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 Cupriavidus campinensis MJ1, 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
NZ_CP0434403,3443,005652743,605,170RefSeq:NZ_CP043440
unnamed12,4872,206122692,786,414RefSeq:NZ_CP043441
unnamed2392352040347,552RefSeq:NZ_CP043439
Total:6,2235,563775836,739,136
Ortholog data available?Yes
Database Contents
Genes6,223
Pathways314
Enzymatic Reactions1,592
Transport Reactions73
Polypeptides5,563
Protein Complexes5
Enzymes1,051
Transporters794
Compounds1,199
Transcription Units4,177
tRNAs61
Protein Features6,986
GO Terms613
Database Version29.0
Sequence SourceGCF_008271425.1
Synonyms Ralstonia campinensis
Wautersia campinensis
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Betaproteobacteria
Burkholderiales
Burkholderiaceae
Cupriavidus
Cupriavidus campinensis
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN12645908
NCBI BioProjectPRJNA224116
NCBI-Taxonomy151783
Environmentsoil
Geographic LocationSouth Korea
Collection Date2019-05-17
Annotation ProviderNCBI RefSeq
Annotation Date2021-09-7
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.2
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

Report Errors or Provide Feedback
Page generated by Pathway Tools version 29.0 (software by SRI International) on Mon May 19, 2025, BIOCYC14A.