Y196_N1.4750.99
260_I264_S1.4730.99
370_F390_V1.4620.99
184_I203_I1.4530.99
212_K216_D1.4370.99
346_M369_E1.4350.99
336_V390_V1.4310.99
134_Y163_A1.4310.99
260_I275_I1.4190.99
74_I78_F1.4150.99
219_A241_G1.4000.99
124_L149_L1.3990.99
357_F364_Y1.3980.99
285_S320_N1.3810.99
101_A205_L1.3770.99
84_T88_Q1.3750.99
329_T333_G1.3510.99
215_R240_L1.3480.98
224_V238_A1.3430.98
34_K37_D1.3420.98
303_S306_R1.3350.98
42_V47_G1.3320.98
123_Y195_L1.3070.98
248_S273_H1.3060.98
136_F139_M1.3050.98
215_R241_G1.3030.98
336_V392_L1.2990.98
184_I193_V1.2840.98
226_N248_S1.2730.98
224_V246_T1.2730.98
315_A344_F1.2710.98
119_Y124_L1.2670.98
222_K296_L1.2610.98
235_S263_F1.2590.98
299_L325_T1.2570.98
209_H373_P1.2510.98
191_Y203_I1.2500.98
123_Y182_I1.2490.98
181_P192_A1.2490.98
83_L117_I1.2440.97
82_K111_G1.2440.97
263_F268_L1.2410.97
366_I393_L1.2380.97
76_Q80_L1.2350.97
286_Y290_K1.2230.97
67_T72_E1.2230.97
334_V367_I1.2190.97
315_A348_K1.2100.97
287_A328_I1.2090.97
241_G296_L1.2070.97
138_D142_S1.1970.97
276_K283_Y1.1950.97
264_S269_D1.1800.96
80_L147_M1.1760.96
213_A216_D1.1710.96
51_A68_R1.1670.96
56_G131_K1.1630.96
40_D49_F1.1610.96
107_G116_T1.1510.96
224_V243_A1.1430.96
29_S33_M1.1400.96
87_A102_F1.1390.96
76_Q139_M1.1380.96
218_Y368_E1.1360.96
247_T274_D1.1200.95
323_K327_A1.1190.95
189_I236_V1.1150.95
277_V309_K1.1130.95
285_S324_E1.1120.95
41_I53_G1.1100.95
239_A263_F1.1090.95
311_T344_F1.1070.95
350_K391_V1.1010.95
11_A44_E1.1010.95
279_D282_N1.0990.95
145_D154_I1.0980.95
87_A91_A1.0970.95
66_L74_I1.0970.95
101_A184_I1.0970.95
274_D292_L1.0880.94
247_T292_L1.0800.94
124_L151_Y1.0780.94
209_H374_E1.0760.94
38_L52_R1.0760.94
81_S85_K1.0750.94
23_K62_V1.0690.94
153_A177_R1.0690.94
345_G348_K1.0560.94
334_V392_L1.0550.93
288_A324_E1.0550.93
207_Q338_S1.0530.93
364_Y393_L1.0470.93
41_I65_T1.0470.93
7_K10_H1.0410.93
137_K156_E1.0370.93
218_Y334_V1.0300.93
304_F317_D1.0300.93
305_A344_F1.0270.93
235_S275_I1.0160.92
33_M55_Y1.0140.92
89_A377_K1.0130.92
80_L143_A1.0050.92
253_N260_I1.0050.92
185_Q188_G1.0040.92
200_M340_N1.0020.92
43_S50_L0.9960.91
322_L326_I0.9950.91
282_N285_S0.9940.91
115_V147_M0.9850.91
152_K176_R0.9840.91
204_F303_S0.9840.91
207_Q210_V0.9820.91
13_K25_A0.9800.91
299_L335_I0.9770.91
31_G37_D0.9760.91
326_I335_I0.9730.90
213_A218_Y0.9720.90
346_M386_N0.9670.90
299_L322_L0.9650.90
236_V240_L0.9580.90
126_I144_L0.9540.90
329_T335_I0.9540.90
181_P194_D0.9530.89
37_D135_T0.9520.89
257_A261_E0.9520.89
299_L337_A0.9450.89
207_Q234_F0.9450.89
303_S341_S0.9440.89
87_A149_L0.9440.89
105_F117_I0.9430.89
11_A43_S0.9350.89
337_A349_F0.9350.89
227_T299_L0.9300.88
88_Q91_A0.9270.88
106_N109_G0.9140.87
120_Y201_T0.9120.87
19_P382_F0.9110.87
20_L61_G0.9110.87
379_I382_F0.9030.87
123_Y152_K0.9030.87
172_F177_R0.9020.87
163_A168_E0.9010.87
155_Y158_K0.9000.87
41_I63_G0.8980.86
303_S342_S0.8980.86
87_A104_L0.8950.86
84_T147_M0.8940.86
236_V268_L0.8930.86
128_W137_K0.8930.86
319_K323_K0.8920.86
228_F321_L0.8900.86
6_L10_H0.8890.86
67_T74_I0.8840.86
256_L275_I0.8830.86
263_F275_I0.8810.85
239_A246_T0.8780.85
77_A80_L0.8770.85
350_K369_E0.8760.85
13_K18_Y0.8710.85
14_I21_I0.8690.85
126_I141_I0.8680.85
54_Y133_I0.8610.84
139_M142_S0.8610.84
350_K366_I0.8600.84
99_T185_Q0.8600.84
175_G178_G0.8580.84
316_K359_E0.8560.84
227_T249_V0.8560.84
115_V140_L0.8560.84
38_L66_L0.8510.83
15_K43_S0.8510.83
10_H24_E0.8480.83
340_N376_F0.8470.83
8_K44_E0.8440.83
65_T68_R0.8400.83
15_K48_E0.8390.82
78_F82_K0.8340.82
23_K60_K0.8330.82
234_F298_I0.8330.82
229_S232_G0.8320.82
117_I126_I0.8320.82
124_L144_L0.8300.82
371_T386_N0.8280.82
214_I298_I0.8270.82
314_A319_K0.8270.82
75_D78_F0.8250.81
145_D151_Y0.8220.81
322_L335_I0.8210.81
142_S146_E0.8110.80
263_F273_H0.8110.80
187_N237_A0.8070.80
322_L325_T0.8070.80
83_L140_L0.8070.80
366_I380_S0.8060.80
128_W133_I0.8050.80
350_K354_D0.8050.80
39_V63_G0.8040.80
258_K261_E0.8040.80
101_A121_D0.8010.79
262_Q265_V0.8000.79
143_A146_E0.7980.79
223_T247_T0.7950.79
136_F140_L0.7940.79
7_K24_E0.7910.79
325_T329_T0.7900.79
129_Y160_F0.7870.78
177_R196_N0.7860.78
214_I218_Y0.7860.78
151_Y154_I0.7810.78
189_I215_R0.7810.78
224_V296_L0.7800.78
351_G354_D0.7800.78
86_A90_R0.7800.78
153_A179_E0.7750.77
246_T275_I0.7710.77
139_M143_A0.7710.77
235_S273_H0.7700.77
188_G212_K0.7700.77
248_S275_I0.7700.77
218_Y336_V0.7690.77
305_A311_T0.7690.77
320_N359_E0.7650.76
366_I384_E0.7640.76
79_F136_F0.7630.76
14_I50_L0.7630.76
45_S48_E0.7620.76
319_K356_A0.7610.76
223_T295_D0.7600.76
226_N235_S0.7590.76
83_L143_A0.7570.76
18_Y384_E0.7570.76
6_L50_L0.7530.75
182_I195_L0.7510.75
33_M37_D0.7450.74
337_A353_I0.7450.74
69_N72_E0.7450.74
338_S370_F0.7440.74
10_H25_A0.7430.74
235_S246_T0.7430.74
317_D320_N0.7420.74
89_A365_T0.7410.74
347_K351_G0.7400.74
320_N324_E0.7390.74
66_L136_F0.7380.74
212_K215_R0.7370.74
21_I41_I0.7350.73
228_F281_F0.7340.73
230_Y305_A0.7310.73
227_T325_T0.7300.73
238_A243_A0.7280.73
141_I173_V0.7240.72
128_W134_Y0.7230.72
316_K319_K0.7220.72
117_I130_S0.7190.72
98_D185_Q0.7110.71
207_Q388_L0.7080.71
140_L143_A0.7080.71
27_A44_E0.7080.71
28_G31_G0.7050.70
26_L31_G0.7050.70
287_A292_L0.7030.70
112_V133_I0.7030.70
8_K12_A0.7020.70
248_S259_T0.7000.70
247_T283_Y0.6960.69
352_F356_A0.6930.69
227_T321_L0.6930.69
246_T273_H0.6920.69
81_S84_T0.6900.69
36_G132_G0.6900.69
288_A327_A0.6890.68
6_L9_A0.6890.68
161_D306_R0.6880.68
344_F352_F0.6870.68
159_R163_A0.6850.68
355_A358_K0.6850.68
239_A273_H0.6830.68
172_F178_G0.6810.68
199_A340_N0.6810.68
203_I237_A0.6810.68
322_L356_A0.6810.68
79_F115_V0.6790.67
222_K295_D0.6780.67
18_Y22_E0.6760.67
211_R231_T0.6760.67
208_R233_A0.6740.67
279_D320_N0.6740.67
47_G50_L0.6730.67
346_M391_V0.6700.66
40_D71_H0.6690.66
366_I378_T0.6670.66
226_N237_A0.6670.66
326_I364_Y0.6670.66
192_A265_V0.6670.66
204_F390_V0.6630.66
214_I334_V0.6610.65
229_S235_S0.6600.65
249_V276_K0.6580.65
199_A255_S0.6570.65
200_M376_F0.6550.65
85_K88_Q0.6550.65
213_A392_L0.6550.65
79_F83_L0.6540.64
10_H22_E0.6520.64
117_I144_L0.6500.64
104_L124_L0.6490.64
170_D214_I0.6470.64
121_D182_I0.6460.64
378_T386_N0.6450.63
77_A81_S0.6440.63
231_T258_K0.6440.63
21_I63_G0.6430.63
156_E171_D0.6430.63
127_Q325_T0.6420.63
322_L357_F0.6410.63
322_L339_T0.6410.63
307_T310_R0.6400.63
353_I393_L0.6400.63
206_D300_D0.6390.63
214_I219_A0.6370.62
76_Q143_A0.6370.62
324_E327_A0.6350.62
53_G67_T0.6340.62
6_L27_A0.6340.62
94_F102_F0.6330.62
67_T78_F0.6300.62
7_K27_A0.6290.61
153_A178_G0.6280.61
215_R237_A0.6270.61
155_Y195_L0.6240.61
10_H19_P0.6240.61
24_E60_K0.6230.61
28_G42_V0.6210.60
203_I211_R0.6200.60
95_E293_R0.6180.60
100_T185_Q0.6170.60
366_I391_V0.6160.60
55_Y63_G0.6160.60
232_G248_S0.6150.60
311_T345_G0.6150.60
199_A303_S0.6120.59
326_I362_E0.6110.59
304_F321_L0.6090.59
109_G385_G0.6080.59
205_L373_P0.6080.59
39_V53_G0.6080.59
218_Y387_Y0.6070.59
348_K352_F0.6060.59
318_Y341_S0.6060.59
204_F306_R0.6050.58
142_S174_K0.6040.58
291_D328_I0.6000.58
79_F143_A0.6000.58
384_E387_Y0.6000.58
49_F69_N0.5990.58
188_G215_R0.5990.58
141_I154_I0.5990.58
369_E386_N0.5970.57
19_P385_G0.5960.57
10_H13_K0.5950.57
77_A185_Q0.5950.57
153_A172_F0.5930.57
142_S152_K0.5930.57
135_T138_D0.5930.57
270_Y274_D0.5920.57
281_F304_F0.5910.57
22_E61_G0.5900.57
226_N231_T0.5890.56
214_I238_A0.5880.56
23_K279_D0.5880.56
186_E262_Q0.5870.56
199_A306_R0.5860.56
98_D188_G0.5850.56
210_V373_P0.5840.56
306_R317_D0.5820.56
342_S382_F0.5800.55
242_G250_D0.5790.55
26_L321_L0.5780.55
269_D272_A0.5780.55
278_M282_N0.5770.55
49_F65_T0.5770.55
244_E247_T0.5750.55
59_N108_E0.5740.55
186_E266_N0.5730.54
105_F144_L0.5720.54
8_K27_A0.5720.54
54_Y132_G0.5710.54
204_F338_S0.5710.54
222_K244_E0.5700.54
155_Y171_D0.5700.54
226_N273_H0.5700.54
320_N323_K0.5690.54
137_K171_D0.5690.54
210_V336_V0.5680.54
284_F328_I0.5680.54
94_F208_R0.5680.54
259_T273_H0.5670.54
86_A112_V0.5660.54
213_A370_F0.5660.54
249_V278_M0.5650.53
22_E25_A0.5640.53
66_L72_E0.5610.53
212_K237_A0.5600.53
256_L259_T0.5590.53
226_N263_F0.5590.53
90_R388_L0.5590.53
210_V234_F0.5580.53
35_E58_Q0.5580.53
319_K348_K0.5580.53
192_A262_Q0.5580.53
6_L14_I0.5570.52
38_L74_I0.5540.52
329_T332_K0.5530.52
200_M255_S0.5530.52
49_F72_E0.5530.52
310_R313_S0.5520.52
259_T263_F0.5520.52
107_G338_S0.5520.52
183_I193_V0.5500.51
252_A255_S0.5490.51
339_T387_Y0.5460.51
42_V71_H0.5450.51
158_K163_A0.5430.51
33_M57_L0.5410.50
21_I26_L0.5410.50
276_K294_F0.5400.50
199_A376_F0.5390.50
303_S343_A0.5390.50
52_R72_E0.5370.50
311_T343_A0.5370.50
237_A241_G0.5370.50
244_E330_A0.5370.50
244_E274_D0.5350.50
176_R291_D0.5340.49
109_G372_L0.5340.49
204_F251_V0.5340.49
8_K11_A0.5330.49
211_R266_N0.5330.49
105_F133_I0.5320.49
288_A328_I0.5310.49
41_I55_Y0.5310.49
108_E234_F0.5310.49
369_E391_V0.5290.49
25_A382_F0.5290.49
170_D173_V0.5280.49
284_F321_L0.5270.49
127_Q158_K0.5260.48
6_L44_E0.5260.48
123_Y179_E0.5260.48
251_V279_D0.5240.48
54_Y136_F0.5230.48
139_M147_M0.5230.48
372_L378_T0.5220.48
315_A350_K0.5210.48
229_S259_T0.5200.48
305_A310_R0.5200.48
157_K197_E0.5200.48
170_D196_N0.5200.48
35_E131_K0.5190.47
129_Y184_I0.5190.47
26_L45_S0.5170.47
45_S332_K0.5160.47
116_T120_Y0.5150.47
186_E226_N0.5130.47
201_T234_F0.5130.47
126_I154_I0.5120.47
123_Y155_Y0.5110.46
117_I133_I0.5090.46
260_I274_D0.5080.46
172_F175_G0.5080.46
281_F311_T0.5070.46
285_S323_K0.5070.46
99_T208_R0.5070.46
34_K135_T0.5070.46
326_I353_I0.5060.46
181_P258_K0.5060.46
348_K351_G0.5060.46
90_R377_K0.5060.46
187_N209_H0.5040.46
71_H74_I0.5030.45
13_K17_G0.5020.45
134_Y137_K0.5000.45
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  
2b78A 1 0.9495 100 0.325 Contact Map
3c0kA 2 0.9924 100 0.34 Contact Map
3vseA 1 0.9798 100 0.356 Contact Map
1wxxA 2 0.9596 100 0.371 Contact Map
2as0A 2 0.9823 100 0.42 Contact Map
4dmgA 2 0.9495 100 0.442 Contact Map
3v97A 1 0.8914 100 0.556 Contact Map
2igtA 4 0.7525 100 0.682 Contact Map
3k6rA 1 0.6439 100 0.687 Contact Map
3a27A 1 0.5429 100 0.703 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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