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 22-Nov-2024 from the annotated genome of Achromobacter veterisilvae AB1, as obtained from RefSeq (annotation date: 05-APR-2024). The PGDB was created computationally by the PathoLogic component of the Pathway Tools software (version 28.5) [Karp11, Karp16] using MetaCyc version 28.5 [Caspi20]. It has not undergone any manual curation or review, and may contain errors.
Genome
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
GEN-EL14787406,0955,99177276,549,044RefSeq:GEN-EL1478740
Ortholog data available?Yes
Database Contents
Genes6,095
Pathways351
Enzymatic Reactions1,962
Transport Reactions83
Polypeptides5,991
Protein Complexes0
Enzymes1,188
Transporters1,259
Compounds1,607
tRNAs60
Protein Features8,331
GO Terms7,871
Database Version29.0
Synonyms Achromobacter sp. LMG 30378
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Betaproteobacteria
Burkholderiales
Alcaligenaceae
Achromobacter
Achromobacter veterisilvae
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN40310765
NCBI BioProjectPRJNA224116
NCBI-Taxonomy2069367
Environmentcompost
Geographic LocationUnited Kingdom
Collection Date2018
Annotation ProviderNCBI RefSeq
Annotation Date2024-04-5
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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