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_TG27327, 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_AMIO0100007430429464353,944RefSeq:NZ_AMIO01000074
NZ_AMIO01000043316302122312,567RefSeq:NZ_AMIO01000043
NZ_AMIO0100003026926315272,577RefSeq:NZ_AMIO01000030
NZ_AMIO0100006021320337215,367RefSeq:NZ_AMIO01000060
NZ_AMIO0100004120520302211,221RefSeq:NZ_AMIO01000041
NZ_AMIO01000020197182114206,342RefSeq:NZ_AMIO01000020
NZ_AMIO0100001917717205181,402RefSeq:NZ_AMIO01000019
NZ_AMIO0100002715915324164,048RefSeq:NZ_AMIO01000027
NZ_AMIO0100001815614781161,007RefSeq:NZ_AMIO01000018
NZ_AMIO0100000115214813155,973RefSeq:NZ_AMIO01000001
NZ_AMIO0100002214814305153,870RefSeq:NZ_AMIO01000022
NZ_AMIO0100010214013172147,110RefSeq:NZ_AMIO01000102
NZ_AMIO0100004713212165140,941RefSeq:NZ_AMIO01000047
NZ_AMIO0100007912312003133,575RefSeq:NZ_AMIO01000079
NZ_AMIO0100009910810512114,200RefSeq:NZ_AMIO01000099
NZ_AMIO010001041009901107,985RefSeq:NZ_AMIO01000104
NZ_AMIO0100000211911612107,071RefSeq:NZ_AMIO01000002
NZ_AMIO0100002667643077,980RefSeq:NZ_AMIO01000026
NZ_AMIO0100003472690372,810RefSeq:NZ_AMIO01000034
NZ_AMIO0100009070690169,788RefSeq:NZ_AMIO01000090
NZ_AMIO0100005467634064,417RefSeq:NZ_AMIO01000054
NZ_AMIO0100005246430354,544RefSeq:NZ_AMIO01000052
NZ_AMIO0100000548470150,376RefSeq:NZ_AMIO01000005
NZ_AMIO0100003537360143,849RefSeq:NZ_AMIO01000035
NZ_AMIO0100005939390042,734RefSeq:NZ_AMIO01000059
NZ_AMIO0100004239370241,301RefSeq:NZ_AMIO01000042
NZ_AMIO0100005333320131,899RefSeq:NZ_AMIO01000053
NZ_AMIO0100008728280026,691RefSeq:NZ_AMIO01000087
NZ_AMIO0100005124240026,206RefSeq:NZ_AMIO01000051
NZ_AMIO0100005824220224,848RefSeq:NZ_AMIO01000058
NZ_AMIO0100000616160019,525RefSeq:NZ_AMIO01000006
NZ_AMIO0100007621150617,565RefSeq:NZ_AMIO01000076
NZ_AMIO0100006712100214,296RefSeq:NZ_AMIO01000067
NZ_AMIO0100003713120114,192RefSeq:NZ_AMIO01000037
NZ_AMIO0100006813120110,413RefSeq:NZ_AMIO01000068
NZ_AMIO010000921410049,513RefSeq:NZ_AMIO01000092
NZ_AMIO010000451010005,529RefSeq:NZ_AMIO01000045
67 Undisplayed Contigs/Replicons157153623155,284
Total:3,8933,713721084,012,960
Ortholog data available?Yes
Database Contents
Genes3,891
Pathways261
Enzymatic Reactions1,292
Transport Reactions111
Polypeptides3,744
Protein Complexes53
Enzymes807
Transporters366
Compounds1,047
Transcription Units2,724
tRNAs64
GO Terms2,409
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii AB_TG27327
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02471232
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1221284
Environmentwound
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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