GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Methyltransf_24 - Methyltransferase domain
Pfam: PF13578 (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: 106
Sequences: 79310
Seq/Len: 748.21
HH_delta: 0.023 (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_T28_S3.782433.138
27_Y70_I3.363072.790
27_Y54_I3.355082.783
95_L99_G3.119872.588
1_L70_I2.60632.162
25_K52_E2.500782.075
33_P55_Q2.487982.064
71_D96_A2.464562.045
11_T28_S2.406981.997
27_Y52_E2.288671.899
31_P57_D2.126141.764
61_F65_L1.966171.631
90_N93_P1.915951.589
11_T26_L1.915241.589
91_A101_I1.908451.583
73_I95_L1.880921.560
72_L100_V1.752441.454
39_Q42_I1.738141.442
83_A86_R1.672621.388
78_D81_Y1.649921.369
39_Q43_K1.633811.355
73_I91_A1.606821.333
15_A50_R1.603011.330
2_E5_T1.572661.305
56_G64_S1.547821.284
41_I44_K1.547351.284
61_F64_S1.546271.283
56_G61_F1.5411.278
57_D60_D1.521141.262
90_N94_R1.495411.241
10_S76_D1.482781.230
85_L89_E1.431231.187
95_L101_I1.426261.183
10_S13_W1.419831.178
13_W16_S1.396711.159
29_V56_G1.393491.156
42_I53_F1.392811.155
69_P96_A1.383651.148
72_L102_V1.351691.121
15_A26_L1.33921.111
56_G60_D1.335841.108
40_E43_K1.333861.107
40_E44_K1.326681.101
29_V54_I1.280791.063
37_Q40_E1.276411.059
13_W17_A1.270761.054
10_S14_L1.265351.050
75_I101_I1.225841.017
39_Q53_F1.217811.010
70_I73_I1.20210.997
12_L16_S1.197990.994
75_I78_D1.177580.977
86_R89_E1.166220.968
37_Q41_I1.161880.964
3_I58_S1.155720.959
2_E28_S1.141030.947
66_P69_P1.130210.938
87_D91_A1.111960.922
86_R90_N1.108510.920
2_E11_T1.106310.918
12_L41_I1.102070.914
14_L18_L1.100760.913
5_T30_D1.07790.894
12_L47_L1.069960.888
28_S53_F1.065590.884
12_L45_A1.049360.871
15_A51_V1.048690.870
96_A99_G1.038790.862
77_G80_S1.036190.860
3_I91_A1.032530.857
5_T11_T0.987010.819
69_P94_R0.983160.816
59_P83_A0.980110.813
38_A41_I0.977960.811
82_E85_L0.970170.805
1_L29_V0.965110.801
11_T15_A0.942260.782
89_E92_L0.936870.777
10_S74_F0.93420.775
89_E93_P0.932030.773
79_H84_V0.916970.761
76_D80_S0.909130.754
3_I87_D0.904720.751
1_L73_I0.903040.749
80_S84_V0.88610.735
38_A53_F0.884370.734
7_S10_S0.874150.725
59_P86_R0.872070.723
77_G81_Y0.86120.714
65_L69_P0.857970.712
16_S45_A0.85190.707
41_I45_A0.85030.705
2_E26_L0.84550.701
31_P55_Q0.839280.696
75_I87_D0.834470.692
9_Y13_W0.83390.692
78_D84_V0.817390.678
80_S83_A0.817270.678
54_I65_L0.816880.678
84_V87_D0.810360.672
39_Q55_Q0.795780.660
61_F90_N0.793880.659
28_S51_V0.790650.656
2_E10_S0.785430.652
14_L74_F0.778740.646
9_Y76_D0.77760.645
7_S37_Q0.773510.642
18_L26_L0.773120.641
52_E55_Q0.773040.641
43_K48_S0.76360.633
93_P96_A0.759890.630
47_L50_R0.757170.628
12_L15_A0.755090.626
59_P90_N0.753250.625
92_L96_A0.749560.622
76_D81_Y0.746890.620
88_L103_F0.74340.617
25_K50_R0.737060.611
76_D79_H0.736350.611
42_I51_V0.732330.608
3_I29_V0.729870.606
15_A18_L0.725420.602
29_V61_F0.722960.600
4_G75_I0.711740.590
30_D53_F0.703090.583
93_P97_P0.692850.575
38_A42_I0.692840.575
12_L42_I0.687470.570
81_Y84_V0.686830.570
70_I94_R0.682090.566
75_I103_F0.677070.562
7_S76_D0.674070.559
2_E8_G0.671920.557
65_L94_R0.666950.553
11_T51_V0.664440.551
19_R50_R0.66410.551
92_L95_L0.663760.551
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
3dr5A0.962399.20.023
4hg2A0.877499.20.032
3r3hA0.962399.20.041
4gekA0.952899.20.047
3kkzA0.943499.20.058
3q7eA0.943499.20.064
3u81A0.971799.20.064
1suiA0.962399.10.071
3f4kA0.943499.10.076
3tfwA0.962399.10.081

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