GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
zf-Apc11 - Anaphase-promoting complex subunit 11 RING-H2 finger
Pfam: PF12861 (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: 85
Sequences: 1330
Seq/Len: 15.65
HH_delta: 0.16 (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
56_F61_I0.597293.065
22_D57_H0.396012.032
10_A14_W0.357251.833
74_C77_C0.353091.812
57_H64_W0.304941.565
73_Q78_R0.302151.550
25_G76_M0.298531.532
9_H13_T0.294131.509
64_W78_R0.287681.476
25_G28_R0.283351.454
47_L57_H0.274431.408
26_I75_P0.264541.357
31_F57_H0.260621.337
64_W73_Q0.25641.316
56_F64_W0.249951.283
27_C60_C0.245451.259
47_L82_K0.243241.248
23_V72_G0.241911.241
63_K67_T0.231331.187
56_F76_M0.231251.187
57_H60_C0.225091.155
8_W16_W0.209271.074
25_G57_H0.207661.066
25_G66_S0.207211.063
51_K82_K0.205361.054
21_D72_G0.200441.028
48_V51_K0.19871.020
47_L50_G0.195741.004
46_P50_G0.194330.997
19_A23_V0.192950.990
50_G81_W0.192280.987
12_A16_W0.192270.987
48_V62_L0.191240.981
20_N30_P0.190870.979
8_W12_A0.190650.978
7_E10_A0.189510.972
72_G81_W0.18620.955
58_M73_Q0.183760.943
54_H65_L0.181660.932
64_W75_P0.180810.928
26_I64_W0.180350.925
8_W13_T0.180020.924
15_K19_A0.174890.897
12_A59_H0.17470.896
28_R76_M0.173430.890
7_E11_V0.173170.889
15_K18_V0.172990.888
24_C54_H0.172530.885
9_H62_L0.169120.868
14_W32_D0.165170.847
55_N79_Q0.163450.839
61_I65_L0.161520.829
49_W55_N0.160860.825
8_W18_V0.158320.812
22_D81_W0.15710.806
64_W81_W0.156920.805
31_F56_F0.156360.802
9_H21_D0.155760.799
55_N59_H0.15510.796
20_N80_P0.155080.796
51_K79_Q0.153870.790
71_K80_P0.152980.785
47_L62_L0.152510.783
10_A67_T0.152180.781
49_W73_Q0.151860.779
32_D46_P0.151710.778
32_D55_N0.150990.775
79_Q82_K0.148630.763
58_M62_L0.148330.761
18_V59_H0.14810.760
23_V81_W0.147990.759
28_R58_M0.147720.758
77_C80_P0.147440.757
11_V14_W0.147430.756
64_W71_K0.146070.749
53_S56_F0.145090.744
8_W63_K0.1450.744
21_D30_P0.142550.731
64_W72_G0.141520.726
7_E18_V0.140380.720
7_E15_K0.139730.717
17_D29_M0.139390.715
63_K66_S0.139290.715
18_V55_N0.139230.714
30_P62_L0.137880.707
28_R49_W0.137370.705
13_T53_S0.136040.698
7_E17_D0.134440.690
9_H12_A0.134280.689
13_T62_L0.133910.687
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
4a0kB0.952999.30.16
3dplR0.952999.30.178
1jm7A0.847199.20.219
2eclA0.894199.10.247
1z6uA0.8235990.286
4aycA0.8118990.289
3fl2A0.8235990.294
2cklB0.8353990.295
3lrqA0.8235990.295
2ct2A0.8235990.299

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