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 Acidiphilium multivorum AIU301, 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
NC_0151863,5083,37257793,749,411RefSeq:NC_015186
pACMV1284252032271,573RefSeq:NC_015178
pACMV266650165,564RefSeq:NC_015187
pACMV3655501054,248RefSeq:NC_015179
pACMV439380140,588RefSeq:NC_015188
pACMV518180014,328RefSeq:NC_015180
pACMV614120212,125RefSeq:NC_015181
pACMV787015,178RefSeq:NC_015189
pACMV833001,729RefSeq:NC_015182
Total:4,0053,822571264,214,744
Ortholog data available?Yes
Database Contents
Genes4,005
Pathways299
Enzymatic Reactions1,537
Transport Reactions43
Polypeptides3,822
Protein Complexes126
Enzymes851
Transporters290
Compounds1,122
Transcription Units2,267
tRNAs47
Protein Features4,858
GO Terms260
Database Version29.0
Sequence SourceGCF_000202835.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Alphaproteobacteria
Rhodospirillales
Acetobacteraceae
Acidiphilium
Acidiphilium multivorum
Acidiphilium multivorum AIU301
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMD00060977
NCBI BioProjectPRJNA224116
NCBI-Taxonomy926570
Annotation ProviderNCBI RefSeq
Annotation Date2021-12-14
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.