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 AB_TG27339, 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_AMIR0100004458657619591,345RefSeq:NZ_AMIR01000044
NZ_AMIR01000015473457124481,001RefSeq:NZ_AMIR01000015
NZ_AMIR01000040404383615419,226RefSeq:NZ_AMIR01000040
NZ_AMIR01000013351338112375,069RefSeq:NZ_AMIR01000013
NZ_AMIR0100001222321229235,222RefSeq:NZ_AMIR01000012
NZ_AMIR0100003020419464222,110RefSeq:NZ_AMIR01000030
NZ_AMIR01000036193178114190,735RefSeq:NZ_AMIR01000036
NZ_AMIR0100003516316021185,626RefSeq:NZ_AMIR01000035
NZ_AMIR0100002713913405157,390RefSeq:NZ_AMIR01000027
NZ_AMIR0100003413612745150,922RefSeq:NZ_AMIR01000034
NZ_AMIR0100001888834188,765RefSeq:NZ_AMIR01000018
NZ_AMIR0100002984811288,639RefSeq:NZ_AMIR01000029
NZ_AMIR0100002178750381,661RefSeq:NZ_AMIR01000021
NZ_AMIR0100002576713279,718RefSeq:NZ_AMIR01000025
NZ_AMIR0100004173683274,095RefSeq:NZ_AMIR01000041
NZ_AMIR0100001182801172,871RefSeq:NZ_AMIR01000011
NZ_AMIR0100003865600567,829RefSeq:NZ_AMIR01000038
NZ_AMIR0100000255513163,905RefSeq:NZ_AMIR01000002
NZ_AMIR0100000752491258,629RefSeq:NZ_AMIR01000007
NZ_AMIR0100004651490256,751RefSeq:NZ_AMIR01000046
NZ_AMIR0100000649480150,523RefSeq:NZ_AMIR01000006
NZ_AMIR0100000373730044,021RefSeq:NZ_AMIR01000003
NZ_AMIR0100001059580137,894RefSeq:NZ_AMIR01000010
NZ_AMIR0100000432260627,932RefSeq:NZ_AMIR01000004
NZ_AMIR0100001429281026,983RefSeq:NZ_AMIR01000014
NZ_AMIR0100003123230021,420RefSeq:NZ_AMIR01000031
20 Undisplayed Contigs/Replicons16881221,231
Total:3,8693,690701093,971,513
Ortholog data available?Yes
Database Contents
Genes3,869
Pathways268
Enzymatic Reactions1,292
Transport Reactions97
Polypeptides3,694
Protein Complexes53
Enzymes777
Transporters356
Compounds1,053
Transcription Units2,688
tRNAs62
GO Terms1,286
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii AB_TG27339
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02471260
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1221287
Environmentsputum
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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