GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Orn_Arg_deC_N - Pyridoxal-dependent decarboxylase pyridoxal binding domain
Pfam: PF02784 (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: CL0036
Length: 251
Sequences: 4018
Seq/Len: 16.01
HH_delta: 0.119 (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
208_V250_A0.912213.931
99_E149_R0.835323.599
109_R156_R0.745073.210
55_E81_E0.721823.110
79_L101_L0.67162.894
22_K239_K0.595782.567
10_R42_E0.594532.562
80_E104_L0.576912.486
80_E107_E0.572262.466
102_A153_L0.561762.420
6_I42_E0.559522.411
81_E85_N0.559432.410
76_D103_E0.551442.376
158_V198_E0.496542.139
144_E187_E0.485832.093
156_R198_E0.463681.998
84_E108_A0.461911.990
58_L85_N0.455921.964
179_E226_A0.450391.941
6_I41_E0.445311.919
12_A247_Y0.4431.909
48_V54_L0.441251.901
95_L146_A0.425961.835
46_F57_A0.419011.805
29_A249_V0.415661.791
39_L248_L0.414261.785
4_R8_R0.412821.779
102_A106_P0.409861.766
80_E84_E0.407461.756
76_D100_R0.406021.749
9_I44_C0.403791.740
79_L90_I0.401691.731
40_A62_F0.401151.728
2_L6_I0.399321.721
46_F62_F0.392091.689
182_L186_E0.38831.673
148_E192_L0.383071.651
162_F181_L0.375481.618
74_K97_E0.37271.606
27_V46_F0.372431.605
5_I249_V0.36721.582
51_P55_E0.365311.574
6_I10_R0.364081.569
109_R158_V0.362671.563
3_D7_E0.359751.550
92_V101_L0.359171.548
111_G199_F0.355231.531
144_E192_L0.354961.529
189_K195_E0.353931.525
150_A157_L0.353121.522
149_R152_E0.351611.515
95_L141_E0.351041.513
9_I39_L0.348741.503
55_E59_K0.347411.497
175_R225_E0.347171.496
83_I104_L0.346191.492
58_L64_P0.34531.488
224_R228_K0.343971.482
4_R7_E0.341291.471
13_W17_L0.33941.462
145_E148_E0.333851.438
89_T199_F0.328061.414
217_E221_E0.323331.393
149_R153_L0.320071.379
79_L104_L0.318741.373
25_Y29_A0.31611.362
175_R222_V0.31571.360
215_D218_E0.314831.357
90_I101_L0.307931.327
51_P78_E0.304711.313
179_E183_D0.295861.275
24_F241_I0.293011.263
14_K18_P0.291791.257
137_I146_A0.290561.252
139_I187_E0.289931.249
37_K41_E0.289031.245
68_I201_D0.288521.243
34_A37_K0.287861.240
39_L44_C0.286681.235
138_D141_E0.284891.228
80_E108_A0.284681.227
202_I242_I0.283781.223
6_I38_I0.283131.220
95_L145_E0.283041.220
103_E107_E0.281611.213
147_L157_L0.281071.211
57_A67_I0.276671.192
11_A217_E0.27541.187
162_F202_I0.272451.174
222_V225_E0.270371.165
63_P66_R0.268291.156
175_R179_E0.268061.155
185_A200_I0.266021.146
5_I39_L0.265261.143
227_L240_L0.265171.143
82_A90_I0.263051.133
92_V110_V0.262241.130
76_D104_L0.260641.123
172_E176_Q0.260461.122
163_H244_P0.259621.119
24_F45_G0.257291.109
35_V249_V0.256671.106
221_E225_E0.255521.101
160_L200_I0.253091.091
22_K66_R0.251911.085
10_R14_K0.250511.079
2_L38_I0.249271.074
24_F68_I0.248211.069
218_E221_E0.247531.067
7_E11_A0.247191.065
92_V98_L0.24641.062
171_A222_V0.245611.058
123_H128_T0.244981.056
164_V177_A0.244971.056
8_R11_A0.244361.053
98_L150_A0.241871.042
83_I101_L0.240991.038
95_L99_E0.239491.032
187_E191_E0.238761.029
98_L153_L0.234221.009
45_G66_R0.234221.009
33_P59_K0.231370.997
99_E153_L0.230980.995
9_I42_E0.229870.990
38_I42_E0.228810.986
98_L110_V0.228550.985
51_P81_E0.227090.978
72_P93_D0.226980.978
19_Y224_R0.224510.967
81_E84_E0.223510.963
150_A153_L0.223220.962
58_L67_I0.22320.962
8_R247_Y0.222310.958
36_L56_L0.22180.956
27_V36_L0.221680.955
64_P67_I0.220950.952
5_I8_R0.220480.950
76_D80_E0.219510.946
99_E103_E0.216360.932
148_E152_E0.215320.928
95_L149_R0.214860.926
69_F87_V0.212320.915
9_I13_W0.21210.914
77_E80_E0.212050.914
105_A108_A0.212040.914
122_S126_I0.210690.908
144_E148_E0.210060.905
102_A154_G0.209370.902
22_K241_I0.209230.902
38_I41_E0.209160.901
174_F219_Y0.208880.900
175_R226_A0.207780.895
88_A239_K0.207610.895
173_A176_Q0.207470.894
111_G159_G0.207080.892
119_G122_S0.205810.887
26_A29_A0.205480.885
33_P56_L0.20480.882
179_E229_E0.203150.875
68_I91_N0.202310.872
31_P36_L0.202230.871
110_V155_L0.200770.865
30_N35_V0.199830.861
27_V31_P0.198940.857
5_I9_I0.198440.855
200_I227_L0.195270.841
51_P77_E0.1950.840
69_F78_E0.194980.840
61_G64_P0.194770.839
191_E195_E0.192480.829
162_F177_A0.190930.823
176_Q179_E0.189890.818
69_F82_A0.189820.818
160_L185_A0.189050.815
95_L137_I0.188710.813
70_T91_N0.188320.811
143_A184_L0.18540.799
198_E239_K0.185080.797
170_D173_A0.185040.797
54_L82_A0.183960.793
5_I38_I0.183960.793
47_D70_T0.183930.793
194_F197_L0.183470.791
180_R183_D0.183430.790
178_I226_A0.182230.785
206_F214_Y0.182140.785
214_Y219_Y0.181690.783
218_E222_V0.180310.777
70_T201_D0.180130.776
216_L220_A0.180080.776
176_Q180_R0.179230.772
185_A197_L0.179230.772
207_G246_R0.176660.761
47_D134_K0.175410.756
40_A66_R0.175210.755
104_L107_E0.174810.753
124_P127_S0.172950.745
40_A46_F0.172650.744
49_A72_P0.171170.738
162_F178_I0.171130.737
145_E149_R0.171040.737
102_A105_A0.170950.737
141_E145_E0.170720.736
18_P224_R0.170530.735
150_A155_L0.170530.735
19_Y228_K0.169730.731
178_I223_I0.169640.731
226_A229_E0.169090.729
163_H166_S0.169070.728
134_K163_H0.168820.727
183_D187_E0.16860.726
128_T134_K0.167890.723
89_T109_R0.166860.719
47_D50_S0.166650.718
23_I44_C0.166450.717
148_E151_K0.166130.716
25_Y50_S0.165950.715
161_H201_D0.165710.714
16_F220_A0.164540.709
104_L108_A0.164490.709
139_I144_E0.164130.707
26_A47_D0.163960.706
144_E191_E0.163440.704
195_E198_E0.163390.704
225_E228_K0.162710.701
50_S53_E0.162530.700
75_S78_E0.162250.699
225_E229_E0.162170.699
26_A161_H0.161910.698
27_V57_A0.161540.696
178_I202_I0.161180.694
137_I143_A0.161150.694
180_R184_L0.160810.693
77_E81_E0.160070.690
13_W16_F0.159520.687
76_D107_E0.158620.683
57_A62_F0.158590.683
14_K217_E0.158350.682
157_L194_F0.157910.680
10_R248_L0.157440.678
83_I105_A0.157270.678
49_A71_G0.156790.676
74_K101_L0.156460.674
28_K163_H0.156260.673
106_P154_G0.155730.671
36_L62_F0.154820.667
86_G109_R0.154410.665
97_E100_R0.154410.665
133_S161_H0.154040.664
7_E10_R0.153890.663
47_D68_I0.153830.663
13_W21_V0.153820.663
57_A60_A0.153560.662
25_Y30_N0.15310.660
134_K246_R0.152290.656
222_V226_A0.152270.656
209_P215_D0.151880.654
166_S177_A0.15180.654
171_A218_E0.151530.653
160_L181_L0.150130.647
92_V112_L0.150.646
91_N111_G0.149970.646
199_F241_I0.149570.644
101_L110_V0.149350.644
28_K113_R0.149040.642
111_G161_H0.148410.639
49_A70_T0.148320.639
25_Y36_L0.148190.639
169_L207_G0.148080.638
116_P119_G0.14750.636
11_A14_K0.147380.635
203_G245_G0.147250.634
71_G74_K0.145960.629
22_K45_G0.145840.628
89_T158_V0.145740.628
185_A189_K0.145580.627
10_R13_W0.145530.627
83_I108_A0.145290.626
62_F67_I0.145160.625
175_R218_E0.145010.625
62_F66_R0.144780.624
52_G55_E0.144450.622
152_E229_E0.144420.622
181_L200_I0.144370.622
111_G115_N0.144290.622
71_G75_S0.14420.621
47_D72_P0.14380.620
157_L197_L0.14380.620
125_K128_T0.143710.619
214_Y222_V0.143140.617
8_R216_L0.143020.616
5_I214_Y0.143020.616
9_I248_L0.142830.615
10_R41_E0.142340.613
49_A91_N0.141590.610
5_I35_V0.141120.608
58_L84_E0.141110.608
14_K17_L0.140990.607
69_F91_N0.140560.606
36_L46_F0.140450.605
90_I108_A0.140450.605
199_F239_K0.139660.602
73_G78_E0.13950.601
31_P49_A0.139470.601
145_E152_E0.139390.601
83_I90_I0.139140.600
70_T133_S0.138890.598
228_K237_G0.138720.598
93_D134_K0.137580.593
33_P37_K0.137380.592
26_A167_Q0.137230.591
37_K40_A0.137220.591
171_A175_R0.13710.591
112_L147_L0.136930.590
100_R103_E0.136460.588
140_E221_E0.136250.587
151_K194_F0.13590.586
200_I240_L0.135530.584
53_E163_H0.134930.581
41_E229_E0.134760.581
227_L239_K0.134620.580
160_L194_F0.134250.578
70_T111_G0.134120.578
223_I238_P0.13370.576
24_F66_R0.133660.576
55_E85_N0.133580.576
27_V56_L0.133240.574
101_L105_A0.132790.572
31_P56_L0.132740.572
170_D213_E0.132560.571
113_R243_E0.131890.568
5_I12_A0.13150.567
72_P135_F0.131490.567
175_R229_E0.131270.566
12_A206_F0.130910.564
73_G93_D0.13090.564
48_V69_F0.130850.564
102_A156_R0.130560.563
172_E175_R0.130530.562
163_H177_A0.130280.561
93_D97_E0.130140.561
40_A60_A0.129990.560
50_S69_F0.129470.558
121_G170_D0.129460.558
123_H126_I0.128430.553
206_F219_Y0.128370.553
114_I139_I0.128260.553
114_I184_L0.128120.552
76_D79_L0.127920.551
111_G158_V0.126690.546
25_Y31_P0.126630.546
5_I13_W0.12650.545
11_A216_L0.126410.545
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
4aibA0.93231000.119
3vabA0.96411000.125
3n2bA0.96811000.129
7odcA0.95221000.136
3nzqA0.98411000.137
3nzpA0.98011000.137
3n2oA0.98411000.139
3mt1A0.91241000.172
3n29A0.90841000.178
2o0tA0.9881000.187

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