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 gerneri CIP 107464, 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
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_KB849544750731514841,291RefSeq:NZ_KB849544
NZ_KB8495435755382314645,261RefSeq:NZ_KB849543
NZ_KB84954255254138610,553RefSeq:NZ_KB849542
NZ_KB849545540514224564,812RefSeq:NZ_KB849545
NZ_KB849549452438131482,049RefSeq:NZ_KB849549
NZ_KB84953732130696363,495RefSeq:NZ_KB849537
NZ_KB84953327226291294,712RefSeq:NZ_KB849533
NZ_KB84953924523852235,360RefSeq:NZ_KB849539
NZ_KB84953818417473188,989RefSeq:NZ_KB849538
NZ_KB84955310491013116,408RefSeq:NZ_KB849553
NZ_KB84955477740379,952RefSeq:NZ_KB849554
NZ_KB84955530290121,068RefSeq:NZ_KB849555
NZ_KB84954722190320,182RefSeq:NZ_KB849547
29 Undisplayed Contigs/Replicons9999017131,040
Total:4,2404,05496904,595,172
Ortholog data available?Yes
Database Contents
Genes4,237
Pathways274
Enzymatic Reactions1,374
Transport Reactions63
Polypeptides4,104
Protein Complexes5
Enzymes817
Transporters403
Compounds1,027
Transcription Units3,090
tRNAs73
Protein Features4,720
GO Terms291
Database Version29.0
Sequence SourceGCF_000368565.1
Synonyms Acinetobacter gerneri CIP 107464
Acinetobacter gerneri DSM 14967
Acinetobacter gerneri MTCC 9824
Acinetobacter gerneri DSM 14967 = CIP 107464 = MTCC 9824
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter gerneri
Acinetobacter gerneri DSM 14967 = CIP 107464 = MTCC 9824
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN01087849
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1120926
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+
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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