Automated reconstruction and manual curation of amino acid biosynthesis pathways in Sulfolobus solfataricus P2
Author
Source
Ibn al-Haitham Journal for Pure and Applied Science
Issue
Vol. 32, Issue 3 (31 Dec. 2019), pp.1-18, 18 p.
Publisher
University of Baghdad College of Education for Pure Science / Ibn al-Haitham
Publication Date
2019-12-31
Country of Publication
Iraq
No. of Pages
18
Main Subjects
Topics
Abstract EN
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.
American Psychological Association (APA)
Khayyat, Barzan Ibrahim. 2019. Automated reconstruction and manual curation of amino acid biosynthesis pathways in Sulfolobus solfataricus P2. Ibn al-Haitham Journal for Pure and Applied Science،Vol. 32, no. 3, pp.1-18.
https://search.emarefa.net/detail/BIM-899929
Modern Language Association (MLA)
Khayyat, Barzan Ibrahim. Automated reconstruction and manual curation of amino acid biosynthesis pathways in Sulfolobus solfataricus P2. Ibn al-Haitham Journal for Pure and Applied Science Vol. 32, no. 3 (Dec. 2019), pp.1-18.
https://search.emarefa.net/detail/BIM-899929
American Medical Association (AMA)
Khayyat, Barzan Ibrahim. Automated reconstruction and manual curation of amino acid biosynthesis pathways in Sulfolobus solfataricus P2. Ibn al-Haitham Journal for Pure and Applied Science. 2019. Vol. 32, no. 3, pp.1-18.
https://search.emarefa.net/detail/BIM-899929
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references : p. 16-18
Record ID
BIM-899929