GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HTH_35 - Winged helix-turn-helix DNA-binding
Pfam: PF13693 (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: 10626
Seq/Len: 136.23
HH_delta: 0.164 (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
11_L36_L3.972193.984
24_E50_A2.402782.410
19_A29_S2.230912.237
10_A14_R2.152882.159
31_T35_A2.000212.006
10_A13_K1.805881.811
29_S33_R1.752461.758
21_L32_L1.630441.635
20_A24_E1.593731.598
19_A23_R1.591511.596
9_A13_K1.54291.547
18_L33_R1.529381.534
30_S33_R1.464921.469
6_D57_E1.388611.393
31_T34_N1.347481.351
16_T20_A1.327561.331
25_A50_A1.307671.311
33_R37_R1.295981.300
21_L51_L1.252591.256
16_T50_A1.235041.239
6_D9_A1.211891.215
17_S20_A1.204731.208
16_T24_E1.194061.198
8_K36_L1.172771.176
10_A53_V1.17171.175
45_R49_D1.115881.119
54_P57_E1.103511.107
35_A43_G1.092041.095
10_A51_L1.059731.063
27_L43_G1.059171.062
8_K12_R1.057061.060
14_R52_G1.056261.059
53_V57_E1.050711.054
40_W43_G0.941560.944
27_L31_T0.928940.932
18_L29_S0.918830.922
20_A23_R0.910340.913
43_G46_I0.895520.898
48_A55_P0.870780.873
27_L32_L0.860880.863
18_L36_L0.832450.835
22_S32_L0.830810.833
44_E48_A0.818260.821
14_R51_L0.816220.819
25_A47_I0.814860.817
48_A58_I0.813630.816
6_D10_A0.807910.810
7_I35_A0.807540.810
44_E55_P0.805270.808
30_S34_N0.802420.805
8_K18_L0.797540.800
35_A39_P0.77630.779
38_R42_K0.771140.773
22_S29_S0.745170.747
39_P43_G0.740060.742
25_A43_G0.731450.734
28_S34_N0.712420.715
16_T21_L0.71020.712
5_A9_A0.709930.712
26_G46_I0.705770.708
56_E60_P0.704460.707
28_S31_T0.702010.704
9_A12_R0.693520.696
10_A57_E0.690250.692
41_P59_W0.677720.680
32_L36_L0.677240.679
27_L35_A0.674460.676
18_L32_L0.66760.670
41_P45_R0.65470.657
31_T43_G0.642170.644
21_L47_I0.625120.627
38_R41_P0.622810.625
11_L16_T0.607710.609
49_D61_S0.600950.603
60_P63_Y0.590940.593
45_R55_P0.587390.589
46_I49_D0.584830.587
46_I50_A0.571080.573
21_L50_A0.571010.573
18_L37_R0.565940.568
32_L35_A0.563360.565
57_E61_S0.550170.552
6_D61_S0.5370.539
48_A53_V0.532590.534
35_A40_W0.52350.525
53_V58_I0.523070.525
45_R56_E0.523020.525
35_A47_I0.513390.515
54_P60_P0.51190.513
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
4ichA1990.164
3op9A198.90.196
3qq6A0.846298.90.201
3mlfA198.90.203
3t76A0.820598.90.212
3g5gA0.897498.90.213
3ivpA198.90.214
1b0nA0.987298.90.217
3lfpA0.961598.90.217
1neqA0.85998.90.218

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