GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Methyltransf_11 - Methyltransferase domain
Pfam: PF08241 (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: 95
Sequences: 79900
Seq/Len: 841.05
HH_delta: -0.08 (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
5_C24_G3.306292.827
23_T61_F3.262892.790
87_L91_G2.948472.521
23_T47_R2.817372.409
62_D88_K2.623362.243
11_A24_G2.459592.103
1_L61_F2.406762.058
32_L36_R2.22571.903
11_A22_V2.184051.868
29_E48_Q2.118351.811
32_L48_Q2.045031.749
68_S71_H1.899791.625
64_V87_L1.883941.611
83_I93_L1.808841.547
66_S69_V1.784411.526
82_E85_R1.770081.514
2_D5_C1.76341.508
29_E33_E1.740491.488
12_A39_L1.725261.475
32_L46_F1.708921.461
35_A46_F1.656581.417
75_D78_A1.649021.410
63_V92_R1.629691.394
66_S93_L1.626921.391
28_S31_M1.610451.377
64_V83_I1.603761.371
27_I50_D1.584361.355
12_A38_R1.567531.340
26_D32_L1.565951.339
34_Q37_K1.508171.290
10_F67_N1.44381.235
87_L93_L1.443381.234
68_S72_H1.421241.215
77_E81_R1.418591.213
82_E86_V1.40461.201
49_G54_L1.403831.200
25_I49_G1.376641.177
50_D53_D1.369471.171
13_A17_R1.347581.152
10_F13_A1.299291.111
63_V94_V1.28811.102
2_D11_A1.28771.101
60_S88_K1.277121.092
78_A81_R1.275521.091
13_A16_K1.21221.037
49_G55_P1.202911.029
15_A22_V1.193291.020
33_E37_K1.179851.009
3_I83_I1.15950.992
36_R39_L1.159210.991
49_G53_D1.143490.978
33_E36_R1.139760.975
1_L64_V1.125430.962
57_P60_S1.11910.957
78_A82_E1.117210.955
26_D31_M1.114980.953
5_C35_A1.114790.953
4_G69_V1.104420.944
19_G22_V1.096860.938
30_E33_E1.092570.934
12_A16_K1.082720.926
7_T34_Q1.078460.922
69_V73_L1.072880.917
2_D10_F1.071810.917
69_V72_H1.043730.893
66_S83_I1.034510.885
79_A83_I1.032630.883
10_F14_L1.030410.881
58_D85_R1.029730.881
39_L46_F1.012580.866
2_D24_G0.996680.852
67_N71_H0.973760.833
60_S86_V0.972670.832
88_K91_G0.972030.831
67_N72_H0.965320.825
81_R84_Y0.951470.814
81_R85_R0.932710.798
52_E75_D0.92640.792
71_H76_P0.924330.790
61_F64_V0.922630.789
30_E34_Q0.913870.781
10_F65_F0.913720.781
36_R40_K0.906980.776
38_R41_N0.903120.772
16_K42_E0.888030.759
52_E78_A0.877370.750
37_K40_K0.876110.749
39_L43_G0.871810.746
25_I47_R0.870120.744
70_L73_L0.867450.742
48_Q51_A0.849320.726
73_L76_P0.842370.720
2_D22_V0.841260.719
1_L25_I0.839050.718
70_L80_L0.826250.707
3_I79_A0.817170.699
3_I51_A0.814930.697
11_A15_A0.811620.694
5_C11_A0.811260.694
34_Q38_R0.810180.693
56_F86_V0.806080.689
58_D86_V0.799620.684
5_C26_D0.793810.679
9_R13_A0.790030.676
14_L65_F0.777040.664
7_T10_F0.768420.657
56_F61_F0.767320.656
2_D66_S0.761130.651
7_T31_M0.759290.649
24_G46_F0.753190.644
9_R67_N0.736520.630
3_I25_I0.734920.628
39_L44_V0.733840.628
85_R89_P0.728220.623
40_K45_S0.728210.623
10_F71_H0.723670.619
8_G35_A0.718370.614
31_M68_S0.716050.612
64_V91_G0.715730.612
85_R88_K0.714040.611
12_A42_E0.71340.610
12_A15_A0.710430.608
38_R42_E0.709340.607
39_L42_E0.703590.602
15_A44_V0.698870.598
40_K43_G0.697930.597
56_F60_S0.693380.593
37_K41_N0.68830.589
61_F86_V0.687730.588
51_A69_V0.6870.587
26_D46_F0.685360.586
76_P79_A0.683060.584
14_L22_V0.678420.580
66_S79_A0.673390.576
54_L82_E0.670780.574
31_M34_Q0.667830.571
64_V93_L0.663170.567
77_E84_Y0.661970.566
46_F49_G0.659860.564
35_A38_R0.659440.564
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
4hg2A0.947499.4-0.08
3g5lA199.4-0.078
4fsdA199.3-0.068
1vl5A0.989599.3-0.062
3kkzA0.989599.3-0.06
3g5tA0.989599.3-0.06
3ujcA199.3-0.054
2o57A199.3-0.054
3busA199.3-0.051
3f4kA0.989599.3-0.049

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