GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Peptidase_C3 - 3C cysteine protease (picornain 3C)
Pfam: PF00548 (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: 172
Sequences: 7895
Seq/Len: 45.9
HH_delta: 0.184 (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
155_S162_K1.747024.298
29_A37_F1.361243.349
42_H149_C1.343543.305
30_L163_I1.223443.010
144_T167_H1.137522.798
103_V155_S1.079662.656
36_Y78_K1.047862.578
41_T68_D1.044752.570
36_Y76_L1.025662.523
30_L166_I0.926972.280
59_D80_P0.858342.112
42_H73_D0.808971.990
65_V68_D0.804241.978
35_R78_K0.786221.934
58_V77_V0.7811.921
43_E51_I0.769651.893
30_L152_P0.710931.749
73_D149_C0.647811.594
50_Y55_E0.64641.590
103_V164_I0.632671.556
98_E101_E0.630521.551
105_L144_T0.629711.549
106_V154_V0.611641.505
103_V153_L0.609911.500
32_I38_L0.601741.480
105_L167_H0.60081.478
90_K162_K0.594241.462
140_Y167_H0.592681.458
74_L166_I0.586051.442
93_P96_I0.577341.420
59_D78_K0.576061.417
102_C118_V0.558221.373
155_S160_Q0.556921.370
33_Y36_Y0.55331.361
30_L38_L0.551581.357
31_G37_F0.525971.294
105_L153_L0.521631.283
58_V64_L0.520411.280
56_Y79_L0.518511.276
48_T57_K0.517561.273
35_R82_N0.515341.268
64_L68_D0.502791.237
140_Y153_L0.499071.228
155_S164_I0.492871.212
89_R163_I0.490371.206
31_G85_F0.481741.185
152_P163_I0.477741.175
145_K148_M0.467611.150
40_P166_I0.461961.136
97_P164_I0.456191.122
69_G72_T0.453531.116
148_M151_S0.453051.115
30_L89_R0.452071.112
31_G83_P0.44711.100
85_F91_F0.445021.095
118_V122_T0.438611.079
37_F79_L0.435891.072
130_S133_T0.430311.059
38_L163_I0.424271.044
42_H147_G0.423161.041
89_R92_F0.421991.038
73_D147_G0.415361.022
39_V75_T0.41441.019
30_L74_L0.413111.016
47_D51_I0.413021.016
40_P43_E0.412581.015
31_G79_L0.411791.013
147_G150_G0.406571.000
84_K87_D0.405270.997
40_P148_M0.404630.995
125_G136_R0.403420.992
40_P149_C0.392940.967
153_L167_H0.390350.960
89_R93_P0.382090.940
108_S113_R0.381620.939
65_V70_V0.378060.930
90_K93_P0.375550.924
140_Y144_T0.372860.917
120_F123_N0.364510.897
40_P167_H0.36340.894
86_R89_R0.360830.888
134_T137_S0.355670.875
118_V126_F0.355340.874
36_Y65_V0.353740.870
59_D65_V0.353050.869
40_P151_S0.351630.865
79_L83_P0.345360.850
85_F90_K0.34190.841
140_Y143_P0.341070.839
49_I64_L0.340350.837
109_T112_P0.340250.837
108_S114_M0.339290.835
43_E149_C0.338440.833
32_I36_Y0.337810.831
155_S161_G0.334630.823
40_P73_D0.330030.812
52_D55_E0.329580.811
126_F139_K0.329480.811
107_N148_M0.328850.809
32_I76_L0.327930.807
46_E51_I0.326470.803
83_P86_R0.324930.799
92_F163_I0.322490.793
128_N134_T0.321380.791
108_S112_P0.321190.790
39_V77_V0.319270.785
149_C167_H0.317880.782
145_K151_S0.317820.782
133_T137_S0.316830.779
41_T75_T0.314590.774
57_K80_P0.311470.766
122_T139_K0.307260.756
30_L92_F0.306070.753
101_E155_S0.305650.752
126_F134_T0.305250.751
153_L165_G0.303430.746
93_P162_K0.301910.743
44_E48_T0.30180.742
112_P115_I0.300430.739
38_L74_L0.300180.738
121_V134_T0.299860.738
46_E49_I0.29740.732
122_T126_F0.294670.725
48_T51_I0.294260.724
39_V149_C0.292980.721
121_V138_L0.290960.716
108_S111_F0.290720.715
127_I135_P0.288150.709
37_F51_I0.287180.706
132_T135_P0.286010.704
129_L134_T0.285390.702
87_D92_F0.282220.694
40_P168_V0.280210.689
67_R70_V0.276990.681
81_R84_K0.276990.681
105_L151_S0.27690.681
43_E46_E0.274440.675
109_T148_M0.271210.667
129_L132_T0.26560.653
34_D82_N0.261330.643
44_E47_D0.261240.643
34_D85_F0.258770.637
138_L153_L0.257250.633
107_N151_S0.257210.633
38_L166_I0.254340.626
32_I91_F0.25370.624
129_L133_T0.253140.623
116_V120_F0.252940.622
123_N139_K0.251440.619
41_T70_V0.250840.617
87_D90_K0.248550.611
123_N126_F0.247720.609
53_G56_Y0.247350.608
119_G122_T0.246170.606
91_F163_I0.246150.606
51_I79_L0.24510.603
34_D136_R0.243310.599
124_F134_T0.242940.598
110_K113_R0.242220.596
113_R137_S0.240960.593
121_V126_F0.240360.591
118_V134_T0.240120.591
121_V124_F0.239750.590
34_D71_D0.23950.589
30_L40_P0.238440.587
131_G135_P0.237180.583
83_P89_R0.233880.575
137_S168_V0.232260.571
148_M152_P0.231740.570
130_S134_T0.231210.569
122_T141_K0.23090.568
117_E122_T0.229530.565
143_P146_P0.22950.565
49_I58_V0.228890.563
104_L163_I0.22830.562
57_K65_V0.227590.560
106_V144_T0.22540.554
104_L116_V0.225390.554
98_E102_C0.22460.553
152_P167_H0.224390.552
133_T136_R0.222510.547
146_P169_A0.222250.547
127_I137_S0.220810.543
89_R154_V0.220270.542
94_E97_P0.219690.540
119_G142_A0.21920.539
119_G141_K0.219190.539
111_F115_I0.21840.537
52_D56_Y0.217890.536
43_E148_M0.216840.533
33_Y87_D0.216460.533
109_T149_C0.215430.530
75_T103_V0.214330.527
116_V119_G0.213770.526
41_T74_L0.212880.524
120_F126_F0.212060.522
103_V121_V0.21170.521
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
3qzrA0.965199.90.184
3q3yA0.965199.90.193
3zveA0.965199.90.194
4dcdA0.965199.90.203
2b0fA0.959399.90.206
1cqqA0.965199.90.234
2ijd10.965199.90.27
2bhgA0.988499.80.297
2halA0.976799.80.348
3stjA0.947799.70.373

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