PMC

Synteny plots between T. fusca (horizontal axis) and five representative genomes of Actinobacteria: Streptomyces coelicolor, Nocardia farcinica, Mycobacterium tuberculosis, and Corynebacterium diphtheriae.

Phylogenetic tree of the cytochrome P450 monooxygenases from T. fusca and their closest homologs together with known hyperthermostable P450s. The multiple sequence alignment was made using ClustalX version 2.0.12. The phylogenetic tree was constructed by the neighbor-joining method and was schematically presented using the ClustalX output and MEGA version 4 (Tamura et al. ). Prefixes in front of the CYP number abbreviate the genus and species of the respective bacterial organism where the enzyme originates from (Tf T. fusca, Nd Nocardiopsis dassonvillei, Nf Nocardia farcinica, Sal Streptomyces albaduncus, Sco Streptomyces coelicolor, Sgr Streptomyces griseoflavus, Shy Streptomyces hygroscopicus, Ssp Streptomyces sp., Sso Sulfolobus solfataricus, Sto Sulfolobus tokodaii, Pt Picrophilus torridus, Tt Thermus thermophilus). P450s from T. fusca are shown in red; hyperthermostable P450s are given in blue. The bar in the lower left corner represents 0.1 amino acid substitutions per amino acid for the branch length

Multiple alignment of Rv0813c homologs. Secondary-structure elements are indicated for Rv0813c (above) and Atlg79260 (below). Invariant residues are in white (red background), and those conserved in at least 70% of the sequences are in red (boxed). Genes and species abbreviations: Rv0813, M. tuberculosis Rv0813c; Nf, Nocardia farcinica; Ml, Mycobacterium leprae; Ma, Mycobacterium avium subsp. paratuberculosis; Cj, Corynebacterium jeikeium; Cd, Corynebacterium diphtheriae; Ce, Corynebacterium efficiens; Cg, Corynebacterium glutamicum; Os, Oryza sativa; Pa, Propionibacterium acnes; Nsp, Nocardioides sp.; Tf, Thermobifida fusca; Sa, Streptomyces avermitilis; Sc, Streptomyces coelicolor; Fsp, Frankia sp.; Kr, Kineococcus radiotolerans; Asp, Arthrobacter sp.; Bl, Brevibacterium linens; Lx, Leifsonia xyli; Mtb, M. tuberculosis Rv2717c; At, Arabidopsis thaliana Atlg79260.

Sequence alignment and secondary structure prediction of Lsr2 proteins in various actinomycetes. The alignment was produced using the CLUSTALW program. The secondary structure was analyzed by using the Jpred program (http://www.compbio.dundee.ac.uk/∼www-jpred/). The arrows represent β-strands and ovals represent α-helices. Species abbreviations: M. tb., Mycobacterium tuberculosis; M. marinum, Mycobacterium marinum; M. ulcerans, Mycobacterium ulcerans; M. avium, Mycobacterium avium; M. paratb, Mycobacterium avium subsp. paratuberculosis; M. leprae, Mycobacterium leprae; M. flavescens, Mycobacterium flavescens; M. gilvum, Mycobacterium gilvum; M. vanbaalenii, Mycobacterium vanbaalenii; M. smegmatis, Mycobacterium smegmatis; M. abscessus, Mycobacterium abscessus; N. farcinica, Nocardia farcinica; R. RHA1, Rhodococcus sp. strain RHA1; S. erythraea, Saccharopolyspora erythraea; S. avermitilis, Streptomyces avermitilis; S. coelicolor, Streptomyces coelicolor; S. griseus, Streptomyces griseus subsp. griseus; J. HTCC, Janibacter sp. strain HTCC2649; A. aurescens, Arthrobacter aurescens; R. salmoninarum, Renibacterium salmoninarum; F. alni, Frankia alni; M. luteus, Micrococcus luteus; Cjw1, Mycobacterium phage Cjw1; C. sepedonicus, Clavibacter michiganensis subsp. sepedonicus; K. rhizophila, Kocuria rhizophila; T. fusca, Thermobifida fusca; Omega, Mycobacterium phage Omega. The H-NS of E. coli is included in the alignment (bottom), but only the predicted secondary structure of Lsr2 is shown.