Database Authors
Pallavi Subhraveti1, Peter Midford1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 01-June-2022 from the annotated genome of Campylobacter helveticus ATCC 51209, 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_CP0204781,8751,79454271,758,726RefSeq:NZ_CP020478
pHELV-191910072,019RefSeq:NZ_CP020479
pHELV-243430034,012RefSeq:NZ_CP020480
pHELV-322003,279RefSeq:NZ_CP020481
pHELV-533001,761RefSeq:NZ_CP020483
pHELV-433001,698RefSeq:NZ_CP020482
Total:2,0171,93654271,871,495
Ortholog data available?Yes
Database Contents
Genes2,017
Pathways167
Enzymatic Reactions921
Transport Reactions33
Polypeptides1,936
Protein Complexes52
Enzymes483
Transporters122
Compounds662
Transcription Units826
tRNAs42
Protein Features2,042
GO Terms102
Database Version29.0
Sequence SourceGCF_002080395.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Campylobacterota
Epsilonproteobacteria
Campylobacterales
Campylobacteraceae
Campylobacter
Campylobacter helveticus
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN03737972
NCBI BioProjectPRJNA224116
NCBI-Taxonomy28898
Environmentfeces
Geographic LocationSwitzerland
Collection Date1992
HostFelis catus
Annotation ProviderNCBI RefSeq
Annotation Date2022-04-11
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version6.1
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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