GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DNA_binding_1 - 6-O-methylguanine DNA methyltransferase DNA binding domain
Pfam: PF01035 (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. )
Length: 85
Sequences: 3526
Seq/Len: 41.48
HH_delta: -0.033 (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
75_A79_A1.569183.151
6_R31_R1.330482.671
58_N64_G1.26832.546
10_A13_Q1.218692.447
20_T28_L1.163282.336
20_T24_E1.12822.265
74_R78_E1.106272.221
23_G59_S1.077812.164
10_A25_I1.018482.045
23_G27_R0.908351.824
20_T25_I0.884841.777
10_A28_L0.876881.761
1_T4_Q0.860931.729
11_V42_L0.859831.726
40_S44_R0.836991.681
14_I56_V0.826061.659
31_R34_A0.771821.550
7_V25_I0.765981.538
14_I20_T0.753971.514
4_Q44_R0.751041.508
10_A29_L0.73061.467
12_R51_I0.707011.420
48_P68_G0.690691.387
45_N53_C0.688911.383
13_Q28_L0.670791.347
40_S43_A0.667541.340
35_A39_G0.66711.339
75_A78_E0.646481.298
3_F7_V0.622721.250
78_E81_G0.620071.245
5_R9_E0.610071.225
24_E27_R0.596771.198
23_G35_A0.583211.171
34_A37_A0.576951.158
9_E12_R0.573221.151
63_L74_R0.558581.122
19_V82_V0.552161.109
4_Q40_S0.545741.096
2_P5_R0.542841.090
4_Q8_W0.536251.077
63_L70_I0.535951.076
20_T56_V0.526831.058
42_L48_P0.508071.020
49_I79_A0.497460.999
10_A20_T0.481340.966
65_G70_I0.480770.965
8_W41_A0.479420.963
58_N62_S0.478130.960
72_R75_A0.475240.954
15_P18_K0.469680.943
48_P72_R0.465930.935
48_P67_R0.46430.932
9_E13_Q0.451150.906
7_V41_A0.449130.902
22_Y36_R0.44440.892
16_Y79_A0.441140.886
8_W42_L0.431990.867
3_F37_A0.431920.867
49_I76_L0.430410.864
3_F41_A0.423590.850
42_L57_V0.420340.844
47_I51_I0.405140.813
66_Y73_K0.403850.811
11_V25_I0.400170.803
78_E82_V0.39910.801
4_Q41_A0.395450.794
27_R32_P0.39450.792
6_R9_E0.392150.787
54_H80_E0.388740.781
68_G72_R0.388070.779
19_V77_L0.381970.767
7_V29_L0.377650.758
8_W11_V0.36550.734
71_E74_R0.359860.723
73_K77_L0.359010.721
23_G39_G0.35540.714
29_L38_V0.348760.700
64_G73_K0.34830.699
67_R72_R0.348070.699
48_P51_I0.344570.692
45_N49_I0.341970.687
2_P6_R0.339980.683
7_V38_V0.336870.676
19_V57_V0.336450.676
24_E28_L0.323720.650
22_Y39_G0.321270.645
35_A40_S0.318390.639
21_T59_S0.316290.635
43_A64_G0.315150.633
65_G73_K0.310830.624
42_L67_R0.298220.599
36_R39_G0.294440.591
30_G36_R0.285710.574
45_N48_P0.281660.566
58_N65_G0.280010.562
53_C69_G0.279890.562
37_A41_A0.278020.558
40_S64_G0.275880.554
74_R81_G0.275750.554
47_I50_I0.272490.547
25_I38_V0.269670.541
29_L41_A0.268610.539
19_V61_G0.267630.537
8_W47_I0.265310.533
70_I74_R0.26280.528
53_C65_G0.262530.527
72_R76_L0.261280.525
66_Y69_G0.26060.523
6_R29_L0.258830.520
43_A67_R0.258040.518
75_A82_V0.255620.513
16_Y50_I0.255260.513
53_C63_L0.254660.511
8_W51_I0.253760.509
66_Y72_R0.251330.505
14_I18_K0.250210.502
33_K36_R0.250210.502
54_H76_L0.247830.498
45_N50_I0.244850.492
51_I66_Y0.244810.492
39_G46_P0.243320.489
53_C73_K0.241560.485
37_A45_N0.240860.484
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
2kifA1100-0.033
3l00A1100-0.031
1sfeA1100-0.03
3gvaA1100-0.029
1eh6A199.9-0.023
4bhbA199.9-0.022
1wrjA0.964799.90.003
1mgtA0.964799.90.012
2g7hA0.964799.90.012
1qgpA0.682493.90.814

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