GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Methyltransf_12 - Methyltransferase domain
Pfam: PF08242 (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: 99
Sequences: 76625
Seq/Len: 773.99
HH_delta: -0.046 (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_C25_G4.182043.435
24_T67_F3.568812.931
93_L97_G3.160292.596
11_L25_G2.858512.348
68_D94_K2.748512.258
1_L67_F2.665912.190
11_L23_Y2.340141.922
50_R53_F2.13851.757
88_N91_R2.129031.749
70_V93_L2.063631.695
89_I99_L2.017091.657
74_N77_H1.998351.641
30_P34_E1.97961.626
50_R54_D1.972421.620
33_L37_R1.92691.583
29_S32_M1.886581.550
2_D5_C1.840111.511
88_N92_L1.754631.441
69_L98_I1.730321.421
12_R40_L1.707071.402
12_R39_R1.652461.357
81_D84_A1.648551.354
70_V89_I1.619271.330
72_A75_V1.607531.320
27_D33_L1.593131.309
10_L73_S1.564481.285
55_V58_L1.525991.253
74_N78_H1.496251.229
13_A17_E1.470671.208
83_E87_R1.466661.205
66_S94_K1.40081.151
93_L99_L1.400731.151
66_S92_L1.396611.147
35_R38_E1.371291.126
5_C36_A1.350721.109
2_D11_L1.329931.092
4_G75_V1.312591.078
15_L23_Y1.308421.075
84_A87_R1.300751.068
13_A16_E1.298131.066
24_T54_D1.292721.062
10_L13_A1.292121.061
1_L70_V1.283031.054
72_A99_L1.277031.049
3_I89_I1.262331.037
16_E43_L1.213310.997
75_V79_L1.208930.993
2_D25_G1.20520.990
57_D60_D1.191080.978
84_A88_N1.187860.976
53_F57_D1.175750.966
56_L61_Y1.169120.960
85_V89_I1.165430.957
31_S34_E1.150730.945
20_D23_Y1.14730.942
34_E37_R1.141480.938
27_D32_M1.136530.934
10_L14_L1.130050.928
34_E38_E1.095920.900
53_F58_L1.095920.900
12_R16_E1.093740.898
73_S78_H1.089380.895
37_R40_L1.081420.888
7_T32_M1.079610.887
7_T35_R1.07540.883
53_F56_L1.070270.879
2_D10_L1.069070.878
73_S77_H1.058980.870
10_L71_V1.051030.863
54_D57_D1.046780.860
39_R42_E1.031150.847
31_S35_R1.015620.834
51_L54_D1.010640.830
40_L44_G1.008370.828
33_L50_R0.998640.820
37_R41_A0.986930.811
11_L15_L0.982480.807
87_R91_R0.979650.805
38_E41_A0.966250.794
77_H82_I0.963950.792
24_T51_L0.960830.789
1_L26_V0.957240.786
87_R90_Y0.938780.771
24_T52_R0.936880.770
72_A89_I0.936560.769
5_C27_D0.936480.769
41_A44_G0.936280.769
75_V78_H0.93040.764
38_E42_E0.928720.763
40_L43_L0.913560.750
5_C11_L0.903530.742
3_I85_V0.899370.739
50_R55_V0.89430.735
76_L79_L0.893350.734
91_R94_K0.887840.729
94_K97_G0.885280.727
35_R39_R0.877460.721
67_F70_V0.860750.707
2_D23_Y0.858090.705
76_L86_L0.858080.705
72_A85_V0.85770.705
39_R43_L0.847450.696
58_L62_D0.837750.688
9_R73_S0.836670.687
58_L61_Y0.82250.676
30_P52_R0.82120.675
40_L45_N0.807930.664
10_L77_H0.807090.663
67_F92_L0.800870.658
9_R13_A0.799140.656
7_T10_L0.790980.650
74_N79_L0.78570.645
4_G72_A0.773850.636
12_R43_L0.771350.634
80_E83_E0.770540.633
3_I26_V0.768230.631
91_R95_P0.766480.630
54_D58_L0.76250.626
86_L90_Y0.760770.625
70_V97_G0.75870.623
14_L71_V0.754610.620
26_V53_F0.753310.619
36_A50_R0.752950.618
86_L89_I0.750880.617
79_L85_V0.745630.612
52_R55_V0.738460.607
56_L59_F0.734620.603
79_L82_I0.730190.600
2_D71_V0.727110.597
59_F88_N0.727070.597
42_E45_N0.723660.594
59_F62_D0.718640.590
50_R56_L0.713680.586
30_P55_V0.709270.583
8_G36_A0.703270.578
21_A24_T0.700070.575
54_D60_D0.699520.575
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
4gekA0.969799.3-0.046
4fsdA199.2-0.044
3gu3A0.959699.2-0.037
3g07A199.2-0.034
4dcmA199.2-0.032
3mggA0.979899.2-0.03
2aotA199.2-0.029
1vl5A0.959699.2-0.02
1nkvA0.969799.2-0.02
4htfA0.969799.2-0.019

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