GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
gag-asp_proteas - gag-polyprotein putative aspartyl protease
Pfam: PF13975 (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: CL0129
Length: 72
Sequences: 1656
Seq/Len: 23
HH_delta: 0.255 (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
13_V22_A0.740353.533
35_E39_K0.482432.302
38_A43_L0.414281.977
34_S37_L0.365531.744
30_H54_V0.344791.645
23_L57_A0.32551.553
20_V37_L0.319951.527
29_T56_L0.312711.492
14_S19_Q0.30391.450
10_Y21_K0.291021.389
8_L29_T0.29041.386
28_A56_L0.272921.302
14_S18_V0.266431.271
52_I65_R0.262371.252
54_V63_E0.259991.241
37_L40_R0.25781.230
18_V41_L0.252591.205
37_L41_L0.243081.160
19_Q67_V0.238841.140
12_P21_K0.237661.134
32_F56_L0.234751.120
12_P19_Q0.233261.113
26_T59_G0.23041.099
22_A59_G0.225091.074
22_A32_F0.219651.048
36_S40_R0.218711.044
9_M32_F0.216821.035
10_Y36_S0.213131.017
9_M28_A0.211621.010
9_M56_L0.207850.992
31_N62_I0.205840.982
17_G59_G0.203150.969
39_K47_K0.196770.939
25_D57_A0.192780.920
43_L47_K0.191840.915
23_L29_T0.191160.912
52_I63_E0.189930.906
36_S39_K0.187290.894
55_K60_S0.184760.882
14_S39_K0.18430.879
27_G59_G0.182910.873
46_E51_P0.180180.860
42_G60_S0.180170.860
18_V40_R0.177390.846
46_E49_P0.176220.841
11_V21_K0.175780.839
35_E47_K0.174880.835
21_K39_K0.173610.828
13_V23_L0.173390.827
19_Q39_K0.173190.826
51_P65_R0.172960.825
44_P49_P0.172640.824
17_G48_P0.171850.820
9_M54_V0.171290.817
45_L48_P0.170780.815
51_P55_K0.17070.815
13_V24_V0.170010.811
23_L55_K0.169940.811
45_L64_I0.167080.797
30_H66_G0.166660.795
10_Y32_F0.166660.795
15_I34_S0.164970.787
19_Q40_R0.164940.787
20_V41_L0.163410.780
32_F64_I0.163030.778
23_L32_F0.16240.775
16_G26_T0.162290.774
29_T55_K0.161110.769
31_N38_A0.160790.767
18_V36_S0.160650.767
12_P51_P0.160450.766
62_I67_V0.159970.763
45_L55_K0.159960.763
46_E62_I0.159920.763
36_S60_S0.158070.754
52_I61_V0.157970.754
8_L23_L0.15730.751
30_H52_I0.156820.748
44_P67_V0.154510.737
38_A45_L0.153630.733
16_G38_A0.151790.724
39_K53_R0.151360.722
12_P39_K0.151220.722
33_I46_E0.150380.718
22_A26_T0.150070.716
23_L56_L0.1490.711
18_V47_K0.148770.710
41_L55_K0.148370.708
52_I62_I0.147870.706
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
3s8iA0.972298.70.255
2i1aA0.958398.50.301
1fmbA0.930697.80.449
3slzA0.902897.80.453
3ka2A0.902896.90.546
2hahA0.944496.80.555
3ec0A0.87596.50.572
2hs1A0.87596.50.575
3sqfA0.958396.20.589
3ka2A0.902895.70.606

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