GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Methyltransf_18 - Methyltransferase domain
Pfam: PF12847 (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: 112
Sequences: 83493
Seq/Len: 745.47
HH_delta: -0.087 (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
10_C30_G3.805272.938
29_V71_F3.124932.413
29_V57_V3.076242.375
3_G73_L3.04552.351
101_L105_G2.884062.227
4_R27_R2.795612.158
6_L71_F2.726242.105
72_D102_K2.546351.966
16_S30_G2.464991.903
35_P58_Q2.397851.851
38_L58_Q2.385321.842
4_R29_V2.278581.759
4_R72_D2.174761.679
16_S28_V2.107751.627
33_I60_D2.070481.599
29_V55_T2.052931.585
38_L42_R2.043671.578
27_R55_T2.009771.552
41_A56_F1.95281.508
96_R99_R1.900821.468
97_I107_L1.877791.450
35_P39_E1.869681.443
7_D10_C1.817961.404
38_L56_F1.816961.403
74_V101_L1.803781.393
17_I45_A1.782441.376
17_I44_R1.712741.322
5_V73_L1.708891.319
4_R71_F1.695411.309
32_D38_L1.664881.285
34_S37_M1.658741.281
3_G26_A1.605281.239
73_L106_R1.579131.219
15_L77_S1.576681.217
96_R100_L1.556711.202
91_R95_E1.502021.160
31_V59_G1.485421.147
6_L31_V1.474991.139
20_A53_R1.449081.119
76_C107_L1.444191.115
3_G72_D1.4371.109
40_I43_E1.412671.091
45_A56_F1.408881.088
74_V97_I1.390121.073
84_L87_L1.374761.061
101_L107_L1.367741.056
5_V19_L1.319761.019
10_C41_A1.307681.010
45_A54_I1.293190.998
73_L108_V1.234740.953
4_R102_K1.233210.952
31_V57_V1.19030.919
92_R95_E1.190140.919
20_A28_V1.185380.915
15_L18_A1.185010.915
70_P102_K1.17790.909
8_L61_A1.175980.908
7_D30_G1.171820.905
93_V97_I1.16620.900
92_R96_R1.158740.895
60_D63_F1.156750.893
4_R26_A1.15450.891
7_D16_S1.143590.883
32_D37_M1.138210.879
5_V28_V1.13310.875
18_A21_R1.126390.870
12_T37_M1.104920.853
14_R77_S1.104750.853
39_E43_E1.104660.853
17_I21_R1.103760.852
15_L19_L1.101770.851
6_L74_V1.087440.840
5_V75_I1.07770.832
45_A49_G1.076990.831
8_L97_I1.07090.827
4_R70_P1.067610.824
39_E42_R1.061780.820
3_G106_R1.060610.819
67_F70_P1.038140.801
42_R45_A1.037130.801
36_E39_E1.029270.795
15_L75_I1.024860.791
30_G56_F1.009310.779
64_D67_F1.007660.778
12_T40_I0.988970.764
76_C93_V0.977370.755
5_V25_G0.961790.743
10_C32_D0.959530.741
42_R56_F0.958960.740
63_F67_F0.957950.740
36_E40_I0.956220.738
13_G41_A0.938260.724
95_E99_R0.937040.723
20_A54_I0.927890.716
76_C109_I0.921340.711
49_G52_D0.919510.710
65_P96_R0.905050.699
78_G87_L0.901280.696
70_P100_L0.900460.695
94_L109_I0.898440.694
59_G66_D0.894840.691
10_C16_S0.894420.691
25_G28_V0.894230.690
102_K105_G0.890010.687
14_R78_G0.889510.687
66_D70_P0.884580.683
9_G78_G0.883260.682
76_C97_I0.879860.679
50_L53_R0.879470.679
19_L75_I0.878240.678
12_T15_L0.875230.676
4_R69_E0.868530.671
7_D15_L0.860670.664
63_F66_D0.849890.656
71_F74_V0.83860.647
7_D28_V0.83150.642
14_R18_A0.828890.640
45_A50_L0.818750.632
9_G61_A0.814610.629
16_S20_A0.813490.628
78_G84_L0.80840.624
6_L100_L0.804510.621
40_I44_R0.802620.620
85_L90_R0.800390.618
9_G76_C0.799550.617
86_P90_R0.784860.606
59_G63_F0.775050.598
12_T78_G0.772460.596
68_L99_R0.770910.595
7_D76_C0.765550.591
87_L90_R0.761960.588
59_G65_P0.757590.585
21_R24_P0.756370.584
90_R93_V0.747870.577
33_I61_A0.746770.577
84_L90_R0.736260.568
16_S54_I0.733370.566
95_E98_R0.733070.566
8_L93_V0.72960.563
99_R103_P0.724780.560
71_F100_L0.711450.549
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
4gekA0.964399.6-0.087
3g07A0.991199.5-0.019
3ocjA0.982199.5-0.015
3kkzA0.946499.5-0.006
3hemA0.955499.40.007
3f4kA0.946499.40.009
3vc1A0.946499.40.014
1nkvA0.946499.40.019
3jwhA0.982199.40.019
2o57A0.955499.40.021

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