Summary of Listeria monocytogenes J0161, version 28.5 Tier 3 Uncurated Database

Database Authors: Pallavi Subhraveti¹, Peter Midford¹, Ingrid Keseler¹, Anamika Kothari¹, Ron Caspi¹, Peter D Karp¹

¹SRI International

Summary:
This Pathway/Genome Database (PGDB) was generated on 13-Mar-2021 from the annotated genome of Listeria monocytogenes J0161, 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 25.0) [Karp16, Karp11] using MetaCyc version 24.5 [Caspi20]. 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.

Sequence Source: GCF_000168635.2

Taxonomic Lineage: cellular organisms, Bacteria <bacteria>, Terrabacteria group, Bacillota, Bacilli, Bacillales, Listeriaceae, Listeria, Listeria monocytogenes, Listeria monocytogenes J0161

Synonyms: Listeria monocytogenes str. J0161, Listeria monocytogenes strain J0161, Listeria monocytogenes J0161

Unification Links: BIOSAMPLE:SAMN00769971, NCBI BioProject:PRJNA224116, NCBI-Taxonomy:393130

Organism or Sample Properties
Annotation Provider:	NCBI RefSeq
Annotation Date:	2020-09-6
Annotation Pipeline:	NCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version:	4.12
Annotation Comment:	Best-placed reference protein set; GeneMarkS-2+

Replicon	Total Genes	Protein Genes	RNA Genes	Pseudogenes	Size (bp)	NCBI Link
NC_017545	3,022	2,931	77	14	3,000,464	NCBI-RefSeq:NC_017545
Ortholog data available?	Yes

Genes:	3,022	SmartTable	Ontology
Pathways:	227	SmartTable	Ontology
Enzymatic Reactions:	1,076
Transport Reactions:	119		Ontology
Polypeptides:	2,931	SmartTable	Ontology
Protein Complexes:	67	SmartTable	Ontology
Enzymes:	678	SmartTable
Transporters:	345	SmartTable
Compounds:	823	SmartTable	Ontology
Transcription Units:	1,720	SmartTable	Ontology
tRNAs:	58		Ontology
Protein Features:	3,917
GO Terms:	1,737		Ontology

Genetic Code Number:
11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)

PGDB Unique ID: 2C86

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References

Caspi20: 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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