Database Authors
Pallavi Subhraveti1, Peter Midford1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 8-Mar-2022 from the annotated genome of Actinomyces sp. HMSC075B09 HMSC075B09, 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_KV808731722694226813,948RefSeq:NZ_KV808731
NZ_KV80873527926577302,353RefSeq:NZ_KV808735
NZ_KV80874317416671199,205RefSeq:NZ_KV808743
NZ_KV80873017216642191,611RefSeq:NZ_KV808730
NZ_KV80874214514122170,695RefSeq:NZ_KV808742
NZ_KV8087391019470112,229RefSeq:NZ_KV808739
NZ_KV80874069672084,685RefSeq:NZ_KV808740
NZ_KV80873323221029,593RefSeq:NZ_KV808733
7 Undisplayed Contigs/Replicons763218,493
Total:1,6961,62155201,922,812
Ortholog data available?No
Database Contents
Genes1,694
Pathways169
Enzymatic Reactions865
Transport Reactions35
Polypeptides1,633
Protein Complexes3
Enzymes468
Transporters223
Compounds597
Transcription Units1,031
tRNAs48
Protein Features2,211
GO Terms148
Database Version29.0
Sequence SourceGCF_001812395.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Actinomycetales
Actinomycetaceae
Actinomyces
unclassified Actinomyces
Actinomyces sp. HMSC075B09
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN04477663
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1739358
Environmenttissue r heel
HostHomo sapiens
Human Microbiome Body Sitenot-specified
Annotation ProviderNCBI RefSeq
Annotation Date2021-09-1
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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