GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Alpha-amylase - Alpha amylase catalytic domain
Pfam: PF00128 (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: CL0058
Length: 316
Sequences: 9278
Seq/Len: 29.36
HH_delta: 0.117 (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
11_D64_R1.65064.751
60_A63_K1.518594.371
55_K160_E1.495544.305
62_H163_D1.465714.219
4_R56_E1.368673.939
50_T53_D1.273843.667
60_A64_R1.211373.487
147_R180_E1.178063.391
4_R53_D1.136473.271
28_E43_A1.054133.034
7_I56_E1.044033.005
13_L18_V1.04022.994
4_R7_I1.001642.883
14_K64_R1.00082.881
268_E306_D0.981862.826
77_T99_Y0.920072.648
7_I60_A0.918122.643
61_A68_V0.915092.634
61_A66_I0.897442.583
54_F58_V0.879282.531
10_L64_R0.834252.401
6_I57_L0.809922.331
21_I61_A0.787612.267
56_E60_A0.744832.144
182_R186_K0.738412.125
155_K184_E0.725232.087
158_I192_F0.716362.062
28_E39_S0.707052.035
42_Y152_D0.697612.008
58_V68_V0.674771.942
54_F162_I0.666251.918
52_E55_K0.655931.888
148_E152_D0.634081.825
28_E46_P0.630061.814
155_K188_E0.624761.798
59_D63_K0.614021.767
149_Y152_D0.607711.749
9_K12_Y0.601411.731
10_L61_A0.59941.725
77_T139_L0.597461.720
54_F70_L0.591561.703
151_I180_E0.578691.666
51_M160_E0.575151.655
276_A286_L0.574331.653
4_R8_D0.563151.621
122_E134_S0.55941.610
155_K159_E0.549431.581
140_N143_N0.546631.573
43_A51_M0.54251.561
151_I184_E0.541451.558
53_D56_E0.532391.532
11_D15_D0.530931.528
42_Y153_V0.525361.512
159_E188_E0.518291.492
69_I164_G0.515671.484
13_L66_I0.514261.480
267_L289_A0.514011.479
139_L146_V0.512441.475
72_V154_L0.5091.465
52_E56_E0.507791.462
80_D135_D0.502471.446
6_I23_L0.501491.443
42_Y156_F0.495841.427
23_L26_I0.494081.422
32_G135_D0.489231.408
74_P150_I0.484681.395
26_I54_F0.481531.386
144_P148_E0.476471.371
57_L61_A0.471441.357
98_Y149_Y0.464381.337
26_I70_L0.463411.334
2_D5_G0.459081.321
156_F160_E0.456261.313
183_D187_E0.455141.310
169_A172_H0.453811.306
51_M156_F0.450441.297
154_L181_F0.447931.289
176_E179_K0.445731.283
40_D43_A0.445591.283
141_Y150_I0.443351.276
145_E148_E0.440741.269
26_I44_V0.440631.268
95_Y98_Y0.437221.258
225_D229_R0.436251.256
184_E187_E0.429661.237
42_Y149_Y0.429561.236
156_F161_G0.425671.225
74_P153_V0.424581.222
51_M55_K0.424481.222
18_V302_I0.423451.219
23_L57_L0.421821.214
10_L57_L0.41411.192
186_K218_D0.402561.159
180_E184_E0.401811.157
14_K66_I0.399561.150
8_D60_A0.399271.149
44_V54_F0.398951.148
55_K59_D0.398471.147
168_D271_D0.397651.145
148_E184_E0.396881.142
3_F44_V0.396491.141
266_F269_N0.393241.132
28_E45_D0.393221.132
20_A67_K0.390411.124
149_Y153_V0.386751.113
28_E40_D0.386011.111
54_F57_L0.385381.109
56_E59_D0.379821.093
244_S248_N0.376071.082
168_D197_E0.373371.075
197_E271_D0.371791.070
67_K163_D0.370831.067
220_V223_F0.369911.065
229_R233_F0.368891.062
79_D137_P0.368731.061
177_F181_F0.367331.057
13_L21_I0.367231.057
221_F224_P0.366661.055
74_P167_L0.365291.051
93_N96_S0.365051.051
166_R271_D0.364611.049
182_R194_L0.362331.043
7_I53_D0.3621.042
27_F70_L0.358521.032
226_Y229_R0.358271.031
180_E183_D0.354661.021
59_D62_H0.353341.017
245_D248_N0.351231.011
35_G48_F0.347331.000
7_I11_D0.345740.995
268_E275_F0.340650.981
184_E188_E0.340490.980
147_R151_I0.336710.969
97_D143_N0.336050.967
118_G122_E0.335040.964
290_L306_D0.33470.963
79_D135_D0.334280.962
227_G230_S0.334050.962
27_F38_P0.33330.959
51_M161_G0.328430.945
158_I189_K0.32670.940
154_L185_V0.324230.933
120_N123_Y0.321590.926
12_Y15_D0.321530.925
3_F26_I0.321450.925
292_F296_S0.320930.924
76_H270_H0.320780.923
44_V157_W0.320590.923
286_L290_L0.320580.923
70_L162_I0.320250.922
220_V224_P0.31840.916
153_V156_F0.318020.915
195_I301_M0.317020.912
11_D60_A0.316590.911
286_L309_G0.316320.910
197_E270_H0.314940.907
8_D11_D0.314830.906
74_P154_L0.314190.904
242_D245_D0.31360.903
179_K183_D0.312850.900
166_R197_E0.310640.894
290_L294_L0.309940.892
151_I181_F0.308110.887
10_L60_A0.307570.885
152_D155_K0.307560.885
248_N251_S0.307330.885
221_F225_D0.306380.882
72_V165_F0.305850.880
20_A69_I0.304420.876
222_D225_D0.30420.876
14_K65_G0.302830.872
3_F54_F0.302810.872
291_A295_T0.301480.868
178_W182_R0.301270.867
225_D228_L0.301050.867
262_R299_I0.299850.863
71_D166_R0.299670.863
38_P41_Y0.298560.859
62_H68_V0.298530.859
61_A64_R0.29780.857
139_L150_I0.297620.857
170_A198_V0.296750.854
118_G121_W0.294290.847
7_I57_L0.293780.846
73_V76_H0.292940.843
294_L300_P0.291340.839
185_V192_F0.290550.836
90_Y93_N0.28970.834
302_I306_D0.289650.834
4_R50_T0.287890.829
264_V301_M0.287360.827
248_N252_S0.287270.827
211_Y214_Y0.285210.821
227_G231_S0.284950.820
41_Y139_L0.284790.820
8_D56_E0.284450.819
168_D270_H0.283670.816
245_D249_W0.282380.813
276_A309_G0.281690.811
144_P147_R0.280910.809
267_L293_L0.27990.806
158_I185_V0.279620.805
151_I155_K0.279480.804
250_L296_S0.278520.802
76_H168_D0.275610.793
199_W272_T0.27560.793
170_A196_G0.275250.792
251_S255_S0.273340.787
75_N138_D0.272380.784
70_L157_W0.272330.784
170_A178_W0.271580.782
222_D226_Y0.271370.781
229_R232_F0.271210.781
89_N93_N0.270220.778
176_E180_E0.268630.773
57_L68_V0.268430.773
275_F279_F0.268180.772
247_A251_S0.266880.768
44_V51_M0.266840.768
185_V189_K0.266520.767
12_Y16_L0.266150.766
36_Y270_H0.263810.759
31_N47_R0.263070.757
32_G80_D0.262840.757
138_D172_H0.262630.756
58_V162_I0.262340.755
58_V62_H0.261080.751
20_A193_F0.258640.744
155_K189_K0.258630.744
179_K216_D0.258440.744
72_V167_L0.256180.737
68_V163_D0.25610.737
62_H67_K0.255920.737
183_D186_K0.255580.736
30_P39_S0.252650.727
69_I195_I0.251220.723
98_Y145_E0.251130.723
118_G123_Y0.250280.720
154_L167_L0.249670.719
45_D48_F0.249340.718
154_L165_F0.249070.717
265_N298_G0.248950.717
189_K192_F0.247580.713
148_E151_I0.246960.711
76_H271_D0.24690.711
181_F185_V0.246450.709
31_N45_D0.24580.707
155_K185_V0.245460.707
177_F180_E0.244880.705
290_L302_I0.244210.703
11_D14_K0.244070.703
166_R270_H0.24350.701
36_Y168_D0.243490.701
294_L302_I0.242890.699
27_F153_V0.24270.699
33_Y37_D0.24260.698
205_D208_Q0.241730.696
244_S247_A0.241670.696
171_K199_W0.241250.694
181_F194_L0.241220.694
18_V66_I0.240620.693
228_L232_F0.240460.692
72_V153_V0.23790.685
100_Y142_E0.235850.679
228_L233_F0.234960.676
290_L293_L0.232380.669
223_F233_F0.232340.669
76_H166_R0.232280.669
280_G285_R0.231010.665
20_A66_I0.230910.665
119_S122_E0.230810.664
41_Y77_T0.230780.664
173_I178_W0.230160.662
211_Y215_F0.22910.659
73_V168_D0.228740.658
97_D100_Y0.228180.657
230_S233_F0.227580.655
32_G37_D0.22550.649
171_K198_V0.225280.648
3_F57_L0.224890.647
83_W149_Y0.224290.646
221_F301_M0.224160.645
6_I61_A0.222620.641
12_Y308_I0.222440.640
7_I64_R0.221990.639
277_S312_G0.221760.638
3_F53_D0.21940.632
251_S254_Q0.218360.629
231_S245_D0.217860.627
221_F226_Y0.217140.625
222_D227_G0.216870.624
169_A173_I0.216790.624
167_L170_A0.215180.619
150_I153_V0.213670.615
253_W257_Y0.213640.615
238_H241_G0.213310.614
178_W181_F0.213250.614
304_Y308_I0.212180.611
28_E47_R0.211950.610
119_S123_Y0.211820.610
76_H197_E0.210880.607
244_S296_S0.210840.607
167_L194_L0.210660.606
285_R289_A0.210440.606
207_R211_Y0.210270.605
39_S80_D0.209950.604
71_D168_D0.209320.602
277_S311_T0.209320.602
3_F45_D0.209290.602
141_Y173_I0.208570.600
254_Q297_P0.208090.599
226_Y230_S0.207720.598
222_D229_R0.207650.598
158_I165_F0.207060.596
69_I193_F0.206770.595
18_V307_E0.206420.594
91_F96_S0.206290.594
224_P229_R0.205630.592
94_P145_E0.20510.590
239_G242_D0.204120.588
269_N272_T0.204120.588
36_Y166_R0.203960.587
249_W252_S0.203950.587
223_F226_Y0.203880.587
73_V271_D0.203550.586
288_L295_T0.202510.583
2_D6_I0.200560.577
224_P228_L0.199280.574
177_F182_R0.198910.573
226_Y231_S0.198650.572
30_P80_D0.197990.570
207_R210_A0.197770.569
226_Y233_F0.197080.567
174_P177_F0.196930.567
147_R176_E0.196910.567
181_F189_K0.196290.565
41_Y149_Y0.195870.564
224_P252_S0.195640.563
55_K156_F0.195520.563
167_L217_L0.195040.561
286_L306_D0.194410.560
225_D230_S0.194180.559
19_N66_I0.192860.555
243_A247_A0.191780.552
78_S136_L0.191620.552
13_L17_G0.190650.549
37_D78_S0.190520.548
36_Y271_D0.189990.547
72_V150_I0.189940.547
94_P98_Y0.189830.546
71_D271_D0.189110.544
7_I10_L0.188950.544
293_L300_P0.187540.540
16_L307_E0.187520.540
90_Y96_S0.187010.538
91_F95_Y0.186860.538
150_I154_L0.186570.537
12_Y18_V0.186490.537
222_D253_W0.186430.537
276_A280_G0.186180.536
171_K201_G0.18540.534
177_F196_G0.185340.533
220_V225_D0.184910.532
36_Y73_V0.184630.531
288_L291_A0.183720.529
210_A215_F0.183670.529
147_R150_I0.182570.525
186_K192_F0.18220.524
147_R174_P0.181990.524
89_N92_D0.181910.524
143_N146_V0.181820.523
52_E59_D0.181520.522
34_H37_D0.18110.521
158_I188_E0.180970.521
3_F6_I0.180960.521
6_I21_I0.180520.520
31_N48_F0.180480.519
268_E289_A0.180350.519
177_F185_V0.180320.519
220_V233_F0.180130.518
206_L209_Y0.180030.518
77_T146_V0.180010.518
96_S99_Y0.179890.518
58_V160_E0.179680.517
27_F41_Y0.179310.516
24_S34_H0.178770.515
276_A279_F0.178550.514
265_N293_L0.177920.512
172_H199_W0.177450.511
252_S256_S0.177330.510
58_V161_G0.17730.510
183_D210_A0.177130.510
38_P78_S0.176920.509
306_D309_G0.176440.508
89_N137_P0.175960.506
186_K189_K0.175890.506
57_L60_A0.175390.505
83_W139_L0.175140.504
224_P230_S0.174870.503
184_E189_K0.174830.503
275_F290_L0.173720.500
144_P180_E0.173670.500
97_D140_N0.173580.500
19_N67_K0.173490.499
54_F157_W0.172790.497
71_D75_N0.172770.497
141_Y174_P0.172350.496
37_D136_L0.172270.496
54_F161_G0.172240.496
186_K194_L0.172150.496
151_I154_L0.172090.495
100_Y140_N0.171710.494
226_Y272_T0.171670.494
147_R184_E0.171540.494
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
1m53A0.99681000.117
4aeeA0.95891000.119
2zicA0.98421000.121
3aj7A0.99681000.121
1uokA0.99681000.122
1zjaA0.99371000.125
3k8kA0.9621000.128
3edfA0.96521000.131
1wzaA0.95891000.131
4aefA0.93991000.135

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