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_2008-15-34-7, 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_AMHK0100011827626646290,673RefSeq:NZ_AMHK01000118
NZ_AMHK0100001622121434245,917RefSeq:NZ_AMHK01000016
NZ_AMHK0100014017816693187,837RefSeq:NZ_AMHK01000140
NZ_AMHK0100000718718403179,596RefSeq:NZ_AMHK01000007
NZ_AMHK0100014712712034136,697RefSeq:NZ_AMHK01000147
NZ_AMHK0100015412712061132,674RefSeq:NZ_AMHK01000154
NZ_AMHK0100013211010622119,105RefSeq:NZ_AMHK01000132
NZ_AMHK0100009510110001108,657RefSeq:NZ_AMHK01000095
NZ_AMHK01000126949202104,649RefSeq:NZ_AMHK01000126
NZ_AMHK01000024919001102,982RefSeq:NZ_AMHK01000024
NZ_AMHK010001121051021299,079RefSeq:NZ_AMHK01000112
NZ_AMHK0100011992901197,548RefSeq:NZ_AMHK01000119
NZ_AMHK0100011587834088,781RefSeq:NZ_AMHK01000115
NZ_AMHK0100010765640177,102RefSeq:NZ_AMHK01000107
NZ_AMHK0100012980762276,292RefSeq:NZ_AMHK01000129
NZ_AMHK0100009268660272,764RefSeq:NZ_AMHK01000092
NZ_AMHK0100008061590264,721RefSeq:NZ_AMHK01000080
NZ_AMHK0100004571655163,260RefSeq:NZ_AMHK01000045
NZ_AMHK0100008658570162,070RefSeq:NZ_AMHK01000086
NZ_AMHK0100011359580160,523RefSeq:NZ_AMHK01000113
NZ_AMHK0100010066650159,818RefSeq:NZ_AMHK01000100
NZ_AMHK0100011766650156,001RefSeq:NZ_AMHK01000117
NZ_AMHK0100014949460350,381RefSeq:NZ_AMHK01000149
NZ_AMHK0100015753510249,840RefSeq:NZ_AMHK01000157
NZ_AMHK0100009847460148,967RefSeq:NZ_AMHK01000098
NZ_AMHK0100005663630046,419RefSeq:NZ_AMHK01000056
NZ_AMHK0100009443411145,760RefSeq:NZ_AMHK01000094
NZ_AMHK0100011140390143,894RefSeq:NZ_AMHK01000111
NZ_AMHK0100009036350143,398RefSeq:NZ_AMHK01000090
NZ_AMHK0100000638353041,153RefSeq:NZ_AMHK01000006
NZ_AMHK0100012835340139,321RefSeq:NZ_AMHK01000128
NZ_AMHK0100015128270137,763RefSeq:NZ_AMHK01000151
NZ_AMHK0100012031283037,482RefSeq:NZ_AMHK01000120
NZ_AMHK0100006437350237,202RefSeq:NZ_AMHK01000064
NZ_AMHK0100007033320136,904RefSeq:NZ_AMHK01000070
NZ_AMHK0100012441390235,801RefSeq:NZ_AMHK01000124
NZ_AMHK0100014132310135,620RefSeq:NZ_AMHK01000141
NZ_AMHK0100013035341035,504RefSeq:NZ_AMHK01000130
NZ_AMHK0100013336341134,825RefSeq:NZ_AMHK01000133
NZ_AMHK0100000134330133,698RefSeq:NZ_AMHK01000001
NZ_AMHK0100009735330231,267RefSeq:NZ_AMHK01000097
NZ_AMHK0100006935320329,877RefSeq:NZ_AMHK01000069
NZ_AMHK0100009125250029,397RefSeq:NZ_AMHK01000091
NZ_AMHK0100010624230128,547RefSeq:NZ_AMHK01000106
NZ_AMHK0100013129244128,244RefSeq:NZ_AMHK01000131
NZ_AMHK0100001826260024,826RefSeq:NZ_AMHK01000018
NZ_AMHK0100014823220124,024RefSeq:NZ_AMHK01000148
NZ_AMHK0100008921190223,482RefSeq:NZ_AMHK01000089
NZ_AMHK0100013520180223,460RefSeq:NZ_AMHK01000135
NZ_AMHK0100001927270023,329RefSeq:NZ_AMHK01000019
NZ_AMHK0100012117170022,008RefSeq:NZ_AMHK01000121
NZ_AMHK0100012716150121,601RefSeq:NZ_AMHK01000127
NZ_AMHK0100010122200220,696RefSeq:NZ_AMHK01000101
NZ_AMHK0100003216151018,385RefSeq:NZ_AMHK01000032
NZ_AMHK0100007319180117,937RefSeq:NZ_AMHK01000073
NZ_AMHK0100000415150017,714RefSeq:NZ_AMHK01000004
NZ_AMHK0100004618180017,670RefSeq:NZ_AMHK01000046
NZ_AMHK0100000914140017,573RefSeq:NZ_AMHK01000009
NZ_AMHK0100003914113014,668RefSeq:NZ_AMHK01000039
NZ_AMHK0100006215150013,366RefSeq:NZ_AMHK01000062
NZ_AMHK0100011613130012,926RefSeq:NZ_AMHK01000116
NZ_AMHK0100010213100312,278RefSeq:NZ_AMHK01000102
NZ_AMHK0100014415150010,085RefSeq:NZ_AMHK01000144
NZ_AMHK010000251514017,525RefSeq:NZ_AMHK01000025
93 Undisplayed Contigs/Replicons193186744207,112
Total:3,8253,636641253,918,675
Ortholog data available?Yes
Database Contents
Genes3,825
Pathways260
Enzymatic Reactions1,285
Transport Reactions111
Polypeptides3,683
Protein Complexes52
Enzymes792
Transporters359
Compounds1,043
Transcription Units2,683
tRNAs56
GO Terms2,188
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii AB_2008-15-34-7
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02471277
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1221255
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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