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 13-Mar-2021 from the annotated genome of Actinomyces denticolens PA, 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 25.0) [Karp16, Karp11] using MetaCyc version 24.5 [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_FQYL01000001322305611390,024RefSeq:NZ_FQYL01000001
NZ_FQYL0100000233532816372,994RefSeq:NZ_FQYL01000002
NZ_FQYL0100000324323076285,551RefSeq:NZ_FQYL01000003
NZ_FQYL01000004233218123272,192RefSeq:NZ_FQYL01000004
NZ_FQYL0100000513012352160,030RefSeq:NZ_FQYL01000005
NZ_FQYL0100000612311463149,548RefSeq:NZ_FQYL01000006
NZ_FQYL0100000713412455148,361RefSeq:NZ_FQYL01000007
NZ_FQYL0100000811511203135,490RefSeq:NZ_FQYL01000008
NZ_FQYL01000009978863104,588RefSeq:NZ_FQYL01000009
NZ_FQYL0100001070672189,042RefSeq:NZ_FQYL01000010
NZ_FQYL0100001165640181,459RefSeq:NZ_FQYL01000011
NZ_FQYL0100001273711180,327RefSeq:NZ_FQYL01000012
NZ_FQYL0100001357542174,193RefSeq:NZ_FQYL01000013
NZ_FQYL0100001459571170,016RefSeq:NZ_FQYL01000014
NZ_FQYL0100001552482268,931RefSeq:NZ_FQYL01000015
NZ_FQYL0100001647450260,522RefSeq:NZ_FQYL01000016
NZ_FQYL0100001748461159,531RefSeq:NZ_FQYL01000017
NZ_FQYL0100001840390154,108RefSeq:NZ_FQYL01000018
NZ_FQYL0100001923230027,904RefSeq:NZ_FQYL01000019
14 Undisplayed Contigs/Replicons39393775,955
Total:2,3152,19560602,760,766
Ortholog data available?Yes
Database Contents
Genes2,309
Pathways181
Enzymatic Reactions876
Transport Reactions68
Polypeptides2,217
Protein Complexes35
Enzymes520
Transporters241
Compounds682
Transcription Units1,625
tRNAs50
Protein Features2,695
Database Version29.0
Sequence SourceGCF_900141725.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Actinomycetales
Actinomycetaceae
Actinomyces
Actinomyces denticolens
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN05216246
NCBI BioProjectPRJNA224116
NCBI-Taxonomy52767
Annotation ProviderNCBI RefSeq
Annotation Date2020-07-8
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.12
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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