Database Authors
Summary This Pathway/Genome Database (PGDB) was generated on 18-Nov-2021 from the annotated genome of Acidithiobacillus ferrooxidans ATCC 23270, 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 25.5) [Karp16, Karp11] using MetaCyc version 25.5 [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_0117613,0752,89392902,982,397RefSeq:NC_011761
Ortholog data available?Yes
Database Contents
Genes3,075
Pathways217
Enzymatic Reactions1,135
Transport Reactions31
Polypeptides2,897
Protein Complexes7
Enzymes704
Transporters267
Compounds778
Transcription Units1,545
tRNAs82
Protein Features4,185
Database Version29.0
Sequence SourceGCF_000021485.1
Synonyms Acidithiobacillus ferrooxidans str. ATCC 23270
Acidithiobacillus ferrooxidans ATCC 23270
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Acidithiobacillia
Acidithiobacillales
Acidithiobacillaceae
Acidithiobacillus
Acidithiobacillus ferrooxidans
Acidithiobacillus ferrooxidans ATCC 23270
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02603974
NCBI BioProjectPRJNA224116
NCBI-Taxonomy243159
Annotation ProviderNCBI RefSeq
Annotation Date2021-01-24
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.0
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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