GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Pyridoxal_deC - Pyridoxal-dependent decarboxylase conserved domain
Pfam: PF00282 (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: CL0061
Length: 373
Sequences: 5591
Seq/Len: 14.99
HH_delta: 0.235 (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
212_P215_E1.15195.151
182_E222_K0.919634.112
169_P180_A0.720813.223
217_A227_L0.709623.173
350_R353_K0.708093.166
180_A183_K0.70443.150
202_A234_G0.676673.026
148_E169_P0.651692.914
198_V220_C0.647032.893
143_V166_R0.626892.803
200_A216_I0.617112.760
171_D175_R0.6112.732
180_A184_A0.599872.682
346_Y350_R0.585952.620
218_D252_R0.575542.574
143_V186_E0.568982.544
87_W326_K0.546182.442
358_E371_R0.53482.391
231_A256_I0.523982.343
178_I219_I0.523882.343
214_E250_I0.499412.233
182_E219_I0.49772.226
143_V164_G0.493382.206
220_C225_I0.490092.192
93_G247_L0.471712.109
360_V371_R0.463942.075
168_I184_A0.455122.035
215_E218_D0.437021.954
217_A221_E0.433581.939
178_I215_E0.431981.932
109_T115_A0.428291.915
177_D180_A0.42151.885
247_L250_I0.420521.880
221_E252_R0.419991.878
345_R349_D0.412651.845
214_E248_F0.409461.831
348_A359_L0.409271.830
166_R184_A0.387761.734
144_I158_A0.385051.722
214_E218_D0.383231.714
231_A235_G0.378841.694
58_D61_A0.378651.693
171_D177_D0.37361.671
258_I272_V0.373361.670
182_E186_E0.373131.669
179_E182_E0.372911.668
217_A252_R0.372671.666
348_A352_R0.369251.651
185_L219_I0.369041.650
116_N228_H0.368371.647
182_E223_Y0.368341.647
200_A213_L0.363411.625
115_A257_T0.357581.599
200_A227_L0.35751.599
349_D353_K0.355241.589
260_P321_L0.353091.579
220_C227_L0.351811.573
218_D222_K0.349291.562
110_S114_E0.348131.557
323_A326_K0.34581.546
339_R343_L0.345281.544
335_E339_R0.343151.534
116_N153_S0.336771.506
198_V216_I0.334651.496
179_E183_K0.326291.459
57_A61_A0.325831.457
143_V188_D0.320821.435
181_L216_I0.314481.406
182_E215_E0.306741.372
334_R338_R0.304631.362
198_V225_I0.303271.356
349_D352_R0.30151.348
354_D357_F0.301131.347
92_F258_I0.294431.317
93_G249_G0.293221.311
145_Y188_D0.289891.296
86_R90_D0.288631.291
213_L229_V0.288091.288
230_D262_K0.287341.285
87_W322_W0.285921.279
197_A228_H0.284991.274
344_A348_A0.284511.272
338_R342_E0.284461.272
79_E83_E0.283451.267
147_S200_A0.282051.261
253_A256_I0.279171.248
145_Y184_A0.279121.248
260_P270_C0.278641.246
58_D62_S0.278581.246
235_G258_I0.277441.241
332_G336_R0.276641.237
112_G232_A0.275011.230
181_L198_V0.274231.226
341_I345_R0.271461.214
87_W90_D0.271061.212
148_E167_K0.270641.210
173_D362_E0.269091.203
214_E252_R0.268481.201
219_I222_K0.268431.200
348_A363_P0.268281.200
235_G246_L0.268091.199
169_P184_A0.264571.183
185_L225_I0.260521.165
92_F248_F0.258191.155
331_E335_E0.255581.143
234_G256_I0.255081.141
46_V367_I0.254881.140
148_E170_T0.254251.137
221_E254_D0.252961.131
203_G365_L0.252451.129
155_E167_K0.24941.115
146_V165_V0.246111.101
344_A368_V0.245231.097
219_I223_Y0.24481.095
146_V167_K0.243511.089
149_Q209_A0.241841.081
145_Y166_R0.240071.074
337_I341_I0.239661.072
181_L185_L0.239071.069
149_Q211_D0.237421.062
91_L330_R0.236661.058
54_S58_D0.236561.058
186_E223_Y0.236251.056
351_L357_F0.234391.048
216_I227_L0.234241.047
221_E227_L0.231651.036
90_D329_G0.23161.036
106_G274_L0.231281.034
184_A187_K0.230771.032
181_L219_I0.2291.024
342_E346_Y0.226361.012
235_G263_W0.22631.012
229_V253_A0.224881.006
202_A213_L0.224781.005
185_L223_Y0.22371.000
166_R186_E0.222630.996
202_A251_E0.222330.994
202_A256_I0.222040.993
168_I180_A0.221620.991
168_I176_M0.22150.990
260_P266_V0.220370.985
84_V318_A0.219770.983
339_R342_E0.218150.975
86_R89_A0.21780.974
220_C224_N0.216780.969
123_A197_A0.216230.967
217_A229_V0.215160.962
347_L351_L0.214060.957
340_C366_N0.213770.956
347_L368_V0.213180.953
119_A255_S0.212850.952
145_Y185_L0.212620.951
342_E345_R0.210880.943
336_R340_C0.208590.933
309_T312_G0.207830.929
335_E338_R0.206520.923
213_L227_L0.20590.921
87_W329_G0.205260.918
270_C321_L0.204270.913
213_L253_A0.20420.913
348_A351_L0.203930.912
351_L370_F0.203430.910
169_P177_D0.202430.905
350_R354_D0.20210.904
151_H261_H0.201870.903
218_D221_E0.201230.900
116_N257_T0.198610.888
331_E334_R0.19810.886
92_F256_I0.197780.884
124_R160_I0.197590.884
88_L108_F0.196350.878
345_R348_A0.195760.875
149_Q170_T0.19370.866
248_F252_R0.193240.864
203_G234_G0.193150.864
45_F49_G0.193120.864
53_A56_L0.192810.862
56_L60_L0.192440.861
166_R188_D0.192140.859
123_A226_W0.191960.858
228_H255_S0.191540.857
164_G186_E0.191310.855
348_A368_V0.191040.854
112_G116_N0.189950.849
92_F274_L0.188810.844
183_K187_K0.188550.843
119_A273_L0.188270.842
277_D280_D0.187480.838
154_I199_V0.186490.834
346_Y349_D0.186350.833
254_D276_R0.185730.831
151_H262_K0.185510.830
158_A165_V0.18510.828
83_E326_K0.182440.816
53_A57_A0.182310.815
44_G47_P0.181010.809
144_I197_A0.179180.801
176_M181_L0.177940.796
332_G335_E0.177170.792
347_L350_R0.176260.788
120_L197_A0.175990.787
208_G271_G0.175750.786
121_L161_L0.175560.785
177_D181_L0.175430.784
113_T153_S0.175130.783
306_G309_T0.174010.778
352_R355_P0.173910.778
146_V150_A0.172550.772
144_I163_L0.17250.771
328_L336_R0.172430.771
90_D93_G0.172360.771
82_R86_R0.171790.768
352_R362_E0.171680.768
117_L160_I0.17160.767
95_P277_D0.171110.765
221_E224_N0.170980.765
111_G292_L0.170620.763
178_I182_E0.169980.760
61_A65_N0.16990.760
304_D307_D0.169480.758
226_W254_D0.169230.757
178_I212_P0.167910.751
197_A226_W0.167580.749
221_E225_I0.167020.747
178_I181_L0.166370.744
157_A161_L0.164990.738
217_A251_E0.164980.738
338_R341_I0.164890.737
351_L359_L0.164840.737
117_L121_L0.16430.735
317_R320_K0.164170.734
275_V281_L0.163180.730
318_A326_K0.162820.728
90_D330_R0.161790.723
175_R364_D0.161010.720
107_V273_L0.160780.719
263_W320_K0.160570.718
42_F47_P0.16040.717
155_E159_R0.160280.717
159_R167_K0.160240.717
87_W325_L0.159630.714
199_V228_H0.159230.712
343_L346_Y0.158650.709
266_V324_T0.158470.709
168_I181_L0.15820.707
145_Y168_I0.158040.707
201_T205_T0.157630.705
248_F256_I0.157510.704
198_V213_L0.157230.703
146_V199_V0.156630.700
256_I274_L0.156070.698
60_L320_K0.155930.697
152_Y312_G0.155430.695
257_T271_G0.155390.695
175_R362_E0.155070.693
306_G313_S0.153770.688
89_A105_G0.15350.686
232_A259_D0.152430.682
94_L105_G0.152180.680
323_A327_S0.15210.680
119_A197_A0.151710.678
54_S57_A0.151260.676
71_W82_R0.150430.673
267_P320_K0.15040.673
181_L184_A0.150180.672
45_F48_G0.150040.671
232_A271_G0.149970.671
181_L220_C0.149770.670
220_C223_Y0.149410.668
53_A323_A0.14920.667
330_R334_R0.148760.665
232_A262_K0.148690.665
360_V369_C0.148680.665
187_K223_Y0.148630.665
149_Q176_M0.148020.662
157_A160_I0.147870.661
228_H257_T0.147580.660
222_K353_K0.146650.656
95_P276_R0.14620.654
120_L124_R0.145970.653
185_L220_C0.145830.652
260_P272_V0.145580.651
114_E118_Y0.145490.651
121_L160_I0.145310.650
215_E219_I0.145110.649
246_L256_I0.144890.648
112_G257_T0.144360.646
42_F50_P0.143460.642
49_G52_P0.143340.641
54_S267_P0.143330.641
233_Y366_N0.143330.641
116_N119_A0.143230.640
269_G317_R0.143130.640
108_F272_V0.143080.640
178_I216_I0.143030.640
265_G328_L0.143010.639
65_N68_G0.142980.639
83_E87_W0.142890.639
336_R339_R0.142770.638
186_E222_K0.142680.638
258_I320_K0.142620.638
320_K323_A0.142240.636
217_A250_I0.142240.636
254_D280_D0.142010.635
115_A271_G0.141880.634
147_S170_T0.141740.634
149_Q207_T0.141690.634
112_G312_G0.140960.630
54_S323_A0.140940.630
252_R276_R0.140630.629
171_D180_A0.140510.628
226_W255_S0.140460.628
109_T271_G0.14020.627
95_P105_G0.139740.625
248_F251_E0.139330.623
74_S78_T0.139140.622
152_Y205_T0.13880.621
200_A229_V0.138480.619
252_R278_K0.138340.619
333_Y336_R0.138180.618
260_P316_F0.137860.616
329_G333_Y0.136860.612
61_A64_L0.136780.612
105_G277_D0.135080.604
335_E349_D0.13490.603
88_L264_L0.134880.603
245_H330_R0.13480.603
214_E335_E0.134670.602
328_L333_Y0.134670.602
115_A261_H0.133820.598
248_F253_A0.133660.598
348_A364_D0.133640.598
120_L144_I0.133620.598
184_A188_D0.13350.597
151_H259_D0.13230.592
65_N306_G0.132060.591
42_F46_V0.131480.588
144_I165_V0.131370.587
84_V322_W0.131230.587
66_Q77_A0.130770.585
352_R359_L0.130480.583
81_E108_F0.130430.583
147_S168_I0.130330.583
304_D308_Y0.130290.583
319_L322_W0.130150.582
45_F265_G0.129610.580
172_E179_E0.129440.579
69_F268_Y0.129430.579
229_V251_E0.129430.579
315_R319_L0.129280.578
122_A226_W0.12910.577
222_K335_E0.128870.576
182_E185_L0.128720.576
86_R96_E0.128290.574
322_W326_K0.128080.573
198_V227_L0.1280.572
83_E86_R0.127730.571
229_V256_I0.127530.570
226_W280_D0.127170.569
71_W74_S0.126890.567
114_E117_L0.126770.567
81_E318_A0.126750.567
47_P50_P0.126730.567
259_D270_C0.126520.566
173_D335_E0.12630.565
340_C343_L0.126180.564
200_A211_D0.125590.562
71_W81_E0.125320.560
116_N154_I0.12530.560
51_S324_T0.12530.560
202_A246_L0.124970.559
173_D364_D0.12490.559
176_M216_I0.124870.558
207_T369_C0.124720.558
209_A361_N0.124540.557
147_S201_T0.124020.555
305_Y308_Y0.124020.555
217_A220_C0.123770.553
104_A277_D0.123720.553
52_P265_G0.123710.553
115_A273_L0.123650.553
325_L329_G0.123510.552
151_H232_A0.12330.551
158_A167_K0.123030.550
279_S282_R0.122820.549
261_H292_L0.122640.548
307_D311_Q0.122180.546
95_P249_G0.121830.545
44_G49_G0.12180.545
156_K160_I0.121330.543
319_L323_A0.120820.540
123_A157_A0.120770.540
348_A362_E0.120730.540
88_L272_V0.12070.540
116_N199_V0.120630.539
145_Y181_L0.120580.539
347_L357_F0.120360.538
105_G281_L0.120340.538
218_D352_R0.120220.538
246_L252_R0.120040.537
156_K293_G0.120.537
226_W279_S0.119940.536
111_G291_Y0.119940.536
54_S332_G0.119880.536
87_W330_R0.119730.535
201_T206_N0.119610.535
174_G209_A0.119450.534
214_E251_E0.119280.533
169_P349_D0.119030.532
158_A253_A0.118850.531
208_G366_N0.118820.531
117_L265_G0.118140.528
260_P271_G0.118040.528
52_P56_L0.117850.527
51_S56_L0.117770.527
158_A163_L0.117620.526
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
3k40A0.9921000.235
4e1oA0.99461000.24
3vp6A0.98391000.248
1js3A11000.277
2jisA0.97861000.279
2okjA0.98391000.285
2qmaA0.97051000.306
2dgkA0.9331000.397
3hbxA0.93031000.426
3mc6A0.93031000.469

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