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 ambivalens LEI 10, 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_CP0454822,6032,390521612,252,027RefSeq:NZ_CP045482
Ortholog data available?Yes
Database Contents
Genes2,603
Pathways90
Enzymatic Reactions611
Transport Reactions25
Polypeptides2,390
Protein Complexes17
Enzymes389
Transporters162
Compounds531
Transcription Units1,617
tRNAs47
Protein Features2,297
Database Version29.0
Sequence SourceGCF_009729015.1
Synonyms Desulfurolobus ambivalens
Sulfolobus ambivalens
Taxonomic Lineage cellular organisms
Archaea
TACK group
Thermoproteota
Thermoprotei
Sulfolobales
Sulfolobaceae
Acidianus
Acidianus ambivalens
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN09933089
NCBI BioProjectPRJNA224116
NCBI-Taxonomy2283
EnvironmentMud
Geographic LocationIceland
Collection Date1984-08
Relationship to Oxygenanaerobe
Trophic Levelchemolithoautotroph
Annotation ProviderNCBI RefSeq
Annotation Date2019-12-6
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.10
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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