GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Trypsin - Trypsin
Pfam: PF00089 (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: 220
Sequences: 12174
Seq/Len: 55.34
HH_delta: 0 (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
122_C186_C2.082864.176
27_C43_C1.894713.798
29_G37_V1.521643.050
11_E141_S1.445062.897
36_W91_L1.430442.868
6_P140_Q1.430322.867
72_S93_K1.394372.795
42_H180_S1.294642.595
36_W93_K1.294442.595
44_V90_A1.287432.581
17_S25_F1.248962.504
70_K95_D1.24432.495
12_F141_S1.238892.484
176_C201_C1.233382.473
30_T191_L1.218362.442
15_V125_V1.201252.408
31_L98_I1.187322.380
54_L98_I1.119482.244
87_N216_Y1.098682.203
38_L191_L1.084312.174
142_V173_G1.06292.131
35_R93_K1.058292.122
35_R97_P1.03442.074
73_K93_K1.024142.053
197_F209_V0.984381.973
94_L98_I0.982761.970
16_V29_G0.975451.956
33_S36_W0.96041.925
152_C166_C0.951281.907
89_I216_Y0.919891.844
6_P138_N0.919661.844
124_V175_A0.906961.818
34_P97_P0.899481.803
12_F125_V0.891821.788
69_I98_I0.88941.783
53_R68_T0.886641.777
100_F106_P0.877541.759
163_N215_S0.865991.736
174_D208_G0.861371.727
71_V92_L0.846351.697
175_A195_V0.842481.689
30_T107_I0.841291.687
125_V185_I0.833371.671
122_C146_V0.813551.631
30_T194_I0.800861.606
14_W108_C0.79661.597
211_T216_Y0.793411.591
72_S95_D0.781611.567
107_I191_L0.780821.565
16_V54_L0.780051.564
69_I95_D0.75951.523
86_D163_N0.758391.520
165_I184_L0.74991.503
136_S140_Q0.738851.481
19_R25_F0.733751.471
53_R56_T0.726181.456
212_R215_S0.722731.449
124_V142_V0.719661.443
7_A12_F0.716741.437
81_D84_T0.716561.437
52_V55_G0.70711.418
148_S151_T0.704881.413
132_D203_S0.69721.398
39_T44_V0.696221.396
107_I185_I0.679021.361
16_V37_V0.661831.327
79_K87_N0.659191.322
56_T66_E0.656711.317
184_L210_Y0.647561.298
149_R212_R0.645071.293
122_C192_V0.642741.289
15_V139_L0.64141.286
128_G179_D0.629411.262
8_S11_E0.626941.257
122_C184_L0.626671.256
42_H88_D0.62371.250
131_S134_G0.621791.247
124_V195_V0.61321.229
121_S143_T0.609661.222
186_C192_V0.601461.206
123_I143_T0.598981.201
54_L104_I0.598841.201
14_W185_I0.595741.194
163_N216_Y0.59231.187
89_I211_T0.589891.183
76_I90_A0.583611.170
40_A194_I0.580071.163
117_N120_T0.574151.151
75_I93_K0.571941.147
86_D161_T0.564221.131
145_P168_G0.561081.125
12_F123_I0.560081.123
164_M197_F0.547141.097
10_G57_Y0.545271.093
124_V144_V0.543611.090
31_L100_F0.543171.089
10_G103_N0.541961.086
15_V28_T0.540641.084
7_A141_S0.539811.082
36_W75_I0.533691.070
118_V148_S0.532791.068
9_P57_Y0.531031.065
195_V198_G0.526451.055
121_S145_P0.521061.045
147_V207_P0.520581.044
77_H87_N0.520241.043
167_A184_L0.51511.033
101_G104_I0.514521.031
51_K68_T0.507631.018
178_G181_G0.505131.013
39_T90_A0.504931.012
40_A43_C0.503181.009
6_P57_Y0.502061.007
69_I96_R0.497340.997
31_L37_V0.496040.994
149_R160_L0.481860.966
44_V76_I0.478950.960
110_P217_L0.478640.960
58_S137_S0.472910.948
37_V52_V0.472220.947
213_V220_I0.47210.946
5_D141_S0.46970.942
60_R137_S0.468530.939
74_I92_L0.46840.939
30_T38_L0.467090.936
44_V74_I0.465040.932
87_N163_N0.464570.931
77_H80_Y0.46440.931
34_P100_F0.463310.929
179_D182_G0.461030.924
28_T182_G0.458820.920
88_D180_S0.452450.907
174_D210_Y0.451710.906
182_G195_V0.448090.898
51_K70_K0.447840.898
161_T164_M0.447110.896
32_I38_L0.446230.895
195_V210_Y0.445990.894
142_V145_P0.442470.887
175_A198_G0.440610.883
67_Q104_I0.438940.880
58_S138_N0.43660.875
18_I52_V0.434480.871
63_D66_E0.433680.869
145_P169_S0.432320.867
125_V141_S0.432090.866
31_L54_L0.431060.864
109_L217_L0.430910.864
194_I211_T0.430170.862
33_S106_P0.425980.854
149_R153_R0.419820.842
15_V183_P0.419780.842
167_A210_Y0.415970.834
100_F104_I0.414670.831
130_T140_Q0.410750.823
19_R53_R0.409910.822
15_V127_W0.405970.814
175_A208_G0.405120.812
200_N203_S0.404680.811
81_D86_D0.404560.811
180_S195_V0.403430.809
31_L106_P0.396360.795
20_Y26_F0.396030.794
74_I90_A0.390770.783
214_S217_L0.390050.782
151_T154_S0.387880.778
171_G204_P0.385950.774
58_S61_N0.384230.770
130_T136_S0.38370.769
31_L94_L0.381480.765
153_R158_D0.381290.764
44_V92_L0.380120.762
129_R177_Q0.377350.756
216_Y220_I0.374440.751
57_Y138_N0.372670.747
75_I91_L0.371750.745
69_I97_P0.370620.743
183_P191_L0.368580.739
16_V52_V0.364650.731
100_F105_Q0.363520.729
162_P215_S0.361460.725
69_I94_L0.356120.714
116_P192_V0.355080.712
174_D202_G0.352490.707
98_I104_I0.352030.706
194_I213_V0.348680.699
199_E206_Y0.345850.693
14_W125_V0.345070.692
164_M209_V0.345070.692
149_R162_P0.342230.686
146_V192_V0.341670.685
193_G210_Y0.33730.676
67_Q99_T0.336770.675
52_V71_V0.335870.673
191_L213_V0.334180.670
54_L69_I0.333060.668
132_D200_N0.330130.662
144_V210_Y0.329840.661
216_Y219_W0.329470.661
26_F50_I0.329440.660
56_T64_G0.328070.658
56_T63_D0.324140.650
86_D164_M0.317130.636
7_A11_E0.314070.630
35_R72_S0.311650.625
18_I92_L0.31050.622
47_A50_I0.308570.619
129_R132_D0.307960.617
178_G182_G0.307530.617
42_H178_G0.305920.613
4_G7_A0.305870.613
175_A210_Y0.30580.613
80_Y85_Y0.30520.612
6_P10_G0.304870.611
16_V20_Y0.304740.611
176_C179_D0.30430.610
155_S206_Y0.304040.610
19_R51_K0.303730.609
186_C189_N0.301230.604
52_V92_L0.301160.604
108_C189_N0.300420.602
28_T40_A0.299120.600
88_D196_S0.29740.596
125_V183_P0.295340.592
83_S86_D0.292410.586
41_A76_I0.290710.583
41_A77_H0.290520.582
105_Q108_C0.290350.582
41_A80_Y0.288580.579
144_V167_A0.288150.578
150_K154_S0.286980.575
124_V184_L0.286340.574
30_T183_P0.286320.574
38_L89_I0.285810.573
11_E57_Y0.285480.572
215_S218_D0.284020.569
17_S26_F0.282230.566
89_I194_I0.282120.566
156_Y206_Y0.279540.560
15_V185_I0.279470.560
139_L142_V0.279130.560
72_S92_L0.278810.559
147_V151_T0.278470.558
7_A10_G0.276820.555
119_G146_V0.276530.554
90_A93_K0.273930.549
160_L164_M0.272580.546
123_I141_S0.271860.545
53_R66_E0.270950.543
55_G104_I0.269770.541
9_P103_N0.268370.538
81_D85_Y0.266740.535
18_I26_F0.266550.534
38_L213_V0.266210.534
44_V50_I0.266040.533
77_H219_W0.265050.531
196_S211_T0.264920.531
50_I74_I0.264330.530
129_R133_N0.262710.527
212_R216_Y0.262490.526
116_P146_V0.262430.526
7_A90_A0.262340.526
27_C40_A0.262270.526
94_L97_P0.261860.525
76_I80_Y0.259450.520
118_V121_S0.257630.516
29_G52_V0.257160.516
166_C176_C0.256940.515
20_Y49_D0.256250.514
28_T42_H0.255810.513
37_V94_L0.255210.512
129_R134_G0.254660.511
32_I91_L0.254570.510
42_H198_G0.254230.510
150_K153_R0.25340.508
155_S205_N0.253260.508
169_S202_G0.252620.506
31_L104_I0.252480.506
111_S114_S0.25220.506
147_V160_L0.252020.505
129_R135_Y0.251780.505
7_A57_Y0.251460.504
112_A218_D0.251210.504
32_I220_I0.251160.504
191_L195_V0.251070.503
70_K96_R0.250560.502
113_G214_S0.25050.502
15_V18_I0.250160.502
180_S198_G0.249930.501
179_D196_S0.246050.493
9_P12_F0.245540.492
99_T102_D0.243960.489
6_P136_S0.242770.487
19_R59_I0.242710.487
12_F15_V0.242030.485
20_Y50_I0.24120.484
165_I212_R0.239160.479
54_L67_Q0.238350.478
202_G205_N0.238290.478
54_L94_L0.237830.477
41_A90_A0.237690.477
180_S196_S0.237160.475
126_G182_G0.236060.473
40_A180_S0.236040.473
13_P16_V0.234540.470
198_G207_P0.23390.469
163_N212_R0.233860.469
40_A179_D0.233230.468
126_G178_G0.233030.467
42_H182_G0.232920.467
20_Y25_F0.232660.466
6_P9_P0.231870.465
19_R68_T0.230620.462
110_P192_V0.229330.460
198_G201_C0.228850.459
164_M167_A0.228560.458
78_P219_W0.228290.458
184_L193_G0.228170.457
79_K218_D0.227850.457
174_D198_G0.227790.457
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
2f83A11000
1autC11000.002
1t8oA0.99091000.003
2olgA11000.005
1fxyA0.98641000.005
2b9lA0.99551000.009
2xxlA11000.009
3nxpA11000.011
4hzhA11000.012
3govB0.99091000.014

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