GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
zf-MIZ - MIZSP-RING zinc finger
Pfam: PF02891 (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: 50
Sequences: 2383
Seq/Len: 47.66
HH_delta: -0.015 (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
8_S31_S1.232093.394
28_D31_S1.184593.263
21_C47_C0.615541.696
8_S28_D0.591751.630
14_I29_L0.573511.580
17_R24_L0.547341.508
23_H44_C0.526431.450
34_E38_R0.514071.416
10_Q13_R0.494761.363
3_L11_R0.479951.322
44_C47_C0.4741.306
5_C31_S0.469291.293
21_C44_C0.468321.290
16_V29_L0.465141.281
33_L37_Q0.438151.207
30_E33_L0.4171.149
32_F36_N0.410481.131
17_R22_K0.404361.114
39_T42_W0.389661.073
12_I24_L0.387751.068
5_C8_S0.371611.024
33_L42_W0.366181.009
13_R30_E0.365981.008
12_I18_G0.34760.958
23_H46_I0.346260.954
37_Q40_P0.340310.938
34_E37_Q0.33990.936
29_L33_L0.338640.933
32_F45_P0.337530.930
12_I17_R0.315750.870
33_L36_N0.315060.868
34_E49_K0.300660.828
29_L32_F0.298510.822
22_K32_F0.298410.822
4_R38_R0.298360.822
14_I24_L0.295660.815
16_V22_K0.293250.808
20_N44_C0.292470.806
27_F32_F0.291180.802
20_N49_K0.287540.792
23_H47_C0.284030.782
4_R11_R0.282570.778
8_S21_C0.281340.775
2_S46_I0.280840.774
12_I28_D0.279130.769
34_E41_K0.275180.758
33_L49_K0.272610.751
9_F39_T0.269730.743
30_E38_R0.268430.740
6_P32_F0.268090.739
36_N43_K0.259520.715
35_S38_R0.258190.711
9_F48_N0.251830.694
23_H48_N0.251670.693
34_E42_W0.251670.693
7_L32_F0.250650.691
36_N40_P0.247890.683
3_L20_N0.245550.676
16_V24_L0.243890.672
2_S20_N0.242790.669
43_K46_I0.241790.666
35_S40_P0.240210.662
38_R42_W0.239070.659
4_R13_R0.23710.653
6_P46_I0.235090.648
40_P43_K0.233680.644
3_L6_P0.232990.642
30_E34_E0.232450.640
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
3i2dA199.2-0.015
4fo9A199.2-0.015
3htkC0.96990.074
2c2lA0.9298.70.199
2f42A0.9298.60.209
1wgmA0.998.60.228
2kreA0.998.60.228
2yu4A0.9698.60.233
2kr4A0.998.50.236
3ztgA0.9698.50.251

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