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 Naval-72, 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_AMFI01000006595569917611,021RefSeq:NZ_AMFI01000006
NZ_AMFI010000105004682111504,942RefSeq:NZ_AMFI01000010
NZ_AMFI0100000436536113386,779RefSeq:NZ_AMFI01000004
NZ_AMFI0100001425824864281,749RefSeq:NZ_AMFI01000014
NZ_AMFI0100001326224868279,997RefSeq:NZ_AMFI01000013
NZ_AMFI01000027247232132267,268RefSeq:NZ_AMFI01000027
NZ_AMFI0100003218217714197,199RefSeq:NZ_AMFI01000032
NZ_AMFI01000023199182125196,903RefSeq:NZ_AMFI01000023
NZ_AMFI0100001212912306141,594RefSeq:NZ_AMFI01000012
NZ_AMFI010000501039364102,364RefSeq:NZ_AMFI01000050
NZ_AMFI0100002693849095,363RefSeq:NZ_AMFI01000026
NZ_AMFI0100000778770191,688RefSeq:NZ_AMFI01000007
NZ_AMFI01000040104952790,649RefSeq:NZ_AMFI01000040
NZ_AMFI0100002977760179,910RefSeq:NZ_AMFI01000029
NZ_AMFI0100002176695279,840RefSeq:NZ_AMFI01000021
NZ_AMFI0100002466630360,856RefSeq:NZ_AMFI01000024
NZ_AMFI0100002053474256,077RefSeq:NZ_AMFI01000020
NZ_AMFI0100003152463355,000RefSeq:NZ_AMFI01000031
NZ_AMFI0100001641400145,330RefSeq:NZ_AMFI01000016
NZ_AMFI0100000841329040,475RefSeq:NZ_AMFI01000008
NZ_AMFI0100003044350939,174RefSeq:NZ_AMFI01000030
NZ_AMFI0100004338360236,788RefSeq:NZ_AMFI01000043
NZ_AMFI0100001533280532,742RefSeq:NZ_AMFI01000015
NZ_AMFI01000041311901218,366RefSeq:NZ_AMFI01000041
28 Undisplayed Contigs/Replicons282802548,379
Total:3,7203,4761071373,840,453
Ortholog data available?Yes
Database Contents
Genes3,720
Pathways267
Enzymatic Reactions1,310
Transport Reactions114
Polypeptides3,490
Protein Complexes51
Enzymes789
Transporters354
Compounds1,057
Transcription Units2,621
tRNAs79
GO Terms1,221
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii Naval-72
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN00761229
NCBI BioProjectPRJNA224116
NCBI-Taxonomy903908
Environmentwound
Geographic LocationUSA
Collection Date2006-08-18
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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