Database Authors
Pallavi Subhraveti1, Peter Midford1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 8-Mar-2022 from the annotated genome of Acidovorax citrulli AAC00-1, 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 26.0) [Karp16, Karp11] using MetaCyc version 26.0 [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_0087524,9594,786651085,352,772RefSeq:NC_008752
Ortholog data available?Yes
Database Contents
Genes4,959
Pathways292
Enzymatic Reactions1,497
Transport Reactions52
Polypeptides4,786
Protein Complexes6
Enzymes902
Transporters550
Compounds1,124
Transcription Units3,192
tRNAs53
Protein Features7,092
GO Terms398
Database Version29.0
Sequence SourceGCF_000015325.1
Synonyms Acidovorax avenae subsp. citrulli AAC00-1
Acidovorax citrulli str. AAC00-1
Acidovorax citrulli strain AAC00-1
Acidovorax citrulli AAC00-1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Betaproteobacteria
Burkholderiales
Comamonadaceae
Paracidovorax
Paracidovorax citrulli
Acidovorax citrulli AAC00-1
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02598334
NCBI BioProjectPRJNA224116
NCBI-Taxonomy397945
Annotation ProviderNCBI RefSeq
Annotation Date2022-01-5
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.3
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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