GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Glyco_hydro_2_C - Glycosyl hydrolases family 2 TIM barrel domain
Pfam: PF02836 (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: 298
Sequences: 6467
Seq/Len: 21.7
HH_delta: 0.194 (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
227_Y284_P1.038643.480
66_D120_H0.958793.213
67_L70_E0.921073.086
43_E71_L0.920783.085
62_P116_R0.912943.059
39_E67_L0.898443.011
52_A254_F0.879552.947
277_D281_R0.850112.849
282_P286_Y0.848132.842
46_K71_L0.80042.682
111_R115_R0.743952.493
42_L71_L0.717512.404
114_V145_V0.703412.357
74_L124_I0.692962.322
111_R144_L0.691312.317
242_A250_V0.690142.313
115_R148_L0.678432.273
69_D120_H0.67452.260
62_P120_H0.67162.250
143_D147_K0.668432.240
42_L68_C0.664252.226
79_I113_M0.653262.189
39_E70_E0.637562.136
43_E47_E0.628432.106
149_D152_R0.626482.099
241_Q244_Q0.620932.081
144_L147_K0.608592.039
41_D280_R0.590151.978
142_Y146_K0.581411.948
107_E140_E0.565441.895
145_V154_V0.544691.825
235_I255_Y0.542841.819
187_E191_E0.541211.814
144_L148_L0.536711.798
48_M286_Y0.536651.798
42_L64_F0.528571.771
237_D240_D0.52711.766
236_W240_D0.525471.761
233_A237_D0.516421.730
39_E63_R0.512531.717
287_Y290_K0.511661.715
107_E111_R0.511181.713
67_L71_L0.496521.664
172_I238_Y0.488171.636
68_C73_I0.485891.628
111_R148_L0.481831.615
39_E43_E0.47491.591
104_E108_Q0.466621.564
214_K281_R0.465531.560
229_E284_P0.460891.544
65_Y120_H0.445951.494
40_R43_E0.444991.491
111_R147_K0.443721.487
289_Y293_W0.437121.465
107_E144_L0.436441.462
66_D69_D0.430871.444
191_E246_R0.426581.429
42_L73_I0.423921.421
62_P66_D0.422171.415
187_E246_R0.421531.413
55_T64_F0.419881.407
184_E241_Q0.417921.400
65_Y69_D0.409691.373
37_A40_R0.408141.368
139_K143_D0.405571.359
142_Y154_V0.40451.355
101_E105_N0.397431.332
68_C75_V0.394921.323
74_L125_M0.394041.320
119_N149_D0.393481.319
187_E244_Q0.392551.315
104_E140_E0.389761.306
282_P287_Y0.384811.289
263_T266_T0.380221.274
53_I73_I0.378491.268
102_F105_N0.377671.266
42_L67_L0.375491.258
62_P117_D0.37051.242
55_T65_Y0.367151.230
229_E233_A0.36541.224
145_V152_R0.365021.223
45_M50_F0.36051.208
76_W125_M0.358181.200
55_T77_Q0.357191.197
276_V286_Y0.353931.186
172_I185_D0.352721.182
115_R118_R0.352071.180
211_Y270_F0.35161.178
124_I151_T0.351311.177
108_Q112_E0.350261.174
153_P200_P0.345231.157
65_Y117_D0.344561.155
104_E107_E0.343311.150
57_H77_Q0.340371.141
138_L157_A0.339781.139
202_I251_A0.338871.136
38_M67_L0.335051.123
110_L114_V0.333471.117
127_S167_D0.330911.109
65_Y77_Q0.327971.099
52_A76_W0.327251.097
146_K154_V0.326331.094
140_E143_D0.324381.087
47_E286_Y0.323631.084
66_D70_E0.317571.064
60_P87_W0.31661.061
38_M63_R0.314881.055
43_E67_L0.311531.044
47_E282_P0.311.039
188_K191_E0.307031.029
39_E71_L0.306591.027
237_D241_Q0.305321.023
77_Q117_D0.303151.016
45_M73_I0.302481.014
232_G236_W0.301471.010
101_E104_E0.2980.999
44_L276_V0.295990.992
206_Y253_E0.295780.991
46_K72_G0.295730.991
232_G288_E0.295530.990
103_R140_E0.29410.986
119_N152_R0.293680.984
58_Y112_E0.2930.982
127_S157_A0.292260.979
140_E144_L0.289470.970
110_L141_L0.289080.969
53_I64_F0.288760.968
77_Q113_M0.288040.965
145_V149_D0.287350.963
105_N108_Q0.287320.963
288_E292_Q0.285380.956
80_P83_G0.284560.954
184_E188_K0.282430.946
44_L47_E0.282360.946
47_E290_K0.282110.945
76_W254_F0.27910.935
190_L248_P0.278120.932
69_D72_G0.277090.929
40_R44_L0.276350.926
233_A236_W0.275480.923
63_R66_D0.274810.921
118_R148_L0.274620.920
200_P251_A0.273430.916
157_A276_V0.27270.914
125_M153_P0.27130.909
44_L282_P0.269720.904
147_K150_P0.269450.903
76_W127_S0.267290.896
118_R149_D0.267050.895
114_V141_L0.264020.885
125_M172_I0.263880.884
50_F258_G0.263170.882
287_Y291_S0.26140.876
112_E116_R0.261210.875
260_D283_K0.260460.873
145_V150_P0.256770.860
76_W202_I0.256590.860
252_G256_W0.253360.849
109_E113_M0.253310.849
110_L144_L0.251780.844
112_E115_R0.251290.842
255_Y275_L0.249840.837
235_I239_Q0.247830.830
277_D283_K0.245830.824
192_D196_Y0.245540.823
54_R130_N0.243780.817
141_L144_L0.242810.814
202_I252_G0.242360.812
171_D204_S0.240810.807
188_K192_D0.240790.807
123_I126_W0.240340.805
44_L280_R0.239680.803
160_G277_D0.237450.796
64_F68_C0.236790.793
110_L145_V0.23670.793
45_M258_G0.234050.784
227_Y230_Y0.233530.783
127_S169_I0.233310.782
215_G227_Y0.232890.780
79_I106_A0.231640.776
286_Y290_K0.230420.772
136_E139_K0.229660.770
52_A74_L0.228530.766
107_E141_L0.227710.763
45_M276_V0.2260.757
160_G181_G0.225820.757
57_H113_M0.224440.752
131_E205_E0.224420.752
138_L276_V0.224390.752
284_P287_Y0.223580.749
43_E46_K0.223560.749
44_L286_Y0.2230.747
126_W149_D0.222640.746
48_M287_Y0.221720.743
107_E143_D0.221370.742
52_A234_F0.22080.740
108_Q111_R0.220310.738
236_W288_E0.219810.737
209_D271_E0.219230.735
239_Q242_A0.218980.734
191_E248_P0.218920.734
113_M117_D0.218450.732
157_A275_L0.218440.732
62_P119_N0.217930.730
69_D75_V0.21790.730
114_V144_L0.217090.727
36_E40_R0.215070.721
276_V282_P0.21490.720
130_N205_E0.213980.717
274_G283_K0.213960.717
114_V152_R0.213350.715
63_R67_L0.212970.714
65_Y75_V0.211720.709
77_Q123_I0.211570.709
107_E110_L0.211240.708
110_L113_M0.209170.701
45_M53_I0.208380.698
169_I204_S0.207570.696
258_G261_F0.207470.695
118_R152_R0.20730.695
234_F238_Y0.207060.694
168_I199_K0.206330.691
184_E244_Q0.205510.689
245_R248_P0.205330.688
69_D124_I0.205130.687
157_A171_D0.204890.687
62_P69_D0.204780.686
50_F293_W0.204670.686
256_W261_F0.203830.683
103_R107_E0.202480.678
100_P104_E0.202470.678
181_G278_Y0.201620.676
36_E39_E0.201270.674
128_L138_L0.200780.673
275_L286_Y0.200680.672
114_V148_L0.200580.672
126_W152_R0.199350.668
37_A279_D0.199280.668
48_M282_P0.19920.668
55_T75_V0.198240.664
258_G276_V0.197890.663
116_R120_H0.196670.659
44_L259_F0.19610.657
275_L289_Y0.195850.656
240_D243_I0.194240.651
36_E43_E0.194120.650
97_A102_F0.193670.649
128_L156_Y0.190880.640
190_L250_V0.189710.636
58_Y268_Y0.189660.636
131_E256_W0.18930.634
263_T273_N0.18860.632
143_D162_D0.188520.632
200_P249_Y0.187830.629
134_Y181_G0.186790.626
184_E187_E0.185650.622
125_M202_I0.184920.620
134_Y159_N0.184910.620
97_A106_A0.184190.617
69_D119_N0.184080.617
138_L142_Y0.183370.614
138_L275_L0.183050.613
142_Y165_V0.182150.610
68_C71_L0.182140.610
229_E232_G0.180540.605
100_P103_R0.180310.604
51_N74_L0.180210.604
57_H117_D0.180160.604
202_I254_F0.179520.602
191_E247_D0.17930.601
191_E195_K0.179230.601
56_H78_E0.178880.599
155_T167_D0.178040.597
207_G214_K0.176910.593
136_E276_V0.176450.591
120_H123_I0.176270.591
75_V124_I0.175030.587
138_L158_S0.174960.586
50_F289_Y0.174730.586
186_F250_V0.174660.585
124_I153_P0.174250.584
137_F276_V0.174210.584
187_E241_Q0.174130.583
166_D169_I0.173270.581
53_I258_G0.173250.581
128_L145_V0.172140.577
255_Y258_G0.171960.576
156_Y159_N0.171670.575
99_D105_N0.171130.573
182_D185_D0.170970.573
57_H78_E0.170510.571
87_W105_N0.170350.571
65_Y123_I0.170060.570
206_Y234_F0.168680.565
128_L141_L0.167940.563
69_D74_L0.166750.559
142_Y145_V0.166440.558
143_D146_K0.166280.557
104_E111_R0.164120.550
78_E127_S0.164110.550
114_V126_W0.16410.550
103_R136_E0.163630.548
260_D274_G0.163080.546
66_D119_N0.16150.541
155_T204_S0.161450.541
65_Y113_M0.161410.541
114_V149_D0.160990.539
137_F275_L0.160450.538
167_D171_D0.159090.533
215_G281_R0.158590.531
81_L106_A0.158460.531
76_W251_A0.158130.530
246_R253_E0.157140.527
107_E147_K0.156730.525
41_D44_L0.156540.525
228_E231_Q0.155860.522
79_I110_L0.155760.522
139_K163_P0.154970.519
247_D252_G0.154880.519
80_P109_E0.154820.519
129_G132_S0.154740.519
208_A230_Y0.154270.517
166_D173_Y0.153860.516
190_L242_A0.153580.515
79_I117_D0.152810.512
169_I173_Y0.152790.512
49_G293_W0.15170.508
207_G283_K0.151690.508
114_V154_V0.151430.507
99_D102_F0.151310.507
136_E215_G0.151150.506
119_N126_W0.150550.504
261_F273_N0.150320.504
68_C72_G0.150310.504
111_R114_V0.150190.503
42_L63_R0.150070.503
209_D273_N0.149480.501
102_F129_G0.149360.500
288_E291_S0.148870.499
129_G156_Y0.148420.497
127_S155_T0.148370.497
168_I173_Y0.146490.491
173_Y201_I0.146320.490
57_H65_Y0.146130.490
208_A212_N0.145830.489
257_T273_N0.145120.486
110_L128_L0.144990.486
210_A230_Y0.144530.484
157_A204_S0.1440.483
49_G290_K0.143750.482
48_M290_K0.143450.481
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
3lpfA0.97991000.194
3hn3A0.95971000.218
3cmgA0.97321000.237
3fn9A0.9431000.242
3obaA0.96981000.261
1yq2A0.90271000.287
3bgaA0.88591000.288
3gm8A0.93961000.289
1jz7A0.90941000.29
2je8A0.9061000.369

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