GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
rRNA_methylase - Putative rRNA methylase
Pfam: PF06962 (v27) Consensus Sequence
Download Alignment
(Note: includes all positions in family; we filtered this alignment to remove sites that had > 75% gaps before running GREMLIN. )
Clan: CL0063
Length: 140
Sequences: 12838
Seq/Len: 91.7
HH_delta: 0.246 (20Jul13)
GREMLIN Results:
Residue pairs sorted by strength in covariance:

Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] gremlin predictions, sequence seperation > 3. The i and j are positions as given in the consensus sequence. Show Scaled Distribution

ij Raw Score Scaled Score
3_Y47_V1.937873.614
48_D83_K1.599612.983
78_A88_I1.511912.819
82_L86_G1.496582.791
3_Y31_I1.42172.651
9_E32_L1.34642.511
12_I32_L1.333492.487
1_K29_T1.280882.388
12_I30_L1.206842.250
15_T30_L1.138312.123
9_E13_E1.106742.064
6_D12_I1.092542.037
50_A78_A1.006021.876
77_A80_E1.004281.873
12_I16_R0.990721.847
19_L28_V0.949551.771
79_L118_F0.888651.657
6_D11_A0.878951.639
33_D37_N0.874621.631
49_A89_T0.874151.630
39_D77_A0.872771.627
4_A28_V0.83691.561
4_A15_T0.831581.551
3_Y29_T0.826411.541
7_I34_S0.806161.503
19_L30_L0.801411.494
52_F88_I0.726841.355
13_E16_R0.699811.305
34_S37_N0.694331.295
8_Q11_A0.686631.280
5_F33_D0.681971.272
77_A81_L0.68051.269
110_L114_D0.661411.233
75_L113_L0.651321.215
10_E13_E0.648121.209
105_A108_E0.640761.195
17_E20_E0.638991.192
82_L88_I0.635431.185
46_P83_K0.631731.178
47_V81_L0.615981.149
4_A30_L0.598671.116
2_V28_V0.592631.105
72_L115_Q0.577691.077
16_R20_E0.574931.072
14_N17_E0.568951.061
111_A115_Q0.567451.058
14_N18_R0.553631.032
43_P46_P0.541881.010
50_A82_L0.541181.009
40_E47_V0.538461.004
112_S115_Q0.535130.998
39_D80_E0.530720.990
54_L57_L0.524010.977
33_D38_L0.521150.972
13_E17_E0.513240.957
47_V50_A0.507150.946
72_L76_E0.506460.944
70_T73_K0.506460.944
52_F55_G0.504570.941
44_E80_E0.503390.939
57_L93_Y0.48690.908
76_E116_K0.485390.905
52_F90_I0.478870.893
83_K86_G0.474630.885
49_A87_I0.465820.869
17_E21_E0.458820.856
52_F74_A0.452470.844
76_E80_E0.449990.839
73_K77_A0.446590.833
53_N92_V0.440180.821
92_V109_F0.43840.817
80_E84_P0.43510.811
18_R21_E0.434720.811
53_N91_V0.431760.805
9_E12_I0.424270.791
68_P71_T0.420920.785
19_L24_L0.418550.780
73_K76_E0.414310.773
57_L92_V0.411260.767
53_N57_L0.40670.758
51_I89_T0.405920.757
44_E81_L0.405110.755
80_E83_K0.405020.755
6_D30_L0.398360.743
50_A86_G0.39780.742
16_R30_L0.39730.741
40_E77_A0.397140.741
122_K125_F0.39710.740
10_E14_N0.391890.731
112_S116_K0.388490.724
111_A114_D0.387030.722
9_E16_R0.383820.716
5_F38_L0.38340.715
54_L91_V0.382860.714
107_E111_A0.378330.705
54_L93_Y0.374630.699
113_L117_E0.374160.698
38_L77_A0.372340.694
72_L116_K0.371610.693
121_L125_F0.370660.691
35_H38_L0.363040.677
5_F31_I0.362720.676
36_E73_K0.36080.673
24_L28_V0.360260.672
11_A52_F0.359080.670
113_L118_F0.355820.664
72_L112_S0.353610.659
54_L92_V0.352960.658
19_L22_A0.34980.652
74_A78_A0.345720.645
67_K70_T0.343190.640
16_R29_T0.340910.636
110_L123_Y0.340080.634
79_L116_K0.338190.631
52_F93_Y0.337820.630
46_P84_P0.334790.624
55_G58_P0.33320.621
16_R19_L0.331060.617
51_I91_V0.328380.612
104_E108_E0.32690.610
50_A88_I0.326520.609
67_K71_T0.325970.608
50_A81_L0.324680.605
4_A19_L0.32440.605
37_N40_E0.324090.604
12_I15_T0.323770.604
104_E107_E0.320480.598
7_I32_L0.316040.589
33_D39_D0.315670.589
92_V124_Q0.312070.582
108_E112_S0.308150.575
40_E80_E0.30780.574
46_P81_L0.307510.573
46_P80_E0.307090.573
56_Y91_V0.306240.571
78_A82_L0.305550.570
19_L23_G0.305410.570
53_N56_Y0.303810.567
109_F113_L0.303670.566
82_L118_F0.303570.566
55_G92_V0.303160.565
56_Y75_L0.293220.547
57_L68_P0.293050.546
35_H55_G0.288360.538
75_L78_A0.287350.536
43_P81_L0.287030.535
106_V109_F0.284150.530
76_E79_L0.282990.528
112_S117_E0.282770.527
58_P71_T0.282230.526
52_F75_L0.282020.526
6_D15_T0.281790.525
55_G74_A0.279270.521
56_Y92_V0.274980.513
120_V123_Y0.273830.511
Legend: The value of the raw score is the function of the learning procedure, L2 normalization and APC (entropic) correction. These are to be used for relative ranking only.
HHsearch Results:
Top (length/2) GREMLIN results overlayed on top 10 PDB hits:

Legend: The grey circles underneath are pdb residue contacts (min distance < 5 Angstroms). The coloring of these circles is based on HHsearch results which uses the overall probability, per-site alignment prob and agreement of top hits weighted by HHsearch score (Note we only consider monomeric contacts, there might be homo-oligomeric contacts in the pdb that are not shown.)
PDB Cov Prob HH_delta
3eeyA0.992999.50.246
3mtiA0.985799.50.253
3lpmA0.935799.40.274
3tmaA0.885799.40.3
4gekA0.999.30.311
3dmgA0.892999.30.318
3ocjA0.921499.30.323
2ozvA0.928699.30.323
3evzA0.921499.30.334
3busA0.921499.30.336

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