GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Peptidase_C39_2 - Peptidase_C39 like family
Pfam: PF13529 (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: CL0125
Length: 144
Sequences: 1856
Seq/Len: 12.89
HH_delta: 0.22 (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
17_G126_Y0.546342.818
95_E100_R0.538922.780
27_Y101_P0.5152.657
24_V128_V0.477952.466
24_V103_I0.440522.272
104_V129_I0.422662.180
23_M141_N0.419352.163
106_V127_V0.417922.156
15_G34_Q0.400052.064
97_D132_Y0.394562.035
20_S128_V0.385041.986
16_C125_H0.381411.968
127_V140_V0.373021.924
23_M143_P0.360751.861
130_I139_Y0.340681.757
105_S126_Y0.337281.740
93_K132_Y0.33521.729
21_A74_L0.328161.693
93_K138_V0.305841.578
94_Q98_A0.304341.570
88_S91_D0.299571.545
33_S36_D0.290811.500
101_P128_V0.285411.472
130_I141_N0.282181.456
89_F93_K0.280781.448
20_S143_P0.278621.437
20_S103_I0.27271.407
15_G19_A0.263091.357
17_G105_S0.259271.337
40_E76_K0.258931.336
94_Q97_D0.25841.333
99_G102_V0.257441.328
91_D94_Q0.245931.269
25_L30_K0.244521.261
132_Y138_V0.238961.233
95_E98_A0.235031.212
92_I102_V0.232291.198
105_S124_G0.229991.186
36_D39_D0.228591.179
96_I132_Y0.228091.177
15_G22_A0.22791.176
18_P38_A0.22641.168
133_D139_Y0.22631.167
90_D93_K0.220241.136
12_T15_G0.21991.134
103_I126_Y0.212751.097
19_A34_Q0.210971.088
15_G38_A0.208251.074
104_V138_V0.200931.037
70_L126_Y0.200371.034
23_M128_V0.20011.032
36_D40_E0.199731.030
93_K97_D0.197841.021
24_V28_Y0.196971.016
18_P37_L0.191030.985
35_E138_V0.190040.980
12_T18_P0.189810.979
12_T34_Q0.188920.975
14_Y105_S0.188680.973
40_E77_Y0.188350.972
73_Y77_Y0.186990.965
34_Q38_A0.180430.931
26_N31_N0.180210.930
39_D43_T0.171340.884
133_D136_G0.169330.873
28_Y100_R0.165820.855
129_I138_V0.165780.855
104_V127_V0.165730.855
67_P70_L0.165470.854
15_G143_P0.161920.835
20_S23_M0.157610.813
136_G139_Y0.155910.804
31_N128_V0.15420.795
22_A37_L0.153870.794
19_A22_A0.153490.792
15_G126_Y0.153320.791
102_V129_I0.152280.786
76_K94_Q0.152060.784
32_I44_N0.151780.783
22_A26_N0.150190.775
27_Y130_I0.147370.760
64_G70_L0.146010.753
90_D94_Q0.1460.753
99_G143_P0.145940.753
42_G45_P0.144280.744
82_T91_D0.144260.744
17_G69_D0.142480.735
84_T87_A0.140930.727
18_P73_Y0.139940.722
14_Y124_G0.139090.717
17_G103_I0.138750.716
14_Y122_Y0.138280.713
17_G21_A0.137750.711
33_S39_D0.137710.710
107_N124_G0.137550.710
25_L37_L0.137520.709
80_K90_D0.136810.706
20_S25_L0.136630.705
95_E102_V0.136370.703
80_K85_S0.136210.703
67_P71_A0.136160.702
26_N141_N0.133450.688
16_C19_A0.133250.687
32_I36_D0.132950.686
68_D133_D0.132010.681
75_E79_Y0.13080.675
70_L103_I0.129930.670
28_Y79_Y0.129760.669
120_G127_V0.129660.669
41_A73_Y0.129620.669
45_P70_L0.129550.668
26_N32_I0.129060.666
32_I37_L0.129010.666
66_S129_I0.128890.665
21_A25_L0.128860.665
70_L105_S0.12780.659
31_N39_D0.126690.654
31_N135_D0.126470.652
40_E79_Y0.126280.651
78_G87_A0.125680.648
40_E130_I0.125310.646
90_D139_Y0.124580.643
106_V124_G0.124350.641
31_N36_D0.124170.641
76_K136_G0.124120.640
14_Y126_Y0.12330.636
39_D93_K0.123260.636
90_D135_D0.123070.635
93_K134_E0.12290.634
14_Y19_A0.121670.628
64_G89_F0.121080.625
120_G140_V0.120810.623
21_A69_D0.120690.623
36_D72_R0.120630.622
17_G64_G0.120590.622
21_A103_I0.120370.621
105_S122_Y0.120150.620
31_N35_E0.120110.620
83_D140_V0.119080.614
22_A34_Q0.118960.614
26_N30_K0.118920.613
87_A97_D0.118730.612
94_Q131_G0.118530.611
19_A23_M0.118170.610
65_T73_Y0.116960.603
18_P105_S0.116760.602
67_P124_G0.116760.602
18_P106_V0.11670.602
18_P126_Y0.116320.600
36_D43_T0.116220.600
82_T86_D0.116150.599
123_G141_N0.115960.598
38_A41_A0.115920.598
27_Y135_D0.115330.595
92_I129_I0.115310.595
40_E73_Y0.11470.592
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
3ervA0.993199.80.22
3k8uA0.770899.20.526
2bu3A0.881999.10.546
3b79A0.687598.80.601
3zuaA0.736198.50.647
3bb7A0.916798.40.655
4d8bA0.881998.30.671
1pxvA0.87598.20.676
1dkiA0.881998.20.682
1x9yA0.87598.10.688

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