Database Authors
Summary This Pathway/Genome Database (PGDB) was generated on 01-June-2020 from the annotated genome of Actinomyces gaoshouyii pika_114, 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 24.5) [Karp16, Karp11] using MetaCyc version 24.1 [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
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_CP0204682,0071,89263522,359,360RefSeq:NZ_CP020468
Ortholog data available?Yes
Database Contents
Genes2,007
Pathways172
Enzymatic Reactions857
Transport Reactions64
Polypeptides1,892
Protein Complexes32
Enzymes478
Transporters191
Compounds674
Transcription Units1,376
tRNAs51
Protein Features2,417
Database Version29.0
Sequence SourceGCF_002076915.1
Synonyms Actinomyces sp. pika_113
Actinomyces sp. pika_114
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Actinomycetales
Actinomycetaceae
Actinomyces
Actinomyces gaoshouyii
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN06640690
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1960083
Geographic LocationChina
Collection Date2015-10-31
Annotation ProviderNCBI RefSeq
Annotation Date2020-04-2
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.11
Annotation CommentBest-placed reference protein set; GeneMarkS-2+
NCBI Genome Typerepresentative


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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