GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
HTH_33 - Winged helix-turn helix
Pfam: PF13592 (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: 60
Sequences: 1064
Seq/Len: 17.73
HH_delta: 0.389 (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
23_S26_G0.497232.320
11_A24_P0.483822.258
26_G29_R0.414061.932
22_Y26_G0.411.913
15_E21_K0.394971.843
11_A27_V0.369881.726
53_Q56_F0.35341.649
7_L28_Y0.351021.638
54_E57_K0.350741.637
14_I27_V0.315561.473
26_G30_L0.312921.460
25_S29_R0.304181.419
48_A53_Q0.300011.400
12_A16_E0.293911.372
6_T9_E0.290291.355
8_K24_P0.28591.334
45_P48_A0.278821.301
38_Y41_P0.267751.249
12_A21_K0.264191.233
50_E54_E0.258841.208
39_Q45_P0.255381.192
25_S28_Y0.254681.188
10_I28_Y0.239771.119
51_E54_E0.229481.071
13_Y17_E0.225321.051
4_R10_I0.224191.046
49_D52_A0.218951.022
50_E57_K0.212590.992
51_E55_A0.207030.966
44_R49_D0.205980.961
4_R7_L0.20540.959
5_W9_E0.205040.957
4_R9_E0.203820.951
28_Y32_K0.202260.944
42_R56_F0.196550.917
34_L43_P0.196540.917
36_F56_F0.194210.906
12_A15_E0.190090.887
4_R40_K0.189580.885
53_Q57_K0.188030.877
24_P28_Y0.177340.828
12_A24_P0.175440.819
20_V27_V0.174480.814
4_R8_K0.173410.809
4_R42_R0.170760.797
46_P52_A0.169780.792
23_S29_R0.166850.779
22_Y30_L0.166750.778
5_W10_I0.163960.765
37_S40_K0.162240.757
14_I20_V0.161450.753
9_E12_A0.161330.753
25_S34_L0.159820.746
10_I56_F0.158950.742
34_L37_S0.157780.736
45_P49_D0.156550.731
39_Q57_K0.155930.728
15_E27_V0.154890.723
48_A52_A0.151040.705
36_F40_K0.150940.704
22_Y25_S0.150840.704
11_A21_K0.150080.700
44_R51_E0.150060.700
52_A55_A0.149630.698
9_E16_E0.148390.692
6_T32_K0.148070.691
25_S47_K0.148030.691
9_E25_S0.147070.686
40_K46_P0.145520.679
7_L10_I0.145350.678
15_E19_G0.14480.676
13_Y47_K0.144010.672
40_K45_P0.143930.672
12_A34_L0.143240.668
19_G22_Y0.142890.667
7_L24_P0.142470.665
24_P32_K0.141080.658
31_L36_F0.140890.657
6_T24_P0.140090.654
37_S47_K0.139950.653
30_L34_L0.1390.649
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
1u78A0.933397.60.389
3hotA0.997.20.437
1pdnC0.5667950.559
1k78A0.683392.10.608
1b4aA0.983387.10.646
2k27A0.966785.10.655
2p5kA0.816785.10.656
2lvsA0.5580.60.672
1iufA171.90.694
2ahqA0.716767.90.703

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