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 Acidianus sulfidivorans JP7, 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_CP0292882,3502,27451252,265,309RefSeq:NZ_CP029288
Ortholog data available?Yes
Database Contents
Genes2,350
Pathways97
Enzymatic Reactions708
Transport Reactions14
Polypeptides2,274
Protein Complexes0
Enzymes455
Transporters197
Compounds579
Transcription Units1,469
tRNAs46
Protein Features2,322
GO Terms123
Database Version29.0
Sequence SourceGCF_003201765.2
Synonyms Acidianus sp. JP7
Acidianus sulfidivorans DSM 18786
Acidianus sulfidivorans JP7
Taxonomic Lineage cellular organisms
Archaea
TACK group
Thermoproteota
Thermoprotei
Sulfolobales
Sulfolobaceae
Acidianus
Acidianus sulfidivorans
Acidianus sulfidivorans JP7
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN09071530
NCBI BioProjectPRJNA224116
NCBI-Taxonomy619593
EnvironmentEdge of acidic hot spring
Geographic LocationPapua New Guinea
Collection Date2002-05
Annotation ProviderNCBI RefSeq
Annotation Date2021-03-3
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.1
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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