Database Authors
Pallavi Subhraveti1, Peter Midford1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 01-June-2022 from the annotated genome of Acidithiobacillus caldus ATCC 51756, 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_CP0059862,7762,66858502,777,717RefSeq:NZ_CP005986
megap mpAca1.1181162019171,972RefSeq:NZ_CP005987
pACA1.130280227,536RefSeq:NZ_CP005988
pACA1.298019,820RefSeq:NZ_CP005989
Total:2,9962,86658722,987,045
Ortholog data available?Yes
Database Contents
Genes2,996
Pathways191
Enzymatic Reactions1,071
Transport Reactions29
Polypeptides2,866
Protein Complexes60
Enzymes647
Transporters218
Compounds718
Transcription Units1,563
tRNAs48
Protein Features3,463
GO Terms1,813
Database Version29.0
Sequence SourceGCF_000175575.2
Synonyms Acidithiobacillus caldus DSM 8584
Acidithiobacillus caldus KU
Acidithiobacillus caldus strain ATCC 51756
Acidithiobacillus caldus str. ATCC 51756
Acidithiobacillus caldus ATCC 51756
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Acidithiobacillia
Acidithiobacillales
Acidithiobacillaceae
Acidithiobacillus
Acidithiobacillus caldus
Acidithiobacillus caldus ATCC 51756
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02469802
NCBI BioProjectPRJNA224116
NCBI-Taxonomy637389
Annotation ProviderNCBI RefSeq
Annotation Date2022-02-12
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version6.0
Annotation CommentBest-placed reference protein set; GeneMarkS-2+

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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Page generated by Pathway Tools version 29.0 (software by SRI International) on Mon Jun 30, 2025, BIOCYC17A.