Database Authors
Pallavi Subhraveti1, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 13-May-2020 from the annotated genome of Acinetobacter baumannii EH, 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 24.0) [Karp16, Karp11] using MetaCyc version 24.0 [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_CP0382583,6893,412951823,752,576RefSeq:NZ_CP038258
pEH_gr13150117033135,229RefSeq:NZ_CP038259
pEH_gr337330425,856RefSeq:NZ_CP038260
pEH_mcr4.321200118,786RefSeq:NZ_CP038261
Total:3,8973,582952203,932,447
Ortholog data available?Yes
Database Contents
Genes3,897
Pathways309
Enzymatic Reactions1,487
Transport Reactions111
Polypeptides3,584
Protein Complexes23
Enzymes870
Transporters364
Compounds1,200
tRNAs73
Protein Features4,457
GO Terms1,221
Database Version29.0
Sequence SourceGCF_004564115.1
Synonyms Acinetobacter genomosp. 2
Acinetobacter genomospecies 2
Bacterium anitratum
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN10386508
NCBI BioProjectPRJNA224116
NCBI-Taxonomy470
Geographic LocationCzech Republic
Latitude/Longitude50.07 N 14.43 E
Collection Date2018
HostHomo sapiens
Human Microbiome Body Sitenot-specified
Annotation ProviderNCBI RefSeq
Annotation Date2019-04-3
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline
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 (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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