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 AB5256, 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_AHAI010000416846571017732,474RefSeq:NZ_AHAI01000041
NZ_AHAI0100002930829486322,870RefSeq:NZ_AHAI01000029
NZ_AHAI0100003525425013262,402RefSeq:NZ_AHAI01000035
NZ_AHAI0100001923622484250,601RefSeq:NZ_AHAI01000019
NZ_AHAI0100003023422446233,321RefSeq:NZ_AHAI01000030
NZ_AHAI0100002217817107190,052RefSeq:NZ_AHAI01000022
NZ_AHAI01000020169151126177,601RefSeq:NZ_AHAI01000020
NZ_AHAI0100000916615592156,735RefSeq:NZ_AHAI01000009
NZ_AHAI0100003112912504143,446RefSeq:NZ_AHAI01000031
NZ_AHAI01000050143127016127,210RefSeq:NZ_AHAI01000050
NZ_AHAI01000025118107101123,786RefSeq:NZ_AHAI01000025
NZ_AHAI0100003311611402120,622RefSeq:NZ_AHAI01000033
NZ_AHAI010000371059906116,110RefSeq:NZ_AHAI01000037
NZ_AHAI0100002392882291,564RefSeq:NZ_AHAI01000023
NZ_AHAI0100003979780184,524RefSeq:NZ_AHAI01000039
NZ_AHAI0100002475713183,420RefSeq:NZ_AHAI01000024
NZ_AHAI0100001379741482,967RefSeq:NZ_AHAI01000013
NZ_AHAI0100001180746081,664RefSeq:NZ_AHAI01000011
NZ_AHAI0100003269660372,056RefSeq:NZ_AHAI01000032
NZ_AHAI0100003656520460,441RefSeq:NZ_AHAI01000036
NZ_AHAI01000049594601356,854RefSeq:NZ_AHAI01000049
NZ_AHAI0100002858514356,309RefSeq:NZ_AHAI01000028
NZ_AHAI0100004354510355,623RefSeq:NZ_AHAI01000043
NZ_AHAI0100003863601254,546RefSeq:NZ_AHAI01000038
NZ_AHAI0100001752475053,319RefSeq:NZ_AHAI01000017
NZ_AHAI0100000751455152,021RefSeq:NZ_AHAI01000007
NZ_AHAI0100001646450149,145RefSeq:NZ_AHAI01000016
NZ_AHAI0100000834286032,610RefSeq:NZ_AHAI01000008
NZ_AHAI0100004530271232,602RefSeq:NZ_AHAI01000045
NZ_AHAI0100001529260330,903RefSeq:NZ_AHAI01000015
NZ_AHAI0100004228271023,104RefSeq:NZ_AHAI01000042
NZ_AHAI0100004816150120,621RefSeq:NZ_AHAI01000048
NZ_AHAI0100004718153017,651RefSeq:NZ_AHAI01000047
NZ_AHAI0100001415150016,450RefSeq:NZ_AHAI01000014
NZ_AHAI0100004414100414,942RefSeq:NZ_AHAI01000044
NZ_AHAI010000261385014,775RefSeq:NZ_AHAI01000026
NZ_AHAI010000211275010,965RefSeq:NZ_AHAI01000021
13 Undisplayed Contigs/Replicons55487751,709
Total:4,0243,7721171354,158,015
Ortholog data available?Yes
Database Contents
Genes4,024
Pathways281
Enzymatic Reactions1,351
Transport Reactions116
Polypeptides3,779
Protein Complexes53
Enzymes812
Transporters393
Compounds1,126
Transcription Units2,781
tRNAs81
GO Terms1,321
Database Version29.0
Synonyms Acinetobacter baumannii MRSN961
Acinetobacter baumannii str. AB5256
Acinetobacter baumannii strain AB5256
Acinetobacter baumannii AB5256
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii AB5256
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02435969
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1116235
Environmentblood
Geographic LocationUSA
Collection Date2009
HostHomo sapiens
Annotation ProviderNCBI
Annotation Date2017-11-22
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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