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 Acidilobus saccharovorans 345-15, 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
NC_0143741,5421,48151101,496,453RefSeq:NC_014374
Ortholog data available?Yes
Database Contents
Genes1,542
Pathways73
Enzymatic Reactions493
Transport Reactions18
Polypeptides1,481
Protein Complexes14
Enzymes285
Transporters123
Compounds441
Transcription Units1,103
tRNAs46
Protein Features1,584
Database Version29.0
Sequence SourceGCF_000144915.1
Synonyms Acidilobus saccharovorans str. 345-15
Acidilobus saccharovorans strain 345-15
Acidilobus sp. 345-15
Acidilobus saccharovorans 345-15
Taxonomic Lineage cellular organisms
Archaea
TACK group
Thermoproteota
Thermoprotei
Acidilobales
Acidilobaceae
Acidilobus
Acidilobus saccharovorans
Acidilobus saccharovorans 345-15
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02603091
NCBI BioProjectPRJNA224116
NCBI-Taxonomy666510
Environmentsolfataric field of Uzon caldera
Geographic LocationRussia
Annotation ProviderNCBI RefSeq
Annotation Date2020-02-17
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.11
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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