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 15-Oct-2019 from the annotated genome of Achromobacter denitrificans PheN1, 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 23.0) [Karp16, Karp11] using MetaCyc version 23.1 [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_CP0337306,5965,973765477,010,850RefSeq:NZ_CP033730
Ortholog data available?Yes
Database Contents
Genes6,596
Pathways295
Enzymatic Reactions1,747
Transport Reactions14
Polypeptides5,973
Protein Complexes36
Enzymes1,049
Transporters1,119
Compounds1,414
Transcription Units4,153
tRNAs59
Protein Features7,826
GO Terms69
Database Version29.0
Synonyms Achromobacter xylosoxidans subsp. denitrificans
Alcaligenes denitrificans
Alcaligenes denitrificans denitrificans
Alcaligenes denitrificans subsp. 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)
BIOSAMPLESAMN10344696
NCBI BioProjectPRJNA224116
NCBI-Taxonomy32002
Environmentreactors
Geographic LocationChina
Latitude/Longitude38.15 N 118.5 E
Collection Date2018-10-5
Annotation ProviderNCBI RefSeq
Annotation Date2018-11-22
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline
Annotation Pipeline Version4.7
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 (2019). "The MetaCyc database of metabolic pathways and enzymes-a 2019 update." Nucleic Acids Res. 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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