Database Authors
Pallavi Subhraveti1, Peter Midford1, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 01-June-2020 from the annotated genome of Acidianus manzaensis YN-25, 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 24.5) [Karp16, Karp11] using MetaCyc version 24.1 [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_CP0204772,7552,63251722,687,463RefSeq:NZ_CP020477
Ortholog data available?Yes
Database Contents
Genes2,755
Pathways91
Enzymatic Reactions642
Transport Reactions27
Polypeptides2,632
Protein Complexes18
Enzymes451
Transporters219
Compounds578
Transcription Units1,760
tRNAs46
Protein Features2,640
Database Version29.0
Sequence SourceGCF_002116695.1
Taxonomic Lineage cellular organisms
Archaea
TACK group
Thermoproteota
Thermoprotei
Sulfolobales
Sulfolobaceae
Acidianus
Acidianus manzaensis
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN06640543
NCBI BioProjectPRJNA224116
NCBI-Taxonomy282676
Environmentvolcanic hot spring
Geographic LocationChina
Collection Date2005-08
Annotation ProviderNCBI RefSeq
Annotation Date2019-09-1
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.9
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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