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 25-Oct-2020 from the annotated genome of Acidovorax sp. JHL-3 JHL-3, 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
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_JAFU010000012,9212,80863503,163,980RefSeq:NZ_JAFU01000001
NZ_JAFU01000004618598713691,256RefSeq:NZ_JAFU01000004
NZ_JAFU0100000310291011114,390RefSeq:NZ_JAFU01000003
NZ_JAFU010000021590618,358RefSeq:NZ_JAFU01000002
Total:3,6563,50670803,987,984
Ortholog data available?No
Database Contents
Genes3,656
Pathways255
Enzymatic Reactions1,326
Transport Reactions72
Polypeptides3,508
Protein Complexes41
Enzymes813
Transporters423
Compounds997
Transcription Units2,419
tRNAs54
Protein Features4,810
GO Terms1
Database Version29.0
Sequence SourceGCF_000526295.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Betaproteobacteria
Burkholderiales
Comamonadaceae
Acidovorax
Acidovorax sp. JHL-3
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02584928
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1276755
Environmentnot provided; submitted under MIGS 2.1
Annotation ProviderNCBI RefSeq
Annotation Date2020-02-5
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.11
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 (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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