GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DPBB_1 - Rare lipoprotein A (RlpA)-like double-psi beta-barrel
Pfam: PF03330 (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: CL0199
Length: 78
Sequences: 2464
Seq/Len: 31.59
HH_delta: 0.225 (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
17_Q43_T0.869742.516
63_F68_D0.829712.401
5_S73_V0.787172.277
34_K39_S0.744512.154
33_C44_V0.702692.033
60_P64_K0.670641.940
3_A77_E0.634561.836
63_F67_A0.624221.806
40_V62_A0.589441.705
68_D74_I0.580951.681
64_K69_P0.572781.657
48_C51_C0.56381.631
11_N21_V0.558761.617
57_D72_G0.555071.606
4_G55_H0.535721.550
7_T54_N0.523031.513
36_G71_A0.5111.478
42_V62_A0.489341.416
33_C56_L0.482371.396
61_A65_A0.463381.341
23_C33_C0.457671.324
24_L40_V0.452691.310
60_P69_P0.451661.307
3_A75_P0.434051.256
21_V60_P0.430941.247
5_S75_P0.429571.243
11_N60_P0.42121.219
17_Q45_V0.417391.208
13_T45_V0.414321.199
58_L62_A0.411731.191
15_C18_C0.411031.189
14_A47_R0.406691.177
40_V66_L0.399181.155
24_L65_A0.392641.136
49_P57_D0.388641.124
6_A76_V0.374811.084
22_T60_P0.369461.069
42_V58_L0.367271.063
38_K66_L0.355251.028
19_Y45_V0.349771.012
34_K41_T0.337990.978
20_Q23_C0.327430.947
35_V38_K0.320380.927
6_A47_R0.318250.921
63_F74_I0.317560.919
40_V65_A0.314730.911
67_A71_A0.310570.899
12_G21_V0.308350.892
5_S71_A0.298930.865
12_G15_C0.297730.861
59_S62_A0.296980.859
20_Q41_T0.285760.827
29_A54_N0.28330.820
19_Y42_V0.282690.818
71_A74_I0.281660.815
24_L61_A0.28160.815
67_A74_I0.273070.790
6_A35_V0.271880.787
61_A64_K0.269530.780
68_D71_A0.26920.779
58_L68_D0.268990.778
22_T77_E0.268450.777
24_L27_A0.267460.774
28_S49_P0.266430.771
29_A51_C0.265370.768
65_A69_P0.264730.766
65_A77_E0.264360.765
36_G75_P0.256740.743
36_G39_S0.253190.733
10_D21_V0.253040.732
28_S35_V0.250080.724
24_L62_A0.248670.719
28_S47_R0.244670.708
67_A70_D0.243490.704
3_A11_N0.240440.696
46_D59_S0.239190.692
4_G8_W0.238570.690
31_G44_V0.23260.673
7_T47_R0.23150.670
62_A66_L0.230550.667
3_A18_C0.225870.653
6_A50_G0.225410.652
8_W12_G0.22540.652
48_C53_P0.225310.652
11_N23_C0.223990.648
63_F69_P0.223760.647
6_A9_Y0.223140.646
24_L29_A0.219910.636
6_A58_L0.219640.635
35_V42_V0.217750.630
31_G34_K0.217370.629
48_C54_N0.215420.623
5_S52_P0.213630.618
55_H73_V0.213320.617
8_W11_N0.211780.613
4_G14_A0.210930.610
18_C64_K0.210020.608
19_Y56_L0.207450.600
14_A17_Q0.206530.598
7_T73_V0.204830.593
63_F66_L0.204330.591
32_T35_V0.202480.586
4_G9_Y0.199930.578
15_C21_V0.197710.572
18_C43_T0.196670.569
5_S55_H0.194990.564
12_G36_G0.194860.564
35_V58_L0.194830.564
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
3d30A0.846299.60.225
2hczX0.910399.60.232
1n10A0.910399.60.249
4avrA199.40.333
1bw3A0.833399.30.373
1wc2A0.974499.20.391
2kqaA0.7949960.736
3sulA0.807795.70.742
3sujA0.846295.20.753
3sukA0.833395.10.754

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