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 ferridurans JCM 18981, 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_AP0187953,0092,86456892,921,399RefSeq:NZ_AP018795
Ortholog data available?Yes
Database Contents
Genes3,009
Pathways203
Enzymatic Reactions1,113
Transport Reactions33
Polypeptides2,864
Protein Complexes49
Enzymes679
Transporters214
Compounds771
Transcription Units1,565
tRNAs46
Protein Features3,405
GO Terms150
Database Version29.0
Sequence SourceGCF_003966655.1
Synonyms Acidithiobacillus sp. D2PG
Acidithiobacillus sp. F221
Acidithiobacillus sp. GG6/10
Acidithiobacillus sp. L11
Acidithiobacillus sp. M12
Acidithiobacillus sp. R10
Acidithiobacillus sp. RIV11
Acidithiobacillus sp. S10
Acidithiobacillus sp. WVa2
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Acidithiobacillia
Acidithiobacillales
Acidithiobacillaceae
Acidithiobacillus
Acidithiobacillus ferridurans
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMD00129984
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1232575
Environmentacidic water
Geographic LocationJapan
Latitude/Longitude35.3164 N 133.9368 E
Collection Date2017-12-8
Annotation ProviderNCBI RefSeq
Annotation Date2021-12-16
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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Page generated by Pathway Tools version 29.0 (software by SRI International) on Mon Jun 30, 2025, BIOCYC17A.