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 25-Oct-2020 from the annotated genome of Achromobacter denitrificans USDA-ARS-USMARC-56712, 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_CP0139235,6635,53871546,226,215RefSeq:NZ_CP013923
Ortholog data available?No
Database Contents
Genes5,663
Pathways297
Enzymatic Reactions1,489
Transport Reactions108
Polypeptides5,538
Protein Complexes88
Enzymes959
Transporters936
Compounds1,064
Transcription Units3,653
tRNAs57
Protein Features7,361
GO Terms1,308
Database Version29.0
Sequence SourceGCF_001514355.1
Synonyms Achromobacter xylosoxidans subsp. denitrificans
Alcaligenes denitrificans denitrificans
Alcaligenes denitrificans subsp. denitrificans
Alcaligenes denitrificans
Alcaligenes xylosoxidans subsp. denitrificans
Alcaligenes xylosoxydans denitrificans
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Betaproteobacteria
Burkholderiales
Alcaligenaceae
Achromobacter
Achromobacter denitrificans
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN04158498
NCBI BioProjectPRJNA224116
NCBI-Taxonomy32002
Environmentmucus
Geographic LocationUSA
Collection Date2013-09-28
HostBos taurus
Annotation ProviderNCBI RefSeq
Annotation Date2020-06-15
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.11
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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