GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PepSY_2 - Peptidase propeptide and YPEB domain
Pfam: PF13670 (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: CL0320
Length: 83
Sequences: 478
Seq/Len: 5.76
HH_delta: 0.559 (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
59_E69_E0.318252.427
34_A38_L0.242891.852
29_L33_Q0.225191.717
73_D76_T0.223791.707
57_E69_E0.221651.690
28_W74_P0.209091.595
34_A72_V0.189941.449
73_D78_E0.182661.393
72_V79_V0.17041.299
23_A73_D0.168361.284
34_A77_G0.166251.268
48_V58_V0.164761.256
58_V70_V0.161071.228
38_L68_V0.16011.221
50_F56_Y0.159111.213
55_C71_Y0.157291.200
56_Y73_D0.155931.189
42_G60_A0.155851.189
29_L77_G0.150471.148
29_L34_A0.148751.134
43_Y77_G0.147421.124
27_D75_A0.146341.116
36_A44_Q0.144591.103
28_W55_C0.144351.101
47_E63_K0.143651.095
9_A13_A0.143331.093
12_A16_F0.14281.089
43_Y60_A0.142651.088
69_E72_V0.142111.084
34_A58_V0.140771.074
35_V48_V0.138491.056
30_S39_E0.138161.054
59_E71_Y0.137981.052
28_W50_F0.13741.048
34_A48_V0.136411.040
10_L64_D0.136391.040
45_V70_V0.136251.039
65_G78_E0.13441.025
20_D80_V0.133811.020
24_P52_D0.133171.016
70_V79_V0.13221.008
29_L36_A0.130260.993
13_A16_F0.128760.982
43_Y70_V0.128760.982
26_A30_S0.128460.980
37_K72_V0.128260.978
52_D58_V0.127750.974
29_L43_Y0.126030.961
49_E59_E0.124260.948
11_L22_D0.122770.936
66_K78_E0.122470.934
31_I35_V0.12220.932
23_A75_A0.120840.922
37_K40_A0.120770.921
62_D66_K0.119750.913
46_R66_K0.11930.910
30_S34_A0.118760.906
55_C74_P0.118650.905
45_V58_V0.118060.900
38_L79_V0.117280.894
33_Q39_E0.117170.894
31_I48_V0.116580.889
38_L50_F0.115890.884
48_V56_Y0.115860.884
67_K78_E0.115320.879
38_L75_A0.115280.879
38_L60_A0.115040.877
8_A80_V0.114710.875
23_A33_Q0.114580.874
11_L16_F0.114230.871
36_A40_A0.114210.871
26_A40_A0.113680.867
10_L13_A0.113280.864
21_S54_G0.112640.859
30_S65_G0.112630.859
76_T82_E0.112540.858
25_P66_K0.112360.857
49_E55_C0.112080.855
72_V77_G0.111820.853
25_P54_G0.111660.852
79_V82_E0.111120.847
47_E73_D0.110570.843
22_D46_R0.110470.842
22_D32_E0.110080.839
14_P36_A0.109860.838
47_E79_V0.109760.837
71_Y81_K0.107890.823
30_S38_L0.10730.818
48_V60_A0.106630.813
32_E36_A0.10630.811
13_A32_E0.105810.807
35_V39_E0.10550.805
57_E71_Y0.10540.804
37_K41_Q0.104940.800
29_L75_A0.104860.800
70_V81_K0.10470.798
38_L43_Y0.103860.792
10_L46_R0.103660.791
14_P17_A0.102820.784
48_V57_E0.102810.784
68_V81_K0.102440.781
24_P28_W0.101660.775
36_A66_K0.101630.775
49_E53_D0.100480.766
11_L27_D0.099370.758
32_E63_K0.099360.758
24_P39_E0.099190.756
68_V71_Y0.09910.756
24_P54_G0.098580.752
28_W65_G0.098460.751
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
4exrA0.915798.20.559
2kgyA0.939897.90.593
4exrA0.975997.90.599
4fr9A0.75992.60.761
4k61A0.662792.30.764
3u1wA0.722990.50.774
4ipbA0.650685.40.792
4hbrA0.650685.30.792
3tdgA0.927781.40.801
4dsdA0.891672.80.815
If you are interested in a protein containing this domain,
drop us a note and we'll try to predict the structure for you.

Page generated in 0.0299 seconds.