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. S6-Spd3 S6-Spd3, 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_JRMV01000281568543205622,275RefSeq:NZ_JRMV01000281
NZ_JRMV0100027226225291311,855RefSeq:NZ_JRMV01000272
NZ_JRMV0100027520019640217,485RefSeq:NZ_JRMV01000275
NZ_JRMV0100027615214921183,909RefSeq:NZ_JRMV01000276
NZ_JRMV0100027914914072167,205RefSeq:NZ_JRMV01000279
NZ_JRMV0100027415915270165,547RefSeq:NZ_JRMV01000274
NZ_JRMV0100019611211020145,164RefSeq:NZ_JRMV01000196
NZ_JRMV0100027766621368,505RefSeq:NZ_JRMV01000277
273 Undisplayed Contigs/Replicons444112114209,066
Total:1,8351,645641262,091,011
Ortholog data available?No
Database Contents
Genes1,825
Pathways157
Enzymatic Reactions855
Transport Reactions34
Polypeptides1,839
Protein Complexes63
Enzymes428
Transporters169
Compounds605
Transcription Units1,316
tRNAs49
Protein Features2,153
GO Terms167
Database Version29.0
Sequence SourceGCF_000758755.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Actinomycetales
Actinomycetaceae
Actinomyces
unclassified Actinomyces
Actinomyces sp. S6-Spd3
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02850923
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1284680
Environmentvagina
HostHomo sapiens
Human Microbiome Body Siteurogenital-tract
Annotation ProviderNCBI RefSeq
Annotation Date2022-01-13
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.