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 01-June-2020 from the annotated genome of Achromobacter xylosoxidans serovar "not known" str. NCTC10807, 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 24.5) [Karp16, Karp11] using MetaCyc version 24.1 [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 16,2856,12971856,813,182RefSeq:NZ_LN831029
Ortholog data available?Yes
Database Contents
Genes6,285
Pathways306
Enzymatic Reactions1,529
Transport Reactions109
Polypeptides6,130
Protein Complexes89
Enzymes1,064
Transporters970
Compounds1,111
Transcription Units4,006
tRNAs57
Protein Features7,992
GO Terms1,735
Database Version29.0
Sequence SourceGCF_001457475.1
Synonyms Achromobacter sp. 2789STDY5608606
Achromobacter sp. 2789STDY5608609
Achromobacter sp. 2789STDY5608611
Achromobacter sp. 2789STDY5608612
Achromobacter sp. 2789STDY5608616
Achromobacter sp. 2789STDY5608618
Achromobacter sp. 2789STDY5608619
Achromobacter sp. 2789STDY5608620
Achromobacter sp. 2789STDY5608622
Achromobacter sp. 2789STDY5608623
Achromobacter sp. 2789STDY5608624
Achromobacter sp. 2789STDY5608629
Achromobacter sp. 2789STDY5608630
Achromobacter sp. 2789STDY5608632
Achromobacter sp. 2789STDY5663426
Achromobacter sp. 2789STDY5663429
Achromobacter sp. 2789STDY5663443
Achromobacter sp. 2789STDY5663447
Achromobacter sp. AHJR1
Achromobacter sp. ES-6
Achromobacter sp. GAD3
Achromobacter sp. HMSC056C09
Achromobacter sp. HMSC057D05
Achromobacter sp. HMSC070F04
Achromobacter sp. HMSC15D03
Achromobacter sp. HMSC18C08
Achromobacter xilosoxidans
Achromobacter xylosoxidans KF701
Achromobacter xylosoxidans subsp. xylosoxidans
Achromobacter xylosoxydans
Alcaligenes denitrificans subsp. xylosoxydans
Alcaligenes xylosoxidans subsp. xylosoxidans
Alcaligenes xylosoxidans
Alcaligenes xylosoxydans
Flavobacterium sp. 650
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Betaproteobacteria
Burkholderiales
Alcaligenaceae
Achromobacter
Achromobacter xylosoxidans
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMEA2517358
NCBI BioProjectPRJNA224116
NCBI-Taxonomy85698
Environmentpus
Geographic LocationJapan
Collection Date1971
HostHomo sapiens
Health/Disease Statedisease: otitis
Human Microbiome Body Sitenot-specified
Annotation ProviderNCBI RefSeq
Annotation Date2020-02-12
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.11
Annotation CommentBest-placed reference protein set; GeneMarkS-2+
NCBI Genome Typerepresentative

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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