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 Achromobacter xylosoxidans A8, 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
NC_0146406,5106,40674307,013,095RefSeq:NC_014640
pA8223823503247,895RefSeq:NC_014642
pA811069601098,156RefSeq:NC_014641
Total:6,8546,73774437,359,146
Ortholog data available?Yes
Database Contents
Genes6,854
Pathways310
Enzymatic Reactions1,560
Transport Reactions112
Polypeptides6,737
Protein Complexes106
Enzymes1,119
Transporters1,120
Compounds1,160
Transcription Units4,210
tRNAs60
Protein Features8,886
GO Terms64
Database Version29.0
Sequence SourceGCF_000165835.1
Synonyms Achromobacter xylosoxidans str. A8
Achromobacter xylosoxidans strain A8
Achromobacter xylosoxidans A8
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Betaproteobacteria
Burkholderiales
Alcaligenaceae
Achromobacter
Achromobacter xylosoxidans
Achromobacter xylosoxidans A8
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02603404
NCBI BioProjectPRJNA224116
NCBI-Taxonomy762376
Annotation ProviderNCBI RefSeq
Annotation Date2021-01-31
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.0
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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