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 sp. S4-C9 S4-C9, 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_JRMU0100001019318652231,911RefSeq:NZ_JRMU01000010
NZ_JRMU0100000120219732230,621RefSeq:NZ_JRMU01000001
NZ_JRMU0100000615815161173,983RefSeq:NZ_JRMU01000006
NZ_JRMU0100001114013622165,386RefSeq:NZ_JRMU01000011
NZ_JRMU0100000415014091163,999RefSeq:NZ_JRMU01000004
NZ_JRMU01000016989611112,289RefSeq:NZ_JRMU01000016
NZ_JRMU010000071019920110,677RefSeq:NZ_JRMU01000007
NZ_JRMU010000021019812103,324RefSeq:NZ_JRMU01000002
NZ_JRMU0100000572702082,664RefSeq:NZ_JRMU01000005
NZ_JRMU0100001877770080,801RefSeq:NZ_JRMU01000018
NZ_JRMU0100001953492267,699RefSeq:NZ_JRMU01000019
NZ_JRMU0100000860545164,192RefSeq:NZ_JRMU01000008
NZ_JRMU0100002047461050,214RefSeq:NZ_JRMU01000020
NZ_JRMU0100000939381043,062RefSeq:NZ_JRMU01000009
NZ_JRMU0100002228271038,035RefSeq:NZ_JRMU01000022
NZ_JRMU0100001329290036,762RefSeq:NZ_JRMU01000013
NZ_JRMU0100002331291136,663RefSeq:NZ_JRMU01000023
NZ_JRMU0100002427261033,331RefSeq:NZ_JRMU01000024
NZ_JRMU0100001225241031,664RefSeq:NZ_JRMU01000012
NZ_JRMU0100001525222129,017RefSeq:NZ_JRMU01000015
NZ_JRMU0100000322211023,946RefSeq:NZ_JRMU01000003
NZ_JRMU0100001413130015,496RefSeq:NZ_JRMU01000014
8 Undisplayed Contigs/Replicons22194129,896
Total:1,7151,64751171,955,632
Ortholog data available?No
Database Contents
Genes1,714
Pathways177
Enzymatic Reactions893
Transport Reactions35
Polypeptides1,655
Protein Complexes68
Enzymes434
Transporters142
Compounds611
Transcription Units1,058
tRNAs45
Protein Features2,232
GO Terms143
Database Version29.0
Sequence SourceGCF_000758775.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Actinomycetales
Actinomycetaceae
Actinomyces
unclassified Actinomyces
Actinomyces sp. S4-C9
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02850924
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1219581
Environmentvagina
HostHomo sapiens
Human Microbiome Body Siteurogenital-tract
Annotation ProviderNCBI RefSeq
Annotation Date2021-12-18
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.