Database Authors
Pallavi Subhraveti1, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 15-Feb-2020 from the annotated genome of Nocardia nova SH22a, 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 24.0) [Karp16, Karp11] using MetaCyc version 23.5 [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_CP0068507,5597,345621528,348,532RefSeq:NZ_CP006850
Ortholog data available?Yes
Database Contents
Genes7,559
Pathways288
Enzymatic Reactions1,417
Transport Reactions53
Polypeptides7,347
Protein Complexes44
Enzymes1,167
Transporters497
Compounds1,131
Transcription Units5,348
tRNAs50
Protein Features8,432
GO Terms1
Database Version29.0
Sequence SourceGCF_000523235.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Mycobacteriales
Nocardiaceae
Nocardia
Nocardia nova
Nocardia nova SH22a
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02641505
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1415166
Annotation ProviderNCBI RefSeq
Annotation Date2019-08-27
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.9
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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