GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
2OG-FeII_Oxy - 2OG-Fe(II) oxygenase superfamily
Pfam: PF03171 (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: 98
Sequences: 4347
Seq/Len: 44.36
HH_delta: -0.049 (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
41_Q50_D1.293144.281
8_R88_E0.784132.596
41_Q80_R0.68922.282
8_R90_Y0.66732.209
64_D76_A0.66652.206
67_E72_G0.658772.181
43_R78_L0.608452.014
54_P57_G0.605692.005
62_F74_Y0.580491.922
81_V89_R0.512071.695
22_T78_L0.512031.695
35_D38_G0.497761.648
31_I58_F0.479611.588
24_D97_R0.475161.573
22_T64_D0.473611.568
36_E86_E0.465891.542
36_E87_G0.422841.400
29_L96_L0.40951.356
41_Q82_V0.407861.350
33_F58_F0.402461.332
5_R19_G0.389451.289
44_D47_E0.370331.226
20_P80_R0.362541.200
3_Q6_L0.360251.193
81_V91_S0.353781.171
40_L81_V0.351231.163
10_P88_E0.344221.140
90_Y93_T0.340371.127
49_V52_P0.335441.110
5_R18_I0.335071.109
18_I27_G0.333871.105
51_V54_P0.333131.103
53_P56_G0.332491.101
84_P87_G0.332081.099
9_Y21_H0.330721.095
28_L65_A0.325531.078
7_N93_T0.324811.075
24_D27_G0.320841.062
28_L69_L0.319991.059
51_V59_I0.319271.057
7_N18_I0.318471.054
27_G97_R0.317611.051
34_Q38_G0.314021.040
7_N90_Y0.308951.023
15_G83_P0.306911.016
4_L94_F0.305411.011
20_P78_L0.304021.006
32_L93_T0.298940.990
23_D30_T0.29860.989
37_V87_G0.291180.964
28_L66_L0.288550.955
38_G52_P0.287510.952
68_I71_N0.283320.938
18_I97_R0.282220.934
24_D65_A0.280090.927
9_Y23_D0.27810.921
27_G30_T0.277580.919
5_R24_D0.269880.893
40_L91_S0.268910.890
24_D77_T0.267980.887
32_L61_N0.267270.885
22_T67_E0.263780.873
4_L92_L0.261530.866
43_R46_G0.261180.865
69_L72_G0.258430.856
38_G50_D0.257980.854
53_P59_I0.257150.851
31_I60_V0.257060.851
48_W80_R0.25630.848
30_T81_V0.251730.833
79_H89_R0.251650.833
52_P55_P0.250370.829
10_P17_G0.249490.826
49_V53_P0.24640.816
16_V20_P0.243540.806
27_G67_E0.241890.801
32_L91_S0.240430.796
70_T74_Y0.23980.794
38_G87_G0.239710.794
40_L43_R0.238970.791
20_P43_R0.234440.776
24_D68_I0.233810.774
84_P94_F0.232710.770
15_G84_P0.230760.764
57_G62_F0.228970.758
34_Q59_I0.22820.755
27_G95_F0.228010.755
37_V83_P0.227250.752
53_P58_F0.226780.751
40_L59_I0.22460.744
5_R20_P0.222890.738
18_I95_F0.220690.731
17_G84_P0.220250.729
44_D78_L0.218290.723
36_E84_P0.218180.722
44_D49_V0.217870.721
56_G61_N0.217850.721
38_G53_P0.215440.713
67_E75_P0.215010.712
28_L33_F0.214760.711
7_N91_S0.213910.708
72_G75_P0.213280.706
41_Q55_P0.212280.703
4_L20_P0.211460.700
90_Y94_F0.211220.699
62_F66_L0.20930.693
16_V82_V0.208530.690
68_I96_L0.206350.683
61_N64_D0.205430.680
16_V88_E0.204970.679
47_E50_D0.204950.679
29_L60_V0.20480.678
5_R95_F0.202490.670
43_R47_E0.201880.668
20_P48_W0.201470.667
34_Q91_S0.200330.663
14_N47_E0.199810.661
3_Q28_L0.198840.658
21_H79_H0.197860.655
3_Q96_L0.197540.654
6_L90_Y0.196510.651
73_R86_E0.195380.647
89_R93_T0.19530.647
17_G80_R0.195270.646
45_D75_P0.194280.643
66_L70_T0.193940.642
51_V61_N0.192810.638
32_L60_V0.192810.638
30_T97_R0.191870.635
81_V95_F0.19070.631
76_A79_H0.19060.631
55_P86_E0.189620.628
55_P58_F0.189420.627
33_F92_L0.188670.625
68_I72_G0.187120.619
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
1gp6A0.979699.9-0.049
1w9yA0.979699.9-0.039
3on7A0.979699.8-0.014
3ooxA0.979699.8-0.007
1dcsA0.979699.8-0.003
1odmA0.959299.8-0.003
3itqA0.918498.90.46
2jigA0.938898.90.472
3dkqA0.846998.80.483
4bqyA0.867398.30.57

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