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 F0530, 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_KE95149026625961321,155RefSeq:NZ_KE951490
NZ_KE95149918417572243,094RefSeq:NZ_KE951499
NZ_KE95150220319805215,278RefSeq:NZ_KE951502
NZ_KE951482158142412175,477RefSeq:NZ_KE951482
NZ_KE95148312211903148,729RefSeq:NZ_KE951483
NZ_KE9514881039733132,951RefSeq:NZ_KE951488
NZ_KE9514941009550118,521RefSeq:NZ_KE951494
NZ_KE9514891049554115,946RefSeq:NZ_KE951489
NZ_KE951485938562107,789RefSeq:NZ_KE951485
NZ_KE951506827921107,351RefSeq:NZ_KE951506
NZ_KE95150369625280,403RefSeq:NZ_KE951503
NZ_KE95147858541364,782RefSeq:NZ_KE951478
NZ_KE95149248480058,676RefSeq:NZ_KE951492
NZ_KE95149857524157,696RefSeq:NZ_KE951498
NZ_KE95148135304134,022RefSeq:NZ_KE951481
NZ_KE95149521210023,572RefSeq:NZ_KE951495
NZ_KE95150413130014,422RefSeq:NZ_KE951504
NZ_KE95149315121214,391RefSeq:NZ_KE951493
11 Undisplayed Contigs/Replicons28253456,697
Total:1,7631,66156462,090,952
Ortholog data available?No
Database Contents
Genes1,763
Pathways143
Enzymatic Reactions749
Transport Reactions29
Polypeptides1,695
Protein Complexes54
Enzymes391
Transporters128
Compounds553
Transcription Units1,173
tRNAs50
Protein Features2,121
GO Terms115
Database Version29.0
Sequence SourceGCF_000466185.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Actinomycetales
Actinomycetaceae
Actinomyces
Actinomyces graevenitzii
Actinomyces graevenitzii F0530
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02436719
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1321817
Environmentoral cavity- mouth
HostHomo sapiens
Human Microbiome Body Sitenot-specified
Annotation ProviderNCBI RefSeq
Annotation Date2021-12-9
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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Page generated by Pathway Tools version 29.0 (software by SRI International) on Mon Jun 30, 2025, BIOCYC18A.