Database Authors
Pallavi Subhraveti1, Peter Midford1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 8-Mar-2022 from the annotated genome of Acidiferrobacter thiooxydans ZJ, 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_CP0806243,0792,96553613,302,271RefSeq:NZ_CP080624
Ortholog data available?Yes
Database Contents
Genes3,079
Pathways229
Enzymatic Reactions1,187
Transport Reactions35
Polypeptides2,965
Protein Complexes1
Enzymes730
Transporters242
Compounds863
Transcription Units1,718
tRNAs46
Protein Features3,624
GO Terms135
Database Version29.0
Sequence SourceGCF_001705075.2
Synonyms Acidithiobacillus ferrooxidans DSM 2392
iron-oxidizing acidophile m-1
Thiobacillus ferrooxidans DSM 2392
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Acidiferrobacterales
Acidiferrobacteraceae
Acidiferrobacter
Acidiferrobacter thiooxydans
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN05526184
NCBI BioProjectPRJNA224116
NCBI-Taxonomy163359
EnvironmentAcid mine drainage
Geographic LocationChina
Latitude/Longitude25.11 N 116.25 E
Collection Date2015-05-1
Annotation ProviderNCBI RefSeq
Annotation Date2021-11-13
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.3
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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