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 OIFC065, 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_AMFV01000016460439156468,640RefSeq:NZ_AMFV01000016
NZ_AMFV0100003434333274366,591RefSeq:NZ_AMFV01000034
NZ_AMFV0100002437536294359,611RefSeq:NZ_AMFV01000024
NZ_AMFV0100004632432013336,379RefSeq:NZ_AMFV01000046
NZ_AMFV0100003226225714275,888RefSeq:NZ_AMFV01000032
NZ_AMFV0100002122922405242,208RefSeq:NZ_AMFV01000021
NZ_AMFV01000017232216106230,647RefSeq:NZ_AMFV01000017
NZ_AMFV0100002720519717210,169RefSeq:NZ_AMFV01000027
NZ_AMFV01000028196177136198,077RefSeq:NZ_AMFV01000028
NZ_AMFV0100000917517122187,628RefSeq:NZ_AMFV01000009
NZ_AMFV0100000211911432128,787RefSeq:NZ_AMFV01000002
NZ_AMFV0100004313813107122,569RefSeq:NZ_AMFV01000043
NZ_AMFV0100003398922493,417RefSeq:NZ_AMFV01000033
NZ_AMFV0100001879780190,345RefSeq:NZ_AMFV01000018
NZ_AMFV0100001390836189,416RefSeq:NZ_AMFV01000013
NZ_AMFV0100004965600566,084RefSeq:NZ_AMFV01000049
NZ_AMFV0100002249423453,281RefSeq:NZ_AMFV01000022
NZ_AMFV0100004248460252,782RefSeq:NZ_AMFV01000042
NZ_AMFV0100000872710152,367RefSeq:NZ_AMFV01000008
NZ_AMFV0100000149471151,672RefSeq:NZ_AMFV01000001
NZ_AMFV0100004146450150,098RefSeq:NZ_AMFV01000041
NZ_AMFV0100003538380043,908RefSeq:NZ_AMFV01000035
NZ_AMFV0100001133293139,937RefSeq:NZ_AMFV01000011
NZ_AMFV0100000349480138,932RefSeq:NZ_AMFV01000003
NZ_AMFV0100003837340331,286RefSeq:NZ_AMFV01000038
NZ_AMFV0100000731283028,317RefSeq:NZ_AMFV01000007
NZ_AMFV0100002624240024,521RefSeq:NZ_AMFV01000026
NZ_AMFV0100002518150321,019RefSeq:NZ_AMFV01000025
NZ_AMFV0100004415122112,729RefSeq:NZ_AMFV01000044
NZ_AMFV0100001412120010,798RefSeq:NZ_AMFV01000014
24 Undisplayed Contigs/Replicons424212051,543
Total:3,9743,786831054,029,646
Ortholog data available?Yes
Database Contents
Genes3,962
Pathways265
Enzymatic Reactions1,303
Transport Reactions115
Polypeptides3,801
Protein Complexes51
Enzymes787
Transporters356
Compounds1,062
Transcription Units2,711
tRNAs61
GO Terms1,380
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii OIFC065
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN00761244
NCBI BioProjectPRJNA224116
NCBI-Taxonomy903932
Environmentpatient left leg
Geographic LocationUSA
Collection Date2003-07-17
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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