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 OIFC035, 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_AMTB010000065545341010618,327RefSeq:NZ_AMTB01000006
NZ_AMTB0100002836736016386,584RefSeq:NZ_AMTB01000028
NZ_AMTB0100001135534465376,482RefSeq:NZ_AMTB01000011
NZ_AMTB01000007347335102370,543RefSeq:NZ_AMTB01000007
NZ_AMTB0100000831330148327,620RefSeq:NZ_AMTB01000008
NZ_AMTB01000026251239012263,030RefSeq:NZ_AMTB01000026
NZ_AMTB01000038241228103259,453RefSeq:NZ_AMTB01000038
NZ_AMTB01000035194177134196,338RefSeq:NZ_AMTB01000035
NZ_AMTB0100001717517212184,096RefSeq:NZ_AMTB01000017
NZ_AMTB0100002412912117114,949RefSeq:NZ_AMTB01000024
NZ_AMTB0100002194862692,436RefSeq:NZ_AMTB01000021
NZ_AMTB0100000478770191,342RefSeq:NZ_AMTB01000004
NZ_AMTB0100000589836089,833RefSeq:NZ_AMTB01000005
NZ_AMTB0100003398943189,281RefSeq:NZ_AMTB01000033
NZ_AMTB0100004284822088,709RefSeq:NZ_AMTB01000042
NZ_AMTB0100002076684488,659RefSeq:NZ_AMTB01000020
NZ_AMTB0100002770682075,797RefSeq:NZ_AMTB01000027
NZ_AMTB0100003450491052,409RefSeq:NZ_AMTB01000034
NZ_AMTB0100004451490251,499RefSeq:NZ_AMTB01000044
NZ_AMTB0100001038380043,874RefSeq:NZ_AMTB01000010
NZ_AMTB0100000928271031,522RefSeq:NZ_AMTB01000009
NZ_AMTB0100003024231022,359RefSeq:NZ_AMTB01000030
NZ_AMTB0100003719181016,544RefSeq:NZ_AMTB01000037
NZ_AMTB0100001316142015,442RefSeq:NZ_AMTB01000013
20 Undisplayed Contigs/Replicons111102025,483
Total:3,7723,59881933,972,611
Ortholog data available?Yes
Database Contents
Genes3,763
Pathways280
Enzymatic Reactions1,342
Transport Reactions106
Polypeptides3,613
Protein Complexes56
Enzymes823
Transporters365
Compounds1,060
Transcription Units2,618
tRNAs62
GO Terms1,393
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii OIFC035
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN00761235
NCBI BioProjectPRJNA224116
NCBI-Taxonomy903926
Environmentgroin wound
Geographic LocationUSA
Collection Date2003-08-28
HostHomo sapiens
Annotation ProviderNCBI
Annotation Date2017-03-15
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline
Annotation Pipeline Version4.1
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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