GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
2OG-FeII_Oxy_4 - 2OG-Fe(II) oxygenase superfamily
Pfam: PF13661 (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: 70
Sequences: 1142
Seq/Len: 16.31
HH_delta: 0.336 (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_W63_D0.408222.073
14_R39_R0.369821.878
58_G62_F0.313731.593
48_N54_D0.307551.561
20_R35_S0.297421.510
19_R22_D0.292661.486
15_F18_Y0.287191.458
22_D26_W0.275871.401
15_F47_L0.273811.390
16_Y24_F0.248241.260
15_F28_V0.24561.247
25_G31_D0.233071.183
16_Y31_D0.22311.133
20_R37_K0.219911.116
17_R22_D0.219841.116
44_L55_F0.21871.110
58_G61_F0.216851.101
12_N32_P0.215261.093
56_G59_E0.212281.078
31_D38_R0.207761.055
26_W43_L0.206431.048
42_T46_Y0.205941.046
14_R18_Y0.204561.039
43_L65_D0.202891.030
30_A33_S0.200221.017
23_F34_S0.197971.005
53_E56_G0.197151.001
16_Y44_L0.195880.994
37_K45_L0.194010.985
11_P26_W0.187820.954
28_V41_L0.185840.944
35_S41_L0.183770.933
24_F33_S0.182050.924
21_G45_L0.181640.922
12_N33_S0.181340.921
12_N16_Y0.179670.912
43_L63_D0.178920.908
33_S43_L0.17850.906
22_D41_L0.176910.898
30_A37_K0.175740.892
11_P38_R0.175640.892
33_S39_R0.175580.891
35_S56_G0.174140.884
25_G44_L0.17380.882
16_Y43_L0.173630.882
32_P35_S0.173470.881
24_F31_D0.173190.879
19_R48_N0.171710.872
23_F30_A0.171070.869
58_G63_D0.170810.867
23_F35_S0.170310.865
35_S43_L0.169320.860
12_N56_G0.168030.853
53_E59_E0.167460.850
42_T45_L0.164890.837
38_R43_L0.164310.834
53_E65_D0.164170.833
34_S40_F0.163380.829
20_R65_D0.161810.822
14_R24_F0.160930.817
20_R48_N0.160270.814
59_E62_F0.15880.806
32_P45_L0.158620.805
31_D37_K0.157490.800
32_P64_D0.156630.795
42_T58_G0.156510.795
34_S37_K0.155780.791
11_P60_L0.153490.779
21_G39_R0.152450.774
20_R34_S0.150660.765
11_P18_Y0.148860.756
26_W34_S0.148160.752
41_L48_N0.148120.752
25_G40_F0.147680.750
24_F42_T0.147070.747
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
2jigA0.9429990.336
3itqA0.9429990.348
3dkqA0.971498.90.363
4bqyA0.957198.80.382
2hbtA0.957198.80.389
3kt7A0.914398.70.406
2rg4A0.8429960.682
2rdqA0.942958.90.811
2opwA0.957153.20.817
3emrA0.957151.70.819

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