Database Authors
Carol A Fulcher1, Suzanne Paley1, Ron Caspi1, Anamika Kothari1, Markus Krummenacker1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated by the PathoLogic [Karp10, Dale10, Caspi14] component of Pathway Tools software version 20.0 and MetaCyc version 19.6 on 27-Jan-2016 16:20:15.

The primary data source for this dataset was the full genome sequence of Corynebacterium glutamicum ATCC 13032, derived from Genbank entry BA000036.3 [Ikeda03].

The PGDB, which integrates the biochemical reaction network and metabolic pathways of the organism with its genome, was improved by limited manual curation.

Genome
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
Chromosome3,1803,0998103,309,401NCBI BioProject:PRJNA307
Ortholog data available?Yes
Database Contents
Genes3,180
Pathways261
Enzymatic Reactions1,319
Transport Reactions99
Polypeptides3,100
Protein Complexes71
Enzymes790
Transporters292
Compounds1,055
Transcription Units2,833
tRNAs60
Protein Features3,397
GO Terms24,008
Database Version29.0
Sequence SourceIkeda03
Synonyms Corynebacterium glutamicum strain ATCC 13032
Corynebacterium glutamicum ATCC 13032
Corynebacterium glutamicum ATCC 13032Ikeda03
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Mycobacteriales
Corynebacteriaceae
Corynebacterium
Corynebacterium glutamicum
Corynebacterium glutamicum ATCC 13032
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
NCBI BioProjectPRJNA307
NCBI-Taxonomy196627
Relationship to Oxygenfacultative
Trophic Levelheterotroph
Temperature Rangemesophile
Biotic Relationshipfree-living
NCBI Genome Typereference
Copyright SRI International 2016. All Rights Reserved.

References

Caspi14: Caspi R, Altman T, Billington R, Dreher K, Foerster H, Fulcher CA, Holland TA, Keseler IM, Kothari A, Kubo A, Krummenacker M, Latendresse M, Mueller LA, Ong Q, Paley S, Subhraveti P, Weaver DS, Weerasinghe D, Zhang P, Karp PD (2014). "The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases." Nucleic Acids Res. 42(1):D459-D471. PMID: 24225315

Dale10: Dale JM, Popescu L, Karp PD (2010). "Machine learning methods for metabolic pathway prediction." BMC Bioinformatics 11;15. PMID: 20064214

Ikeda03: Ikeda M, Nakagawa S (2003). "The Corynebacterium glutamicum genome: features and impacts on biotechnological processes." Appl Microbiol Biotechnol 62(2-3);99-109. PMID: 12743753

Karp10: Karp PD, Paley SM, Krummenacker M, Latendresse M, Dale JM, Lee TJ, Kaipa P, Gilham F, Spaulding A, Popescu L, Altman T, Paulsen I, Keseler IM, Caspi R (2010). "Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology." Brief Bioinform 11(1);40-79. PMID: 19955237

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