Database Authors
Pallavi Subhraveti1, Anamika Kothari1, Peter Midford1, Ron Caspi1, Lisa Moore1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 29-Oct-2024 from the annotated genome of Achromobacter xylosoxidans NH44784-1996, as obtained from RefSeq (annotation date: 01-APR-2024). The PGDB was created computationally by the PathoLogic component of the Pathway Tools software (version 28.5) [Karp11, Karp16] using MetaCyc version 28.1 [Caspi20]. It has not undergone any manual curation or review, and may contain errors.
Genome
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
Chromosome I6,4616,34463546,916,670RefSeq:NC_021285
Ortholog data available?No
Database Contents
Genes6,461
Pathways352
Enzymatic Reactions1,953
Transport Reactions115
Polypeptides6,348
Protein Complexes214
Enzymes1,159
Transporters819
Compounds1,596
Transcription Units4,239
tRNAs54
Protein Features8,323
GO Terms9,450
Database Version29.0
Sequence SourceGCF_000967095.2
Synonyms Achromobacter xylosoxidans strain NH44784-1996
Achromobacter xylosoxidans str. NH44784-1996
Achromobacter xylosoxidans NH44784-1996
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Betaproteobacteria
Burkholderiales
Alcaligenaceae
Achromobacter
Achromobacter xylosoxidans
Achromobacter xylosoxidans NH44784-1996
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMEA3283131
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1167634
Annotation ProviderNCBI RefSeq
Annotation Date2024-04-1
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version6.7
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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Page generated by Pathway Tools version 29.0 (software by SRI International) on Mon Jun 30, 2025, BIOCYC17A.