Abstract
The efficient sequencing techniques have significantly increased the number of genomes
that are now available, including the Crenarchaeon Sulfolobus solfataricus P2 genome. The
genome-scale metabolic pathways in Sulfolobus solfataricus P2 were predicted by
implementing the “Pathway Tools” software using MetaCyc database as reference knowledge
base. A Pathway/Genome Data Base (PGDB) specific for Sulfolobus solfataricus P2 was
created. A curation approach was carried out regarding all the amino acids biosynthetic
pathways. Experimental literatures as well as homology-, orthology- and context-based
protein function prediction methods were followed for the curation process. The
“PathoLogic” component of the “Pathway Tools” programme was able to predict many amino
acid biosynthetic metabolic pathways. The total number of the metabolic pathways was
modified to 168 pathways by adding extra pathways that have not been detected by the
“PathoLogic”. Amino acid biosynthetic pathways such as alpha-aminoadipic acid (AAA)
pathway of Lysine biosynthesis and Alanine biosynthesis as well as the super-pathway of
Phenylalanine, Tyrosine and Tryptophan biosynthesis variation II were added to the
Pathway/Genome data base of Sulfolobus solfataricus P2. Discovery of the missing enzymes
that have to fill in the metabolic holes in the pathways under study was the main curation task.
This approach and the curated amino acid biosynthetic pathways in the PGDB of Sulfolobus
solfataricus P2 can be used for genomic annotations and metabolic pathway reconstructions
of closely related Bacteria and Archaea.
that are now available, including the Crenarchaeon Sulfolobus solfataricus P2 genome. The
genome-scale metabolic pathways in Sulfolobus solfataricus P2 were predicted by
implementing the “Pathway Tools” software using MetaCyc database as reference knowledge
base. A Pathway/Genome Data Base (PGDB) specific for Sulfolobus solfataricus P2 was
created. A curation approach was carried out regarding all the amino acids biosynthetic
pathways. Experimental literatures as well as homology-, orthology- and context-based
protein function prediction methods were followed for the curation process. The
“PathoLogic” component of the “Pathway Tools” programme was able to predict many amino
acid biosynthetic metabolic pathways. The total number of the metabolic pathways was
modified to 168 pathways by adding extra pathways that have not been detected by the
“PathoLogic”. Amino acid biosynthetic pathways such as alpha-aminoadipic acid (AAA)
pathway of Lysine biosynthesis and Alanine biosynthesis as well as the super-pathway of
Phenylalanine, Tyrosine and Tryptophan biosynthesis variation II were added to the
Pathway/Genome data base of Sulfolobus solfataricus P2. Discovery of the missing enzymes
that have to fill in the metabolic holes in the pathways under study was the main curation task.
This approach and the curated amino acid biosynthetic pathways in the PGDB of Sulfolobus
solfataricus P2 can be used for genomic annotations and metabolic pathway reconstructions
of closely related Bacteria and Archaea.
Keywords
Amino acid biosynthesis
Crenarchaeon
Metabolic pathways reconstruction
Pathway Tools
Protein function prediction.