GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Peptidase_C1 - Papain family cysteine protease
Pfam: PF00112 (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: CL0125
Length: 219
Sequences: 4234
Seq/Len: 19.33
HH_delta: -0.012 (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
195_D200_R1.209144.290
8_R184_I0.760382.698
33_A170_L0.751912.668
176_D181_G0.748932.657
126_I136_V0.663462.354
13_R40_A0.662492.350
184_I200_R0.649252.303
30_A137_V0.637042.260
26_C167_H0.630952.238
59_S63_N0.61512.182
72_F117_K0.605032.146
127_K203_Y0.570422.024
32_A84_I0.53721.906
138_A169_V0.52671.869
18_R52_E0.524381.860
15_T186_K0.52211.852
177_E200_R0.513181.821
170_L186_K0.510041.809
185_V199_F0.503591.787
27_W55_L0.49581.759
139_S168_A0.490631.741
191_T196_N0.48681.727
2_P131_M0.475741.688
5_F131_M0.469011.664
57_D90_Y0.466651.656
181_G204_D0.461521.637
93_N101_K0.460921.635
140_I199_F0.460721.634
156_D202_S0.461.632
30_A168_A0.448181.590
171_I185_V0.44771.588
25_S92_Y0.447691.588
13_R41_I0.447091.586
27_W74_A0.446941.586
140_I147_F0.445671.581
71_P168_A0.441431.566
172_V198_Y0.440981.564
54_Y77_Y0.440091.561
131_M174_Y0.43781.553
39_L50_L0.433641.538
130_L171_I0.432741.535
3_K176_D0.429871.525
23_C66_C0.426951.515
175_D182_Y0.426141.512
202_S205_Y0.416831.479
71_P139_S0.416471.478
186_K198_Y0.407241.445
38_R134_G0.401131.423
124_E127_K0.401071.423
122_D125_D0.400531.421
138_A171_I0.397891.412
125_D128_K0.392071.391
49_D87_E0.391761.390
147_F199_F0.388071.377
123_I203_Y0.387331.374
25_S56_I0.387141.373
38_R42_Q0.387141.373
102_S107_S0.387011.373
140_I169_V0.37771.340
181_G203_Y0.373461.325
34_A170_L0.371931.319
5_F10_K0.367081.302
19_D190_G0.364641.294
35_L78_I0.358911.273
16_P49_D0.351871.248
15_T47_N0.350921.245
49_D52_E0.35081.245
18_R49_D0.343751.220
54_Y85_V0.340551.208
93_N98_P0.339731.205
172_V184_I0.339191.203
53_Q57_D0.33451.187
33_A36_E0.333241.182
14_I37_S0.331391.176
17_V198_Y0.326571.159
171_I183_W0.326311.158
58_C100_C0.325421.154
70_S73_D0.319311.133
7_W41_I0.31811.129
18_R36_E0.314041.114
144_S157_P0.313781.113
139_S165_G0.311861.106
128_K132_K0.311291.104
5_F174_Y0.311191.104
130_L136_V0.311121.104
58_C66_C0.310211.101
180_K202_S0.310211.101
85_V89_D0.308061.093
169_V185_V0.307771.092
127_K174_Y0.30651.087
142_V166_G0.303571.077
167_H187_N0.302871.074
130_L183_W0.301531.070
35_L112_I0.298141.058
29_F52_E0.296741.053
4_S9_D0.295351.048
125_D129_A0.293691.042
182_Y200_R0.2891.025
15_T18_R0.28741.020
24_G68_G0.284911.011
103_K106_N0.282041.001
156_D180_K0.281851.000
76_K80_N0.281630.999
86_T89_D0.280040.994
59_S62_Y0.278770.989
71_P137_V0.278520.988
150_Y153_G0.278050.986
126_I130_L0.276620.981
40_A47_N0.275340.977
176_D203_Y0.274610.974
20_Q188_S0.274530.974
20_Q167_H0.273150.969
17_V186_K0.271110.962
39_L48_V0.270650.960
155_Y199_F0.267480.949
39_L110_V0.266870.947
16_P191_T0.266690.946
141_D166_G0.266140.944
20_Q26_C0.265990.944
78_I84_I0.263540.935
183_W203_Y0.263140.934
126_I129_A0.26280.932
175_D200_R0.262630.932
156_D205_Y0.262370.931
127_K183_W0.262260.930
39_L43_N0.260270.923
126_I171_I0.259980.922
3_K9_D0.257760.914
194_G197_G0.255510.906
31_A74_A0.252670.896
29_F33_A0.251490.892
18_R29_F0.250780.890
53_Q93_N0.248820.883
152_S195_D0.24880.883
30_A71_P0.248190.881
142_V148_Q0.247460.878
14_I186_K0.247320.877
123_I127_K0.247270.877
127_K131_M0.246990.876
190_G197_G0.24660.875
7_W14_I0.24640.874
48_V86_T0.246010.873
73_D76_K0.244880.869
147_F155_Y0.243340.863
24_G189_W0.243330.863
75_L137_V0.242690.861
32_A55_L0.242460.860
32_A50_L0.241050.855
89_D106_N0.240340.853
37_S170_L0.239510.850
135_P170_L0.238260.845
43_N46_K0.238090.845
33_A186_K0.236120.838
35_L50_L0.235860.837
129_A136_V0.234910.833
140_I201_I0.234570.832
55_L74_A0.233940.830
140_I155_Y0.232160.824
23_C53_Q0.231870.823
138_A185_V0.230860.819
123_I181_G0.22950.814
175_D203_Y0.228410.810
76_K115_Y0.227590.807
53_Q56_I0.22690.805
86_T109_Y0.226890.805
24_G142_V0.226530.804
136_V171_I0.22630.803
130_L133_Y0.224060.795
37_S135_P0.221530.786
23_C69_G0.221010.784
129_A133_Y0.220690.783
64_K67_D0.219570.779
18_R87_E0.219430.778
17_V191_T0.218480.775
167_H188_S0.217050.770
36_E52_E0.215990.766
24_G167_H0.215510.765
54_Y102_S0.212390.753
76_K79_K0.212380.753
32_A52_E0.210620.747
144_S148_Q0.209810.744
123_I126_I0.209570.743
4_S175_D0.207560.736
39_L46_K0.206560.733
101_K104_K0.205180.728
143_S165_G0.205060.727
193_W199_F0.204270.725
26_C168_A0.203130.721
13_R37_S0.202640.719
32_A170_L0.202390.718
5_F9_D0.202310.718
70_S139_S0.201740.716
176_D179_G0.201070.713
27_W69_G0.199970.709
28_A32_A0.199490.708
124_E128_K0.199450.708
185_V201_I0.199320.707
119_K125_D0.198110.703
141_D161_S0.196090.696
104_K107_S0.194830.691
6_D184_I0.194780.691
26_C187_N0.194640.691
52_E186_K0.19450.690
119_K122_D0.194280.689
37_S41_I0.194010.688
99_T103_K0.193810.688
176_D180_K0.192610.683
56_I65_G0.192350.682
23_C58_C0.192060.681
169_V199_F0.191740.680
71_P75_L0.19110.678
36_E186_K0.190320.675
29_F92_Y0.189980.674
69_G167_H0.189450.672
37_S40_A0.189050.671
141_D163_E0.188670.669
2_P174_Y0.187770.666
35_L84_I0.187760.666
20_Q24_G0.187720.666
52_E87_E0.187330.665
8_R14_I0.187230.664
26_C189_W0.18660.662
72_F76_K0.185880.659
55_L78_I0.185830.659
66_C100_C0.183950.653
63_N73_D0.183320.650
15_T49_D0.183080.650
54_Y90_Y0.181990.646
17_V20_Q0.181840.645
18_R33_A0.181440.644
26_C68_G0.181390.644
40_A45_G0.18030.640
34_A38_R0.180260.640
185_V188_S0.178850.635
123_I204_D0.177630.630
127_K130_L0.177530.630
85_V106_N0.177070.628
33_A52_E0.17670.627
112_I115_Y0.175260.622
53_Q94_G0.174740.620
25_S29_F0.174380.619
66_C150_Y0.174210.618
28_A55_L0.174180.618
109_Y112_I0.173480.615
150_Y194_G0.173240.615
38_R41_I0.17320.614
79_K112_I0.172970.614
29_F36_E0.172460.612
68_G167_H0.172430.612
141_D165_G0.172130.611
40_A43_N0.172060.610
3_K127_K0.171890.610
34_A75_L0.171470.608
88_E99_T0.171120.607
175_D181_G0.17030.604
85_V105_S0.169830.603
67_D164_S0.168780.599
24_G67_D0.167660.595
28_A56_I0.164810.585
6_D17_V0.163630.581
93_N99_T0.16340.580
41_I134_G0.163390.580
144_S164_S0.163390.580
70_S168_A0.162950.578
167_H189_W0.162940.578
16_P47_N0.162740.577
8_R172_V0.162530.577
7_W13_R0.161710.574
24_G187_N0.161510.573
102_S105_S0.16150.573
141_D144_S0.16140.573
21_G190_G0.160780.570
23_C27_W0.160750.570
157_P161_S0.160590.570
95_N99_T0.160480.569
87_E91_P0.160450.569
37_S186_K0.160240.568
31_A137_V0.160170.568
127_K176_D0.159670.566
127_K181_G0.159570.566
33_A37_S0.159150.565
15_T36_E0.158850.564
193_W197_G0.15850.562
85_V102_S0.158230.561
55_L59_S0.15820.561
110_V113_K0.158110.561
127_K204_D0.157930.560
17_V31_A0.157440.559
32_A78_I0.15680.556
28_A74_A0.156780.556
126_I204_D0.156410.555
116_G120_D0.156050.554
177_E180_K0.155850.553
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
3qt4A0.968100-0.012
3qj3A0.968100-0.012
2o6xA0.9726100-0.005
1by8A0.9772100-0.004
2c0yA0.9772100-0.001
1cs8A0.97721000.003
3kwzA0.97721000.01
1xkgA0.95431000.011
3ovxA0.97721000.016
1pciA0.96351000.02

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