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 WC-692, 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_AMGG0100000334232967364,569RefSeq:NZ_AMGG01000003
NZ_AMGG0100000229928586310,179RefSeq:NZ_AMGG01000002
NZ_AMGG0100005628427815291,566RefSeq:NZ_AMGG01000056
NZ_AMGG0100002822922423249,867RefSeq:NZ_AMGG01000028
NZ_AMGG0100002120920504219,954RefSeq:NZ_AMGG01000021
NZ_AMGG0100001820619916203,556RefSeq:NZ_AMGG01000018
NZ_AMGG01000046188175121190,779RefSeq:NZ_AMGG01000046
NZ_AMGG0100001019218327187,580RefSeq:NZ_AMGG01000010
NZ_AMGG0100007217016181187,130RefSeq:NZ_AMGG01000072
NZ_AMGG0100005317216903176,725RefSeq:NZ_AMGG01000053
NZ_AMGG0100003915414914150,549RefSeq:NZ_AMGG01000039
NZ_AMGG0100004914113272145,551RefSeq:NZ_AMGG01000049
NZ_AMGG0100001312912405140,653RefSeq:NZ_AMGG01000013
NZ_AMGG0100003012311481116,463RefSeq:NZ_AMGG01000030
NZ_AMGG01000007969204109,797RefSeq:NZ_AMGG01000007
NZ_AMGG0100002774720270,713RefSeq:NZ_AMGG01000027
NZ_AMGG0100001450434367,240RefSeq:NZ_AMGG01000014
NZ_AMGG0100004863570667,168RefSeq:NZ_AMGG01000048
NZ_AMGG0100001661580365,434RefSeq:NZ_AMGG01000016
NZ_AMGG0100003765575363,436RefSeq:NZ_AMGG01000037
NZ_AMGG0100001584830162,713RefSeq:NZ_AMGG01000015
NZ_AMGG0100004162564261,436RefSeq:NZ_AMGG01000041
NZ_AMGG0100006056478161,255RefSeq:NZ_AMGG01000060
NZ_AMGG0100007159516257,544RefSeq:NZ_AMGG01000071
NZ_AMGG0100004544383347,731RefSeq:NZ_AMGG01000045
NZ_AMGG0100005443410247,555RefSeq:NZ_AMGG01000054
NZ_AMGG0100006944380642,737RefSeq:NZ_AMGG01000069
NZ_AMGG0100002635285237,757RefSeq:NZ_AMGG01000026
NZ_AMGG0100003434275236,676RefSeq:NZ_AMGG01000034
NZ_AMGG0100006831280335,115RefSeq:NZ_AMGG01000068
NZ_AMGG0100007733275132,330RefSeq:NZ_AMGG01000077
NZ_AMGG0100002032260628,985RefSeq:NZ_AMGG01000020
NZ_AMGG0100002345420328,152RefSeq:NZ_AMGG01000023
NZ_AMGG0100006526250127,932RefSeq:NZ_AMGG01000065
NZ_AMGG0100003818170120,764RefSeq:NZ_AMGG01000038
NZ_AMGG0100006219145019,181RefSeq:NZ_AMGG01000062
NZ_AMGG0100005919171116,425RefSeq:NZ_AMGG01000059
NZ_AMGG0100005017140316,038RefSeq:NZ_AMGG01000050
NZ_AMGG0100007514110314,709RefSeq:NZ_AMGG01000075
NZ_AMGG0100003212110111,131RefSeq:NZ_AMGG01000032
NZ_AMGG0100007411110010,175RefSeq:NZ_AMGG01000074
NZ_AMGG010000311813058,797RefSeq:NZ_AMGG01000031
37 Undisplayed Contigs/Replicons656504479,399
Total:4,1123,8361071694,183,446
Ortholog data available?Yes
Database Contents
Genes4,112
Pathways268
Enzymatic Reactions1,314
Transport Reactions110
Polypeptides3,865
Protein Complexes52
Enzymes803
Transporters367
Compounds1,075
Transcription Units2,821
tRNAs79
GO Terms1,337
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii WC-692
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN00761214
NCBI BioProjectPRJNA224116
NCBI-Taxonomy903913
Environmentintact skin surface
Geographic LocationIraq
Collection Date2008-05-29
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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