Database Authors
Pallavi Subhraveti1, Peter Midford1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 8-Mar-2022 from the annotated genome of Staphylococcus aureus ATCC 25923, as obtained from RefSeq (see the RefSeq entry for the authors of the original genome sequence). The PGDB was created computationally by the PathoLogic component of the Pathway Tools software (version 26.0) [Karp16, Karp11] using MetaCyc version 26.0 [Caspi19]. It has not undergone any manual curation or review, and may contain errors. Development of this PGDB was supported by grant GM080746 from the National Institutes of Health.
Genome
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_CP0093612,7442,58381802,778,854RefSeq:NZ_CP009361
pS194530270327,491RefSeq:NZ_CP009362
Total:2,7742,61081832,806,345
Ortholog data available?Yes
Database Contents
Genes2,774
Pathways253
Enzymatic Reactions1,238
Transport Reactions83
Polypeptides2,610
Protein Complexes4
Enzymes687
Transporters344
Compounds881
Transcription Units1,702
tRNAs58
Protein Features3,392
GO Terms2,229
Database Version29.0
Sequence SourceGCF_000756205.1
Synonyms Micrococcus aureus
Micrococcus pyogenes
Staphlococcus pyogenes citreus
Staphylococcus aureus subsp. anaerobius
Staphylococcus aureus subsp. aureus
Staphylococcus pyogenes aureus
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Bacillota
Bacilli
Bacillales
Staphylococcaceae
Staphylococcus
Staphylococcus aureus
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN03009478
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1280
EnvironmentClinical
Geographic LocationUSA
Collection Date1945
HostHomo sapiens
Annotation ProviderNCBI RefSeq
Annotation Date2022-01-20
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.3
Annotation CommentBest-placed reference protein set; GeneMarkS-2+

References

Caspi19: Caspi R, Billington R, Keseler IM, Kothari A, Krummenacker M, Midford PE, Ong WK, Paley S, Subhraveti P, Karp PD (2020). "The MetaCyc database of metabolic pathways and enzymes - a 2019 update." Nucleic Acids Res 48(D1);D445-D453. PMID: 31586394

Karp11: Karp PD, Latendresse M, Caspi R (2011). "The pathway tools pathway prediction algorithm." Stand Genomic Sci 5(3);424-9. PMID: 22675592

Karp16: Karp PD, Latendresse M, Paley SM, Krummenacker M, Ong QD, Billington R, Kothari A, Weaver D, Lee T, Subhraveti P, Spaulding A, Fulcher C, Keseler IM, Caspi R (2016). "Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology." Brief Bioinform 17(5);877-90. PMID: 26454094

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