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-116, 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_AMGF01000017681665106685,051RefSeq:NZ_AMGF01000017
NZ_AMGF01000005459438147468,623RefSeq:NZ_AMGF01000005
NZ_AMGF0100001237236615388,660RefSeq:NZ_AMGF01000012
NZ_AMGF0100002534233165364,345RefSeq:NZ_AMGF01000025
NZ_AMGF0100003323422707245,621RefSeq:NZ_AMGF01000033
NZ_AMGF0100000320820152227,177RefSeq:NZ_AMGF01000003
NZ_AMGF01000024190176104198,461RefSeq:NZ_AMGF01000024
NZ_AMGF01000026195177135197,163RefSeq:NZ_AMGF01000026
NZ_AMGF0100000413913423147,600RefSeq:NZ_AMGF01000004
NZ_AMGF0100000211911360126,399RefSeq:NZ_AMGF01000002
NZ_AMGF0100002113813008122,568RefSeq:NZ_AMGF01000021
NZ_AMGF0100003411010712116,361RefSeq:NZ_AMGF01000034
NZ_AMGF0100001097900794,556RefSeq:NZ_AMGF01000010
NZ_AMGF0100000879780190,348RefSeq:NZ_AMGF01000008
NZ_AMGF0100002998902687,101RefSeq:NZ_AMGF01000029
NZ_AMGF0100002768583774,994RefSeq:NZ_AMGF01000027
NZ_AMGF0100000962580465,943RefSeq:NZ_AMGF01000009
NZ_AMGF0100001152474154,458RefSeq:NZ_AMGF01000011
NZ_AMGF0100003139380143,185RefSeq:NZ_AMGF01000031
NZ_AMGF0100001849480138,030RefSeq:NZ_AMGF01000018
NZ_AMGF0100000736340231,860RefSeq:NZ_AMGF01000007
NZ_AMGF0100001530282028,301RefSeq:NZ_AMGF01000015
NZ_AMGF0100002321182119,579RefSeq:NZ_AMGF01000023
NZ_AMGF010000371290312,770RefSeq:NZ_AMGF01000037
16 Undisplayed Contigs/Replicons121221423,357
Total:3,8583,673831023,952,511
Ortholog data available?Yes
Database Contents
Genes3,849
Pathways265
Enzymatic Reactions1,298
Transport Reactions115
Polypeptides3,682
Protein Complexes53
Enzymes784
Transporters359
Compounds1,061
Transcription Units2,652
tRNAs63
GO Terms1,335
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii IS-116
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN00761231
NCBI BioProjectPRJNA224116
NCBI-Taxonomy903912
Environmentwound
Geographic LocationIraq
Collection Date2008-02
HostHomo sapiens
Annotation ProviderNCBI
Annotation Date2017-11-23
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline
Annotation Pipeline Version4.3
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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