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 Acinetobacter lwoffii FDAARGOS_552, 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_CP0462963,1582,953111943,247,623RefSeq:NZ_CP046296
unnamed1220170050221,520RefSeq:NZ_CP046295
unnamed499006,691RefSeq:NZ_CP046299
unnamed388006,573RefSeq:NZ_CP046298
unnamed233003,065RefSeq:NZ_CP046297
Total:3,3983,1431111443,485,472
Ortholog data available?Yes
Database Contents
Genes3,398
Pathways243
Enzymatic Reactions1,259
Transport Reactions53
Polypeptides3,143
Protein Complexes6
Enzymes761
Transporters290
Compounds931
Transcription Units2,350
tRNAs86
Protein Features4,018
GO Terms208
Database Version29.0
Sequence SourceGCF_009730095.1
Synonyms Acinetobacter genomosp. 9
Acinetobacter genomospecies 9
Acinetobacter mesopotamicus
Acinetobacter sp. GC2
Moraxella lwoffi
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter lwoffii
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN10163245
NCBI BioProjectPRJNA224116
NCBI-Taxonomy28090
Environmentclinical isolate
Geographic LocationUSA
HostHomo sapiens
Annotation ProviderNCBI RefSeq
Annotation Date2021-11-14
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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