GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
RVP - Retroviral aspartyl protease
Pfam: PF00077 (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: 100
Sequences: 6529
Seq/Len: 65.29
HH_delta: 0.188 (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
28_S90_D1.309663.564
28_S76_F1.094072.977
10_V19_A1.087972.960
27_V90_D1.048512.853
21_L92_L0.974292.651
13_N64_E0.893732.432
34_D38_L0.844622.298
11_K66_K0.80792.198
17_I30_I0.696121.894
32_E80_P0.692751.885
64_E73_N0.686491.868
64_E71_E0.66581.812
66_K71_E0.652411.775
48_V57_I0.646641.760
9_T16_K0.632771.722
11_K16_K0.631381.718
87_L91_F0.610081.660
49_R55_S0.597711.626
17_I33_K0.561161.527
91_F95_L0.553071.505
72_F91_F0.536891.461
66_K69_G0.500791.363
32_E36_K0.493791.344
74_H91_F0.482661.313
47_T56_S0.479091.304
34_D85_N0.476231.296
22_D25_A0.458221.247
31_S34_D0.452891.232
17_I34_D0.435571.185
92_L97_A0.425731.158
65_V91_F0.419831.142
72_F95_L0.417831.137
10_V17_I0.41641.133
17_I32_E0.409891.115
49_R84_M0.389761.061
25_A28_S0.387311.054
49_R54_S0.385561.049
33_K78_V0.375771.022
29_I79_V0.374721.020
55_S84_M0.367371.000
9_T18_K0.362650.987
10_V87_L0.35850.975
65_V74_H0.356670.971
67_I97_A0.346850.944
27_V48_V0.344760.938
30_I35_W0.343110.934
13_N36_K0.333130.906
88_G92_L0.33290.906
63_V74_H0.326080.887
20_L86_I0.321730.875
58_L61_T0.319340.869
62_T75_T0.318210.866
44_T59_G0.316790.862
49_R53_G0.313990.854
30_I33_K0.307040.835
89_R92_L0.306760.835
12_I17_I0.305250.831
25_A29_I0.301890.821
28_S91_F0.299380.815
9_T14_G0.298870.813
26_D89_R0.298040.811
35_W38_L0.293710.799
11_K14_G0.293220.798
20_L29_I0.290020.789
56_S59_G0.28650.780
11_K15_K0.286480.780
74_H94_K0.285620.777
64_E74_H0.284460.774
10_V30_I0.284340.774
46_I57_I0.282580.769
49_R52_G0.27870.758
89_R93_K0.274210.746
30_I34_D0.272890.743
72_F94_K0.268740.731
29_I48_V0.264230.719
27_V77_L0.263620.717
32_E58_L0.263320.716
94_K97_A0.259450.706
31_S85_N0.258990.705
70_K95_L0.253940.691
76_F87_L0.248120.675
33_K37_K0.247680.674
25_A77_L0.242740.660
54_S72_F0.242460.660
91_F97_A0.242420.660
21_L90_D0.240050.653
62_T73_N0.239190.651
19_A87_L0.239030.650
43_K46_I0.238410.649
12_I30_I0.237770.647
28_S74_H0.237690.647
26_D50_G0.233310.635
36_K62_T0.23310.634
60_S75_T0.231120.629
67_I87_L0.230930.628
18_K37_K0.229070.623
8_I11_K0.227450.619
13_N73_N0.227420.619
8_I31_S0.226480.616
19_A35_W0.225250.613
48_V77_L0.224180.610
47_T77_L0.223850.609
51_A89_R0.223690.609
74_H92_L0.220190.599
63_V76_F0.220060.599
70_K91_F0.219230.597
20_L92_L0.218760.595
30_I84_M0.218660.595
44_T58_L0.217610.592
19_A85_N0.216350.589
50_G88_G0.214560.584
48_V79_V0.213610.581
57_I77_L0.21310.580
52_G88_G0.21260.578
20_L51_A0.211390.575
8_I72_F0.211220.575
13_N16_K0.210630.573
57_I79_V0.209690.571
51_A86_I0.209140.569
65_V95_L0.204030.555
56_S80_P0.201910.549
12_I15_K0.198860.541
71_E74_H0.198390.540
34_D37_K0.197440.537
76_F80_P0.196620.535
76_F79_V0.195470.532
69_G88_G0.19530.531
58_L80_P0.194650.530
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
3s8iA199.30.188
1fmbA0.9899.30.191
2i1aA199.30.202
3slzA0.9699.30.212
3ec0A0.9599.20.225
2hs1A0.9599.20.234
2hahA0.9699.20.242
3ka2A0.9599.20.253
3sqfA199.10.281
3ka2A0.9599.10.286

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