GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DUF1495 - Winged helix DNA-binding domain (DUF1495)
Pfam: PF07381 (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: 20370
Seq/Len: 226.33
HH_delta: 0.194 (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
25_P78_R2.532882.533
68_E78_R2.293322.293
27_Y30_E2.023812.024
60_V67_E1.955781.956
66_E78_R1.951951.952
70_E76_Y1.772881.773
17_Y34_S1.678611.678
11_R62_L1.670631.671
19_C87_A1.651381.651
25_P76_Y1.612241.612
21_I26_A1.481341.481
19_C79_L1.461561.461
80_T83_G1.401051.401
21_I34_S1.38191.382
66_E80_T1.324341.324
11_R58_S1.300051.300
25_P68_E1.282351.282
19_C84_K1.282291.282
46_L77_Y1.266671.267
14_V42_V1.242561.242
26_A30_E1.206461.206
63_G82_K1.193391.193
28_P77_Y1.181621.182
40_S43_L1.166241.166
37_S41_N1.151081.151
32_A39_Y1.150031.150
29_S33_R1.148991.149
64_L86_I1.128381.128
10_V37_S1.119361.119
28_P46_L1.099421.099
9_K13_K1.095251.095
82_K86_I1.074741.075
38_D41_N1.073481.073
30_E34_S1.018631.019
26_A34_S1.001431.001
18_L65_V0.991120.991
17_Y21_I0.986760.987
41_N45_A0.977520.977
47_R61_G0.969250.969
82_K85_R0.935070.935
43_L47_R0.933260.933
17_Y26_A0.929810.930
67_E77_Y0.927760.928
17_Y35_V0.925850.926
38_D44_G0.925510.925
39_Y43_L0.92340.923
42_V46_L0.921890.922
8_S11_R0.916430.916
46_L65_V0.905050.905
14_V31_I0.901610.902
81_E85_R0.897660.898
84_K88_E0.896530.896
14_V45_A0.887420.887
68_E76_Y0.883220.883
11_R45_A0.882650.883
32_A42_V0.879530.879
28_P42_V0.877080.877
29_S39_Y0.84680.847
30_E33_R0.836550.836
10_V45_A0.823890.824
19_C88_E0.822790.823
64_L82_K0.821120.821
28_P43_L0.815170.815
18_L26_A0.810.810
16_E20_S0.809880.810
13_K35_V0.808620.809
12_K16_E0.805080.805
12_K87_A0.803240.803
40_S44_G0.802340.802
8_S45_A0.80110.801
58_S62_L0.787040.787
69_E74_F0.768660.769
17_Y31_I0.757690.758
81_E84_K0.750560.751
60_V65_V0.74270.743
79_L83_G0.739070.739
37_S42_V0.733850.734
13_K17_Y0.727070.727
15_L64_L0.718730.719
70_E73_G0.715670.716
47_R74_F0.701370.701
21_I30_E0.698490.698
41_N44_G0.694640.695
44_G58_S0.692360.692
85_R88_E0.68920.689
79_L84_K0.685630.686
15_L79_L0.684580.685
44_G47_R0.682190.682
16_E87_A0.668250.668
47_R60_V0.662930.663
45_A58_S0.656530.656
83_G86_I0.650280.650
59_L64_L0.643120.643
28_P39_Y0.641070.641
47_R67_E0.628540.628
13_K16_E0.624150.624
10_V13_K0.619510.619
71_K76_Y0.61380.614
62_L82_K0.609840.610
15_L87_A0.590730.591
11_R59_L0.587050.587
62_L86_I0.584720.585
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
1hsjA0.8889990.194
1p4xA0.8889990.207
1p4xA0.8889990.221
4hblA0.8667990.228
3hsrA0.8667990.228
4em2A0.8667990.228
2fxaA0.866798.90.23
3zmdA0.888998.90.231
3jw4A0.888998.90.232
4aikA0.877898.90.233

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