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Figure 3 | BMC Microbiology

Figure 3

From: Novel aromatic ring-hydroxylating dioxygenase genes from coastal marine sediments of Patagonia

Figure 3

Phylogenetic analysis of the deduced amino acid sequences of ARHD genes found in the libraries. The tree was constructed by using the neighbor-joining method in MEGA 3.1 [57] using clone sequences and related proteins, corresponding to positions 45–192 of NahAc in P. putida NCIB 9816-4. Bootstrap values were calculated as percentage of 1000 replicates, and values greater than 50% are shown at branching points. The scale bar represents 0.1 inferred amino acid changes per position. Branches containing sequences found in this study are indicated with a rectangle, with shading indicating novel ARHD gene types. The sequence abbreviations (protein name and strain number), species and accession numbers from GenBank are as follows: BphA IAM 12620: Porphyrobacter sanguineus IAM 12620 [BAB55875]; PhnA1a CHY-1: Sphingomonas sp. CHY-1 [CAG17576]; BphA1f B1: Sphingomonas yanoikuyae B1 [ABM91740]; PhnA1 A5: Cycloclasticus sp. A5 [BAC81541]; PhnAc AFK2 type: includes PhnAc A. faecalis AFK2 [BAA76323], PhnAc Burkholderia sp. Eh1-1 [AAQ84686], PhnAc Burkholderia sp. Cs1-4 [AAQ84685], PhnAc Burkholderia sp. Ch3-5 [AAQ84684] and sequences from this work; ArhA1 A4: Sphingomonas sp. A4 [BAD34447]; PhnAc RP007: Burkholderia sp. RP007 [AAD09872]; NagAc type: includes NagAc Ralstonia sp. U2 [AAD12610], NbzAc Comamonas sp. JS765 [AAL76202], NtdAc Acidovorax sp. JS42 [AAB40383]; NahAc type: includes NahAc P. putida NCIB 9816-4 [AAO64274], NahAc P. putida G7 [BAE92156], NahAc Pseudomonas sp. ND6 [AAP44288] and sequences from this work; CarAa CB3: Sphingomonas sp. CB3 [AAC38616]; XylC1 RB1: Cycloclasticus oligotrophus RB1 [AAC44161]; BphAa RHA1: Rhodococcus sp. RHA1 [YP707265]; CumA1 IP01: Pseudomonas fluorescens IP01 [BAA07074]; BphA1 B4: Pseudomonas sp. B4 [CAB93965]; BphA LB400: Burkholderia sp. LB400 [AAB63425]; NidA PYR-1: Mycobacterium vanbaalenii PYR-1 [AAT51751]; PhtA1 DBF63: Terrabacter sp. DBF63 [BAC54156]; NarA NCIMB12038: Rhodococcus sp. NCIMB 12038 [AAD28100]; NidA I24: Rhodococcus sp. I24 [AAD25395]; PhdA KP7: Nocardioides sp. KP7 [BAA94708]; DitA BKME-9: Pseudomonas abietaniphila BKME-9 [AAD21063]; DbfA1 DBF63: Terrabacter sp. DBF63 [BAB55886]; XylX pWW0: P. putida pWW0 [AAA26047]; XylX B1: Sphingomonas yanoikuyae B1 [ABM79785]. The arrow corresponds to sequences CarAa CA10: Pseudomonas resinovorans CA10 [BAB32766] and Pht3 NMH102-2: Pseudomonas putida NMH102-2 [BAA02511].

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