GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
zf-rbx1 - RING-H2 zinc finger
Pfam: PF12678 (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: 73
Sequences: 2431
Seq/Len: 33.3
HH_delta: 0.001 (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
69_C72_C0.75362.516
56_F60_S0.479021.599
54_F59_I0.470441.571
61_Q65_Q0.465541.554
8_N12_L0.465011.553
26_R71_L0.462381.544
45_I55_H0.4521.509
62_W68_T0.441141.473
23_A71_L0.439781.468
55_H58_C0.435811.455
68_T73_R0.435151.453
45_I48_G0.421511.407
9_A13_W0.418061.396
13_W16_D0.388471.297
10_V13_W0.377891.262
23_A26_R0.372121.242
25_C58_C0.362061.209
55_H63_L0.361611.207
43_C48_G0.354161.183
50_C72_C0.353261.180
47_W52_H0.352031.175
24_I62_W0.351911.175
8_N11_A0.335121.119
58_C69_C0.328951.098
12_L17_I0.327791.094
25_C50_C0.324641.084
59_I70_P0.320081.069
29_L55_H0.314711.051
11_A15_W0.309121.032
26_R61_Q0.297380.993
9_A12_L0.297320.993
29_L45_I0.296310.989
62_W66_N0.287260.959
26_R60_S0.284390.950
62_W73_R0.282910.945
10_V14_S0.273940.915
47_W53_I0.270860.904
59_I63_L0.266160.889
16_D51_G0.265860.888
43_C57_H0.263730.881
14_S17_I0.262130.875
22_C52_H0.261470.873
23_A52_H0.260490.870
8_N15_W0.254740.851
11_A17_I0.254180.849
12_L16_D0.251060.838
22_C50_C0.248280.829
55_H59_I0.247670.827
10_V16_D0.246530.823
22_C72_C0.245890.821
12_L15_W0.245750.821
61_Q64_K0.245260.819
28_P60_S0.239960.801
43_C55_H0.239630.800
54_F62_W0.237860.794
19_D71_L0.234060.782
20_D28_P0.232680.777
54_F70_P0.23080.771
50_C58_C0.230370.769
61_Q66_N0.230170.769
44_P48_G0.229370.766
26_R73_R0.227630.760
42_E48_G0.226610.757
57_H60_S0.225220.752
13_W17_I0.224940.751
42_E47_W0.224780.751
56_F64_K0.224730.750
22_C25_C0.223230.745
25_C55_H0.223170.745
8_N14_S0.221710.740
64_K67_N0.22050.736
56_F68_T0.216080.721
19_D53_I0.21440.716
17_I64_K0.214170.715
29_L56_F0.213570.713
22_C58_C0.212780.710
24_I73_R0.212220.709
14_S19_D0.212050.708
9_A15_W0.211580.706
46_V60_S0.211090.705
19_D64_K0.210660.703
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
4a0kB199.50.001
3dplR199.40.013
2eclA0.945299.20.13
1v87A1990.21
2l0bA0.863990.213
1x4jA0.86398.90.228
2y1nA0.821998.90.241
2ectA0.808298.90.252
2ep4A0.808298.90.253
2kizA0.794598.90.258

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