Database Authors
Pallavi Subhraveti1, Peter Midford, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 15-Feb-2019 from the annotated genome of Acinetobacter baumannii Ab11111, 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 23.0 [Caspi18]. 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 Institutess of Health.
Genome
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_JH8155572,3372,24738522,462,629RefSeq:NZ_JH815557
NZ_JH8155535204892011542,454RefSeq:NZ_JH815553
NZ_JH815558455434147479,474RefSeq:NZ_JH815558
NZ_JH815555251236132266,817RefSeq:NZ_JH815555
NZ_JH815559165151113175,204RefSeq:NZ_JH815559
NZ_JH81555612211615110,965RefSeq:NZ_JH815556
NZ_JH81555434286032,726RefSeq:NZ_JH815554
NZ_JH81556165014,030RefSeq:NZ_JH815561
NZ_JH81556011003,243RefSeq:NZ_JH815560
NZ_JH81556244002,789RefSeq:NZ_JH815562
Total:3,8953,711103814,080,331
Ortholog data available?Yes
Database Contents
Genes3,894
Pathways259
Enzymatic Reactions1,296
Transport Reactions113
Polypeptides3,720
Protein Complexes53
Enzymes812
Transporters363
Compounds1,059
Transcription Units2,676
tRNAs77
GO Terms2,439
Database Version29.0
Synonyms Acinetobacter baumannii str. Ab11111
Acinetobacter baumannii strain Ab11111
Acinetobacter baumannii Ab11111
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii Ab11111
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02596915
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1168588
Annotation ProviderNCBI
Annotation Date2017-03-15
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline
Annotation Pipeline Version4.1
Annotation CommentBest-placed reference protein set; GeneMarkS+

References

Caspi18: Caspi R, Billington R, Fulcher CA, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Midford PE, Ong Q, Ong WK, Paley S, Subhraveti P, Karp PD (2018). "The MetaCyc database of metabolic pathways and enzymes." Nucleic Acids Res 46(D1);D633-D639. PMID: 29059334

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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