GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Trypsin_2 - Trypsin-like peptidase domain
Pfam: PF13365 (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: CL0124
Length: 120
Sequences: 11187
Seq/Len: 93.22
HH_delta: 0.226 (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
1_G18_V2.306083.931
112_D116_R1.909793.256
17_H106_S1.776973.029
3_G12_I1.754762.991
4_F117_V1.724772.940
11_Y63_K1.690032.881
19_V60_A1.562132.663
16_A52_F1.502952.562
11_Y61_L1.469842.506
4_F120_I1.27122.167
7_G11_Y1.246812.125
4_F109_P1.143881.950
9_D63_K1.114981.901
17_H58_D0.898951.532
6_I13_L0.857111.461
14_T19_V0.833011.420
4_F13_L0.820521.399
59_L120_I0.784431.337
48_E65_D0.783981.336
66_P69_G0.778561.327
102_R105_S0.755341.288
5_L64_V0.744691.269
58_D106_S0.73581.254
15_A18_V0.731.244
99_A102_R0.729881.244
48_E63_K0.721551.230
2_T108_G0.717911.224
34_E42_R0.710451.211
47_A62_L0.707881.207
5_L12_I0.707841.207
31_S36_V0.693991.183
72_G75_R0.692111.180
105_S108_G0.684161.166
12_I64_V0.670761.143
15_A105_S0.668831.140
84_S87_S0.665071.134
50_V63_K0.659021.123
97_T101_T0.64891.106
16_A20_E0.63911.089
97_T110_V0.630991.076
15_A120_I0.624211.064
19_V62_L0.622811.062
49_V52_F0.615171.049
76_V80_T0.607821.036
97_T100_D0.597461.018
66_P70_V0.596481.017
78_G81_S0.587871.002
76_V79_S0.587131.001
34_E37_F0.583980.995
47_A53_D0.582350.993
75_R78_G0.577580.985
77_P80_T0.577150.984
36_V40_G0.574640.980
53_D57_Y0.571350.974
109_P117_V0.568680.969
47_A55_D0.567840.968
31_S34_E0.559710.954
49_V53_D0.559550.954
17_H104_G0.558470.952
32_S44_P0.558010.951
33_V36_V0.5580.951
70_V75_R0.546930.932
92_R95_Y0.546470.932
67_W72_G0.542680.925
100_D103_P0.539370.919
91_N95_Y0.536470.915
13_L117_V0.53370.910
80_T88_T0.526260.897
13_L59_L0.523740.893
37_F43_V0.523290.892
30_N33_V0.517810.883
73_G76_V0.510180.870
72_G76_V0.504730.860
71_G75_R0.49930.851
34_E44_P0.496560.846
11_Y50_V0.494970.844
80_T83_V0.491650.838
71_G74_V0.48690.830
6_I61_L0.48650.829
75_R80_T0.483140.824
74_V77_P0.481030.820
69_G72_G0.476270.812
20_E29_D0.473140.807
70_V73_G0.472260.805
14_T60_A0.469960.801
75_R79_S0.464860.792
31_S35_V0.463280.790
16_A60_A0.462560.789
47_A50_V0.458650.782
79_S82_G0.458380.781
84_S88_T0.455280.776
36_V42_R0.453010.772
67_W70_V0.452550.771
69_G73_G0.451460.770
40_G43_V0.450550.768
29_D32_S0.449710.767
47_A54_P0.447270.762
37_F41_R0.446480.761
68_T72_G0.445770.760
80_T84_S0.437350.746
15_A108_G0.433950.740
74_V80_T0.433640.739
110_V119_G0.431140.735
2_T105_S0.430240.733
74_V78_G0.429380.732
112_D118_V0.427220.728
111_F117_V0.426520.727
35_V38_P0.423770.722
83_V88_T0.421950.719
43_V64_V0.421630.719
90_D93_M0.419750.716
67_W74_V0.417910.712
5_L37_F0.41340.705
91_N94_L0.413110.704
2_T15_A0.407180.694
13_L61_L0.406750.693
1_G4_F0.406610.693
4_F108_G0.405650.692
1_G17_H0.405250.691
50_V53_D0.404440.689
87_S90_D0.403370.688
70_V74_V0.403130.687
81_S84_S0.395160.674
66_P73_G0.394560.673
38_P42_R0.393270.670
69_G75_R0.392780.670
6_I11_Y0.390880.666
52_F55_D0.389550.664
8_P11_Y0.388660.663
73_G79_S0.388610.662
50_V54_P0.387630.661
82_G88_T0.384290.655
75_R81_S0.383680.654
16_A19_V0.37730.643
51_Y61_L0.376690.642
1_G15_A0.375370.640
82_G85_P0.374170.638
72_G77_P0.373570.637
4_F59_L0.372550.635
90_D94_L0.372550.635
1_G105_S0.372290.635
33_V49_V0.370030.631
98_D102_R0.365420.623
112_D115_G0.361240.616
16_A54_P0.3610.615
68_T73_G0.35490.605
88_T92_R0.353690.603
71_G76_V0.350330.597
86_T90_D0.3480.593
71_G81_S0.346730.591
102_R108_G0.338920.578
72_G88_T0.33880.578
81_S85_P0.338340.577
89_N92_R0.335930.573
89_N95_Y0.33540.572
76_V83_V0.33430.570
79_S83_V0.333990.569
77_P81_S0.333730.569
89_N93_M0.333670.569
85_P88_T0.330190.563
49_V55_D0.328710.560
100_D110_V0.328250.560
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
3tjoA0.908399.60.226
4ic5A0.991799.50.233
3stiA0.908399.50.236
3numA0.908399.50.237
3lgiA0.908399.50.239
3stjA0.908399.50.24
1lcyA0.999.50.24
1te0A0.908399.50.242
3qo6A0.908399.50.247
1y8tA0.966799.50.249

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