GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
zf-Nse - Zinc-finger of the MIZ type in Nse subunit
Pfam: PF11789 (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: CL0229
Length: 57
Sequences: 12788
Seq/Len: 224.35
HH_delta: -0.112 (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
17_T38_A2.046113.138
35_E38_A1.695692.601
17_T35_E1.555562.386
34_F39_I1.434412.200
15_P53_V1.414282.169
36_K40_L1.176271.804
14_C17_T1.116881.713
13_K18_L1.113421.708
29_K32_H1.085331.665
42_Y49_K1.017341.560
12_L20_P0.984131.509
13_K20_P0.902121.384
15_P18_L0.830041.273
21_F35_E0.790731.213
39_I52_P0.757341.162
34_F53_V0.749831.150
21_F24_P0.745721.144
26_K33_T0.72221.108
14_C38_A0.694611.065
21_F33_T0.690741.059
43_I49_K0.667661.024
11_S20_P0.649140.996
27_S30_C0.64720.993
27_S32_H0.636620.976
23_D36_K0.603350.925
37_E40_L0.602830.925
16_I52_P0.595310.913
42_Y50_R0.562910.863
12_L33_T0.56140.861
11_S31_G0.558880.857
24_P28_K0.536110.822
18_L53_V0.532510.817
26_K40_L0.519580.797
30_C51_C0.514470.789
16_I19_Q0.509290.781
43_I48_S0.495550.760
39_I43_I0.494560.759
41_Q46_N0.476240.730
24_P27_S0.467670.717
27_S33_T0.463050.710
16_I42_Y0.45790.702
34_F52_P0.437130.670
33_T36_K0.43310.664
16_I34_F0.433080.664
21_F43_I0.425620.653
37_E41_Q0.418760.642
36_K47_G0.412750.633
21_F25_V0.402450.617
11_S33_T0.400790.615
38_A51_C0.400570.614
32_H51_C0.396710.608
9_T20_P0.395420.606
29_K51_C0.390190.598
19_Q41_Q0.382750.587
24_P33_T0.382040.586
46_N50_R0.378940.581
22_E33_T0.375180.575
26_K30_C0.372450.571
25_V36_K0.356910.547
24_P36_K0.356660.547
22_E37_E0.355310.545
19_Q22_E0.354570.544
15_P34_F0.349970.537
23_D37_E0.34760.533
29_K40_L0.345210.529
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
3htkC198.9-0.112
3knvA0.929898.50.061
2cklB0.947498.50.065
3lrqA0.947498.40.075
2cklA0.929898.40.079
3ztgA0.947498.40.079
3fl2A0.929898.40.086
1z6uA0.929898.40.09
2yurA0.947498.40.09
4aycA0.912398.40.095

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