GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
ZapA - Cell division protein ZapA
Pfam: PF05164 (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. )
Length: 89
Sequences: 1035
Seq/Len: 11.63
HH_delta: 0.054 (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
11_Y51_V0.468812.068
22_Y59_D0.426831.882
31_N35_N0.426111.879
33_K60_E0.425371.876
3_K10_E0.41241.819
30_I54_A0.400361.766
30_I58_A0.37551.656
5_T10_E0.366121.615
34_I50_A0.343931.517
29_L57_L0.338931.495
33_K36_E0.335731.481
4_V27_A0.331291.461
9_R48_R0.330771.459
60_E65_K0.327521.444
67_E72_E0.32751.444
26_A62_L0.326471.440
29_L62_L0.325021.433
28_E32_E0.320791.415
20_E24_R0.312331.377
34_I49_L0.304521.343
7_L49_L0.296551.308
22_Y63_K0.293551.295
18_E63_K0.291521.286
69_D72_E0.281061.240
21_E25_K0.27891.230
45_S48_R0.277921.226
13_I59_D0.27341.206
29_L33_K0.268541.184
37_I49_L0.264321.166
64_L68_L0.260541.149
6_I11_Y0.259831.146
16_P19_D0.253841.120
68_L72_E0.251021.107
25_K28_E0.250841.106
5_T8_G0.242581.070
7_L34_I0.242411.069
6_I13_I0.237331.047
16_P56_N0.23691.045
2_V44_L0.233421.029
3_K12_R0.226160.997
68_L71_L0.22440.990
36_E40_K0.221970.979
63_K66_R0.220520.973
28_E31_N0.218230.962
13_I45_S0.216850.956
32_E39_K0.214840.948
61_L65_K0.214540.946
70_E73_E0.213880.943
30_I50_A0.213570.942
61_L64_L0.213340.941
19_D23_L0.212670.938
22_Y26_A0.211660.933
17_D26_A0.203280.897
67_E70_E0.201020.887
10_E25_K0.200810.886
2_V24_R0.199390.879
21_E24_R0.196190.865
9_R47_E0.193950.855
34_I51_V0.190810.842
21_E28_E0.188590.832
8_G35_N0.186110.821
29_L58_A0.185150.817
38_K49_L0.184920.816
37_I41_Y0.182620.805
11_Y52_L0.181510.801
26_A56_N0.179010.789
68_L73_E0.177770.784
46_P50_A0.17760.783
32_E70_E0.177560.783
3_K19_D0.17750.783
26_A59_D0.175150.772
25_K66_R0.173910.767
34_I45_S0.1720.759
34_I53_A0.170430.752
4_V16_P0.169090.746
63_K68_L0.167110.737
13_I56_N0.167070.737
16_P55_L0.164440.725
45_S52_L0.16370.722
7_L48_R0.163350.720
35_N39_K0.163330.720
58_A61_L0.161780.714
35_N66_R0.161150.711
57_L61_L0.16020.707
50_A55_L0.159840.705
6_I51_V0.159660.704
65_K69_D0.158170.698
2_V37_I0.156780.691
2_V20_E0.156490.690
9_R46_P0.15640.690
9_R45_S0.156330.689
16_P23_L0.15590.688
4_V34_I0.155740.687
27_A31_N0.155530.686
24_R39_K0.155490.686
10_E45_S0.155020.684
23_L59_D0.152240.671
69_D73_E0.150510.664
64_L67_E0.149880.661
57_L68_L0.148650.656
36_E67_E0.147950.653
25_K65_K0.147710.651
36_E56_N0.146420.646
7_L51_V0.14570.643
53_A73_E0.144520.637
56_N59_D0.143270.632
17_D32_E0.143190.632
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
1t3uA0.977599.70.054
3hnwA0.966399.50.145
1k1gA0.7303380.84
3hs8A0.38232.50.846
3eikA0.449430.90.847
4jkvA1260.853
1kyfA0.38218.20.862
1rm1A0.449417.90.862
4e29A0.943816.80.865
1ytbA0.449416.40.865

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