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 UMB003, 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_AEPM01000007265249610286,932RefSeq:NZ_AEPM01000007
NZ_AEPM0100001819718197217,557RefSeq:NZ_AEPM01000018
NZ_AEPM01000036203193010216,805RefSeq:NZ_AEPM01000036
NZ_AEPM01000015179168110181,077RefSeq:NZ_AEPM01000015
NZ_AEPM0100000615915126176,210RefSeq:NZ_AEPM01000006
NZ_AEPM01000005156145110156,988RefSeq:NZ_AEPM01000005
NZ_AEPM0100002413612727145,466RefSeq:NZ_AEPM01000024
NZ_AEPM0100000211711034131,890RefSeq:NZ_AEPM01000002
NZ_AEPM0100003412111407128,889RefSeq:NZ_AEPM01000034
NZ_AEPM0100002911310625127,988RefSeq:NZ_AEPM01000029
NZ_AEPM0100002513412554126,750RefSeq:NZ_AEPM01000025
NZ_AEPM0100000912110957126,727RefSeq:NZ_AEPM01000009
NZ_AEPM0100000311811512126,458RefSeq:NZ_AEPM01000003
NZ_AEPM010000331009028125,747RefSeq:NZ_AEPM01000033
NZ_AEPM01000012938238108,946RefSeq:NZ_AEPM01000012
NZ_AEPM0100006512312003107,356RefSeq:NZ_AEPM01000065
NZ_AEPM0100001485780796,577RefSeq:NZ_AEPM01000014
NZ_AEPM0100004084780692,687RefSeq:NZ_AEPM01000040
NZ_AEPM0100003177730487,849RefSeq:NZ_AEPM01000031
NZ_AEPM0100000479702784,634RefSeq:NZ_AEPM01000004
NZ_AEPM0100003080740684,536RefSeq:NZ_AEPM01000030
NZ_AEPM0100003881763283,879RefSeq:NZ_AEPM01000038
NZ_AEPM0100002165603267,011RefSeq:NZ_AEPM01000021
NZ_AEPM0100000859560359,942RefSeq:NZ_AEPM01000008
NZ_AEPM0100002851460558,476RefSeq:NZ_AEPM01000028
NZ_AEPM0100005855471755,793RefSeq:NZ_AEPM01000058
NZ_AEPM0100002657551154,496RefSeq:NZ_AEPM01000026
NZ_AEPM0100001344400451,069RefSeq:NZ_AEPM01000013
NZ_AEPM0100000148443148,796RefSeq:NZ_AEPM01000001
NZ_AEPM0100002743390446,747RefSeq:NZ_AEPM01000027
NZ_AEPM0100001939380145,804RefSeq:NZ_AEPM01000019
NZ_AEPM0100003546432144,372RefSeq:NZ_AEPM01000035
NZ_AEPM0100001641363241,976RefSeq:NZ_AEPM01000016
NZ_AEPM0100001137330441,828RefSeq:NZ_AEPM01000011
NZ_AEPM0100004229280135,719RefSeq:NZ_AEPM01000042
NZ_AEPM0100004137305233,977RefSeq:NZ_AEPM01000041
NZ_AEPM0100001025230233,524RefSeq:NZ_AEPM01000010
NZ_AEPM0100004328270131,673RefSeq:NZ_AEPM01000043
NZ_AEPM0100002226240231,183RefSeq:NZ_AEPM01000022
NZ_AEPM0100004623220128,750RefSeq:NZ_AEPM01000046
NZ_AEPM0100003924231027,823RefSeq:NZ_AEPM01000039
NZ_AEPM0100003230262227,273RefSeq:NZ_AEPM01000032
NZ_AEPM0100004423220124,807RefSeq:NZ_AEPM01000044
NZ_AEPM0100002022200223,775RefSeq:NZ_AEPM01000020
NZ_AEPM0100004722220022,488RefSeq:NZ_AEPM01000047
NZ_AEPM0100004518131420,647RefSeq:NZ_AEPM01000045
NZ_AEPM0100005220200017,863RefSeq:NZ_AEPM01000052
NZ_AEPM0100003717150217,739RefSeq:NZ_AEPM01000037
NZ_AEPM0100006016160017,063RefSeq:NZ_AEPM01000060
NZ_AEPM0100005922210116,353RefSeq:NZ_AEPM01000059
NZ_AEPM0100005715140113,245RefSeq:NZ_AEPM01000057
NZ_AEPM01000048109019,180RefSeq:NZ_AEPM01000048
NZ_AEPM010000491511047,250RefSeq:NZ_AEPM01000049
43 Undisplayed Contigs/Replicons8073911110,119
Total:3,9213,630782134,188,709
Ortholog data available?Yes
Database Contents
Genes3,913
Pathways245
Enzymatic Reactions1,261
Transport Reactions43
Polypeptides3,732
Protein Complexes31
Enzymes847
Transporters377
Compounds1,085
Transcription Units2,763
tRNAs59
GO Terms1,267
Database Version29.0
Synonyms Acinetobacter baumannii str. UMB003
Acinetobacter baumannii strain UMB003
Acinetobacter baumannii UMB003
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii UMB003
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02436014
NCBI BioProjectPRJNA190221
NCBI-Taxonomy933265
Environmentwound
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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