Database Authors
Pallavi Subhraveti1, Peter Midford1, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 15-Oct-2019 from the annotated genome of Acinetobacter johnsonii IC001, 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 23.0) [Karp16, Karp11] using MetaCyc version 23.1 [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_CP0222983,5503,2241132133,610,322RefSeq:NZ_CP022298
pIC001A987802094,476RefSeq:NZ_CP022299
pIC001B29240522,605RefSeq:NZ_CP022300
pIC001C99006,970RefSeq:NZ_CP022301
pIC001D22001,859RefSeq:NZ_CP022302
Total:3,6883,3371132383,736,232
Ortholog data available?Yes
Database Contents
Genes3,688
Pathways231
Enzymatic Reactions1,405
Transport Reactions7
Polypeptides3,339
Protein Complexes27
Enzymes701
Transporters320
Compounds1,155
Transcription Units2,603
tRNAs88
Protein Features4,117
GO Terms9
Database Version29.0
Synonyms Acinetobacter genomosp. 7
Acinetobacter genomospecies 7
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter johnsonii
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN07298690
NCBI BioProjectPRJNA224116
NCBI-Taxonomy40214
Environmentwater
Geographic LocationJapan
Latitude/Longitude35.689487 N 139.69171 E
Collection Date2003-02
Annotation ProviderNCBI RefSeq
Annotation Date2019-01-14
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline
Annotation Pipeline Version4.7
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 (2019). "The MetaCyc database of metabolic pathways and enzymes-a 2019 update." Nucleic Acids Res. 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

Report Errors or Provide Feedback
Page generated by Pathway Tools version 29.0 (software by SRI International) on Mon Jun 30, 2025, BIOCYC18A.