Database Authors
Pallavi Subhraveti1, Peter Midford1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 01-June-2022 from the annotated genome of Actinomyces graevenitzii C83, 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 [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
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_JH4703381,5251,42854431,784,751RefSeq:NZ_JH470338
NZ_JH47033926225525281,181RefSeq:NZ_JH470339
NZ_JH470340847842111,643RefSeq:NZ_JH470340
NZ_JH47034115131115,660RefSeq:NZ_JH470341
6 Undisplayed Contigs/Replicons624112,490
Total:1,8931,77665522,205,725
Ortholog data available?No
Database Contents
Genes1,888
Pathways142
Enzymatic Reactions736
Transport Reactions29
Polypeptides1,792
Protein Complexes54
Enzymes382
Transporters131
Compounds540
Transcription Units1,258
tRNAs50
Protein Features2,191
GO Terms116
Database Version29.0
Sequence SourceGCF_000239695.1
Synonyms Actinomyces graevenitzii strain C83
Actinomyces graevenitzii str. C83
Actinomyces sp. C83
Actinomyces graevenitzii C83
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Actinomycetales
Actinomycetaceae
Actinomyces
Actinomyces graevenitzii
Actinomyces graevenitzii C83
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02463758
NCBI BioProjectPRJNA224116
NCBI-Taxonomy435830
Environmentbiological product [ENVO:02000043]
HostHomo sapiens
Human Microbiome Body Sitenot-specified
Annotation ProviderNCBI RefSeq
Annotation Date2021-12-8
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.3
Annotation CommentBest-placed reference protein set; GeneMarkS-2+

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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