GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Peptidase_M3_N - Oligopeptidase F
Pfam: PF08439 (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. )
Length: 70
Sequences: 1031
Seq/Len: 14.73
HH_delta: 0.38 (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
39_S42_E0.799773.722
42_E45_L0.599322.789
24_R28_E0.500622.330
60_Y64_S0.496762.312
7_E11_E0.491372.286
6_P9_K0.481022.238
55_A59_L0.419831.954
31_R34_K0.369471.719
7_E31_R0.368221.713
9_K13_L0.340121.583
21_K24_R0.334781.558
38_L42_E0.326711.520
3_L37_T0.318771.483
56_W59_L0.292511.361
6_P12_S0.288081.341
25_F29_E0.283191.318
2_L10_L0.264071.229
50_S56_W0.257931.200
8_E12_S0.248991.159
52_G56_W0.245671.143
28_E32_R0.242811.130
9_K12_S0.235481.096
29_E32_R0.2341.089
2_L30_I0.232591.082
4_S40_E0.229851.070
49_L52_G0.221651.031
7_E34_K0.215841.004
59_L63_L0.212970.991
11_E14_I0.211910.986
58_N62_T0.207190.964
36_H41_E0.206970.963
5_L10_L0.206760.962
18_P21_K0.206410.960
38_L46_L0.19980.930
16_E19_E0.196240.913
6_P34_K0.196160.913
16_E28_E0.195440.909
2_L27_L0.195240.909
16_E21_K0.191820.893
1_E34_K0.191690.892
47_A67_D0.190880.888
22_E54_S0.190760.888
1_E35_K0.189410.881
25_F28_E0.188790.878
26_Y45_L0.188590.878
41_E45_L0.18760.873
17_D68_M0.185710.864
23_Y36_H0.185420.863
5_L9_K0.182660.850
10_L14_I0.182040.847
64_S68_M0.181150.843
1_E30_I0.180250.839
11_E24_R0.179280.834
34_K50_S0.179140.834
37_T63_L0.175360.816
9_K22_E0.171350.797
57_S64_S0.171010.796
30_I38_L0.170990.796
49_L56_W0.170650.794
30_I33_Y0.170340.793
16_E24_R0.168210.783
50_S54_S0.167530.780
47_A61_D0.166640.775
59_L62_T0.166530.775
63_L68_M0.163570.761
17_D21_K0.163390.760
13_L69_K0.161690.752
25_F48_K0.161460.751
12_S16_E0.159920.744
50_S67_D0.159290.741
23_Y70_F0.159240.741
33_Y44_K0.157090.731
49_L62_T0.156880.730
36_H39_S0.156570.729
52_G59_L0.154470.719
3_L34_K0.153380.714
1_E5_L0.153120.713
14_I27_L0.152190.708
31_R59_L0.151490.705
58_N69_K0.15090.702
30_I37_T0.15060.701
44_K63_L0.147970.689
7_E35_K0.147210.685
45_L64_S0.14720.685
10_L27_L0.145660.678
26_Y29_E0.14560.678
53_L62_T0.145450.677
25_F55_A0.14420.671
28_E70_F0.144070.670
25_F59_L0.143810.669
50_S53_L0.143270.667
1_E70_F0.142570.663
46_L70_F0.142330.662
10_L31_R0.142320.662
25_F52_G0.14170.659
3_L30_I0.14160.659
32_R57_S0.141450.658
49_L53_L0.140590.654
54_S57_S0.140140.652
8_E35_K0.139990.651
23_Y60_Y0.139770.650
3_L38_L0.139560.649
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
2qr4A198.50.38
3ce2A0.985798.40.394
3ahnA0.957195.40.649
3sksA0.914384.50.735
2o3eA0.985741.70.802
2o36A0.985736.90.808
1uz3A0.957116.30.837
1y7910.971412.40.844
2fmmE0.95719.90.851
1cnt10.95715.30.867

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