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 insolitus NCTC13520, 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
Chromosome 15,9785,82774776,472,476RefSeq:NZ_LR134361
Ortholog data available?No
Database Contents
Genes5,978
Pathways292
Enzymatic Reactions1,788
Transport Reactions12
Polypeptides5,827
Protein Complexes30
Enzymes1,041
Transporters1,136
Compounds1,427
Transcription Units3,807
tRNAs57
Protein Features7,882
GO Terms57
Database Version29.0
Synonyms Achromobacter sp. AR476-2
Achromobacter sp. KCJK1724
Achromobacter sp. KCJK1731
Achromobacter sp. LMG 6003
Achromobacter sp. UBA1170
Achromobacter sp. UBA1582
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Betaproteobacteria
Burkholderiales
Alcaligenaceae
Achromobacter
Achromobacter insolitus
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMEA4384063
NCBI BioProjectPRJNA224116
NCBI-Taxonomy217204
EnvironmentLeg
Geographic LocationChina
Latitude/Longitude30.0 N 110.0 E
Collection Date1984-12-31/1900-01-1
Health/Disease Statenot available: to be reported later
Annotation ProviderNCBI RefSeq
Annotation Date2018-12-27
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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