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 AB4857, 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_AHAG01000049343316225367,162RefSeq:NZ_AHAG01000049
NZ_AHAG01000041309288516330,937RefSeq:NZ_AHAG01000041
NZ_AHAG01000018236213518253,834RefSeq:NZ_AHAG01000018
NZ_AHAG01000016237216714239,251RefSeq:NZ_AHAG01000016
NZ_AHAG01000026203183713225,228RefSeq:NZ_AHAG01000026
NZ_AHAG01000013197176813217,373RefSeq:NZ_AHAG01000013
NZ_AHAG01000034173162110191,150RefSeq:NZ_AHAG01000034
NZ_AHAG01000044171160011189,409RefSeq:NZ_AHAG01000044
NZ_AHAG01000043158145013165,145RefSeq:NZ_AHAG01000043
NZ_AHAG01000012169148912160,243RefSeq:NZ_AHAG01000012
NZ_AHAG01000045149137012152,325RefSeq:NZ_AHAG01000045
NZ_AHAG01000051126115110141,919RefSeq:NZ_AHAG01000051
NZ_AHAG0100003012511375129,511RefSeq:NZ_AHAG01000030
NZ_AHAG010000191039454117,622RefSeq:NZ_AHAG01000019
NZ_AHAG0100002582770592,141RefSeq:NZ_AHAG01000025
NZ_AHAG0100002089815391,258RefSeq:NZ_AHAG01000020
NZ_AHAG0100001484763590,691RefSeq:NZ_AHAG01000014
NZ_AHAG01000033816911184,061RefSeq:NZ_AHAG01000033
NZ_AHAG0100001776676380,276RefSeq:NZ_AHAG01000017
NZ_AHAG0100000956478158,332RefSeq:NZ_AHAG01000009
NZ_AHAG0100003152435456,165RefSeq:NZ_AHAG01000031
NZ_AHAG0100005245402355,693RefSeq:NZ_AHAG01000052
NZ_AHAG01000038695601355,618RefSeq:NZ_AHAG01000038
NZ_AHAG0100002851434455,084RefSeq:NZ_AHAG01000028
NZ_AHAG0100004249470250,611RefSeq:NZ_AHAG01000042
NZ_AHAG0100003633283242,660RefSeq:NZ_AHAG01000036
NZ_AHAG0100001035258235,931RefSeq:NZ_AHAG01000010
NZ_AHAG0100004734320232,842RefSeq:NZ_AHAG01000047
NZ_AHAG0100003526201532,399RefSeq:NZ_AHAG01000035
NZ_AHAG0100002125205028,546RefSeq:NZ_AHAG01000021
NZ_AHAG0100003218180019,523RefSeq:NZ_AHAG01000032
NZ_AHAG0100002411100116,931RefSeq:NZ_AHAG01000024
NZ_AHAG0100004016133016,142RefSeq:NZ_AHAG01000040
NZ_AHAG0100000716130316,061RefSeq:NZ_AHAG01000007
NZ_AHAG010000291485115,160RefSeq:NZ_AHAG01000029
NZ_AHAG0100002224240013,459RefSeq:NZ_AHAG01000022
NZ_AHAG0100001114110312,870RefSeq:NZ_AHAG01000011
NZ_AHAG0100003918170110,588RefSeq:NZ_AHAG01000039
NZ_AHAG0100000420190110,191RefSeq:NZ_AHAG01000004
NZ_AHAG0100005098019,830RefSeq:NZ_AHAG01000050
NZ_AHAG01000008119029,461RefSeq:NZ_AHAG01000008
13 Undisplayed Contigs/Replicons30300749,011
Total:3,7943,4171162614,022,644
Ortholog data available?Yes
Database Contents
Genes3,794
Pathways238
Enzymatic Reactions1,235
Transport Reactions42
Polypeptides3,486
Protein Complexes30
Enzymes832
Transporters350
Compounds1,070
Transcription Units2,678
tRNAs83
GO Terms1,315
Database Version29.0
Synonyms Acinetobacter baumannii MRSN939
Acinetobacter baumannii str. AB4857
Acinetobacter baumannii strain AB4857
Acinetobacter baumannii AB4857
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii AB4857
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02435900
NCBI BioProjectPRJNA190310
NCBI-Taxonomy1116233
Environmentisolated from a bone infection
Geographic LocationUSA
Collection Date2009
HostHomo sapiens
Annotation ProviderNCBI
Annotation Date2014-06-21
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline
Annotation Pipeline Version2.6 (rev. 437773)
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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