GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
Pyridox_oxase_2 - Pyridoxamine 5-phosphate oxidase
Pfam: PF12766 (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: 100
Sequences: 4372
Seq/Len: 43.72
HH_delta: 0.142 (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
26_A37_V1.225692.902
34_S76_R1.187062.811
24_Q37_V1.147292.716
77_V96_A1.002222.373
27_T69_Q0.958662.270
29_D32_D0.930442.203
23_F79_L0.851032.015
25_L77_V0.834281.975
28_V74_N0.798681.891
36_R69_Q0.784721.858
24_Q82_W0.736311.743
70_L96_A0.734151.738
37_V80_V0.715911.695
76_R95_R0.701441.661
71_A98_I0.649721.538
31_P73_A0.635481.505
60_T66_K0.615331.457
13_K18_H0.605821.434
46_D55_L0.594591.408
24_Q39_T0.593471.405
29_D34_S0.571931.354
28_V35_P0.571191.352
78_E91_R0.565851.340
38_R69_Q0.563051.333
70_L77_V0.557851.321
36_R93_R0.553091.310
40_V58_F0.551011.305
62_A98_I0.547651.297
78_E93_R0.51161.211
27_T70_L0.501721.188
17_S81_F0.500551.185
25_L70_L0.4931.167
37_V78_E0.487611.154
36_R65_P0.455441.078
24_Q80_V0.454041.075
58_F94_G0.452761.072
34_S93_R0.448441.062
47_P55_L0.44371.051
42_L81_F0.440841.044
75_P95_R0.433921.027
79_L92_I0.433191.026
67_V71_A0.430351.019
25_L66_K0.427391.012
65_P69_Q0.424051.004
60_T67_V0.422741.001
40_V66_K0.414590.982
22_Y41_V0.411380.974
42_L79_L0.392750.930
12_L90_F0.387090.916
26_A35_P0.385580.913
83_F88_E0.384910.911
42_L56_L0.383520.908
11_A14_K0.380640.901
56_L79_L0.375340.889
59_H64_S0.373960.885
68_A71_A0.362870.859
26_A78_E0.3620.857
18_H45_F0.360180.853
81_F90_F0.354910.840
65_P93_R0.347450.823
28_V34_S0.346460.820
68_A73_A0.338890.802
23_F58_F0.338630.802
23_F42_L0.336630.797
83_F86_T0.328320.777
14_K19_P0.328150.777
16_R20_F0.318260.754
41_V61_D0.3110.736
62_A67_V0.310550.735
75_P97_S0.310450.735
48_D55_L0.299330.709
38_R60_T0.299310.709
29_D93_R0.29760.705
28_V33_G0.292190.692
34_S74_N0.292020.691
29_D36_R0.289110.685
39_T82_W0.284780.674
27_T38_R0.280270.664
28_V73_A0.280210.663
77_V94_G0.277860.658
41_V60_T0.275270.652
28_V76_R0.27430.649
18_H84_P0.273310.647
37_V91_R0.271810.644
63_R67_V0.271310.642
61_D64_S0.268220.635
28_V31_P0.267720.634
33_G76_R0.267460.633
57_T99_I0.265930.630
44_G57_T0.264680.627
48_D95_R0.262550.622
20_F83_F0.259180.614
33_G73_A0.259180.614
56_L92_I0.258660.612
74_N94_G0.258270.611
18_H85_E0.257770.610
42_L45_F0.257220.609
20_F42_L0.255380.605
36_R78_E0.255150.604
38_R89_Q0.254370.602
80_V91_R0.253110.599
13_K47_P0.252760.598
63_R68_A0.248310.588
22_Y84_P0.247870.587
21_R41_V0.247590.586
16_R85_E0.246840.584
70_L75_P0.244050.578
13_K48_D0.242870.575
23_F81_F0.242370.574
22_Y82_W0.239210.566
64_S89_Q0.238940.566
71_A75_P0.238590.565
36_R91_R0.2380.563
29_D69_Q0.237810.563
80_V89_Q0.237530.562
45_F55_L0.236650.560
39_T80_V0.23660.560
11_A88_E0.236380.560
62_A71_A0.23570.558
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
1dnlA0.9199.60.142
2i51A0.9399.60.147
1nrgA0.9299.50.183
1ty9A0.8899.50.19
2ou5A0.9199.50.191
2re7A0.999.50.198
2i02A0.9299.50.199
3u35A0.9199.50.214
1ci0A0.9299.50.215
3f7eA0.8699.40.219

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