GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Amidase - Amidase
Pfam: PF01425 (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. )
Length: 441
Sequences: 6635
Seq/Len: 15.05
HH_delta: 0.044 (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
81_D89_R1.311174.400
4_E29_L1.095693.677
265_E268_E1.070193.592
123_N126_R0.97713.279
81_D86_Q0.956853.211
11_E25_F0.918953.084
86_Q90_A0.867792.912
35_L49_H0.861572.891
433_R436_S0.855632.872
432_G436_S0.852792.862
110_T133_G0.829052.782
244_R276_E0.826122.772
194_A200_L0.8122.725
165_V193_M0.807582.710
146_L203_L0.762522.559
436_S439_K0.760512.552
275_V364_Y0.755412.535
135_S147_A0.728182.444
53_I146_L0.720442.418
405_A431_V0.712392.391
88_L93_A0.708072.376
166_V200_L0.693222.326
24_D27_E0.693212.326
7_L25_F0.687252.306
430_L440_L0.679092.279
168_L437_D0.645612.167
22_E65_P0.639352.146
156_I167_G0.637162.138
432_G440_L0.635982.134
239_R273_E0.63362.126
87_R209_G0.63022.115
166_V197_V0.626522.103
110_T118_T0.624052.094
241_G364_Y0.622462.089
121_P163_C0.608722.043
240_I366_A0.598232.008
38_R49_H0.595041.997
7_L23_V0.574881.929
412_A431_V0.569521.911
54_S99_T0.561531.885
257_R261_E0.556571.868
126_R424_L0.545561.831
47_P91_A0.545221.830
55_V85_V0.545161.830
24_D64_L0.542921.822
46_G49_H0.541421.817
368_L430_L0.540971.816
242_V264_A0.539991.812
30_A33_R0.539821.812
20_F54_S0.539191.810
180_V190_V0.532551.787
65_P75_D0.530741.781
334_S337_E0.518991.742
196_S199_D0.517951.738
139_V193_M0.517211.736
57_D98_K0.512361.720
264_A274_V0.512241.719
245_D278_D0.505211.696
166_V413_I0.501891.684
66_T98_K0.501641.684
264_A368_L0.499711.677
10_I143_F0.494731.660
3_V28_A0.492141.652
13_Y143_F0.482271.619
175_V207_L0.478761.607
53_I95_I0.478711.607
18_N116_G0.477491.602
359_E362_E0.476991.601
4_E8_A0.476831.600
126_R378_P0.472431.585
410_L431_V0.469461.576
17_L137_A0.465481.562
60_D66_T0.464261.558
371_T414_S0.461741.550
266_A269_A0.45941.542
54_S144_V0.456341.531
259_A426_V0.454171.524
162_F372_T0.451921.517
58_N101_M0.450381.511
68_A181_F0.45031.511
125_S378_P0.450131.511
38_R45_R0.446621.499
169_K406_N0.445521.495
261_E265_E0.443041.487
91_A206_V0.441251.481
17_L141_A0.438111.470
54_S138_A0.437371.468
136_A163_C0.431031.447
3_V94_I0.429241.441
375_P420_D0.423791.422
10_I23_V0.423571.422
111_S380_G0.423441.421
168_L441_L0.423391.421
52_P145_P0.420011.410
59_I190_V0.41981.409
61_V78_P0.41891.406
151_D157_R0.412861.386
174_R204_L0.409151.373
31_Q89_R0.404361.357
378_P381_E0.40271.351
259_A417_V0.402211.350
413_I440_L0.401521.348
156_I192_P0.401071.346
33_R37_A0.399131.339
149_G193_M0.398341.337
355_R359_E0.398131.336
3_V29_L0.396241.330
86_Q89_R0.395811.328
275_V363_E0.391471.314
70_S104_F0.391341.313
59_I148_I0.389881.308
61_V98_K0.389671.308
22_E64_L0.387671.301
10_I96_I0.387431.300
122_W419_F0.385551.294
61_V66_T0.382241.283
132_S135_S0.37971.274
83_P86_Q0.379671.274
84_V148_I0.379271.273
30_A34_E0.37791.268
8_A12_A0.377541.267
9_R13_Y0.377241.266
100_N112_N0.376321.263
160_A193_M0.37451.257
35_L38_R0.374351.256
137_A141_A0.371711.247
255_E420_D0.371621.247
31_Q34_E0.369131.239
258_R262_E0.368851.238
369_T431_V0.368471.237
265_E269_A0.368081.235
3_V96_I0.367781.234
54_S135_S0.366321.229
60_D76_N0.366011.228
21_V69_G0.364911.225
27_E64_L0.363981.222
150_T190_V0.363891.221
358_D434_P0.363521.220
237_G272_A0.359991.208
89_R95_I0.359961.208
20_F97_G0.358641.204
259_A418_G0.356911.198
344_L348_R0.354561.190
48_L93_A0.35411.188
255_E421_P0.353421.186
412_A429_Q0.352521.183
268_E273_E0.352271.182
168_L413_I0.34941.173
34_E38_R0.349311.172
204_L437_D0.348741.170
119_R124_P0.348641.170
119_R379_I0.346731.164
121_P137_A0.345871.161
164_G419_F0.344731.157
148_I207_L0.344411.156
14_N19_A0.343321.152
2_L51_I0.342781.150
117_R379_I0.342671.150
192_P203_L0.341131.145
168_L204_L0.340181.142
64_L78_P0.339151.138
241_G360_L0.338521.136
32_A36_D0.33771.133
6_Y144_V0.337181.132
433_R439_K0.335511.126
256_V426_V0.334571.123
27_E89_R0.33391.121
71_P74_A0.333851.120
83_P87_R0.333561.119
34_E37_A0.331191.111
218_L435_G0.331021.111
139_V147_A0.329551.106
415_V430_L0.328851.104
171_T434_P0.32841.102
405_A412_A0.328351.102
6_Y96_I0.327971.101
142_G195_R0.327921.101
260_F264_A0.326041.094
263_A428_V0.325751.093
6_Y145_P0.325541.093
414_S427_G0.323321.085
21_V100_N0.322511.082
38_R43_K0.322221.081
152_T188_D0.321441.079
240_I272_A0.319131.071
14_N143_F0.318581.069
149_G156_I0.317231.065
200_L441_L0.315691.059
58_N105_A0.314851.057
28_A32_A0.314461.055
29_L32_A0.313951.054
129_G158_I0.313581.052
244_R261_E0.312851.050
7_L11_E0.311911.047
239_R275_V0.31111.044
61_V64_L0.311061.044
86_Q213_W0.310991.044
186_S296_E0.310531.042
27_E31_Q0.307871.033
28_A94_I0.307631.032
10_I14_N0.306671.029
17_L124_P0.306631.029
55_V95_I0.30611.027
235_L272_A0.305651.026
252_V257_R0.305591.026
53_I203_L0.305141.024
254_P258_R0.304321.021
60_D78_P0.303691.019
84_V190_V0.302031.014
87_R90_A0.301831.013
127_T162_F0.299451.005
161_A372_T0.298621.002
54_S147_A0.298351.001
292_I296_E0.298311.001
288_A349_R0.297030.997
238_L439_K0.296690.996
148_I190_V0.296030.993
243_P246_D0.295480.992
266_A270_A0.294970.990
162_F376_A0.294550.989
237_G273_E0.294150.987
240_I368_L0.294130.987
174_R208_A0.293990.987
31_Q35_L0.293750.986
315_R318_P0.293620.985
252_V401_Y0.292750.982
53_I93_A0.292520.982
281_D356_R0.292190.981
166_V415_V0.291950.980
308_A312_A0.291230.977
6_Y143_F0.291220.977
16_E124_P0.291180.977
87_R176_S0.291010.977
14_N18_N0.288090.967
62_A81_D0.287790.966
354_R358_D0.287490.965
262_E266_A0.286380.961
144_V147_A0.285430.958
343_Y347_Q0.28520.957
138_A143_F0.284340.954
258_R261_E0.2830.950
99_T147_A0.281170.944
262_E265_E0.280250.941
420_D426_V0.279860.939
347_Q350_R0.278810.936
100_N115_Y0.278360.934
264_A268_E0.277860.933
118_T137_A0.27670.929
65_P77_P0.276010.926
2_L6_Y0.275170.923
64_L98_K0.274670.922
359_E363_E0.272760.915
298_A331_A0.27110.910
171_T435_G0.270260.907
361_F433_R0.269890.906
277_V360_L0.269110.903
284_E349_R0.268660.902
417_V426_V0.267570.898
259_A262_E0.266940.896
55_V148_I0.266810.895
174_R438_E0.266770.895
8_A11_E0.266710.895
214_D217_S0.265420.891
24_D31_Q0.264510.888
417_V428_V0.264070.886
59_I150_T0.263210.883
83_P178_D0.262840.882
175_V204_L0.262290.880
45_R49_H0.261820.879
139_V165_V0.261610.878
3_V7_L0.26110.876
174_R437_D0.26040.874
101_M105_A0.260210.873
27_E30_A0.259540.871
168_L200_L0.259090.870
235_L238_L0.25820.867
242_V260_F0.257310.864
82_A85_V0.256950.862
260_F417_V0.255070.856
145_P199_D0.25390.852
99_T138_A0.253660.851
168_L440_L0.253320.850
238_L272_A0.252550.848
20_F144_V0.252490.847
244_R278_D0.251880.845
70_S103_E0.250870.842
61_V81_D0.249430.837
108_P158_I0.247040.829
135_S138_A0.24680.828
136_A193_M0.245980.826
160_A167_G0.244690.821
48_L202_L0.244280.820
241_G277_V0.244140.819
361_F410_L0.243980.819
29_L33_R0.243850.818
210_P217_S0.241620.811
211_D214_D0.241390.810
351_A355_R0.240240.806
146_L194_A0.240180.806
118_T128_P0.239750.805
126_R376_A0.238720.801
366_A439_K0.237980.799
369_T412_A0.237970.799
371_T427_G0.23750.797
100_N116_G0.237080.796
49_H92_G0.236680.794
324_R328_E0.236460.794
17_L143_F0.234120.786
254_P257_R0.234110.786
102_P107_G0.233410.783
362_E433_R0.232360.780
352_R355_R0.232140.779
169_K189_T0.231810.778
261_E268_E0.231780.778
55_V61_V0.231780.778
136_A140_A0.231610.777
366_A432_G0.23120.776
51_I145_P0.231170.776
109_T377_P0.230190.773
60_D80_E0.229660.771
7_L29_L0.22950.770
355_R358_D0.22930.770
161_A427_G0.229050.769
413_I441_L0.228560.767
19_A143_F0.228450.767
38_R92_G0.22830.766
9_R12_A0.228280.766
67_T75_D0.228160.766
119_R125_S0.228160.766
432_G439_K0.228040.765
352_R356_R0.22770.764
376_A424_L0.227210.763
350_R354_R0.227110.762
24_D28_A0.227090.762
246_D282_L0.226830.761
368_L428_V0.22630.759
105_A188_D0.225320.756
80_E86_Q0.225260.756
44_P49_H0.225060.755
140_A165_V0.224690.754
199_D202_L0.224230.753
171_T437_D0.223950.752
293_F297_G0.223780.751
20_F99_T0.223110.749
11_E23_V0.22310.749
99_T135_S0.222910.748
253_D420_D0.222580.747
351_A354_R0.222530.747
356_R359_E0.221670.744
61_V89_R0.221490.743
81_D85_V0.221270.743
437_D440_L0.220510.740
59_I180_V0.219890.738
202_L205_D0.219310.736
60_D98_K0.218710.734
366_A430_L0.218570.734
183_L293_F0.21830.733
96_I144_V0.217510.730
405_A410_L0.216880.728
2_L145_P0.215160.722
3_V6_Y0.214980.721
358_D433_R0.214930.721
59_I82_A0.21490.721
42_G45_R0.214780.721
345_Q348_R0.214420.720
105_A152_T0.214030.718
85_V95_I0.214010.718
320_S323_V0.213930.718
10_I20_F0.213860.718
64_L95_I0.212990.715
267_L270_A0.212090.712
150_T180_V0.211960.711
20_F143_F0.211820.711
239_R365_D0.21170.710
261_E264_A0.211130.709
367_L431_V0.210140.705
255_E422_D0.210110.705
256_V375_P0.209730.704
42_G46_G0.20950.703
156_I191_G0.209210.702
2_L52_P0.208980.701
128_P137_A0.208130.698
253_D375_P0.207350.696
268_E271_G0.207220.695
4_E33_R0.206910.694
175_V192_P0.206020.691
239_R364_Y0.205840.691
241_G365_D0.20560.690
360_L363_E0.205540.690
162_F377_P0.205190.689
357_F408_A0.205150.688
65_P74_A0.205140.688
238_L366_A0.205060.688
205_D208_A0.203570.683
7_L10_I0.203430.683
5_A8_A0.203370.683
241_G361_F0.202780.681
185_P300_N0.201830.677
277_V367_L0.201780.677
203_L207_L0.201620.677
47_P205_D0.200640.673
322_I325_S0.200530.673
255_E426_V0.200230.672
291_R346_A0.200150.672
135_S139_V0.200120.672
198_E202_L0.199990.671
63_G77_P0.199520.670
83_P176_S0.19950.670
349_R352_R0.199130.668
61_V95_I0.199120.668
353_L408_A0.198930.668
137_A163_C0.198340.666
153_G289_Y0.198340.666
68_A73_L0.197920.664
271_G274_V0.197330.662
67_T100_N0.1970.661
58_N150_T0.196990.661
242_V274_V0.196240.659
358_D410_L0.195130.655
268_E274_V0.19490.654
42_G49_H0.194710.653
51_I199_D0.194230.652
3_V32_A0.193860.651
20_F96_I0.193270.649
18_N118_T0.192810.647
122_W425_P0.192590.646
174_R436_S0.192270.645
84_V175_V0.192150.645
82_A179_G0.19170.643
29_L36_D0.19120.642
295_S333_I0.191050.641
263_A417_V0.191020.641
69_G101_M0.190990.641
274_V364_Y0.190530.639
156_I160_A0.189590.636
161_A414_S0.189440.636
56_K155_S0.188920.634
279_L360_L0.188440.632
201_A205_D0.187810.630
155_S159_P0.187670.630
267_L368_L0.187630.630
195_R199_D0.187330.629
156_I193_M0.187180.628
238_L365_D0.186530.626
54_S97_G0.186240.625
14_N20_F0.185870.624
80_E178_D0.185740.623
410_L434_P0.185240.622
47_P206_V0.184130.618
375_P424_L0.183840.617
112_N117_R0.18290.614
17_L118_T0.182780.613
279_L282_L0.182660.613
196_S200_L0.182530.613
112_N116_G0.18240.612
110_T128_P0.182030.611
59_I84_V0.181770.610
135_S148_I0.181640.610
33_R36_D0.181070.608
21_V114_L0.1810.607
172_R189_T0.180710.606
243_P369_T0.179640.603
177_R211_D0.178620.599
298_A330_G0.178510.599
122_W164_G0.178150.598
240_I267_L0.17760.596
149_G192_P0.177540.596
204_L441_L0.177430.595
234_S237_G0.177380.595
436_S440_L0.177360.595
120_N128_P0.177210.595
62_A80_E0.177040.594
97_G138_A0.176630.593
53_I85_V0.176340.592
26_D33_R0.176260.592
56_K131_S0.176080.591
253_D256_V0.176060.591
268_E276_E0.175960.591
102_P133_G0.17470.586
197_V200_L0.174630.586
158_I372_T0.174570.586
309_R313_K0.174030.584
13_Y17_L0.173740.583
1_E4_E0.17370.583
289_Y293_F0.172330.578
81_D84_V0.170910.574
153_G157_R0.170790.573
98_K101_M0.170570.572
158_I402_T0.170450.572
20_F23_V0.170010.571
406_N412_A0.169750.570
57_D101_M0.169350.568
15_P18_N0.16930.568
73_L76_N0.169240.568
52_P199_D0.169110.568
58_N68_A0.16880.567
6_Y9_R0.168690.566
121_P124_P0.168540.566
260_F368_L0.16850.565
126_R377_P0.16820.564
69_G100_N0.168040.564
160_A165_V0.167980.564
93_A203_L0.167970.564
6_Y20_F0.167930.564
74_A114_L0.167920.564
168_L194_A0.167650.563
102_P109_T0.16760.562
6_Y142_G0.16760.562
67_T74_A0.166420.559
263_A267_L0.166250.558
117_R128_P0.166240.558
138_A144_V0.1660.557
148_I203_L0.165950.557
192_P207_L0.165340.555
13_Y16_E0.164850.553
4_E25_F0.164840.553
118_T133_G0.164270.551
437_D441_L0.164260.551
56_K132_S0.163280.548
1_E5_A0.16320.548
132_S139_V0.16320.548
19_A138_A0.162930.547
43_K49_H0.162920.547
166_V194_A0.16240.545
35_L42_G0.162290.545
354_R434_P0.162180.544
25_F29_L0.162140.544
31_Q95_I0.162040.544
67_T115_Y0.161980.544
357_F410_L0.161730.543
127_T379_I0.161380.542
197_V415_V0.161360.542
333_I337_E0.161050.540
13_Y141_A0.160760.540
277_V280_P0.160570.539
26_D30_A0.160540.539
88_L203_L0.160430.538
18_N117_R0.160070.537
35_L94_I0.159980.537
154_G158_I0.159570.536
353_L356_R0.159350.535
241_G275_V0.159150.534
14_N23_V0.15890.533
123_N424_L0.158890.533
156_I175_V0.158870.533
371_T429_Q0.158560.532
2_L5_A0.158530.532
335_S343_Y0.158470.532
66_T78_P0.158420.532
277_V364_Y0.158130.531
281_D284_E0.157820.530
78_P81_D0.157540.529
411_P432_G0.157370.528
119_R123_N0.157330.528
18_N21_V0.15670.526
308_A311_L0.15660.526
122_W140_A0.156140.524
27_E62_A0.155660.522
106_M153_G0.155650.522
12_A15_P0.155510.522
405_A408_A0.155240.521
284_E287_D0.155160.521
138_A147_A0.154830.520
372_T376_A0.154790.519
135_S193_M0.154580.519
31_Q81_D0.154410.518
47_P92_G0.154390.518
151_D158_I0.154070.517
35_L46_G0.153260.514
272_A365_D0.153230.514
296_E300_N0.153170.514
329_Q332_A0.153130.514
410_L432_G0.153070.514
179_G188_D0.152670.512
62_A86_Q0.152610.512
61_V85_V0.152540.512
323_V326_R0.152370.511
247_G260_F0.152190.511
58_N180_V0.152080.510
177_R190_V0.151870.510
184_S296_E0.151730.509
100_N118_T0.151710.509
24_D95_I0.151310.508
296_E299_A0.150980.507
62_A79_T0.150930.507
347_Q351_A0.150630.506
260_F428_V0.150210.504
241_G276_E0.150110.504
168_L171_T0.150.503
177_R214_D0.149870.503
238_L241_G0.149820.503
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
3ip4A0.97511000.044
3h0lA0.96371000.064
2dc0A0.91611000.076
3kfuE0.95011000.077
3a2qA0.95691000.084
2gi3A0.94331000.09
1m22A0.94781000.095
tr|CX0.93421000.099
3a1kA0.98641000.101
4gysA0.9321000.116

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