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 Acidovorax avenae ATCC 19860, 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_0151384,8704,75364535,482,170RefSeq:NC_015138
Ortholog data available?Yes
Database Contents
Genes4,870
Pathways291
Enzymatic Reactions1,508
Transport Reactions84
Polypeptides4,753
Protein Complexes55
Enzymes928
Transporters606
Compounds1,129
Transcription Units3,199
tRNAs52
Protein Features6,345
GO Terms2
Database Version29.0
Sequence SourceGCF_000176855.2
Synonyms Acidovorax avenae subsp. avenae str. ATCC 19860
Acidovorax avenae subsp. avenae strain ATCC 19860
Acidovorax avenae subsp. avenae ATCC 19860
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Betaproteobacteria
Burkholderiales
Comamonadaceae
Paracidovorax
Paracidovorax avenae
Acidovorax avenae avenae
Acidovorax avenae avenae ATCC 19860
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN00006197
NCBI BioProjectPRJNA224116
NCBI-Taxonomy643561
Environmentmaize leaf
Geographic LocationUSA
Collection Date1909
Relationship to Oxygenaerobe
Temperature Rangemesophile
Biotic Relationshipfree-living
Annotation ProviderNCBI RefSeq
Annotation Date2020-07-16
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.12
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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