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 Canada BC1, 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_AMSZ01000028331315214331,250RefSeq:NZ_AMSZ01000028
NZ_AMSZ0100006528427455287,076RefSeq:NZ_AMSZ01000065
NZ_AMSZ01000039287269153276,126RefSeq:NZ_AMSZ01000039
NZ_AMSZ0100005724523807256,983RefSeq:NZ_AMSZ01000057
NZ_AMSZ0100006421921621244,277RefSeq:NZ_AMSZ01000064
NZ_AMSZ01000061231218211243,689RefSeq:NZ_AMSZ01000061
NZ_AMSZ01000010198180135198,162RefSeq:NZ_AMSZ01000010
NZ_AMSZ0100004918017802190,509RefSeq:NZ_AMSZ01000049
NZ_AMSZ0100004418817774187,683RefSeq:NZ_AMSZ01000044
NZ_AMSZ0100005115614664171,540RefSeq:NZ_AMSZ01000051
NZ_AMSZ0100005616416013167,516RefSeq:NZ_AMSZ01000056
NZ_AMSZ0100004011410905113,430RefSeq:NZ_AMSZ01000040
NZ_AMSZ0100000296960099,469RefSeq:NZ_AMSZ01000002
NZ_AMSZ0100002584810395,659RefSeq:NZ_AMSZ01000025
NZ_AMSZ0100002695901495,512RefSeq:NZ_AMSZ01000026
NZ_AMSZ0100002788831494,413RefSeq:NZ_AMSZ01000027
NZ_AMSZ0100006389835191,369RefSeq:NZ_AMSZ01000063
NZ_AMSZ0100001372682276,586RefSeq:NZ_AMSZ01000013
NZ_AMSZ0100000763600371,183RefSeq:NZ_AMSZ01000007
NZ_AMSZ0100003255484368,116RefSeq:NZ_AMSZ01000032
NZ_AMSZ0100002362564258,821RefSeq:NZ_AMSZ01000023
NZ_AMSZ0100006052470556,016RefSeq:NZ_AMSZ01000060
NZ_AMSZ0100000145421247,816RefSeq:NZ_AMSZ01000001
NZ_AMSZ0100005043410244,481RefSeq:NZ_AMSZ01000050
NZ_AMSZ0100004129243236,219RefSeq:NZ_AMSZ01000041
NZ_AMSZ0100000843410235,082RefSeq:NZ_AMSZ01000008
NZ_AMSZ0100001727270034,810RefSeq:NZ_AMSZ01000017
NZ_AMSZ0100001632292133,009RefSeq:NZ_AMSZ01000016
NZ_AMSZ0100001148400832,042RefSeq:NZ_AMSZ01000011
NZ_AMSZ0100005533285029,356RefSeq:NZ_AMSZ01000055
NZ_AMSZ0100004633290429,082RefSeq:NZ_AMSZ01000046
NZ_AMSZ0100005224220224,725RefSeq:NZ_AMSZ01000052
NZ_AMSZ0100005330291017,383RefSeq:NZ_AMSZ01000053
NZ_AMSZ0100003728280017,252RefSeq:NZ_AMSZ01000037
NZ_AMSZ010000031492314,401RefSeq:NZ_AMSZ01000003
31 Undisplayed Contigs/Replicons565263065,361
Total:3,8703,633901473,936,404
Ortholog data available?Yes
Database Contents
Genes3,864
Pathways268
Enzymatic Reactions1,292
Transport Reactions109
Polypeptides3,646
Protein Complexes52
Enzymes786
Transporters356
Compounds1,044
Transcription Units2,686
tRNAs70
GO Terms2,273
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii Canada BC1
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN00761234
NCBI BioProjectPRJNA224116
NCBI-Taxonomy903924
Environmentpatient affected by a nosocomial spread of war-related MDR-ABC in a Canadian civilian hospital with origin from soldier evacuated via Landstuhl Regional Medical Center
Geographic LocationCanada
Collection Date2007
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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