GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
2OG-FeII_Oxy_3 - 2OG-Fe(II) oxygenase superfamily
Pfam: PF13640 (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: CL0029
Length: 100
Sequences: 4027
Seq/Len: 40.27
HH_delta: 0.176 (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
40_E89_G1.025612.950
45_E82_G0.889772.560
67_K70_R0.88772.554
43_E84_T0.795012.287
83_V92_R0.771072.218
14_P82_G0.762622.194
5_R93_Y0.748382.153
28_L97_F0.710132.043
28_L71_L0.703472.024
31_Y66_P0.698982.011
30_L71_L0.686161.974
5_R91_R0.627231.804
34_D68_P0.606481.745
34_D67_K0.571311.643
26_V73_I0.570571.641
44_L83_V0.569821.639
7_P91_R0.566681.630
41_G86_V0.554091.594
45_E84_T0.552261.589
86_V90_G0.549481.581
45_E58_E0.527271.517
47_Y82_G0.522491.503
40_E88_E0.47741.373
14_P47_Y0.471691.357
7_P10_G0.468161.347
30_L69_G0.461791.328
43_E60_E0.460851.326
24_R98_W0.457631.316
29_L74_F0.427641.230
4_N94_S0.415641.196
4_N29_L0.40041.152
14_P80_L0.383431.103
81_H92_R0.37751.086
8_P89_G0.376311.083
15_H81_H0.372381.071
19_S23_H0.35851.031
14_P45_E0.356121.024
83_V86_V0.350221.007
28_L73_I0.348051.001
31_Y72_V0.346380.996
43_E58_E0.338640.974
36_E90_G0.335860.966
12_F17_D0.329950.949
13_G19_S0.323410.930
27_T76_S0.321450.925
33_N93_Y0.320130.921
16_T80_L0.318540.916
75_P78_N0.316020.909
6_Y12_F0.3150.906
40_E90_G0.314150.904
19_S22_P0.309240.890
4_N98_W0.304210.875
24_R96_T0.300650.865
35_P68_P0.296990.854
27_T98_W0.292490.841
60_E66_P0.291890.840
29_L94_S0.291480.839
83_V94_S0.289390.832
12_F27_T0.286770.825
18_N27_T0.284960.820
11_F82_G0.28440.818
60_E67_K0.278160.800
29_L96_T0.271090.780
57_R60_E0.268210.772
48_P55_V0.266930.768
41_G83_V0.265720.764
26_V75_P0.257720.741
17_D81_H0.256120.737
92_R96_T0.254760.733
42_G66_P0.252860.727
4_N27_T0.24950.718
48_P57_R0.247350.712
76_S79_S0.247020.711
24_R29_L0.246480.709
55_V58_E0.246290.709
74_F96_T0.246240.708
3_L93_Y0.243980.702
22_P93_Y0.241290.694
55_V59_V0.237310.683
18_N22_P0.2340.673
18_N80_L0.233720.672
55_V60_E0.232050.668
25_R78_N0.231720.667
58_E84_T0.230430.663
12_F76_S0.230290.662
13_G20_Y0.230170.662
75_P79_S0.230080.662
12_F98_W0.22970.661
6_Y10_G0.228950.659
11_F18_N0.227320.654
88_E91_R0.226420.651
16_T21_D0.22420.645
18_N78_N0.22340.643
17_D41_G0.222350.640
11_F85_P0.222230.639
76_S96_T0.222060.639
44_L94_S0.217870.627
15_H92_R0.217370.625
4_N10_G0.215830.621
36_E89_G0.214660.618
24_R46_F0.213870.615
18_N21_D0.213720.615
6_Y17_D0.21250.611
20_Y80_L0.211820.609
76_S92_R0.211560.609
54_D59_V0.211480.608
4_N19_S0.209920.604
42_G86_V0.20960.603
11_F84_T0.208350.599
43_E46_F0.208130.599
70_R84_T0.207210.596
3_L96_T0.20620.593
47_Y80_L0.205660.592
33_N91_R0.20560.591
49_S57_R0.205590.591
6_Y15_H0.205220.590
56_S60_E0.204630.589
54_D57_R0.204610.589
54_D68_P0.20320.585
25_R75_P0.201390.579
56_S59_V0.201360.579
26_V78_N0.200760.578
54_D58_E0.200640.577
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
3dkqA0.8899.60.176
4bqyA0.999.60.179
2hbtA0.999.50.198
3kt7A0.9799.50.218
2jigA0.9699.50.228
3itqA0.8599.50.229
2rg4A0.9299.40.263
2a1xA0.9798.40.515
2fctA0.9798.30.535
2opwA0.9798.30.537

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