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 13-Mar-2021 from the annotated genome of Acidithiobacillus caldus SM-1, 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 25.0) [Karp16, Karp11] using MetaCyc version 24.5 [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_0158502,9312,80457702,932,225RefSeq:NC_015850
megaplasmid253224029251,782RefSeq:NC_015851
pLAtc332310129,704RefSeq:NC_015854
pLAtc215150014,110RefSeq:NC_015853
pLAtc1119029,778RefSeq:NC_015852
Total:3,2423,083571023,237,599
Ortholog data available?Yes
Database Contents
Genes3,242
Pathways190
Enzymatic Reactions1,018
Transport Reactions43
Polypeptides3,083
Protein Complexes42
Enzymes661
Transporters226
Compounds721
Transcription Units1,748
tRNAs47
Protein Features3,674
GO Terms991
Database Version29.0
Sequence SourceGCF_000221025.1
Synonyms Acidithiobacillus caldus str. SM-1
Acidithiobacillus caldus strain SM-1
Acidithiobacillus caldus SM-1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Acidithiobacillia
Acidithiobacillales
Acidithiobacillaceae
Acidithiobacillus
Acidithiobacillus caldus
Acidithiobacillus caldus SM-1
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02603220
NCBI BioProjectPRJNA224116
NCBI-Taxonomy990288
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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