GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
P_proprotein - Proprotein convertase P-domain
Pfam: PF01483 (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: CL0202
Length: 87
Sequences: 894
Seq/Len: 10.28
HH_delta: -0.006 (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_H78_G0.503512.562
12_H70_D0.481572.451
24_S58_E0.415722.115
14_Y17_D0.409822.085
21_T31_T0.395082.010
28_T58_E0.389521.982
66_L83_W0.382371.946
23_I67_R0.369011.878
11_T79_T0.348021.771
6_V32_L0.345751.759
9_D81_N0.343291.747
14_Y76_D0.320671.632
11_T81_N0.314431.600
21_T29_R0.306971.562
22_L66_L0.289561.473
12_H18_L0.28441.447
66_L80_L0.273591.392
70_D78_G0.270051.374
29_R67_R0.253131.288
19_R35_R0.24721.258
15_R39_D0.24391.241
68_V80_L0.243721.240
5_Q49_T0.239251.217
21_T67_R0.239161.217
53_V56_W0.230541.173
19_R69_T0.230371.172
9_D47_N0.226051.150
23_I65_T0.225571.148
52_S55_F0.22481.144
18_L70_D0.221941.129
30_S55_F0.221541.127
33_K36_R0.221061.125
9_D82_S0.217191.105
15_R33_K0.216131.100
7_S49_T0.214841.093
30_S52_S0.21171.077
30_S58_E0.209081.064
15_R56_W0.207191.054
17_D70_D0.205381.045
24_S64_W0.20431.040
52_S58_E0.201171.024
10_I20_I0.21.018
15_R36_R0.197311.004
13_P76_D0.195330.994
28_T33_K0.190780.971
44_G51_T0.188520.959
36_R56_W0.188140.957
3_H48_W0.187080.952
36_R39_D0.186950.951
7_S86_T0.185480.944
8_V20_I0.185040.942
52_S56_W0.183730.935
35_R72_N0.18110.922
21_T69_T0.180840.920
13_P75_G0.17830.907
63_T75_G0.178110.906
84_S87_F0.177240.902
3_H56_W0.17540.893
7_S11_T0.174470.888
5_Q51_T0.174150.886
10_I18_L0.174120.886
28_T55_F0.168810.859
34_D72_N0.166960.850
48_W56_W0.165680.843
3_H53_V0.161640.823
4_V55_F0.160130.815
11_T43_S0.159260.810
18_L59_S0.159010.809
6_V66_L0.158990.809
30_S54_A0.158640.807
12_H17_D0.158460.806
55_F59_S0.15670.797
36_R50_F0.156280.795
30_S80_L0.155120.789
31_T34_D0.152720.777
69_T74_P0.152430.776
3_H52_S0.152110.774
16_G39_D0.152050.774
51_T55_F0.150860.768
23_I29_R0.150110.764
60_A77_T0.149790.762
36_R53_V0.149350.760
7_S84_S0.149040.758
13_P32_L0.147720.752
24_S28_T0.146710.747
20_I68_V0.145520.741
23_I63_T0.144930.737
18_L78_G0.144870.737
19_R31_T0.144670.736
73_S77_T0.144230.734
81_N86_T0.142370.724
80_L83_W0.14230.724
20_I66_L0.142040.723
48_W52_S0.141640.721
73_S76_D0.141620.721
36_R54_A0.1410.718
4_V30_S0.139970.712
14_Y18_L0.138760.706
74_P77_T0.13860.705
10_I68_V0.137910.702
67_R87_F0.135610.690
17_D76_D0.134920.687
45_F51_T0.134790.686
39_D56_W0.134040.682
27_G46_L0.133760.681
35_R46_L0.133670.680
27_G63_T0.133490.679
18_L46_L0.133390.679
31_T70_D0.13210.672
17_D34_D0.131330.668
36_R44_G0.130840.666
47_N50_F0.130780.665
63_T77_T0.130690.665
3_H51_T0.130570.664
59_S63_T0.130570.664
72_N75_G0.129870.661
9_D54_A0.129670.660
20_I33_K0.129630.660
4_V60_A0.129420.659
42_G77_T0.128370.653
36_R48_W0.128330.653
8_V50_F0.128270.653
35_R73_S0.127670.650
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
2id4A0.988599.9-0.006
3hjrA0.988599.90
2oxaA0.988599.90.007
1p8jA0.988599.80.055
3afgA0.804694.10.77
1wmdA0.93189.80.797
2pn5A0.862172.50.832
2p9rA0.862172.20.833
2hr0A0.896670.40.834
2b39A0.896664.10.841

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