GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HrcA_DNA-bdg - Winged helix-turn-helix transcription repressor HrcA DNA-binding
Pfam: PF03444 (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: 78
Sequences: 26928
Seq/Len: 345.23
HH_delta: 0.195 (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
48_E55_S2.112262.442
25_G28_T1.95932.265
12_A32_E1.649681.907
30_A37_P1.387021.603
26_S41_R1.384531.600
41_R45_A1.279511.479
27_K37_P1.250721.446
45_A48_E1.24311.437
27_K31_E1.217781.408
28_T32_E1.208541.397
35_R39_T1.202371.390
26_S37_P1.201081.388
38_A41_R1.193811.380
39_T43_E1.185741.371
45_A55_S1.166661.349
45_A49_E1.157721.338
54_E66_T1.154761.335
7_R11_K1.147891.327
23_P64_I1.122561.298
54_E64_I1.120111.295
68_K71_R1.111981.285
39_T42_N1.104541.277
14_V65_P1.084661.254
36_S39_T1.075191.243
9_I43_E1.069271.236
10_L50_L1.054851.219
12_A33_L1.024361.184
30_A40_I1.012031.170
67_D71_R1.004391.161
24_V28_T0.997261.153
8_E12_A0.969451.121
56_Q64_I0.95981.109
44_M53_V0.950711.099
51_G68_K0.928091.073
67_D70_Y0.92531.070
35_R40_I0.894041.033
66_T69_A0.880331.018
58_H61_G0.877151.014
14_V70_Y0.877041.014
8_E11_K0.858890.993
68_K72_A0.856730.990
21_G24_V0.845730.978
28_T31_E0.832130.962
36_S42_N0.823520.952
37_P41_R0.819950.948
23_P56_Q0.816640.944
10_L14_V0.81530.942
65_P69_A0.795460.919
11_K15_E0.790620.914
24_V32_E0.790330.914
26_S40_I0.789150.912
42_N46_D0.784140.906
46_D50_L0.78260.905
56_Q60_S0.781370.903
42_N45_A0.781040.903
21_G32_E0.778820.900
8_E33_L0.774060.895
43_E46_D0.732660.847
9_I40_I0.723610.836
38_A42_N0.72290.836
29_I44_M0.716310.828
69_A72_A0.689890.797
46_D49_E0.674650.780
48_E53_V0.673890.779
29_I40_I0.645110.746
27_K30_A0.640610.740
26_S44_M0.627180.725
58_H64_I0.606790.701
57_P62_G0.597540.691
9_I33_L0.587330.679
55_S63_R0.581880.673
44_M48_E0.579820.670
40_I44_M0.579050.669
48_E54_E0.564910.653
41_R48_E0.552710.639
20_T23_P0.552080.638
11_K14_V0.541290.626
50_L54_E0.536050.620
12_A29_I0.529140.612
7_R10_L0.5280.610
57_P61_G0.527510.610
13_L53_V0.525190.607
9_I14_V0.522890.604
52_L72_A0.518410.599
33_L36_S0.515990.596
38_A43_E0.513670.594
45_A62_G0.510190.590
65_P70_Y0.505020.584
52_L68_K0.502940.581
13_L24_V0.498660.576
9_I44_M0.493960.571
55_S62_G0.489710.566
11_K42_N0.487750.564
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
1stzA0.987298.60.195
4aikA0.948798.50.208
1hsjA0.961598.50.211
1p4xA0.961598.50.218
3fm5A0.948798.50.218
3echA0.935998.50.219
2wteA0.923198.50.219
4hblA0.935998.50.22
3k0lA0.935998.50.22
3zmdA0.961598.50.221

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