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 boissieri ANC 4422, 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_FMYL01000001429417120471,130RefSeq:NZ_FMYL01000001
NZ_FMYL0100000228227174291,452RefSeq:NZ_FMYL01000002
NZ_FMYL0100000326225516265,498RefSeq:NZ_FMYL01000003
NZ_FMYL0100000422121371233,939RefSeq:NZ_FMYL01000004
NZ_FMYL01000005192175125214,614RefSeq:NZ_FMYL01000005
NZ_FMYL0100000619719061204,378RefSeq:NZ_FMYL01000006
NZ_FMYL0100000719818882190,201RefSeq:NZ_FMYL01000007
NZ_FMYL0100000817316652188,234RefSeq:NZ_FMYL01000008
NZ_FMYL01000009125108116128,199RefSeq:NZ_FMYL01000009
NZ_FMYL01000010969303104,811RefSeq:NZ_FMYL01000010
NZ_FMYL0100001178771085,422RefSeq:NZ_FMYL01000011
NZ_FMYL0100001275730276,133RefSeq:NZ_FMYL01000012
NZ_FMYL0100001354530156,293RefSeq:NZ_FMYL01000013
NZ_FMYL0100001447470056,209RefSeq:NZ_FMYL01000014
NZ_FMYL0100001547470047,192RefSeq:NZ_FMYL01000015
NZ_FMYL0100001628250319,311RefSeq:NZ_FMYL01000016
NZ_FMYL0100001714110316,903RefSeq:NZ_FMYL01000017
NZ_FMYL0100001814130112,821RefSeq:NZ_FMYL01000018
11 Undisplayed Contigs/Replicons21165527,465
Total:2,5582,43865552,690,205
Ortholog data available?Yes
Database Contents
Genes2,558
Pathways221
Enzymatic Reactions1,151
Transport Reactions57
Polypeptides2,447
Protein Complexes6
Enzymes636
Transporters276
Compounds855
Transcription Units1,692
tRNAs58
Protein Features3,117
GO Terms200
Database Version29.0
Sequence SourceGCF_900096955.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter boissieri
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN05421733
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1219383
Annotation ProviderNCBI RefSeq
Annotation Date2021-05-17
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.2
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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