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. oral taxon 170 F0386, 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_GL88254440338698471,173RefSeq:NZ_GL882544
NZ_GL88257328226778339,694RefSeq:NZ_GL882573
NZ_GL88253827026307275,912RefSeq:NZ_GL882538
NZ_GL88251122521735265,922RefSeq:NZ_GL882511
NZ_GL88253917116551202,023RefSeq:NZ_GL882539
NZ_GL88251611811602138,140RefSeq:NZ_GL882516
NZ_GL88254010610132137,005RefSeq:NZ_GL882540
NZ_GL882517979133112,763RefSeq:NZ_GL882517
NZ_GL882530827912111,342RefSeq:NZ_GL882530
NZ_GL882555948491103,301RefSeq:NZ_GL882555
NZ_GL882506968655103,029RefSeq:NZ_GL882506
NZ_GL88253661572279,375RefSeq:NZ_GL882536
NZ_GL88257262610168,745RefSeq:NZ_GL882572
NZ_GL88251956550165,473RefSeq:NZ_GL882519
NZ_GL88253447411550,151RefSeq:NZ_GL882534
NZ_GL88255343401249,822RefSeq:NZ_GL882553
NZ_GL88252642390346,814RefSeq:NZ_GL882526
NZ_GL88253238370139,321RefSeq:NZ_GL882532
NZ_GL88251426260033,978RefSeq:NZ_GL882514
NZ_GL88252918180032,746RefSeq:NZ_GL882529
NZ_GL88252829252230,996RefSeq:NZ_GL882528
NZ_GL88253121190225,158RefSeq:NZ_GL882531
NZ_GL88252217170024,149RefSeq:NZ_GL882522
NZ_GL88253718170120,747RefSeq:NZ_GL882537
NZ_GL88250811110020,525RefSeq:NZ_GL882508
NZ_GL88250719181020,245RefSeq:NZ_GL882507
NZ_GL88256615150017,773RefSeq:NZ_GL882566
NZ_GL88250914130116,955RefSeq:NZ_GL882509
NZ_GL88254712120016,461RefSeq:NZ_GL882547
NZ_GL88251812110116,258RefSeq:NZ_GL882518
NZ_GL88250415140115,855RefSeq:NZ_GL882504
NZ_GL88254113130015,548RefSeq:NZ_GL882541
NZ_GL88250513120113,775RefSeq:NZ_GL882505
NZ_GL88256312120013,656RefSeq:NZ_GL882563
42 Undisplayed Contigs/Replicons8380322140,314
Total:2,6632,51855903,135,144
Ortholog data available?No
Database Contents
Genes2,663
Pathways194
Enzymatic Reactions943
Transport Reactions55
Polypeptides2,560
Protein Complexes91
Enzymes548
Transporters225
Compounds728
Transcription Units1,949
tRNAs50
Protein Features3,070
GO Terms207
Database Version29.0
Sequence SourceGCF_000195595.1
Synonyms Actinomyces sp. oral taxon 170 strain F0386
Actinomyces sp. oral taxon 170 str. F0386
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Actinomycetales
Actinomycetaceae
Actinomyces
unclassified Actinomyces
Actinomyces sp. oral taxon 170
Actinomyces sp. oral taxon 170 F0386
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN00189093
NCBI BioProjectPRJNA224116
NCBI-Taxonomy762963
Environmentbiological product [ENVO:02000043]
HostHomo sapiens
Human Microbiome Body Sitenot-specified
Annotation ProviderNCBI RefSeq
Annotation Date2021-06-20
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.2
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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