GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Methyltransf_30 - S-adenosyl-L-methionine-dependent methyltransferase
Pfam: PF05430 (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: 124
Sequences: 8151
Seq/Len: 65.73
HH_delta: 0.301 (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
80_S84_G1.65023.425
52_D81_K1.576653.273
5_E37_F1.143782.374
75_K78_R1.131092.348
5_E9_Q1.084952.252
76_L86_L1.068052.217
15_P35_L0.924751.919
70_E101_Q0.917371.904
8_E35_L0.905041.879
11_L35_L0.893941.855
2_E8_E0.89311.854
96_R100_Q0.888271.844
77_A104_F0.887431.842
73_F99_L0.885991.839
8_E37_F0.878851.824
70_E98_A0.854241.773
54_W80_S0.769771.598
97_R101_Q0.764831.587
8_E12_A0.732121.520
51_F54_W0.684071.420
15_P33_L0.682671.417
54_W76_L0.663431.377
4_A7_A0.651961.353
50_R81_K0.645241.339
48_D78_R0.615041.277
12_A16_P0.597831.241
56_L88_T0.588511.222
70_E74_K0.579331.202
38_G42_E0.578051.200
39_D42_E0.57191.187
57_D89_Y0.563921.170
58_G61_P0.55741.157
3_L39_D0.555241.152
88_T99_L0.553031.148
53_A87_A0.548431.138
71_E75_K0.539921.121
6_L9_Q0.539081.119
45_P75_K0.537391.115
75_K79_L0.528871.098
69_S90_S0.527761.095
61_P90_S0.50641.051
12_A15_P0.506381.051
77_A102_A0.498961.036
74_K102_A0.498181.034
8_E11_L0.489351.016
41_R79_L0.489071.015
80_S86_L0.475740.987
56_L69_S0.475380.987
53_A85_T0.4740.984
73_F98_A0.46380.963
13_Q16_P0.453930.942
71_E74_K0.45210.938
96_R108_K0.4470.928
80_S104_F0.441560.917
69_S88_T0.429060.891
73_F102_A0.427710.888
38_G45_P0.425820.884
98_A101_Q0.424260.881
40_A72_L0.423760.880
46_Q51_F0.422380.877
14_W58_G0.42080.873
57_D61_P0.420550.873
97_R100_Q0.408680.848
9_Q12_A0.405630.842
42_E46_Q0.40220.835
62_A90_S0.396650.823
58_G89_Y0.393040.816
7_A14_W0.386310.802
4_A8_E0.385140.799
86_L99_L0.384020.797
94_A98_A0.382430.794
38_G46_Q0.38130.791
72_L76_L0.378520.786
39_D71_E0.368390.765
58_G92_A0.366870.761
99_L104_F0.36680.761
94_A97_R0.36610.760
61_P91_S0.359940.747
92_A95_V0.358910.745
76_L104_F0.358340.744
78_R82_P0.357450.742
41_R72_L0.356050.739
50_R79_L0.355760.738
14_W57_D0.355630.738
57_D72_L0.351420.729
55_Y58_G0.350.726
44_L79_L0.34920.725
3_L37_F0.348910.724
10_L13_Q0.347170.721
58_G90_S0.344180.714
6_L10_L0.342750.711
81_K84_G0.340880.708
61_P89_Y0.33970.705
51_F79_L0.338970.704
44_L75_K0.338830.703
96_R106_V0.337580.701
54_W86_L0.335570.697
69_S98_A0.334570.694
90_S95_V0.333760.693
58_G91_S0.331870.689
70_E102_A0.33080.687
42_E45_P0.329250.683
40_A71_E0.328990.683
74_K77_A0.325950.677
41_R71_E0.323630.672
10_L14_W0.322520.669
98_A102_A0.317430.659
13_Q17_L0.312650.649
89_Y111_G0.311250.646
57_D91_S0.311120.646
62_A91_S0.306990.637
40_A75_K0.305160.633
65_P95_V0.304960.633
7_A65_P0.302640.628
5_E12_A0.302580.628
9_Q13_Q0.301550.626
56_L76_L0.300610.624
40_A63_K0.298760.620
41_R44_L0.296570.616
36_W51_F0.295960.614
56_L72_L0.29460.611
62_A89_Y0.29420.611
77_A103_G0.294010.610
45_P78_R0.290780.604
100_Q105_E0.288430.599
57_D111_G0.287750.597
38_G44_L0.286230.594
58_G62_A0.286190.594
49_A79_L0.284280.590
93_G97_R0.281060.583
2_E7_A0.278710.578
7_A10_L0.276210.573
12_A34_T0.275590.572
73_F95_V0.274270.569
56_L86_L0.273610.568
57_D69_S0.273290.567
34_T50_R0.271080.563
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
2qy6A199.40.301
3vywA0.959799.30.311
3o4fA0.959799.20.347
2qfmA0.975899.20.358
4gekA0.895299.20.359
3bwcA0.951699.20.366
1iy9A0.943599.20.366
3adnA0.951699.20.368
3ocjA0.911399.20.371
3pvcA199.20.371

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