GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Myb_DNA-bind_4 - MybSANT-like DNA-binding domain
Pfam: PF13837 (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: CL0123
Length: 90
Sequences: 1160
Seq/Len: 12.89
HH_delta: 0.208 (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
8_E51_R0.734773.745
9_T59_K0.700153.568
16_W60_W0.475842.425
59_K62_N0.469792.394
41_A56_C0.459072.340
37_W56_C0.432112.202
15_L43_E0.377791.925
43_E46_E0.359081.830
57_R61_K0.356681.818
6_D10_K0.326161.662
18_E43_E0.315291.607
45_A50_N0.298841.523
15_L40_I0.295761.507
41_A53_P0.27331.393
11_L15_L0.25711.310
58_N62_N0.246761.258
55_Q63_L0.245011.249
44_L56_C0.243511.241
13_I60_W0.241181.229
11_L44_L0.23121.178
29_G32_R0.225631.150
50_N76_K0.208621.063
67_Y71_K0.207471.057
12_L56_C0.205351.047
15_L44_L0.205241.046
37_W60_W0.20491.044
70_I73_R0.192120.979
15_L18_E0.190660.972
16_W59_K0.190290.970
74_N77_S0.190090.969
11_L47_H0.189720.967
10_K14_E0.187440.955
53_P57_R0.186990.953
25_F37_W0.186610.951
42_E46_E0.180940.922
69_K74_N0.179650.916
15_L33_N0.17860.910
52_T55_Q0.177160.903
25_F59_K0.175420.894
63_L67_Y0.175140.893
29_G34_K0.174570.890
4_W55_Q0.174480.889
34_K37_W0.171940.876
12_L37_W0.171890.876
17_K73_R0.171740.875
59_K66_K0.170980.871
43_E49_Y0.167180.852
9_T63_L0.165230.842
13_I17_K0.164610.839
38_K42_E0.160230.817
58_N65_K0.159420.812
29_G33_N0.158380.807
22_E26_D0.158290.807
48_G52_T0.157760.804
14_E18_E0.157010.800
41_A52_T0.156190.796
11_L43_E0.156160.796
65_K69_K0.155860.794
7_E47_H0.155260.791
12_L72_D0.15360.783
55_Q66_K0.153570.783
21_M25_F0.153550.783
16_W25_F0.153410.782
5_T66_K0.152810.779
58_N61_K0.152690.778
34_K69_K0.151070.770
6_D52_T0.148460.757
32_R39_E0.147970.754
44_L49_Y0.147460.752
41_A45_A0.147420.751
53_P56_C0.147410.751
24_R50_N0.145160.740
61_K68_K0.144920.739
52_T65_K0.144640.737
16_W36_V0.144620.737
44_L48_G0.144490.736
14_E46_E0.144050.734
32_R36_V0.143890.733
42_E50_N0.143180.730
33_N57_R0.142910.728
41_A67_Y0.142470.726
38_K53_P0.141230.720
7_E10_K0.140590.717
30_K42_E0.139860.713
66_K70_I0.13970.712
9_T62_N0.139680.712
14_E45_A0.139470.711
17_K32_R0.139370.710
29_G62_N0.138520.706
13_I67_Y0.137310.700
13_I62_N0.137290.700
47_H50_N0.135340.690
3_N58_N0.134840.687
47_H71_K0.133430.680
61_K64_K0.131950.672
54_E58_N0.13170.671
7_E71_K0.130430.665
18_E76_K0.129780.661
23_L78_G0.129710.661
7_E70_I0.129210.659
51_R56_C0.127790.651
10_K76_K0.127390.649
14_E39_E0.126480.645
25_F36_V0.126440.644
15_L36_V0.126040.642
35_K68_K0.123570.630
33_N37_W0.122910.626
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
2ebiA0.911199.50.208
2juhA0.8111970.678
3sjmA0.6970.678
2ajeA0.822296.90.683
2rohA0.811196.80.689
2llkA0.566796.70.689
1w0tA0.577896.70.692
3osgA0.722296.50.699
1ignA0.866796.50.702
2yusA0.666796.40.702

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