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 Acidibrevibacterium fodinaquatile G45-3, 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_CP0291763,7053,56856813,907,406RefSeq:NZ_CP029176
unnamed168600868,344RefSeq:NZ_CP029177
unnamed250490145,771RefSeq:NZ_CP029178
unnamed315110416,090RefSeq:NZ_CP029179
Total:3,8383,68856944,037,611
Ortholog data available?Yes
Database Contents
Genes3,838
Pathways257
Enzymatic Reactions1,445
Transport Reactions42
Polypeptides3,688
Protein Complexes5
Enzymes820
Transporters413
Compounds1,095
Transcription Units2,166
tRNAs49
Protein Features4,680
GO Terms281
Database Version29.0
Sequence SourceGCF_003352165.1
Synonyms Acidisphaera sp. G45-3
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Alphaproteobacteria
Rhodospirillales
Acetobacteraceae
Acidibrevibacterium
Acidibrevibacterium fodinaquatile
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN09005679
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1969806
Environmentacidic mine water
Geographic LocationChina
Collection Date2015
Annotation ProviderNCBI RefSeq
Annotation Date2021-02-25
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.1
Annotation CommentBest-placed reference protein set; GeneMarkS-2+
NCBI Genome Typerepresentative

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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