GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Asp_protease_2 - Aspartyl protease
Pfam: PF13650 (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: 90
Sequences: 6544
Seq/Len: 72.71
HH_delta: 0.117 (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
12_F84_G1.757214.514
3_V12_F1.369253.517
21_S89_D1.299663.339
20_I89_D1.164762.992
21_S73_F1.0872.792
6_N60_S1.086782.792
4_K62_T0.913312.346
60_S70_N0.701181.801
2_P9_P0.696091.788
10_V23_I0.67661.738
10_V30_K0.658031.690
62_T67_T0.621671.597
60_S67_T0.61751.586
45_S51_V0.598811.538
62_T65_G0.594911.528
4_K9_P0.558851.436
3_V10_V0.554991.426
10_V31_L0.550661.415
44_V53_V0.525071.349
45_S83_D0.504711.296
32_G36_R0.493661.268
23_I84_G0.493181.267
3_V84_G0.46741.201
45_S50_S0.456561.173
22_V76_V0.446011.146
54_Y58_V0.443531.139
61_I71_V0.439031.128
56_G59_D0.427591.098
18_A22_V0.424531.091
19_S88_M0.415021.066
35_P38_K0.411791.058
13_L85_I0.397151.020
43_S52_T0.394411.013
51_V83_D0.381510.980
63_I86_L0.377580.970
20_I44_V0.376650.968
44_V76_V0.375220.964
44_V74_L0.370250.951
46_G87_G0.366120.940
10_V83_D0.365560.939
73_F84_G0.36060.926
5_V10_V0.355360.913
6_N34_K0.351520.903
45_S48_G0.349940.899
2_P11_R0.341550.877
55_R72_P0.339490.872
65_G87_G0.33540.862
3_V86_L0.335280.861
10_V84_G0.335070.861
57_R72_P0.333990.858
34_K37_P0.333320.856
66_I70_N0.329710.847
52_T55_R0.322830.829
84_G88_M0.320210.823
52_T57_R0.318190.817
18_A74_L0.317580.816
22_V44_V0.317450.815
6_N59_D0.316350.813
81_P84_G0.309510.795
3_V23_I0.306960.789
46_G50_S0.305850.786
34_K77_D0.299780.770
71_V89_D0.292990.753
53_V56_G0.292570.752
15_D18_A0.291560.749
38_K41_P0.285780.734
58_V70_N0.284660.731
4_K8_K0.282980.727
76_V82_I0.2810.722
60_S71_V0.277890.714
61_I68_L0.276770.711
55_R58_V0.275910.709
36_R66_I0.267210.686
18_A46_G0.266520.685
36_R57_R0.264480.679
7_G62_T0.264260.679
56_G73_F0.263380.677
68_L71_V0.260040.668
33_L37_P0.259250.666
45_S49_G0.25910.666
67_T70_N0.257390.661
51_V68_L0.253060.650
64_G71_V0.251760.647
82_I88_M0.243560.626
23_I75_V0.242090.622
48_G87_G0.242080.622
11_R29_K0.241420.620
14_I83_D0.239870.616
14_I21_S0.238260.612
55_R59_D0.236830.608
10_V87_G0.235360.605
57_R70_N0.235040.604
54_Y59_D0.233550.600
46_G76_V0.231750.595
82_I85_I0.230840.593
46_G85_I0.226680.582
21_S71_V0.224180.576
45_S87_G0.222750.572
12_F86_L0.221180.568
3_V63_I0.221140.568
64_G86_L0.220370.566
35_P75_V0.217640.559
42_I55_R0.215540.554
23_I51_V0.21510.553
8_K11_R0.215040.552
43_S74_L0.213620.549
29_K34_K0.212280.545
20_I42_I0.212220.545
22_V89_D0.210860.542
63_I68_L0.210720.541
42_I52_T0.210260.540
31_L75_V0.210070.540
73_F89_D0.208170.535
62_T66_I0.206970.532
41_P74_L0.203950.524
4_K7_G0.203920.524
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
2i1aA0.9667990.117
3s8iA0.9778990.119
1fmbA0.933398.50.285
3slzA0.888998.30.339
3ka2A0.877898.20.357
3ec0A0.877898.10.37
2hs1A0.877898.10.373
2hahA0.944498.10.378
3ka2A0.877897.90.41
3sqfA0.933397.70.445

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