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 AB_909-02-7, 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_AMHZ01000075298284410326,492RefSeq:NZ_AMHZ01000075
NZ_AMHZ0100007428928414298,483RefSeq:NZ_AMHZ01000074
NZ_AMHZ0100008725024901260,343RefSeq:NZ_AMHZ01000087
NZ_AMHZ0100008324323553244,040RefSeq:NZ_AMHZ01000083
NZ_AMHZ01000041234222111241,719RefSeq:NZ_AMHZ01000041
NZ_AMHZ0100005317416482177,645RefSeq:NZ_AMHZ01000053
NZ_AMHZ0100007612612510156,835RefSeq:NZ_AMHZ01000076
NZ_AMHZ0100005814113623150,168RefSeq:NZ_AMHZ01000058
NZ_AMHZ0100004712611853138,985RefSeq:NZ_AMHZ01000047
NZ_AMHZ0100002212712511138,572RefSeq:NZ_AMHZ01000022
NZ_AMHZ0100001212312201119,618RefSeq:NZ_AMHZ01000012
NZ_AMHZ0100005912111830114,536RefSeq:NZ_AMHZ01000059
NZ_AMHZ0100008211010244114,064RefSeq:NZ_AMHZ01000082
NZ_AMHZ010000131059915112,588RefSeq:NZ_AMHZ01000013
NZ_AMHZ0100000495921294,913RefSeq:NZ_AMHZ01000004
NZ_AMHZ0100003280780291,721RefSeq:NZ_AMHZ01000032
NZ_AMHZ0100006879750485,059RefSeq:NZ_AMHZ01000068
NZ_AMHZ0100005481755182,300RefSeq:NZ_AMHZ01000054
NZ_AMHZ0100004374712173,290RefSeq:NZ_AMHZ01000043
NZ_AMHZ0100002969680167,639RefSeq:NZ_AMHZ01000029
NZ_AMHZ0100005664630166,031RefSeq:NZ_AMHZ01000056
NZ_AMHZ0100002058570161,485RefSeq:NZ_AMHZ01000020
NZ_AMHZ0100003158561160,630RefSeq:NZ_AMHZ01000031
NZ_AMHZ0100004960554157,663RefSeq:NZ_AMHZ01000049
NZ_AMHZ0100000953520157,243RefSeq:NZ_AMHZ01000009
NZ_AMHZ0100003959553151,909RefSeq:NZ_AMHZ01000039
NZ_AMHZ0100007342410143,520RefSeq:NZ_AMHZ01000073
NZ_AMHZ0100003039390043,391RefSeq:NZ_AMHZ01000030
NZ_AMHZ0100004444401338,011RefSeq:NZ_AMHZ01000044
NZ_AMHZ0100000830273035,482RefSeq:NZ_AMHZ01000008
NZ_AMHZ0100005729290032,030RefSeq:NZ_AMHZ01000057
NZ_AMHZ0100002827260130,175RefSeq:NZ_AMHZ01000028
NZ_AMHZ0100005226260027,289RefSeq:NZ_AMHZ01000052
NZ_AMHZ0100006128280026,427RefSeq:NZ_AMHZ01000061
NZ_AMHZ0100003622191220,213RefSeq:NZ_AMHZ01000036
NZ_AMHZ0100004528280017,059RefSeq:NZ_AMHZ01000045
NZ_AMHZ0100005128271016,663RefSeq:NZ_AMHZ01000051
NZ_AMHZ0100006318160216,125RefSeq:NZ_AMHZ01000063
NZ_AMHZ0100007919150415,321RefSeq:NZ_AMHZ01000079
NZ_AMHZ0100009816160014,968RefSeq:NZ_AMHZ01000098
NZ_AMHZ0100006912100214,359RefSeq:NZ_AMHZ01000069
NZ_AMHZ0100007214120212,162RefSeq:NZ_AMHZ01000072
56 Undisplayed Contigs/Replicons696473282,473
Total:3,8223,643651143,929,639
Ortholog data available?Yes
Database Contents
Genes3,820
Pathways268
Enzymatic Reactions1,290
Transport Reactions107
Polypeptides3,662
Protein Complexes52
Enzymes790
Transporters351
Compounds1,047
Transcription Units2,652
tRNAs56
GO Terms2,284
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii AB_909-02-7
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02471282
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1221270
Environmentsputum
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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