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 Halioglobus pacificus RR3-57, 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_CP0190464,2444,191531144,847,776RefSeq:NZ_CP019046
pRR3-5713813806155,799RefSeq:NZ_CP019045
Total:4,5024,329531205,003,575
Ortholog data available?No
Database Contents
Genes4,382
Pathways240
Enzymatic Reactions1,335
Transport Reactions42
Polypeptides4,329
Protein Complexes2
Enzymes832
Transporters335
Compounds980
Transcription Units2,759
tRNAs43
Protein Features5,532
GO Annotations220
Database Version29.6
Sequence SourceGCF_001953075.1
Synonyms gamma proteobacterium S1-72
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadati
Pseudomonadota
Gammaproteobacteria
Cellvibrionales
Halieaceae
Halioglobus
Halioglobus pacificus
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN06199441
NCBI BioProjectPRJNA224116
NCBI-Taxonomy930806
EnvironmentRecirculating aquaculture system
Geographic LocationSouth Korea
Collection Date2015-04-14
Annotation ProviderNCBI RefSeq
Annotation Date2021-12-19
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.3
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 29.5 (software by SRI International) on Thu Apr 30, 2026, BIOCYC14A.