GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
RVP_2 - Retroviral aspartyl protease
Pfam: PF08284 (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: 135
Sequences: 2432
Seq/Len: 18.01
HH_delta: 0.281 (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
44_S111_D0.783644.182
35_V106_V0.686813.665
27_L86_S0.609493.252
26_F35_V0.584873.121
44_S96_L0.568483.033
48_S100_D0.451542.409
121_D124_T0.398172.125
84_P91_E0.396152.114
51_A56_L0.377632.015
86_S89_G0.355911.899
86_S91_E0.347351.853
50_F54_L0.333711.781
33_A50_F0.333631.780
108_L112_W0.315261.682
46_I106_V0.314421.678
121_D128_T0.307721.642
25_T32_P0.305341.629
37_I113_L0.303641.620
48_S52_K0.265571.417
84_P93_V0.26191.398
112_W116_H0.250481.337
113_L118_P0.242541.294
51_A55_G0.2361.259
119_V130_N0.233471.246
27_L32_P0.233251.245
45_F99_L0.232051.238
41_A44_S0.229791.226
119_V128_T0.229781.226
33_A106_V0.226231.207
92_F112_W0.224261.197
42_T110_M0.221981.184
26_F106_V0.221461.182
38_D41_A0.221451.182
65_I68_S0.221411.181
31_I53_K0.21841.165
49_S53_K0.215551.150
36_L107_I0.213511.139
87_I108_L0.208991.115
47_S50_F0.207991.110
85_L94_V0.204231.090
26_F33_A0.196341.048
42_T69_A0.193661.033
66_V71_G0.191181.020
36_L45_F0.190111.014
23_T34_S0.18751.001
41_A97_L0.183930.981
37_I127_V0.183870.981
24_G37_I0.183570.980
50_F106_V0.181910.971
92_F116_H0.180940.966
43_H67_V0.171660.916
74_I79_V0.171230.914
39_S122_W0.170170.908
43_H97_L0.169610.905
111_D115_K0.168810.901
46_I98_V0.167770.895
28_I35_V0.16730.893
63_R67_V0.166990.891
33_A37_I0.166140.887
112_W122_W0.166020.886
117_N130_N0.161060.859
72_G75_N0.160050.854
115_K127_V0.159490.851
47_S105_D0.15860.846
33_A105_D0.158210.844
44_S112_W0.157670.841
118_P122_W0.157650.841
46_I50_F0.1570.838
46_I51_A0.156470.835
94_V112_W0.155710.831
57_P80_C0.155540.830
26_F85_L0.15550.830
36_L104_Y0.154820.826
43_H104_Y0.154490.824
37_I114_K0.153820.821
43_H111_D0.153630.820
110_M114_K0.153620.820
113_L117_N0.152340.813
49_S91_E0.151080.806
120_I130_N0.150620.804
46_I56_L0.15050.803
28_I85_L0.150460.803
123_A126_T0.149910.800
36_L113_L0.149410.797
25_T30_S0.148260.791
26_F36_L0.148050.790
119_V124_T0.14690.784
41_A45_F0.146150.780
74_I77_E0.145680.777
110_M122_W0.145470.776
29_N83_V0.145440.776
50_F57_P0.145140.774
92_F129_F0.144720.772
64_P68_S0.143650.767
68_S124_T0.142950.763
74_I89_G0.142640.761
110_M113_L0.142110.758
27_L30_S0.141920.757
122_W125_K0.141830.757
83_V112_W0.141330.754
55_G59_E0.14080.751
64_P67_V0.139760.746
83_V96_L0.138660.740
118_P129_F0.138430.739
96_L111_D0.138320.738
67_V97_L0.138120.737
34_S46_I0.13650.728
50_F53_K0.135820.725
41_A104_Y0.13510.721
49_S101_L0.135060.721
75_N78_G0.134440.717
123_A128_T0.133970.715
90_H130_N0.133330.711
55_G91_E0.133220.711
76_C99_L0.13320.711
117_N123_A0.132610.708
37_I53_K0.132140.705
45_F76_C0.131480.702
25_T79_V0.131210.700
23_T104_Y0.130830.698
31_I73_S0.130570.697
66_V72_G0.130180.695
116_H129_F0.129920.693
30_S93_V0.129820.693
27_L83_V0.129810.693
37_I111_D0.129760.692
48_S114_K0.129350.690
24_G47_S0.128390.685
43_H79_V0.127670.681
46_I115_K0.127480.680
32_P73_S0.127410.680
48_S102_G0.127350.680
63_R68_S0.127170.679
31_I50_F0.126920.677
82_D96_L0.126720.676
68_S73_S0.126540.675
33_A101_L0.125970.672
32_P86_S0.125580.670
37_I104_Y0.124670.665
119_V126_T0.124050.662
66_V69_A0.12370.660
37_I110_M0.123620.660
56_L60_P0.123220.658
24_G28_I0.12260.654
34_S105_D0.121970.651
35_V128_T0.121820.650
58_L114_K0.12110.646
115_K126_T0.120940.645
42_T100_D0.120620.644
52_K129_F0.120530.643
30_S126_T0.120440.643
72_G85_L0.120440.643
65_I75_N0.120440.643
51_A110_M0.120210.641
44_S107_I0.119820.639
45_F75_N0.11920.636
88_Q91_E0.118970.635
41_A111_D0.118130.630
64_P86_S0.118110.630
94_V111_D0.1180.630
28_I75_N0.117340.626
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
3s8iA0.955699.70.281
2i1aA0.985299.60.334
3slzA0.918598.90.543
1fmbA0.770498.80.556
3ec0A0.733398.50.604
2hahA0.814898.50.604
2hs1A0.733398.50.607
3ka2A0.777898.40.625
3sqfA0.829698.20.648
2rspA0.8074980.666

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