GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
PALP - Pyridoxal-phosphate dependent enzyme
Pfam: PF00291 (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. )
Length: 306
Sequences: 11795
Seq/Len: 38.55
HH_delta: 0.127 (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
75_A82_C2.008654.494
25_N299_R1.570123.513
263_E267_R1.444673.232
12_R25_N1.410263.155
156_I301_V1.312722.937
256_E285_K1.263222.826
50_R54_K1.255842.810
92_P96_K1.248682.794
81_K104_E1.207642.702
58_T83_T1.184462.650
7_P158_E1.143152.558
118_D121_E1.138322.547
88_E109_P1.128862.526
52_K80_L1.123632.514
146_I150_A1.10962.483
201_E253_S1.104222.471
253_S256_E1.097732.456
149_Y187_E1.040522.328
27_Y299_R1.039792.326
83_T104_E1.031922.309
49_S78_L1.030572.306
202_G254_D1.026692.297
279_A302_V0.982592.198
121_E125_E0.937722.098
10_L301_V0.929132.079
122_L125_E0.862081.929
154_L184_G0.85951.923
168_V185_L0.856911.917
264_L272_V0.843321.887
172_V197_G0.838581.876
7_P159_Q0.836421.871
260_A281_A0.835471.869
12_R27_Y0.835011.868
83_T106_I0.831881.861
198_V282_A0.815441.825
63_S68_G0.81121.815
182_A195_V0.802111.795
168_V181_I0.801281.793
58_T81_K0.790071.768
149_Y183_A0.780161.746
52_K78_L0.776861.738
23_G296_A0.7761.736
165_P196_I0.773761.731
263_E284_L0.769531.722
281_A285_K0.765771.713
45_Y49_S0.761361.704
36_T73_Y0.750131.678
27_Y160_L0.739641.655
50_R144_N0.712271.594
183_A238_D0.702371.572
255_E259_E0.695021.555
153_G184_G0.692271.549
28_L304_L0.691061.546
256_E281_A0.686841.537
250_V282_A0.686171.535
120_Q124_K0.674411.509
92_P95_L0.657511.471
260_A280_L0.653071.461
153_G185_L0.642791.438
227_L278_A0.641831.436
89_D110_G0.635311.421
96_K99_R0.631481.413
260_A284_L0.629221.408
153_G181_I0.628891.407
259_E263_E0.627561.404
250_V285_K0.626851.403
201_E251_G0.619941.387
118_D122_L0.619761.387
85_V122_L0.618791.385
264_L280_L0.616081.378
252_V281_A0.615451.377
262_R266_E0.613991.374
117_D121_E0.605541.355
49_S53_E0.605181.354
244_E289_R0.588281.316
50_R53_E0.583011.304
99_R104_E0.579151.296
95_L107_L0.575851.288
59_V75_A0.573271.283
285_K288_E0.571961.280
124_K128_E0.569511.274
169_V198_V0.56721.269
256_E259_E0.562571.259
178_A195_V0.559691.252
68_G98_M0.557591.248
182_A245_Y0.556431.245
125_E129_L0.555471.243
48_L59_V0.554821.241
204_D251_G0.548761.228
46_Y150_A0.542161.213
272_V304_L0.529291.184
207_Y251_G0.526121.177
169_V286_L0.52441.173
11_V30_R0.52391.172
95_L105_V0.523851.172
160_L301_V0.521881.168
207_Y249_V0.519471.162
185_L193_V0.51841.160
13_L28_L0.514631.151
196_I250_V0.509661.140
114_G118_D0.50931.140
88_E113_E0.507791.136
86_V107_L0.504521.129
276_S304_L0.499491.118
121_E124_K0.499441.117
95_L99_R0.495161.108
157_Y190_L0.493191.103
181_I303_V0.491281.099
98_M103_A0.48971.096
240_E244_E0.485811.087
187_E190_L0.482121.079
24_A298_K0.481591.078
122_L126_R0.479711.073
10_L160_L0.475651.064
148_G152_I0.471111.054
265_A271_L0.471011.054
150_A154_L0.470621.053
165_P194_R0.468841.049
204_D207_Y0.46561.042
164_D298_K0.464651.040
172_V178_A0.463421.037
182_A241_L0.462521.035
280_L302_V0.461591.033
239_L242_I0.461321.032
178_A197_G0.459411.028
260_A263_E0.457941.025
18_L22_G0.456741.022
147_A150_A0.455841.020
286_L289_R0.455111.018
157_Y184_G0.454551.017
184_G190_L0.452531.013
86_V98_M0.45221.012
116_F120_Q0.451321.010
25_N297_G0.450111.007
73_Y101_L0.45011.007
48_L78_L0.447451.001
156_I181_I0.446610.999
169_V283_A0.445680.997
9_P33_L0.445210.996
13_L280_L0.442370.990
179_A236_E0.440560.986
284_L288_E0.440170.985
178_A242_I0.439930.984
106_I122_L0.439610.984
272_V276_S0.439430.983
47_L142_N0.436830.977
46_Y49_S0.436550.977
154_L158_E0.435540.974
50_R143_P0.433910.971
61_G84_I0.430860.964
17_L20_E0.430250.963
88_E110_G0.429990.962
183_A187_E0.428660.959
19_S22_G0.427950.958
26_I283_A0.427580.957
44_A70_A0.425760.953
149_Y184_G0.422760.946
119_A123_A0.419050.938
17_L267_R0.417460.934
46_Y50_R0.417460.934
184_G187_E0.416830.933
8_T34_N0.416570.932
48_L74_A0.414610.928
169_V196_I0.414310.927
261_I277_A0.41420.927
157_Y160_L0.413140.924
168_V303_V0.410470.918
290_G298_K0.408440.914
280_L304_L0.408050.913
76_A82_C0.405410.907
240_E243_D0.405070.906
164_D299_R0.40130.898
71_L82_C0.401020.897
160_L299_R0.39910.893
197_G249_V0.398910.893
24_A297_G0.398580.892
29_K155_E0.394840.883
179_A183_A0.394650.883
44_A74_A0.394580.883
283_A302_V0.394050.882
30_R304_L0.393740.881
276_S305_T0.390090.873
196_I286_L0.389280.871
181_I185_L0.385370.862
46_Y147_A0.384350.860
171_P305_T0.38410.859
12_R18_L0.383290.858
194_R298_K0.381410.853
258_L274_P0.380710.852
114_G117_D0.379720.850
279_A305_T0.378380.847
225_A257_A0.37420.837
213_G243_D0.371620.831
20_E23_G0.369110.826
28_L302_V0.365820.819
116_F119_A0.36050.807
30_R33_L0.360480.807
165_P300_V0.358960.803
8_T42_R0.358640.802
165_P298_K0.357890.801
141_N236_E0.355670.796
234_P237_L0.354430.793
285_K289_R0.354240.793
31_E42_R0.353720.791
287_A290_G0.352590.789
85_V106_I0.351180.786
21_L288_E0.349060.781
111_D114_G0.34860.780
17_L22_G0.348420.780
10_L156_I0.347220.777
152_I303_V0.346110.774
69_R97_Q0.34580.774
96_K100_A0.344760.771
146_I149_Y0.344230.770
286_L290_G0.34390.769
142_N145_V0.341250.764
11_V270_I0.339750.760
109_P114_G0.339130.759
154_L190_L0.338990.758
146_I183_A0.338680.758
145_V149_Y0.338620.758
59_V82_C0.337250.755
69_R98_M0.336510.753
76_A101_L0.336110.752
257_A278_A0.333820.747
115_A118_D0.332670.744
42_R155_E0.331210.741
72_A103_A0.330950.740
123_A126_R0.330850.740
82_C103_A0.329630.738
55_G80_L0.326150.730
73_Y77_R0.325370.728
194_R244_E0.322440.721
117_D120_Q0.322130.721
259_E266_E0.321440.719
56_G81_K0.321120.718
252_V282_A0.320860.718
264_L304_L0.320830.718
206_L249_V0.320450.717
59_V80_L0.318870.713
250_V289_R0.318550.713
75_A80_L0.318090.712
165_P286_L0.317820.711
165_P301_V0.316970.709
261_I274_P0.316520.708
282_A286_L0.316510.708
152_I156_I0.315430.706
198_V250_V0.315090.705
58_T125_E0.314670.704
169_V282_A0.313590.702
28_L264_L0.313420.701
120_Q123_A0.312210.699
72_A98_M0.311870.698
70_A74_A0.311850.698
160_L165_P0.311730.697
264_L268_E0.310850.696
129_L132_P0.310410.695
170_V181_I0.30920.692
6_G35_P0.309080.692
181_I195_V0.309010.691
86_V95_L0.30890.691
57_R81_K0.30850.690
162_K299_R0.306590.686
84_I98_M0.305780.684
52_K55_G0.304580.681
200_P227_L0.303940.680
168_V195_V0.302990.678
223_T228_G0.302230.676
65_G68_G0.301960.676
29_K42_R0.301640.675
196_I244_E0.300930.673
227_L275_S0.299890.671
28_L280_L0.299130.669
43_G47_L0.298490.668
163_P299_R0.297980.667
8_T29_K0.297260.665
237_L240_E0.296630.664
83_T127_A0.296540.663
152_I177_T0.295950.662
20_E267_R0.295730.662
147_A151_T0.294110.658
155_E159_Q0.293510.657
171_P279_A0.292730.655
36_T101_L0.292410.654
206_L242_I0.292010.653
31_E34_N0.291480.652
24_A300_V0.291270.652
198_V278_A0.290750.651
206_L234_P0.288930.646
236_E240_E0.288590.646
36_T70_A0.288220.645
141_N144_N0.288080.645
19_S23_G0.287730.644
163_P301_V0.287470.643
41_D73_Y0.287310.643
147_A183_A0.28640.641
24_A287_A0.286240.640
12_R19_S0.285810.639
146_I241_L0.285570.639
35_P41_D0.285090.638
62_A87_P0.284170.636
152_I181_I0.283350.634
224_I258_L0.282280.632
272_V280_L0.281680.630
144_N148_G0.281040.629
239_L243_D0.27950.625
241_L245_Y0.279130.625
223_T254_D0.278670.624
85_V125_E0.27860.623
21_L267_R0.278160.622
68_G84_I0.277090.620
18_L21_L0.27690.620
205_P230_P0.275130.616
117_D124_K0.274810.615
97_Q100_A0.274060.613
225_A228_G0.273520.612
85_V108_V0.273340.612
257_A277_A0.273270.611
162_K193_V0.272630.610
18_L23_G0.272340.609
6_G34_N0.271360.607
187_E191_P0.270320.605
25_N162_K0.270280.605
157_Y161_G0.269710.603
21_L263_E0.269360.603
253_S285_K0.267660.599
252_V257_A0.267460.598
196_I282_A0.267340.598
17_L268_E0.266510.596
264_L270_I0.265590.594
66_N70_A0.265090.593
83_T126_R0.26310.589
176_G180_G0.262850.588
39_F177_T0.262340.587
99_R107_L0.261890.586
110_G114_G0.261680.585
199_E205_P0.260480.583
160_L163_P0.260450.583
24_A296_A0.260430.583
114_G121_E0.260120.582
276_S302_V0.259390.580
283_A287_A0.259390.580
10_L159_Q0.259220.580
157_Y185_L0.258830.579
54_K143_P0.258690.579
276_S279_A0.258350.578
272_V277_A0.257360.576
186_K192_P0.256340.574
108_V118_D0.256160.573
127_A130_L0.255990.573
64_S226_G0.255480.572
254_D257_A0.255470.572
302_V305_T0.25530.571
168_V301_V0.255020.571
265_A268_E0.254940.570
28_L270_I0.254180.569
158_E161_G0.253450.567
23_G297_G0.252840.566
97_Q101_L0.252830.566
202_G222_S0.252250.564
60_V127_A0.251970.564
10_L27_Y0.250720.561
226_G275_S0.250330.560
286_L300_V0.249360.558
48_L80_L0.249240.558
43_G145_V0.24920.558
84_I103_A0.248850.557
57_R132_P0.248350.556
46_Y146_I0.248040.555
282_A285_K0.247220.553
47_L145_V0.246150.551
172_V249_V0.24550.549
39_F303_V0.24480.548
100_A271_L0.24460.547
259_E262_R0.244130.546
11_V32_D0.24410.546
47_L144_N0.243790.545
238_D241_L0.243320.544
254_D258_L0.243280.544
60_V126_R0.243220.544
60_V85_V0.243110.544
163_P193_V0.241870.541
156_I163_P0.241210.540
131_S142_N0.241110.539
169_V300_V0.241110.539
172_V206_L0.240020.537
273_E306_G0.239430.536
39_F43_G0.239370.536
168_V193_V0.239260.535
55_G58_T0.238740.534
156_I303_V0.23780.532
34_N41_D0.23660.529
154_L187_E0.236410.529
32_D272_V0.235820.528
179_A238_D0.235440.527
185_L195_V0.234750.525
43_G67_H0.234710.525
85_V118_D0.234370.524
61_G71_L0.234080.524
154_L157_Y0.233820.523
20_E263_E0.233780.523
37_G101_L0.233760.523
86_V90_V0.23350.522
104_E126_R0.233220.522
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
1tdjA0.94771000.127
2gn0A0.94771000.128
3l6bA0.94771000.131
1p5jA0.96081000.132
4h27A0.96411000.133
1v71A0.94121000.139
3ss7X0.97061000.141
3iauA0.94771000.141
2rkbA0.95751000.152
2d1fA0.94771000.152

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