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 Amycolatopsis orientalis B-37, 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
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_CP0161748,3578,292651269,490,992RefSeq:NZ_CP016174
Ortholog data available?Yes
Database Contents
Genes8,483
Pathways313
Enzymatic Reactions1,539
Transport Reactions67
Polypeptides8,292
Protein Complexes55
Enzymes1,175
Transporters648
Compounds1,177
Transcription Units5,550
tRNAs50
Protein Features9,908
GO Terms79
Database Version29.0
Sequence SourceGCF_000943515.2
Synonyms Actinoplanes sp. ATCC 53771
Amycolatopsis orientalis orientalis
Amycolatopsis orientalis subsp. orientalis
Nocardia orientalis
Streptomyces orientalis
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Pseudonocardiales
Pseudonocardiaceae
Amycolatopsis
Amycolatopsis orientalis
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN03273949
NCBI BioProjectPRJNA224116
NCBI-Taxonomy31958
Environmentsoil sample
Geographic LocationChina
Collection Date1960-01-31
Annotation ProviderNCBI RefSeq
Annotation Date2021-01-25
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.0
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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