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 brierleyi DSM 1651, 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_CP0292893,1552,944511602,947,244RefSeq:NZ_CP029289
Ortholog data available?Yes
Database Contents
Genes3,155
Pathways94
Enzymatic Reactions714
Transport Reactions12
Polypeptides2,944
Protein Complexes0
Enzymes478
Transporters245
Compounds587
Transcription Units2,058
tRNAs46
Protein Features2,806
GO Terms163
Database Version29.0
Sequence SourceGCF_003201835.2
Synonyms Sulfolobus brierleyi
Taxonomic Lineage cellular organisms
Archaea
TACK group
Thermoproteota
Thermoprotei
Sulfolobales
Sulfolobaceae
Acidianus
Acidianus brierleyi
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN09071529
NCBI BioProjectPRJNA224116
NCBI-Taxonomy41673
Environmentdrainage system from an acidic hot spring
Geographic LocationUSA
Collection Date1966
Annotation ProviderNCBI RefSeq
Annotation Date2021-04-16
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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