GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Peptidase_A24 - Type IV leader peptidase family
Pfam: PF01478 (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: CL0130
Length: 106
Sequences: 2455
Seq/Len: 23.16
HH_delta: 0.274 (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
22_N76_K1.033533.981
10_I20_I0.984693.793
28_L80_A0.951723.666
72_G75_V0.62792.419
51_G82_G0.612012.358
12_V16_K0.584232.251
6_F24_L0.536832.068
81_L93_I0.535812.064
25_L80_A0.518641.998
13_I21_P0.507161.954
52_A83_L0.453051.745
72_G76_K0.442991.706
56_F79_A0.400841.544
98_S102_I0.397111.530
78_L93_I0.38911.499
96_I100_L0.375311.446
20_I77_L0.371181.430
85_L89_G0.36271.397
20_I25_L0.362621.397
59_F78_L0.357261.376
22_N72_G0.35551.369
32_G84_W0.351.348
21_P24_L0.34411.326
59_F94_L0.340431.311
36_S83_L0.329761.270
55_G82_G0.308221.187
9_I24_L0.307081.183
73_G77_L0.30581.178
56_F60_L0.29841.149
7_L77_L0.296571.142
68_G72_G0.289761.116
93_I97_A0.288671.112
51_G55_G0.28761.108
59_F75_V0.282421.088
51_G86_G0.280581.081
45_L49_L0.279711.077
13_I16_K0.273281.053
50_L53_L0.271721.047
11_S15_I0.268021.032
13_I17_T0.264921.021
85_L93_I0.262461.011
15_I18_R0.254790.981
6_F28_L0.254560.981
10_I70_M0.252440.972
7_L81_L0.251140.967
14_D74_D0.250230.964
70_M75_V0.24850.957
97_A100_L0.248480.957
94_L98_S0.240270.926
23_R27_P0.239180.921
19_R22_N0.238350.918
19_R76_K0.238290.918
10_I24_L0.237520.915
42_L46_L0.232520.896
50_L54_I0.232460.895
38_F50_L0.229850.885
57_L79_A0.229630.885
26_I54_I0.22940.884
97_A101_G0.228680.881
13_I24_L0.225910.870
73_G76_K0.225050.867
22_N25_L0.224110.863
47_E87_W0.223080.859
8_L12_V0.221950.855
21_P76_K0.221140.852
52_A79_A0.220020.848
11_S16_K0.219360.845
27_P31_L0.218870.843
5_I96_I0.217720.839
71_G74_D0.217350.837
55_G90_A0.217130.836
32_G59_F0.215830.831
59_F69_G0.213820.824
36_S42_L0.212890.820
30_I34_I0.212820.820
55_G79_A0.212720.819
58_I61_L0.212130.817
55_G70_M0.211670.815
52_A82_G0.210220.810
9_I13_I0.209410.807
5_I17_T0.208840.804
80_A84_W0.207210.798
55_G59_F0.206890.797
89_G92_L0.205140.790
60_L72_G0.204370.787
58_I94_L0.203850.785
60_L75_V0.203490.784
25_L29_L0.201720.777
47_E50_L0.200120.771
89_G93_I0.197310.760
95_F98_S0.196710.758
10_I25_L0.196620.757
22_N26_I0.194440.749
78_L94_L0.192890.743
54_I57_L0.191570.738
51_G83_L0.189370.729
28_L32_G0.188240.725
8_L11_S0.187820.724
44_S47_E0.186550.719
56_F72_G0.186530.719
83_L86_G0.186350.718
75_V79_A0.185840.716
30_I33_L0.185640.715
80_A83_L0.18430.710
55_G78_L0.183420.707
65_F69_G0.183230.706
13_I19_R0.182860.704
33_L48_A0.18170.700
38_F47_E0.181660.700
18_R65_F0.180670.696
57_L94_L0.179290.691
56_F75_V0.176760.681
79_A90_A0.175570.676
36_S48_A0.174480.672
25_L32_G0.17350.668
92_L100_L0.173070.667
19_R77_L0.172990.666
86_G89_G0.172710.665
19_R72_G0.172590.665
65_F68_G0.171240.660
12_V46_L0.169940.655
59_F70_M0.169270.652
99_I103_I0.1680.647
6_F27_P0.167990.647
16_K35_Y0.167310.645
20_I73_G0.166260.640
5_I9_I0.165610.638
65_F72_G0.161910.624
54_I87_W0.16180.623
82_G86_G0.161340.622
10_I32_G0.161190.621
32_G79_A0.160990.620
18_R102_I0.159750.615
34_I42_L0.159640.615
81_L85_L0.15840.610
64_L67_R0.158320.610
32_G80_A0.157210.606
20_I24_L0.157070.605
57_L61_L0.156270.602
31_L34_I0.155910.601
39_S43_I0.155790.600
70_M95_F0.155750.600
35_Y39_S0.155490.599
46_L49_L0.153770.592
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
3s0xA0.9717990.274
3tijA0.95289.10.861
4ev6A0.51.70.901
4i0uA0.51.70.902
4kppA0.86791.40.905
2qjyB0.33961.20.908
2iubA0.66041.20.909
3cx5D0.33961.10.91
2k9jB0.16980.90.914
4kjsA0.60380.80.918

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