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 IS-123, 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_ALII010000107777193028787,833RefSeq:NZ_ALII01000010
NZ_ALII010000076546131031658,707RefSeq:NZ_ALII01000007
NZ_ALII01000017569527933583,886RefSeq:NZ_ALII01000017
NZ_ALII01000011351324225366,410RefSeq:NZ_ALII01000011
NZ_ALII010000163493181714361,162RefSeq:NZ_ALII01000016
NZ_ALII01000003322311011341,416RefSeq:NZ_ALII01000003
NZ_ALII01000012308289811335,764RefSeq:NZ_ALII01000012
NZ_ALII01000005303274920319,035RefSeq:NZ_ALII01000005
NZ_ALII01000002132116106140,907RefSeq:NZ_ALII01000002
pIS123-6792870567,025RefSeq:NZ_ALII01000020
NZ_ALII0100001533310231,269RefSeq:NZ_ALII01000015
NZ_ALII01000008382701125,771RefSeq:NZ_ALII01000008
pIS123-1823220117,984RefSeq:NZ_ALII01000019
pIS123-1215130211,600RefSeq:NZ_ALII01000018
6 Undisplayed Contigs/Replicons770514,312
Total:3,9783,678952054,063,081
Ortholog data available?Yes
Database Contents
Genes3,978
Pathways248
Enzymatic Reactions1,251
Transport Reactions110
Polypeptides3,682
Protein Complexes53
Enzymes754
Transporters361
Compounds1,017
Transcription Units2,709
tRNAs73
GO Terms1,385
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii IS-123
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02436485
NCBI BioProjectPRJNA224116
NCBI-Taxonomy903899
Geographic LocationIraq
Collection Date2009-02-9
HostHomo sapiens
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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