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 15-Oct-2019 from the annotated genome of Actinomyces israelii NCTC12972, 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 23.0) [Karp16, Karp11] using MetaCyc version 23.1 [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.
Genome
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
Chromosome 12,1612,04465522,572,997RefSeq:NZ_LR134357
Ortholog data available?Yes
Database Contents
Genes2,161
Pathways167
Enzymatic Reactions866
Transport Reactions3
Polypeptides2,045
Protein Complexes19
Enzymes444
Transporters200
Compounds701
Transcription Units1,497
tRNAs53
Protein Features2,509
GO Terms1
Database Version29.0
Synonyms Actinobacterium israeli
Brevistreptothrix israeli
Cohnistreptothrix israeli
Corynebacterium israeli
Discomyces israeli
Nocardia israeli
Oospora israeli
Proactinomyces israeli
Streptothrix israeli
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Actinomycetales
Actinomycetaceae
Actinomyces
Actinomyces israelii
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMEA4364212
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1659
Environmenthuman
Geographic LocationUSA
Collection Date1948
HostHomo sapiens
Health/Disease Statedisease
Human Microbiome Body Sitenot-specified
Annotation ProviderNCBI RefSeq
Annotation Date2018-12-27
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline
Annotation Pipeline Version4.7
Annotation CommentBest-placed reference protein set; GeneMarkS-2+
NCBI Genome Typerepresentative

References

Caspi20: Caspi R, Billington R, Keseler IM, Kothari A, Krummenacker M, Midford PE, Ong WK, Paley S, Subhraveti P, Karp PD (2019). "The MetaCyc database of metabolic pathways and enzymes-a 2019 update." Nucleic Acids Res. 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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