GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Epimerase_2 - UDP-N-acetylglucosamine 2-epimerase
Pfam: PF02350 (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: CL0113
Length: 346
Sequences: 16050
Seq/Len: 46.39
HH_delta: 0.193 (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
185_V259_A2.000254.115
216_P242_R1.874033.855
228_S232_I1.734573.568
125_L148_F1.409722.900
262_V273_A1.399692.880
134_R138_L1.377972.835
212_R313_E1.375912.831
208_A309_I1.372782.824
204_E234_K1.261182.595
206_L217_V1.1492.364
204_E305_P1.135192.335
181_P216_P1.104812.273
208_A306_E1.086432.235
311_A314_K1.053492.167
314_K321_F0.989932.037
318_D321_F0.964891.985
183_I218_I0.930461.914
336_N340_R0.922131.897
131_E134_R0.91941.891
307_A311_A0.909021.870
210_A240_N0.906411.865
134_R149_V0.904231.860
314_K318_D0.896171.844
182_Y316_L0.895461.842
322_Y326_K0.891551.834
208_A305_P0.891121.833
186_T199_L0.886561.824
336_N339_E0.87891.808
305_P309_I0.869571.789
222_H228_S0.868261.786
262_V278_K0.861761.773
294_E297_S0.856851.763
321_F324_K0.856261.762
304_D307_A0.854611.758
302_G307_A0.849721.748
313_E317_S0.847261.743
227_G230_I0.842121.732
235_L243_L0.83511.718
220_P255_L0.828771.705
131_E135_E0.809231.665
134_R147_I0.803411.653
251_E254_S0.801371.649
284_R302_G0.796291.638
135_E139_Q0.793371.632
234_K238_Y0.771831.588
202_I263_V0.771481.587
143_P146_R0.77141.587
198_R201_Q0.762231.568
218_I244_I0.752281.548
131_E149_V0.72841.499
248_G251_E0.728321.498
148_F344_I0.727861.497
125_L344_I0.727791.497
184_L312_I0.724831.491
183_I216_P0.709611.460
209_L313_E0.708331.457
128_A147_I0.703271.447
323_R327_N0.702911.446
307_A310_Q0.695851.432
128_A134_R0.695041.430
60_A89_Y0.693451.427
202_I217_V0.689511.419
205_A308_I0.688731.417
64_E90_L0.686661.413
229_D233_E0.674611.388
208_A211_E0.674421.387
259_A278_K0.668231.375
340_R343_E0.666231.371
218_I242_R0.663161.364
229_D232_I0.662461.363
207_K238_Y0.66231.363
135_E138_L0.661761.361
301_V311_A0.651161.340
333_G336_N0.633141.303
72_L97_I0.631021.298
127_F344_I0.630011.296
62_V66_E0.62921.294
209_L215_V0.62581.287
71_V87_A0.624841.285
233_E237_K0.620541.277
261_L312_I0.618591.273
138_L144_P0.615761.267
319_K322_Y0.615591.266
206_L215_V0.615431.266
200_E234_K0.61111.257
127_F341_I0.608921.253
220_P244_I0.604441.243
293_R299_V0.602151.239
281_V311_A0.601041.236
181_P214_N0.594591.223
292_G298_N0.591411.217
73_V94_V0.584081.202
61_D65_R0.58091.195
128_A137_L0.578711.191
182_Y261_L0.578381.190
252_Y256_L0.577031.187
319_K323_R0.575191.183
247_L251_E0.57361.180
218_I255_L0.573131.179
310_Q314_K0.564981.162
154_G160_Q0.559781.152
60_A90_L0.55711.146
86_A90_L0.556051.144
184_L261_L0.555871.144
96_H99_A0.555811.143
234_K237_K0.553431.139
328_R331_P0.552271.136
323_R326_K0.544861.121
93_P124_H0.54271.116
85_L89_Y0.542531.116
263_V312_I0.541861.115
60_A64_E0.541.111
339_E343_E0.539721.110
309_I313_E0.538391.108
180_K214_N0.537491.106
253_L276_L0.533031.097
156_D160_Q0.532161.095
257_K276_L0.524721.079
284_R289_R0.524571.079
187_L252_Y0.522141.074
207_K210_A0.521371.073
131_E291_E0.520031.070
180_K216_P0.517051.064
201_Q305_P0.515731.061
123_A126_H0.515371.060
127_F150_V0.515011.060
278_K326_K0.512251.054
256_L276_L0.511121.052
57_I61_D0.510491.050
203_L235_L0.509321.048
247_L255_L0.508441.046
294_E298_N0.50421.037
129_P152_N0.501511.032
205_A309_I0.501211.031
199_L219_F0.500251.029
232_I236_K0.500161.029
220_P247_L0.498761.026
181_P260_D0.497241.023
253_L257_K0.496981.022
204_E207_K0.49541.019
315_A325_L0.495091.019
218_I259_A0.494141.017
63_L68_P0.493921.016
299_V314_K0.493471.015
208_A212_R0.489061.006
233_E236_K0.486711.001
288_E291_E0.486671.001
273_A278_K0.48170.991
182_Y260_D0.478650.985
306_E310_Q0.477860.983
200_E204_E0.477680.983
261_L315_A0.476970.981
207_K211_E0.476290.980
183_I258_N0.472330.972
182_Y215_V0.471050.969
201_Q308_I0.463270.953
222_H225_P0.46290.952
230_I234_K0.45950.945
299_V311_A0.459280.945
293_R298_N0.456790.940
190_V219_F0.456310.939
212_R309_I0.456120.938
249_Y252_Y0.455940.938
72_L341_I0.455480.937
187_L256_L0.45320.932
74_L99_A0.450670.927
321_F325_L0.449770.925
254_S257_K0.449020.924
230_I233_E0.446590.919
334_D337_A0.443830.913
183_I260_D0.443680.913
182_Y258_N0.44350.912
284_R290_Q0.44290.911
70_A95_A0.440350.906
225_P228_S0.440230.906
283_I301_V0.440060.905
318_D324_K0.438510.902
201_Q303_T0.4380.901
206_L240_N0.436890.899
95_A127_F0.436680.898
129_P133_A0.436520.898
184_L263_V0.43550.896
198_R265_D0.433360.892
217_V241_V0.432630.890
209_L312_I0.432280.889
281_V312_I0.432010.889
215_V316_L0.431020.887
212_R317_S0.430820.886
87_A124_H0.429870.884
337_A340_R0.426730.878
333_G337_A0.421170.866
218_I258_N0.420690.865
132_E135_E0.419360.863
273_A280_V0.418970.862
244_I255_L0.417480.859
96_H100_G0.416950.858
281_V301_V0.416310.856
279_P315_A0.416210.856
136_R139_Q0.414910.854
134_R144_P0.414220.852
334_D338_S0.41010.844
87_A94_V0.409590.843
201_Q204_E0.4080.839
274_P280_V0.407610.839
155_I160_Q0.406550.836
310_Q313_E0.4050.833
261_L281_V0.404120.831
320_D323_R0.401890.827
244_I247_L0.400250.823
154_G158_L0.399860.823
337_A341_I0.398180.819
315_A318_D0.396530.816
256_L273_A0.395480.814
300_L311_A0.394090.811
191_T196_P0.393760.810
197_E266_S0.39230.807
83_A87_A0.392280.807
159_L253_L0.390670.804
160_Q276_L0.390650.804
204_E208_A0.39050.803
286_S290_Q0.387760.798
220_P252_Y0.387230.797
67_K92_I0.386860.796
70_A93_P0.38640.795
314_K317_S0.385770.794
209_L309_I0.383170.788
88_F122_L0.382590.787
235_L238_Y0.381390.785
301_V308_I0.378640.779
216_P240_N0.377760.777
235_L241_V0.376050.774
184_L215_V0.375580.773
178_A181_P0.375370.772
166_E258_N0.374230.770
83_A86_A0.374150.770
338_S342_V0.373690.769
73_V83_A0.373390.768
254_S258_N0.372630.767
189_P196_P0.371330.764
212_R310_Q0.371180.764
162_K257_K0.369180.760
150_V344_I0.368310.758
204_E238_Y0.36790.757
222_H246_P0.366740.754
281_V315_A0.364660.750
261_L322_Y0.363760.748
68_P92_I0.362730.746
322_Y325_L0.361620.744
309_I312_I0.360680.742
324_K327_N0.360570.742
151_G332_Y0.359980.741
182_Y216_P0.358350.737
156_D159_L0.357660.736
197_E268_G0.356850.734
58_E61_D0.356610.734
151_G337_A0.356010.732
306_E309_I0.355490.731
206_L209_L0.355460.731
205_A305_P0.354110.728
128_A133_A0.353750.728
301_V307_A0.352260.725
293_R297_S0.351260.723
245_E248_G0.351240.723
256_L278_K0.351130.722
120_D126_H0.350940.722
261_L316_L0.350430.721
186_T262_V0.350210.720
154_G157_A0.350020.720
90_L93_P0.349730.719
295_R299_V0.349570.719
166_E173_G0.348990.718
318_D322_Y0.348720.717
274_P326_K0.348050.716
154_G334_D0.347410.715
315_A322_Y0.346760.713
289_R292_G0.345910.712
73_V96_H0.344580.709
320_D324_K0.344350.708
128_A149_V0.344340.708
282_N293_R0.343340.706
99_A129_P0.342730.705
160_Q253_L0.339990.699
150_V341_I0.338630.697
232_I243_L0.337940.695
138_L146_R0.33730.694
57_I89_Y0.336630.693
185_V256_L0.336150.692
264_G269_I0.335440.690
260_D322_Y0.335090.689
187_L220_P0.33260.684
215_V260_D0.33220.683
72_L95_A0.331740.682
185_V255_L0.331490.682
138_L147_I0.330240.679
300_L314_K0.329830.679
56_I85_L0.32920.677
206_L312_I0.328410.676
189_P197_E0.327630.674
97_I100_G0.327580.674
185_V220_P0.327380.674
340_R344_I0.327350.673
264_G268_G0.326890.672
231_I234_K0.326830.672
155_I158_L0.326270.671
339_E342_V0.325190.669
75_G78_N0.324870.668
221_L245_E0.324560.668
231_I243_L0.323330.665
68_P71_V0.323110.665
294_E299_V0.322420.663
72_L96_H0.321150.661
192_N227_G0.320490.659
203_L234_K0.318220.655
203_L231_I0.316740.652
277_G327_N0.316710.652
87_A90_L0.315420.649
94_V98_E0.312650.643
71_V92_I0.312140.642
182_Y185_V0.311830.642
99_A268_G0.311090.640
88_F91_N0.3110.640
268_G273_A0.310670.639
184_L206_L0.310080.638
148_F151_G0.309950.638
73_V80_A0.309650.637
256_L262_V0.308680.635
287_G290_Q0.308490.635
201_Q283_I0.30840.634
279_P322_Y0.307850.633
186_T202_I0.307760.633
205_A208_A0.306930.631
209_L316_L0.306820.631
214_N240_N0.305880.629
228_S245_E0.305730.629
148_F340_R0.305460.628
181_P215_V0.304640.627
96_H123_A0.302060.621
74_L129_P0.302030.621
265_D308_I0.301950.621
210_A215_V0.301810.621
95_A99_A0.301130.620
255_L259_A0.299370.616
282_N300_L0.298890.615
191_T226_R0.298640.614
315_A326_K0.296980.611
155_I275_S0.296640.610
232_I235_L0.296640.610
262_V268_G0.296610.610
282_N298_N0.295810.609
205_A263_V0.294980.607
74_L97_I0.293980.605
173_G242_R0.29380.604
207_K237_K0.292120.601
256_L269_I0.291870.600
57_I65_R0.291580.600
207_K234_K0.291350.599
174_I218_I0.290620.598
184_L217_V0.290190.597
138_L141_G0.289520.596
260_D316_L0.287910.592
282_N289_R0.287490.591
220_P245_E0.287210.591
283_I308_I0.286240.589
315_A321_F0.286130.589
80_A119_I0.284910.586
277_G326_K0.284470.585
312_I316_L0.284370.585
255_L258_N0.284140.585
113_E116_R0.283160.583
120_D123_A0.282870.582
247_L252_Y0.282010.580
56_I60_A0.281980.580
295_R300_L0.281430.579
63_L90_L0.280890.578
274_P298_N0.280310.577
249_Y255_L0.278340.573
286_S289_R0.278330.573
130_T133_A0.277640.571
86_A89_Y0.273990.564
238_Y241_V0.272240.560
277_G329_P0.271820.559
202_I265_D0.271710.559
190_V228_S0.271610.559
215_V240_N0.270910.557
210_A239_D0.269620.555
162_K276_L0.269110.554
252_Y255_L0.269060.554
57_I60_A0.268990.553
256_L272_E0.268480.552
250_E254_S0.268060.551
186_T265_D0.267750.551
99_A102_R0.267750.551
64_E89_Y0.267650.551
200_E230_I0.267610.551
185_V188_H0.267070.549
210_A214_N0.266990.549
157_A333_G0.265360.546
62_V65_R0.265250.546
285_D288_E0.265010.545
266_S272_E0.2650.545
182_Y214_N0.26430.544
137_L147_I0.263730.543
279_P326_K0.263360.542
198_R283_I0.262880.541
198_R267_S0.262620.540
222_H226_R0.260270.535
75_G99_A0.259770.534
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
4fkzA0.97111000.193
1vgvA0.96821000.225
3dzcA0.98271000.235
1v4vA0.96531000.237
3beoA0.9741000.244
2jjmA0.9481000.252
3c48A0.96241000.254
2r60A0.96241000.257
3froA0.96821000.26
3ot5A0.97691000.261

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