plosone-phylo
Figure 3
Unrooted phylogenetic tree obtained from a crystal structure-based sequence alignment of 25 α-subunits of related Rieske Oxygenases.Bootstrap values out of 100 replicates are indicated. The proteins are abbreviated using the gene name and strain as follows: biphenyl dioxygenase from Pandoraea pnomenusa B-356 (BphAB356, GenPeptID: AAC44526), Burkholderia xenovorans LB400 (BphALB400, GenPeptID: YP_556409), Rhodococcus globerulus P6 (BphA1P6, GenPeptID: CAA56346), Rhodococcus jostii RHA1 (BphA1RHA1, GenPeptID: BAA06868), and Sphingobium yanoikuyae B1 (BphA1fB1, GenPeptID: ABM91740); benzene dioxygenase from Pseudomonas putida ML2 (BedC1ML2, GenPeptID: Q07944); benzoate dioxygenase from P. putida F1 (BnzAF1, GenPeptID: A5W4F2); cumene dioxygenase from Pseudomonas fluorescens IP01 (CumA1IP01, GenPeptID: BAA07074); dibenzofuran dioxygenase from Terrabacter sp. YK3 (DfdA1YK3, GenPeptID: BAC06602); diterpenoid dioxygenase from Pseudomonas abietaniphila BKME (DitABKME, GenPeptID: AAD21063); dinitrotoluene dioxygenase from Burkholderia cepacia R34 (DntAcR34, GenPeptID: AAL50021); dibenzo-p-dioxin dioxygenase from Sphignomonas (DxnA1RW1, GenPeptID: CAA51365); ethylbenzene dioxygenase from R jostii RHA1 (EbdA1RHA1, GenPeptID: BAC92718); 3-phenylpropionate dioxygenase from E. coli K-12 (HcaEK12, GenPeptID: ACB03690); naphthalene dioxygenase from Rhodococcus sp. NCIMB 12038 (NarA12038, GenPeptID: AAD28100) and Pseudomonas putida 9816-4 (NdoB9816, GenPeptID: P0A110); nitrobenzene dioxygenase from Comomonas sp. JS765 (NbzA JS765, GenPeptID: AAL76202); polyaromatic hydrocarbon dioxygenase from Mycobacterium vanbaalenii PYR-1(NidAPYR1, GenPeptID: AAF75991, NidA3PYR1, GenPeptID: AAY85176) and Burkholderia sp. RP007 (PhnAcRP07, GenPeptID: AAD09872); phthalate dioxygenase from R. jostii RHA1 (PadAaRHA1, GenPeptID: ABG99212) and Terrabacter sp. DBF63 (PhtADBF63, GenPeptID: BAC54156); phenanthrene dioxygenase from Nocardioides sp. KP7 (PhdAKP7, GenPeptID: BAA94708) and Sphingomonas sp. CHY1 (PhnA1CHY1, GenPeptID: CAG17576); and tetraline dioxygenase from Sphingomonas macrogoltabidus TFA (ThnA1TFA, GenPeptID: AAN26443). Proteins for which the crystal structure was used for alignment are indicated in bold text in the figure.
Figure 3
Unrooted phylogenetic tree obtained from a crystal structure-based sequence alignment of 25 α-subunits of related Rieske Oxygenases.Bootstrap values out of 100 replicates are indicated. The proteins are abbreviated using the gene name and strain as follows: biphenyl dioxygenase from Pandoraea pnomenusa B-356 (BphAB356, GenPeptID: AAC44526), Burkholderia xenovorans LB400 (BphALB400, GenPeptID: YP_556409), Rhodococcus globerulus P6 (BphA1P6, GenPeptID: CAA56346), Rhodococcus jostii RHA1 (BphA1RHA1, GenPeptID: BAA06868), and Sphingobium yanoikuyae B1 (BphA1fB1, GenPeptID: ABM91740); benzene dioxygenase from Pseudomonas putida ML2 (BedC1ML2, GenPeptID: Q07944); benzoate dioxygenase from P. putida F1 (BnzAF1, GenPeptID: A5W4F2); cumene dioxygenase from Pseudomonas fluorescens IP01 (CumA1IP01, GenPeptID: BAA07074); dibenzofuran dioxygenase from Terrabacter sp. YK3 (DfdA1YK3, GenPeptID: BAC06602); diterpenoid dioxygenase from Pseudomonas abietaniphila BKME (DitABKME, GenPeptID: AAD21063); dinitrotoluene dioxygenase from Burkholderia cepacia R34 (DntAcR34, GenPeptID: AAL50021); dibenzo-p-dioxin dioxygenase from Sphignomonas (DxnA1RW1, GenPeptID: CAA51365); ethylbenzene dioxygenase from R jostii RHA1 (EbdA1RHA1, GenPeptID: BAC92718); 3-phenylpropionate dioxygenase from E. coli K-12 (HcaEK12, GenPeptID: ACB03690); naphthalene dioxygenase from Rhodococcus sp. NCIMB 12038 (NarA12038, GenPeptID: AAD28100) and Pseudomonas putida 9816-4 (NdoB9816, GenPeptID: P0A110); nitrobenzene dioxygenase from Comomonas sp. JS765 (NbzA JS765, GenPeptID: AAL76202); polyaromatic hydrocarbon dioxygenase from Mycobacterium vanbaalenii PYR-1(NidAPYR1, GenPeptID: AAF75991, NidA3PYR1, GenPeptID: AAY85176) and Burkholderia sp. RP007 (PhnAcRP07, GenPeptID: AAD09872); phthalate dioxygenase from R. jostii RHA1 (PadAaRHA1, GenPeptID: ABG99212) and Terrabacter sp. DBF63 (PhtADBF63, GenPeptID: BAC54156); phenanthrene dioxygenase from Nocardioides sp. KP7 (PhdAKP7, GenPeptID: BAA94708) and Sphingomonas sp. CHY1 (PhnA1CHY1, GenPeptID: CAG17576); and tetraline dioxygenase from Sphingomonas macrogoltabidus TFA (ThnA1TFA, GenPeptID: AAN26443). Proteins for which the crystal structure was used for alignment are indicated in bold text in the figure.