Database Authors
Pallavi Subhraveti1, Peter Midford1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 01-June-2022 from the annotated genome of Acinetobacter baumannii 6013113, 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 26.0) [Karp16, Karp11] using MetaCyc version 26.0 [Caspi20]. 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 Institutes of Health.
Genome
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_GL891580347329108349,645RefSeq:NZ_GL891580
NZ_GL89160831230516296,550RefSeq:NZ_GL891608
NZ_GL89150621921315223,244RefSeq:NZ_GL891506
NZ_GL89160722621637214,135RefSeq:NZ_GL891607
NZ_GL89159918117623196,391RefSeq:NZ_GL891599
NZ_GL89161318417455189,876RefSeq:NZ_GL891613
NZ_GL89160917817314186,103RefSeq:NZ_GL891609
NZ_GL89161014113407162,212RefSeq:NZ_GL891610
NZ_GL89153613212714130,516RefSeq:NZ_GL891536
NZ_GL89158911511113126,851RefSeq:NZ_GL891589
NZ_GL89161211911702123,937RefSeq:NZ_GL891612
NZ_GL891512989701111,855RefSeq:NZ_GL891512
NZ_GL89155190881195,381RefSeq:NZ_GL891551
NZ_GL89153881780384,215RefSeq:NZ_GL891538
NZ_GL89155265604168,168RefSeq:NZ_GL891552
NZ_GL89153163584162,512RefSeq:NZ_GL891531
NZ_GL89160150433455,338RefSeq:NZ_GL891601
NZ_GL89152153500355,211RefSeq:NZ_GL891521
NZ_GL89152251500152,093RefSeq:NZ_GL891522
NZ_GL89156335340149,007RefSeq:NZ_GL891563
NZ_GL89154042420046,680RefSeq:NZ_GL891540
NZ_GL89152449430644,586RefSeq:NZ_GL891524
NZ_GL89152942420042,600RefSeq:NZ_GL891529
NZ_GL89160239371140,079RefSeq:NZ_GL891602
NZ_GL89160436340239,017RefSeq:NZ_GL891604
NZ_GL89157736320438,686RefSeq:NZ_GL891577
NZ_GL89155937334038,520RefSeq:NZ_GL891559
NZ_GL89155025250036,948RefSeq:NZ_GL891550
NZ_GL89157534330136,723RefSeq:NZ_GL891575
NZ_GL89156835341035,460RefSeq:NZ_GL891568
NZ_GL89150230300035,312RefSeq:NZ_GL891502
NZ_GL89158133320134,974RefSeq:NZ_GL891581
NZ_GL89158540400034,971RefSeq:NZ_GL891585
NZ_GL89156237352034,914RefSeq:NZ_GL891562
NZ_GL89157332293034,529RefSeq:NZ_GL891573
NZ_GL89157028253033,336RefSeq:NZ_GL891570
NZ_GL89152733330032,800RefSeq:NZ_GL891527
NZ_GL89156124230132,790RefSeq:NZ_GL891561
NZ_GL89155632281330,413RefSeq:NZ_GL891556
NZ_GL89149929290029,568RefSeq:NZ_GL891499
NZ_GL89150025240126,189RefSeq:NZ_GL891500
NZ_GL89159025250025,601RefSeq:NZ_GL891590
NZ_GL89150423230025,221RefSeq:NZ_GL891504
NZ_GL89160020190125,133RefSeq:NZ_GL891600
NZ_GL89155726250124,457RefSeq:NZ_GL891557
NZ_GL89156718170122,571RefSeq:NZ_GL891567
NZ_GL89153922210122,390RefSeq:NZ_GL891539
NZ_GL89153713130020,089RefSeq:NZ_GL891537
NZ_GL89159316140217,029RefSeq:NZ_GL891593
NZ_GL89160317170016,648RefSeq:NZ_GL891603
NZ_GL89150813120114,053RefSeq:NZ_GL891508
NZ_GL89151913110210,631RefSeq:NZ_GL891519
66 Undisplayed Contigs/Replicons134132437182,883
Total:3,8373,645561363,999,041
Ortholog data available?Yes
Database Contents
Genes3,835
Pathways301
Enzymatic Reactions1,465
Transport Reactions84
Polypeptides3,759
Protein Complexes78
Enzymes828
Transporters352
Compounds1,105
Transcription Units2,622
tRNAs49
Protein Features4,361
GO Terms2,292
Database Version29.0
Sequence SourceGCF_000163375.2
Synonyms Acinetobacter sp. 6013113
Acinetobacter baumannii 6013113
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii 6013113
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN00189090
NCBI BioProjectPRJNA224116
NCBI-Taxonomy592014
Environmentskin
HostHomo sapiens
Human Microbiome Body Siteskin
Annotation ProviderNCBI RefSeq
Annotation Date2021-11-7
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.3
Annotation CommentBest-placed reference protein set; GeneMarkS-2+

References

Caspi20: Caspi R, Billington R, Keseler IM, Kothari A, Krummenacker M, Midford PE, Ong WK, Paley S, Subhraveti P, Karp PD (2020). "The MetaCyc database of metabolic pathways and enzymes - a 2019 update." Nucleic Acids Res 48(D1);D445-D453. PMID: 31586394

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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