GREMLIN Database
YFIF - Uncharacterized tRNA/rRNA methyltransferase YfiF
UniProt: P0AGJ5 Sequences:
Download Alignment
We filter this alignment to remove sites that have many gaps before running GREMLIN.

Date: 2015_01
EcoGene: EG11786
Length: 345 (283)
Sequences: 1534 (1079)
Seq/√Len: 64.2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:
i j Sco Prob
338_E341_R4.9371.00
218_C223_V4.8791.00
201_A293_V3.8581.00
296_L328_I3.7051.00
330_V333_G3.4291.00
215_M226_V3.3691.00
274_T311_N3.3511.00
214_M332_T3.0971.00
305_D309_D2.9301.00
274_T303_L2.5661.00
266_R312_D2.5641.00
200_L223_V2.4511.00
130_A176_F2.4451.00
275_T335_L2.4381.00
63_K66_D2.4251.00
296_L332_T2.2901.00
273_V292_M2.2221.00
172_G207_N2.2141.00
143_A174_V2.2051.00
110_V119_L2.2011.00
338_E342_Q2.1961.00
61_D64_W2.0781.00
200_L218_C2.0361.00
259_V310_P1.9911.00
201_A262_L1.9711.00
274_T314_R1.9531.00
199_V265_F1.9111.00
68_P73_S1.8771.00
73_S77_G1.8641.00
263_D310_P1.8501.00
186_V265_F1.8251.00
66_D69_W1.8151.00
219_A250_V1.8081.00
69_W73_S1.7891.00
60_R63_K1.7521.00
276_S314_R1.7491.00
295_V311_N1.7230.99
68_P71_T1.7110.99
200_L214_M1.7090.99
270_Y293_V1.7070.99
63_K70_R1.6950.99
225_G253_I1.6910.99
185_T188_Q1.6880.99
127_I176_F1.6760.99
62_R70_R1.6700.99
62_R66_D1.6520.99
201_A258_I1.6250.99
213_G329_S1.6120.99
166_S175_C1.6020.99
221_F334_V1.6010.99
219_A321_G1.5810.99
262_L293_V1.5790.99
65_E68_P1.5550.99
259_V307_A1.5500.99
294_L339_W1.5400.99
116_C176_F1.5360.99
186_V255_G1.5360.99
65_E71_T1.5220.99
129_R155_H1.5210.99
69_W74_R1.5200.99
65_E69_W1.4930.98
215_M239_A1.4930.98
71_T75_A1.4710.98
281_K313_L1.4580.98
61_D66_D1.4570.98
170_H241_R1.4500.98
61_D70_R1.4470.98
276_S308_R1.4230.98
70_R73_S1.4180.98
256_D260_N1.3920.98
71_T76_P1.3900.97
200_L336_L1.3900.97
282_P285_K1.3830.97
203_E304_P1.3830.97
265_F293_V1.3780.97
68_P72_V1.3770.97
63_K68_P1.3750.97
60_R66_D1.3750.97
199_V227_V1.3710.97
197_D291_K1.3690.97
71_T77_G1.3630.97
61_D67_S1.3410.97
66_D70_R1.3240.97
215_M250_V1.3210.97
62_R65_E1.3120.96
60_R65_E1.3030.96
69_W72_V1.2990.96
128_V179_K1.2990.96
270_Y291_K1.2930.96
64_W72_V1.2930.96
262_L310_P1.2870.96
294_L335_L1.2860.96
223_V250_V1.2810.96
190_V270_Y1.2780.96
246_G323_V1.2780.96
199_V268_A1.2700.96
62_R69_W1.2660.96
273_V315_V1.2480.95
70_R74_R1.2430.95
202_L211_L1.2430.95
195_A224_K1.2430.95
62_R68_P1.2400.95
238_A329_S1.2400.95
67_S70_R1.2380.95
257_N260_N1.2350.95
127_I130_A1.2340.95
72_V75_A1.2160.95
205_E342_Q1.2110.94
219_A323_V1.2070.94
60_R64_W1.2010.94
136_V204_N1.1580.93
62_R71_T1.1530.93
76_P80_T1.1450.93
64_W70_R1.1390.92
67_S73_S1.1310.92
84_A87_G1.1280.92
62_R67_S1.1200.92
66_D72_V1.1180.92
91_G100_L1.1140.92
217_S221_F1.1110.91
286_T315_V1.1070.91
117_Q142_E1.1050.91
263_D267_Q1.0910.91
273_V313_L1.0870.91
260_N306_A1.0860.90
91_G99_V1.0820.90
75_A78_D1.0810.90
159_E163_T1.0680.90
196_Q290_A1.0650.90
76_P79_E1.0620.89
187_Q264_D1.0600.89
73_S76_P1.0570.89
62_R72_V1.0500.89
123_R150_N1.0460.89
221_F283_L1.0410.89
284_F341_R1.0380.88
124_P248_E1.0370.88
61_D65_E1.0290.88
88_G94_F1.0200.87
308_R314_R1.0090.87
161_E164_K1.0070.87
66_D73_S1.0070.87
66_D76_P1.0070.87
118_A249_H1.0020.87
311_N314_R1.0020.87
103_Q107_E1.0000.86
266_R272_V1.0000.86
111_Y118_A0.9940.86
78_D83_K0.9930.86
61_D68_P0.9900.86
236_S248_E0.9890.86
162_L175_C0.9790.85
88_G91_G0.9760.85
264_D267_Q0.9740.85
227_V255_G0.9710.85
87_G90_S0.9600.84
63_K76_P0.9590.84
207_N300_Y0.9530.84
65_E77_G0.9510.84
80_T87_G0.9470.83
69_W76_P0.9420.83
190_V268_A0.9390.83
274_T295_V0.9340.82
88_G92_K0.9330.82
240_I247_A0.9300.82
204_N298_Q0.9250.82
287_S290_A0.9250.82
280_G316_K0.9210.82
65_E70_R0.9130.81
109_R175_C0.9050.80
67_S71_T0.8990.80
63_K75_A0.8980.80
87_G91_G0.8980.80
62_R75_A0.8950.80
209_H242_T0.8910.79
283_L335_L0.8900.79
67_S74_R0.8820.79
203_E303_L0.8780.78
64_W71_T0.8770.78
87_G96_D0.8730.78
241_R337_G0.8700.78
77_G83_K0.8600.77
153_A227_V0.8580.77
64_W68_P0.8530.76
71_T78_D0.8510.76
79_E83_K0.8500.76
242_T329_S0.8480.76
63_K69_W0.8470.76
72_V78_D0.8460.76
136_V140_F0.8420.75
189_W253_I0.8370.75
339_W342_Q0.8330.75
203_E295_V0.8310.74
68_P75_A0.8280.74
186_V227_V0.8270.74
72_V76_P0.8250.74
83_K90_S0.8240.74
73_S78_D0.8230.74
287_S342_Q0.8140.73
162_L171_H0.8120.73
70_R75_A0.8110.73
78_D82_E0.8100.72
85_D90_S0.8060.72
228_V234_L0.8050.72
64_W67_S0.8050.72
68_P77_G0.8020.72
295_V307_A0.7990.71
63_K71_T0.7980.71
275_T324_A0.7930.71
243_A307_A0.7920.71
117_Q143_A0.7910.71
62_R77_G0.7830.70
92_K95_I0.7780.69
295_V303_L0.7770.69
279_Q316_K0.7770.69
220_H319_G0.7760.69
82_E86_H0.7750.69
69_W77_G0.7700.69
74_R78_D0.7670.68
65_E72_V0.7670.68
146_W150_N0.7650.68
243_A298_Q0.7650.68
119_L241_R0.7650.68
219_A246_G0.7620.68
240_I248_E0.7620.68
166_S333_G0.7610.68
298_Q301_E0.7590.68
74_R79_E0.7580.67
84_A95_I0.7560.67
70_R77_G0.7530.67
280_G313_L0.7510.67
104_R107_E0.7500.67
196_Q224_K0.7490.66
222_G332_T0.7480.66
60_R67_S0.7480.66
259_V263_D0.7470.66
66_D75_A0.7460.66
194_G270_Y0.7460.66
115_A238_A0.7440.66
64_W73_S0.7430.66
66_D71_T0.7420.66
65_E76_P0.7410.66
189_W225_G0.7400.66
299_E302_G0.7370.65
86_H89_I0.7360.65
77_G80_T0.7310.65
262_L269_G0.7290.64
142_E146_W0.7230.64
69_W75_A0.7200.63
62_R73_S0.7190.63
271_T313_L0.7190.63
80_T83_K0.7180.63
63_K73_S0.7170.63
258_I307_A0.7110.62
63_K72_V0.7100.62
121_Q142_E0.7070.62
110_V169_E0.7070.62
262_L312_D0.7050.62
65_E74_R0.7040.62
110_V178_I0.7010.61
91_G96_D0.7010.61
271_T292_M0.6980.61
99_V105_A0.6970.61
202_L207_N0.6960.61
68_P76_P0.6930.60
82_E91_G0.6930.60
60_R70_R0.6930.60
303_L311_N0.6910.60
64_W78_D0.6910.60
276_S301_E0.6880.60
172_G274_T0.6860.60
264_D268_A0.6850.60
62_R76_P0.6820.59
209_H213_G0.6810.59
212_G245_G0.6780.59
201_A227_V0.6780.59
202_L226_V0.6750.58
129_R177_L0.6730.58
181_R235_E0.6670.58
60_R69_W0.6640.57
243_A247_A0.6620.57
219_A320_T0.6610.57
205_E233_L0.6580.57
209_H248_E0.6580.57
277_S319_G0.6580.57
288_L313_L0.6540.56
206_S300_Y0.6530.56
76_P83_K0.6520.56
99_V103_Q0.6520.56
109_R174_V0.6520.56
260_N263_D0.6500.56
266_R271_T0.6490.55
90_S93_S0.6450.55
209_H238_A0.6450.55
131_W155_H0.6400.54
261_V268_A0.6390.54
189_W197_D0.6370.54
202_L214_M0.6340.54
82_E85_D0.6310.53
73_S79_E0.6300.53
60_R71_T0.6290.53
86_H92_K0.6260.53
108_T177_L0.6260.53
71_T79_E0.6240.53
99_V102_R0.6230.52
199_V225_G0.6230.52
119_L337_G0.6180.52
86_H90_S0.6160.52
60_R75_A0.6140.51
67_S72_V0.6140.51
60_R72_V0.6130.51
83_K86_H0.6130.51
108_T243_A0.6120.51
303_L316_K0.6120.51
115_A244_E0.6120.51
302_G325_G0.6110.51
262_L266_R0.6090.51
297_G302_G0.6080.51
204_N304_P0.6080.51
235_E240_I0.6070.51
70_R78_D0.6070.51
105_A285_K0.6050.50
224_K267_Q0.6030.50
75_A193_A0.6030.50
215_M247_A0.6020.50
87_G92_K0.6020.50
83_K87_G0.6010.50
70_R76_P0.6010.50
222_G334_V0.6000.50
140_F289_P0.5980.50
72_V95_I0.5970.49
220_H323_V0.5960.49
295_V304_P0.5950.49
61_D69_W0.5920.49
134_Q141_K0.5920.49
64_W76_P0.5910.49
65_E75_A0.5910.49
84_A93_S0.5910.49
74_R77_G0.5900.49
79_E86_H0.5890.49
224_K270_Y0.5880.48
262_L307_A0.5880.48
215_M219_A0.5870.48
187_Q191_S0.5840.48
134_Q158_D0.5840.48
206_S233_L0.5830.48
86_H94_F0.5810.48
272_V293_V0.5810.48
82_E96_D0.5810.48
85_D88_G0.5810.48
306_A309_D0.5800.47
262_L295_V0.5790.47
211_L239_A0.5790.47
68_P83_K0.5780.47
308_R329_S0.5780.47
201_A265_F0.5780.47
117_Q174_V0.5750.47
183_G231_A0.5750.47
287_S313_L0.5740.47
159_E243_A0.5710.46
72_V85_D0.5690.46
170_H232_A0.5650.46
198_C292_M0.5640.46
118_A276_S0.5620.45
78_D86_H0.5620.45
131_W177_L0.5600.45
91_G94_F0.5570.45
75_A83_K0.5530.44
71_T80_T0.5510.44
60_R68_P0.5510.44
67_S75_A0.5510.44
62_R89_I0.5500.44
115_A242_T0.5490.44
63_K74_R0.5490.44
213_G333_G0.5480.44
288_L292_M0.5480.44
299_E325_G0.5470.44
84_A90_S0.5470.44
320_T323_V0.5470.44
72_V77_G0.5440.43
323_V335_L0.5410.43
75_A89_I0.5400.43
208_P296_L0.5380.43
144_L174_V0.5380.43
249_H321_G0.5320.42
179_K254_T0.5300.42
61_D71_T0.5290.42
69_W78_D0.5290.42
68_P74_R0.5270.41
302_G331_A0.5270.41
228_V231_A0.5270.41
90_S96_D0.5250.41
281_K286_T0.5240.41
111_Y168_T0.5230.41
79_E82_E0.5220.41
215_M235_E0.5220.41
96_D145_R0.5220.41
145_R148_A0.5210.41
108_T241_R0.5200.41
160_A163_T0.5200.41
167_G175_C0.5200.41
71_T74_R0.5190.41
207_N244_E0.5180.40
168_T238_A0.5170.40
147_M152_K0.5160.40
111_Y167_G0.5150.40
318_D338_E0.5130.40
68_P78_D0.5120.40
64_W69_W0.5110.40
110_V165_A0.5100.40
77_G81_P0.5100.40
81_P87_G0.5090.39
167_G296_L0.5070.39
96_D99_V0.5070.39
208_P239_A0.5040.39
282_P342_Q0.5040.39
284_F334_V0.5030.39
135_S140_F0.5030.39
202_L205_E0.5030.39
78_D81_P0.5020.39
101_R267_Q0.5020.39
210_N299_E0.5000.38
209_H239_A0.5000.38
334_V341_R0.5000.38
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  
1ipaA 1 0.7449 100 0.304 Contact Map
3nk6A 2 0.742 100 0.313 Contact Map
1gz0A 2 0.7188 100 0.313 Contact Map
1x7oA 2 0.7333 100 0.333 Contact Map
2i6dA 2 0.7072 100 0.353 Contact Map
1v2xA 2 0.4899 100 0.506 Contact Map
1zjrA 2 0.487 100 0.507 Contact Map
4kgnA 2 0.4377 100 0.51 Contact Map
2ha8A 2 0.4435 100 0.519 Contact Map
3n4jA 2 0.4348 100 0.521 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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