GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
DIOX_N - non-haem dioxygenase in morphine synthesis N-terminal
Pfam: PF14226 (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: 116
Sequences: 3605
Seq/Len: 31.08
HH_delta: 0.078 (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
22_D26_E1.25383.919
5_D34_N1.21073.784
21_R25_E0.911122.848
59_E62_K0.909732.844
57_L61_Q0.907682.837
15_E19_Q0.823572.574
39_Q43_D0.802512.508
24_C30_F0.673292.104
70_R94_G0.586871.834
4_I16_V0.579691.812
38_P41_L0.542291.695
16_V19_Q0.537271.679
9_D12_D0.529011.654
44_R47_A0.526861.647
8_P12_D0.522081.632
40_E44_R0.51311.604
6_L32_L0.501961.569
14_E18_E0.497991.557
53_F89_E0.493991.544
48_A51_E0.485161.516
44_R48_A0.474291.482
50_R54_A0.464421.452
51_E54_A0.429211.342
18_E22_D0.428011.338
73_S78_E0.424271.326
56_P59_E0.424091.326
18_E21_R0.422281.320
23_A30_F0.414721.296
19_Q22_D0.4111.285
16_V20_L0.409821.281
47_A51_E0.408371.276
55_L59_E0.402641.259
8_P16_V0.402531.258
20_L30_F0.396411.239
61_Q72_Y0.394121.232
15_E18_E0.389131.216
88_K92_N0.386931.209
6_L34_N0.370321.158
52_F91_F0.368891.153
58_E61_Q0.368711.152
61_Q74_P0.360621.127
52_F55_L0.353491.105
52_F63_Y0.347121.085
17_A21_R0.340351.064
61_Q64_A0.332051.038
10_P13_R0.318890.997
46_F49_A0.316460.989
43_D47_A0.316120.988
46_F50_R0.313290.979
2_P27_W0.306440.958
79_S82_G0.302170.944
75_P78_E0.301820.943
11_A14_E0.296950.928
60_K89_E0.293020.916
2_P23_A0.286040.894
80_T92_N0.285970.894
59_E63_Y0.280430.877
14_E17_A0.279480.874
12_D15_E0.276880.865
42_I46_F0.26430.826
63_Y93_I0.263210.823
2_P5_D0.262220.820
52_F60_K0.261740.818
73_S90_S0.25970.812
21_R24_C0.256280.801
27_W87_W0.255540.799
6_L23_A0.25480.796
75_P90_S0.254690.796
4_I19_Q0.253510.792
37_I41_L0.252460.789
71_G86_D0.250280.782
74_P77_S0.249950.781
3_V31_Y0.249430.780
69_Y90_S0.245980.769
48_A54_A0.245670.768
73_S92_N0.244030.763
7_S34_N0.241520.755
29_F32_L0.239390.748
81_D90_S0.238690.746
23_A27_W0.237480.742
42_I45_V0.236560.739
78_E86_D0.234630.733
74_P78_E0.233620.730
69_Y88_K0.231540.724
9_D13_R0.23080.721
8_P15_E0.230440.720
57_L74_P0.230210.720
78_E88_K0.227370.711
88_K91_F0.226750.709
31_Y92_N0.226650.708
74_P90_S0.226370.708
41_L48_A0.225750.706
44_R51_E0.224930.703
53_F72_Y0.222990.697
53_F60_K0.221720.693
69_Y92_N0.2210.691
73_S88_K0.220510.689
47_A50_R0.220040.688
4_I20_L0.218140.682
86_D89_E0.216950.678
70_R96_D0.215120.672
15_E47_A0.209610.655
63_Y91_F0.20670.646
13_R16_V0.205040.641
41_L44_R0.204290.639
6_L36_G0.19890.622
73_S76_G0.198440.620
2_P6_L0.198130.619
45_V78_E0.19710.616
69_Y72_Y0.196820.615
77_S81_D0.196140.613
86_D92_N0.194870.609
7_S43_D0.193010.603
4_I23_A0.192170.601
4_I30_F0.191580.599
37_I42_I0.191190.598
35_H42_I0.187830.587
49_A52_F0.187520.586
55_L63_Y0.187240.585
5_D33_V0.187070.585
1_I78_E0.18690.584
32_L87_W0.186670.583
32_L42_I0.186430.583
10_P14_E0.184360.576
79_S84_K0.183570.574
45_V94_G0.183340.573
20_L23_A0.181490.567
27_W35_H0.180610.565
89_E93_I0.17960.561
65_R82_G0.179540.561
18_E44_R0.178560.558
77_S80_T0.17770.555
92_N96_D0.175720.549
3_V23_A0.175080.547
74_P87_W0.174490.545
75_P81_D0.173740.543
8_P20_L0.173440.542
69_Y80_T0.173350.542
73_S77_S0.173190.541
1_I30_F0.172620.540
79_S86_D0.172320.539
43_D51_E0.172190.538
39_Q51_E0.171950.537
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
3ooxA0.991499.90.078
1gp6A0.93199.90.134
1odmA0.939799.90.155
1w9yA0.879399.90.163
1dcsA0.870799.90.188
3on7A0.81999.80.277
2dbnA0.965580.60.856
1e4cP0.775945.50.885
2irpA0.56942.90.887
2fk5A0.663839.80.889

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