PMC:3368417 / 10207-12924
Annnotations
{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/3368417","sourcedb":"PMC","sourceid":"3368417","source_url":"http://www.ncbi.nlm.nih.gov/pmc/3368417","text":"Genome properties\nThe genome consists of a circular chromosome (6,346,587 bp) and two circular plasmids, pHAU01 (339,639 bp) and pHAU02 (88,204 bp), respectively with an overall G+C content of 50.9% (Table 3, Figure 3, Figure 4, Figure 5 and Figure 6). These are the only plasmids that have been identified to date among the seventeen Chloroflexi strains whose genomes have been sequenced. Interestingly, the GC content of the chromosome (50.7%) is notably lower than that of pHAU01 (53.7%) or pHAU02 (53.1%). Plasmid pHAU02 is predicted to encode 71 proteins, and pHAU01 is predicted to encode 231 potential proteins, which included a variety of transposases, phage recombinases and integrases, a CRISPR and CRISPR-associated gene cluster, and a variety of predicted transcription regulators. Neither plasmid encodes a product known to be essential for cell viability. Of the 5,654 genes predicted, 5,577 were protein-coding genes, and 77 encoded RNAs; 82 pseudogenes were identified. The majority of the protein-coding genes (67.4%) were assigned a putative function while the remaining ones were annotated as hypothetical proteins. The distribution of genes into COGs functional categories is presented in Table 4.\nTable 3 Genome Statistics\nFigure 3 Graphical circular map of the chromosome (not drawn to scale with plasmids). From outside to the center: Genes on forward strand (color by COG categories), Genes on reverse strand (color by COG categories), RNA genes (tRNAs green, rRNAs red, other RNAs black), GC content, GC skew.\nFigure 4 Graphical circular map of the plasmid pHAU01. From outside to the center: Genes on forward strand (color by COG categories), Genes on reverse strand (color by COG categories), RNA genes (tRNAs green, rRNAs red, other RNAs black), GC content, GC skew.\nFigure 5 Graphical circular map of the plasmid pHAU02 (not drawn to scale with chromosome). From outside to the center: Genes on forward strand (color by COG categories), Genes on reverse strand (color by COG categories), RNA genes (tRNAs green, rRNAs red, other RNAs black), GC content, GC skew.\nFigure 6 Chromosome of H. aurantiacus strain 114-95T oriented to the dnaA gene (top). The inner ring shows a normalized plot of GC skew, while the center ring shows a normalized plot of GC content. The outer circle shows the distribution of secondary metabolite gene clusters. Biosynthetic gene clusters associated with thiotemplate-based assembly (PKS, NRPS) are depicted in red and bacteriocin loci are marked in black.\nTable 4 Number of genes associated with the general COG functional categories * manual annotation yielded 6.4% genes in the secondary metabolites biosynthesis, transport and catabolism category.\n\n","divisions":[{"label":"Title","span":{"begin":0,"end":17}},{"label":"Table caption","span":{"begin":1218,"end":1246}},{"label":"Title","span":{"begin":1227,"end":1244}},{"label":"Figure caption","span":{"begin":1245,"end":1538}},{"label":"Figure caption","span":{"begin":1537,"end":1799}},{"label":"Figure caption","span":{"begin":1798,"end":2097}},{"label":"Figure caption","span":{"begin":2096,"end":2520}},{"label":"Table caption","span":{"begin":2519,"end":2716}},{"label":"Title","span":{"begin":2528,"end":2597}}],"tracks":[{"project":"MicrobeTaxon","denotations":[{"id":"T112","span":{"begin":2120,"end":2149},"obj":"65"}],"namespaces":[{"prefix":"_base","uri":"http://purl.bioontology.org/ontology/NCBITAXON/"}],"attributes":[{"subj":"T112","pred":"source","obj":"MicrobeTaxon"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"MicrobeTaxon","color":"#c9ec93","default":true}]}]}}