Assembly and annotation of the P. aeruginosa strain CCBH4851 genome - Curated versions
Assembly: The assembly was done using the hybrid assembler MaSuRCA (http://www.genome.umd.edu/masurca.html). The inputs were reads from Illumina (300 cycles and 500 cycles) and PacBio platforms. The combination of Illumina and PacBio reads generated a single contig that, after careful analysis, was adopted to represent the genome of the CCBH4851 strain.
Annotation: The annotation was made using a set of protocols. First, annotation of genes exhibiting homology with PAO1 (NC_002516), PA7790 (NZ_CP014999), PA11803 (NZ_CP015003) strains was transferred to CCBH4851 using the RATT program (http://ratt.sourceforge.net). Predictions were made with the GenemarkS (http://exon.gatech.edu/GeneMark) and Glimmer (https://ccb.jhu.edu/software/glimmer) programs, and the ORFs that were left unmarked were submitted to BLASTp searches and were annotated accordingly. Predictions for rRNA and tRNA were also made with the RNAmmer programs (http://www.cbs.dtu.dk/services/RNAmmer) and tRNAscan-SE (http://lowelab.ucsc.edu/tRNAscan-SE ), respectively. Discrepant annotations, e.g. ORFs detected or transferred in the same region but with different transcription directions, were analyzed individually and manually, through BLASTp searches and queries to conserved protein domain databases, taking into account the most significant results (identity, greater number of homologues, conserved domains, experimental evidence) and also the genetic context depending on the known function of neighboring genes. Finally, to designate an EC number for annotated proteins, the PRIAM program (http://priam.prabi.fr/REL_MAR15/index_mar15.html) was used and only EC numbers detected with probability greater than 0.9 were assigned to the respective proteins.
* Locus_tag nomenclature may change after submission to NCBI.
Metabolic Network Model of P.aeruginosa CCBH4851
Metabolic Network v2: This SBML model of the metabolic network of P. aeruginosa CCBH4851 was generated by the NETGen system. This system performs genomic scale reconstructions having the genome annotation and a reference model as inputs. For the reconstruction of the metabolic network of P.aeruginosa CCBH4851, the metabolic network model of P.aeruginosa strain PAO1, published in 2017, was used as reference. The P.aeruginosa CCBH4851 metabolic network is represented as a SBML Level 3 file, and this second version encompasses 1139 genes, 1450 reactions,1280 metabolites and 576 EC numbers. The biomass reaction flux generated in the FBA simulation of this metabolic network model is 12.470973 mmol/gDCW/h.
Knowledge base - Metabolic Network v2: The knowledge base is a database created in MySQL to support and store the data of all reconstructions executed by NETGen. This knowledge base has a relational structure containing information of the following entities: reconstructions, organisms, genomes, genes, proteins, reactions, GPRs relations, enzymes and metabolites. A snapshot of this database, generated after the reconstruction of the P.aeruginosa CCBH4851 metabolic network model v2, is available as an Excel spreadsheet.
Metabolic Network v3: This SBML model of the metabolic network of P. aeruginosa CCBH4851 is a curated version of the metabolic network v2 . This P.aeruginosa CCBH4851 metabolic network is represented as a SBML Level 3 file, and the biomass reaction flux generated in the FBA simulation of this metabolic network model is 1.036524 mmol/gDCW/h.