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 baumannii ACICU, 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_CP0313803,7513,59194663,919,274RefSeq:NZ_CP031380
pACICU295930270,101RefSeq:NZ_CP031382
pACICU1342301124,268RefSeq:NZ_CP031381
Total:3,8803,70794794,013,643
Ortholog data available?Yes
Database Contents
Genes3,880
Pathways259
Enzymatic Reactions1,292
Transport Reactions107
Polypeptides3,709
Protein Complexes46
Enzymes770
Transporters376
Compounds1,064
Transcription Units2,671
tRNAs72
Protein Features4,541
GO Terms2,251
Database Version29.0
Sequence SourceCP031380
Synonyms Acinetobacter baumannii str. ACICU
Acinetobacter baumannii strain ACICU
Acinetobacter baumannii ACICU
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii ACICU
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN09302593
NCBI BioProjectPRJNA224116
NCBI-Taxonomy405416
Environmentcerebrospinal fluid
Geographic LocationItaly
Latitude/Longitude41.8857 N 12.5024 E
Collection Date2005-12-31/2004-12-31
HostHomo sapiens
Human Microbiome Body Sitecentral-nervous-system
Annotation ProviderNCBI RefSeq
Annotation Date2019-05-22
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.8
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

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