GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Pyrid_oxidase_2 - Pyridoxamine 5-phosphate oxidase
Pfam: PF13883 (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: CL0336
Length: 170
Sequences: 2513
Seq/Len: 14.78
HH_delta: 0.214 (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
108_E145_R0.914133.972
23_S37_G0.790253.434
108_E147_E0.761953.311
74_V146_L0.656522.853
53_R145_R0.629892.737
24_T67_N0.584812.541
106_R149_E0.567852.467
21_T37_G0.565782.458
105_G146_L0.516262.243
14_L78_I0.478762.080
12_T16_Q0.451031.960
54_P76_L0.44021.913
42_Y78_I0.436691.897
74_V107_A0.402441.749
103_L151_V0.399481.736
68_L107_A0.386351.679
109_P144_Y0.372211.617
34_Y73_R0.368441.601
21_T77_T0.367581.597
119_R123_L0.35981.563
10_A153_L0.357261.552
37_G75_S0.348881.516
73_R106_R0.341921.486
106_R147_E0.341.477
38_S64_H0.335491.458
53_R147_E0.332311.444
20_G42_Y0.330021.434
21_T79_S0.327221.422
13_L17_S0.322851.403
104_T150_R0.321781.398
9_L12_T0.319971.390
107_A146_L0.31891.386
20_G76_L0.294671.280
17_S42_Y0.293391.275
25_L35_P0.292361.270
56_F144_Y0.288341.253
109_P142_F0.286991.247
8_E12_T0.285741.242
24_T64_H0.279921.216
68_L74_V0.273981.190
58_L65_T0.264721.150
49_D52_G0.262671.141
76_L146_L0.259841.129
103_L146_L0.252721.098
57_L98_C0.250161.087
80_E99_P0.246861.073
25_L71_D0.245991.069
23_S77_T0.244981.064
39_V102_T0.242891.055
51_T147_E0.241091.048
78_I103_L0.236751.029
117_A121_A0.236391.027
61_L140_D0.23621.026
14_L103_L0.233321.014
43_A118_A0.228430.993
17_S78_I0.227070.987
24_T74_V0.224720.976
39_V100_R0.224690.976
60_P142_F0.224160.974
25_L33_G0.222030.965
9_L13_L0.220540.958
55_I145_R0.21850.949
11_R52_G0.217960.947
13_L99_P0.217250.944
58_L144_Y0.216150.939
26_S34_Y0.215750.937
10_A151_V0.215060.934
59_S62_A0.213540.928
42_Y76_L0.21350.928
15_H48_C0.213160.926
11_R15_H0.211160.917
75_S102_T0.211160.917
69_K72_P0.210770.916
24_T38_S0.208350.905
118_A122_Y0.206710.898
26_S67_N0.206480.897
38_S56_F0.205610.893
119_R134_P0.205220.892
10_A101_V0.203930.886
37_G77_T0.203410.884
73_R104_T0.203260.883
42_Y56_F0.201320.875
52_G148_I0.199970.869
63_Q104_T0.199920.869
103_L148_I0.197680.859
65_T144_Y0.197270.857
19_W82_Q0.196210.853
39_V77_T0.195080.848
40_V56_F0.193490.841
33_G67_N0.191790.833
59_S154_V0.190990.830
34_Y71_D0.190320.827
120_A124_S0.189930.825
23_S75_S0.187740.816
112_P115_A0.18720.813
20_G78_I0.186740.811
115_A143_F0.186180.809
38_S102_T0.186030.808
40_V58_L0.185740.807
22_L64_H0.185370.805
56_F146_L0.185270.805
59_S140_D0.185050.804
60_P69_K0.184780.803
107_A144_Y0.184510.802
22_L40_V0.184160.800
69_K109_P0.183860.799
22_L74_V0.183360.797
43_A125_R0.182090.791
43_A121_A0.180930.786
110_V145_R0.180110.783
75_S104_T0.174980.760
57_L62_A0.174940.760
59_S141_F0.171950.747
34_Y104_T0.16960.737
18_R82_Q0.169450.736
66_R69_K0.169360.736
19_W98_C0.168380.732
66_R150_R0.1660.721
49_D53_R0.16560.720
34_Y149_E0.164650.715
19_W79_S0.163460.710
120_A130_K0.163080.709
41_S64_H0.162080.704
77_T102_T0.161270.701
97_A144_Y0.161250.701
111_P116_A0.161110.700
118_A121_A0.161070.700
13_L153_L0.160810.699
118_A125_R0.16040.697
132_W135_F0.16030.696
110_V114_E0.160190.696
60_P111_P0.159330.692
116_A120_A0.158880.690
76_L103_L0.157630.685
127_P132_W0.157420.684
62_A100_R0.15740.684
69_K142_F0.157050.682
56_F65_T0.155910.677
8_E11_R0.15530.675
65_T142_F0.154990.673
118_A123_L0.154690.672
78_I101_V0.154440.671
56_F107_A0.152420.662
122_Y143_F0.151840.660
139_H142_F0.151750.659
36_F64_H0.151260.657
114_E117_A0.150650.655
83_G97_A0.150170.652
101_V153_L0.149890.651
18_R97_A0.149580.650
27_T70_A0.148680.646
13_L80_E0.148380.645
57_L141_F0.148050.643
27_T33_G0.147650.642
50_S121_A0.147630.641
13_L41_S0.147280.640
148_I151_V0.146930.638
121_A124_S0.146910.638
56_F105_G0.146880.638
84_G97_A0.146630.637
82_Q99_P0.146190.635
76_L148_I0.144670.629
113_D117_A0.143840.625
27_T106_R0.14360.624
114_E145_R0.143160.622
54_P57_L0.142870.621
38_S100_R0.142490.619
73_R149_E0.142070.617
14_L101_V0.141870.616
60_P139_H0.141440.615
131_H134_P0.14140.614
122_Y126_H0.141270.614
57_L100_R0.140640.611
117_A120_A0.140250.609
111_P114_E0.139540.606
119_R122_Y0.139460.606
36_F67_N0.138790.603
22_L26_S0.138770.603
60_P140_D0.138170.600
123_L127_P0.137930.599
72_P106_R0.137880.599
58_L64_H0.137840.599
48_C54_P0.137270.596
70_A113_D0.137190.596
14_L17_S0.137050.595
38_S67_N0.136980.595
65_T68_L0.136350.592
16_Q80_E0.135990.591
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
1xhnA0.958899.90.214
3dnhA0.882499.90.226
2arzA0.894199.90.256
3swjA0.888299.90.286
3gasA0.888299.90.315
1vl7A0.829499.80.356
2vpaA0.929499.80.395
2ol5A0.917699.80.397
2furA0.923599.80.405
2fg9A0.905999.80.411

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