GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Cu_bind_like - Plastocyanin-like domain
Pfam: PF02298 (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: CL0026
Length: 85
Sequences: 1184
Seq/Len: 13.93
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
75_C80_H0.704513.270
34_H75_C0.639562.968
41_K45_D0.617632.866
38_E71_H0.547952.543
24_T62_T0.476812.213
40_S43_D0.472572.193
39_V74_I0.467272.169
19_F65_L0.424621.971
79_G83_K0.415061.926
34_H80_H0.4041.875
33_Q77_V0.398581.850
58_T61_D0.368641.711
29_Y61_D0.351111.629
37_V76_G0.34671.609
49_S74_I0.346381.608
28_N60_N0.342371.589
24_T64_T0.330051.532
80_H85_Q0.321111.490
67_K71_H0.298011.383
56_Y61_D0.279731.298
35_S76_G0.275721.280
13_W19_F0.271491.260
26_V60_N0.262041.216
26_V62_T0.256031.188
41_K72_Y0.24981.159
19_F25_L0.249051.156
70_P85_Q0.244351.134
19_F23_D0.239941.114
77_V80_H0.237031.100
36_V73_F0.233921.086
34_H85_Q0.233531.084
44_Y47_C0.232921.081
30_D46_S0.227331.055
75_C85_Q0.225441.046
13_W25_L0.217131.008
21_V66_T0.207370.962
13_W23_D0.206610.959
16_G65_L0.206590.959
14_A19_F0.206020.956
55_T58_T0.205710.955
29_Y60_N0.203850.946
21_V68_P0.202320.939
29_Y80_H0.202110.938
81_C84_G0.199550.926
20_R23_D0.197380.916
31_S77_V0.194240.901
43_D48_N0.191090.887
79_G85_Q0.181330.842
39_V49_S0.18090.840
48_N83_K0.179110.831
37_V49_S0.173440.805
29_Y76_G0.172730.802
38_E53_I0.166140.771
29_Y46_S0.163820.760
20_R68_P0.163280.758
56_Y63_V0.162810.756
40_S45_D0.16270.755
45_D60_N0.162620.755
13_W69_G0.160950.747
41_K53_I0.159880.742
29_Y59_G0.159430.740
47_C81_C0.157070.729
35_S70_P0.156050.724
44_Y72_Y0.155240.720
41_K70_P0.15450.717
29_Y36_V0.153760.714
50_S53_I0.152570.708
32_G55_T0.152040.706
38_E82_Q0.151750.704
50_S56_Y0.148930.691
35_S77_V0.14850.689
38_E50_S0.147050.682
37_V55_T0.145270.674
15_S72_Y0.143570.666
25_L44_Y0.142830.663
43_D74_I0.142760.663
28_N48_N0.140130.650
28_N56_Y0.140.650
32_G85_Q0.139920.649
23_D73_F0.139620.648
22_G61_D0.137790.639
43_D70_P0.137080.636
69_G73_F0.136890.635
27_F63_V0.13640.633
35_S75_C0.136070.631
72_Y80_H0.134930.626
39_V44_Y0.134220.623
36_V76_G0.133510.620
52_P76_G0.133170.618
25_L63_V0.132410.615
45_D83_K0.132270.614
40_S52_P0.131620.611
52_P74_I0.130010.603
73_F81_C0.129940.603
46_S57_S0.129820.602
40_S50_S0.129590.601
36_V57_S0.129570.601
41_K44_Y0.129350.600
79_G82_Q0.128940.598
27_F66_T0.128760.598
77_V82_Q0.127810.593
54_S63_V0.127390.591
15_S62_T0.127210.590
34_H77_V0.127080.590
25_L65_L0.126130.585
46_S70_P0.126020.585
40_S73_F0.124690.579
37_V71_H0.124310.577
54_S57_S0.123870.575
31_S45_D0.123580.574
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
1jerA199.90.001
1ws8A0.988299.90.01
1x9uA199.90.011
2cbpA0.929499.90.058
1f56A0.917699.90.08
1qhqA198.50.606
2calA0.988298.50.609
4dp9X0.976598.30.632
1bxvA0.929498.20.642
3tu6A0.917698.20.65

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