GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Methyltransf_25 - Methyltransferase domain
Pfam: PF13649 (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: 101
Sequences: 74484
Seq/Len: 737.47
HH_delta: -0.051 (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
6_C29_G4.151663.044
28_I54_V3.614332.650
28_I68_F3.411932.501
97_L101_G3.208632.352
19_F25_S3.105872.277
12_T29_G2.962062.172
2_L68_F2.931032.149
34_P55_Q2.786142.043
69_D98_R2.683781.968
37_L55_Q2.658281.949
28_I52_R2.585621.896
12_T27_V2.532791.857
26_R52_R2.468511.810
32_I57_D2.366611.735
40_A53_F2.117011.552
37_L53_F2.0871.530
37_L41_K2.053151.505
13_R44_F2.012261.475
76_L79_H2.004971.470
92_R95_R1.998581.465
3_D6_C1.979021.451
13_R43_R1.939621.422
71_V97_L1.907981.399
33_S36_M1.861621.365
34_P38_E1.8121.328
92_R96_L1.743251.278
30_V56_A1.721631.262
16_A50_K1.683151.234
31_D37_L1.630811.196
87_E91_R1.60611.178
6_C40_A1.595141.169
75_G79_H1.584181.161
71_V93_I1.546961.134
17_R47_D1.50171.101
44_F53_F1.490321.093
75_G78_L1.486141.090
14_A18_R1.4751.081
57_D60_D1.47161.079
14_A17_R1.466551.075
44_F51_V1.463051.073
56_A60_D1.448781.062
1_I70_L1.445581.060
56_A62_P1.41121.035
82_S85_E1.403351.029
30_V54_V1.377481.010
67_K98_R1.375851.009
2_L30_V1.372361.006
44_F49_P1.332970.977
11_V14_A1.324140.971
3_D12_T1.304340.956
19_F27_V1.302120.955
1_I15_L1.292670.948
4_L93_I1.271510.932
16_A27_V1.270510.931
4_L58_A1.25840.923
11_V15_L1.242520.911
88_A91_R1.24080.910
39_L42_K1.234990.905
85_E88_A1.230430.902
13_R17_R1.215430.891
8_T39_L1.202380.882
11_V72_V1.196220.877
3_D11_V1.19350.875
76_L80_H1.189590.872
88_A92_R1.188230.871
64_S67_K1.176220.862
65_D95_R1.168270.857
2_L71_V1.16480.854
89_L93_I1.144070.839
13_R47_D1.139450.835
3_D29_G1.120810.822
1_I27_V1.120780.822
41_K44_F1.115320.818
35_E38_E1.101660.808
1_I72_V1.094080.802
75_G80_H1.094070.802
68_F71_V1.091380.800
29_G53_F1.088350.798
72_V75_G1.080110.792
31_D36_M1.079960.792
15_L72_V1.071040.785
5_G58_A1.070260.785
15_L19_F1.068860.784
38_E42_K1.065480.781
16_A51_V1.056820.775
38_E41_K1.048880.769
73_C76_L1.034690.759
41_K53_F1.02670.753
43_R46_E1.017740.746
8_T36_M1.015650.745
62_P92_R1.003720.736
41_K45_S0.994530.729
42_K46_E0.986790.723
12_T16_A0.983630.721
63_F68_F0.982430.720
9_G40_A0.980680.719
6_C12_T0.978180.717
42_K45_S0.975360.715
39_L43_R0.97510.715
91_R94_A0.971910.713
35_E39_L0.968410.710
67_K96_L0.961370.705
59_R88_A0.948230.695
91_R95_R0.932340.684
43_R47_D0.919040.674
73_C93_I0.906780.665
10_R14_A0.898220.659
93_I97_L0.892730.655
90_L94_A0.892610.654
32_I58_A0.886450.650
5_G73_C0.880790.646
63_F96_L0.880460.646
37_L40_A0.880440.645
73_C89_L0.874970.641
79_H86_L0.869020.637
32_I55_Q0.860010.631
61_L92_R0.857330.629
78_L90_L0.849830.623
63_F67_K0.846590.621
4_L89_L0.843850.619
59_R85_E0.839770.616
56_A61_L0.839390.615
8_T11_V0.82910.608
13_R49_P0.824640.605
1_I25_S0.820950.602
95_R99_P0.788710.578
98_R101_G0.787720.578
12_T51_V0.786530.577
58_A81_L0.785660.576
26_R50_K0.780770.572
94_A98_R0.778890.571
52_R55_Q0.778170.571
71_V101_G0.777980.570
65_D96_L0.773270.567
54_V63_F0.772120.566
81_L85_E0.766620.562
29_G51_V0.766460.562
76_L81_L0.764430.560
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
4gekA0.960499.4-0.051
1pjzA0.940699.3-0.033
2gb4A0.940699.3-0.019
3g2mA0.940699.3-0.01
4fsdA0.950599.3-0.003
3m70A0.930799.3-0.001
4hg2A0.861499.30.002
3dtnA0.940699.30.003
1vl5A0.920899.30.009
3g5tA0.940699.20.013

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