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 AB058, 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_ADHA0100000441410041,000RefSeq:NZ_ADHA01000004
NZ_ADHA0100014026241127,796RefSeq:NZ_ADHA01000140
NZ_ADHA0100026138380026,135RefSeq:NZ_ADHA01000261
NZ_ADHA0100001219190026,101RefSeq:NZ_ADHA01000012
NZ_ADHA0100026428261125,779RefSeq:NZ_ADHA01000264
NZ_ADHA0100008426251025,299RefSeq:NZ_ADHA01000084
NZ_ADHA0100019723210224,784RefSeq:NZ_ADHA01000197
NZ_ADHA0100012928270123,368RefSeq:NZ_ADHA01000129
NZ_ADHA0100005316160022,861RefSeq:NZ_ADHA01000053
NZ_ADHA0100017525250022,726RefSeq:NZ_ADHA01000175
NZ_ADHA0100016020170322,629RefSeq:NZ_ADHA01000160
NZ_ADHA0100014918170122,339RefSeq:NZ_ADHA01000149
NZ_ADHA0100002820200021,970RefSeq:NZ_ADHA01000028
NZ_ADHA0100035714130121,844RefSeq:NZ_ADHA01000357
NZ_ADHA0100012123230021,451RefSeq:NZ_ADHA01000121
NZ_ADHA0100015222220021,420RefSeq:NZ_ADHA01000152
NZ_ADHA0100009023230021,351RefSeq:NZ_ADHA01000090
NZ_ADHA0100000520190121,283RefSeq:NZ_ADHA01000005
NZ_ADHA0100000922210120,780RefSeq:NZ_ADHA01000009
NZ_ADHA0100009621200119,754RefSeq:NZ_ADHA01000096
NZ_ADHA0100013420200019,449RefSeq:NZ_ADHA01000134
NZ_ADHA0100015519190019,065RefSeq:NZ_ADHA01000155
NZ_ADHA0100008317160119,002RefSeq:NZ_ADHA01000083
NZ_ADHA0100002516150118,907RefSeq:NZ_ADHA01000025
NZ_ADHA0100033515140118,557RefSeq:NZ_ADHA01000335
NZ_ADHA0100021114130118,413RefSeq:NZ_ADHA01000211
NZ_ADHA0100014813120117,997RefSeq:NZ_ADHA01000148
NZ_ADHA0100022916150117,762RefSeq:NZ_ADHA01000229
NZ_ADHA0100017328270117,693RefSeq:NZ_ADHA01000173
NZ_ADHA0100005921190217,679RefSeq:NZ_ADHA01000059
NZ_ADHA0100006518170117,280RefSeq:NZ_ADHA01000065
NZ_ADHA0100010317170017,262RefSeq:NZ_ADHA01000103
NZ_ADHA0100004315150016,881RefSeq:NZ_ADHA01000043
NZ_ADHA0100011914130116,807RefSeq:NZ_ADHA01000119
NZ_ADHA0100026014131016,539RefSeq:NZ_ADHA01000260
NZ_ADHA0100016514130116,323RefSeq:NZ_ADHA01000165
NZ_ADHA0100002916160016,230RefSeq:NZ_ADHA01000029
NZ_ADHA0100032516160016,096RefSeq:NZ_ADHA01000325
NZ_ADHA0100022718180015,773RefSeq:NZ_ADHA01000227
NZ_ADHA0100045216160015,716RefSeq:NZ_ADHA01000452
NZ_ADHA0100010420190115,645RefSeq:NZ_ADHA01000104
NZ_ADHA0100003330290115,628RefSeq:NZ_ADHA01000033
NZ_ADHA0100000717150215,581RefSeq:NZ_ADHA01000007
NZ_ADHA0100024213110215,382RefSeq:NZ_ADHA01000242
NZ_ADHA0100011414140015,365RefSeq:NZ_ADHA01000114
NZ_ADHA0100002415140114,892RefSeq:NZ_ADHA01000024
NZ_ADHA0100015312110114,886RefSeq:NZ_ADHA01000153
NZ_ADHA0100008214130114,482RefSeq:NZ_ADHA01000082
NZ_ADHA0100001912110114,203RefSeq:NZ_ADHA01000019
NZ_ADHA0100016814140014,151RefSeq:NZ_ADHA01000168
NZ_ADHA0100027417170014,149RefSeq:NZ_ADHA01000274
NZ_ADHA0100033714130114,031RefSeq:NZ_ADHA01000337
NZ_ADHA0100023712120013,710RefSeq:NZ_ADHA01000237
NZ_ADHA0100004214140013,656RefSeq:NZ_ADHA01000042
NZ_ADHA0100030114140013,428RefSeq:NZ_ADHA01000301
NZ_ADHA0100002212110113,428RefSeq:NZ_ADHA01000022
NZ_ADHA0100017715140113,427RefSeq:NZ_ADHA01000177
NZ_ADHA0100062612100213,349RefSeq:NZ_ADHA01000626
NZ_ADHA0100021313120113,194RefSeq:NZ_ADHA01000213
NZ_ADHA0100020313120112,952RefSeq:NZ_ADHA01000203
NZ_ADHA0100012012110112,942RefSeq:NZ_ADHA01000120
NZ_ADHA0100040416160012,894RefSeq:NZ_ADHA01000404
NZ_ADHA0100030012120012,827RefSeq:NZ_ADHA01000300
NZ_ADHA0100005013110212,652RefSeq:NZ_ADHA01000050
NZ_ADHA0100004613120112,565RefSeq:NZ_ADHA01000046
NZ_ADHA0100005812100212,455RefSeq:NZ_ADHA01000058
NZ_ADHA0100007711100112,436RefSeq:NZ_ADHA01000077
NZ_ADHA0100030918170112,386RefSeq:NZ_ADHA01000309
NZ_ADHA0100014613120112,327RefSeq:NZ_ADHA01000146
NZ_ADHA0100021613130012,138RefSeq:NZ_ADHA01000216
NZ_ADHA0100001812110112,054RefSeq:NZ_ADHA01000018
NZ_ADHA0100043712120011,828RefSeq:NZ_ADHA01000437
NZ_ADHA0100047712120011,820RefSeq:NZ_ADHA01000477
NZ_ADHA0100007012110111,707RefSeq:NZ_ADHA01000070
NZ_ADHA0100023911100111,206RefSeq:NZ_ADHA01000239
NZ_ADHA0100032112110111,094RefSeq:NZ_ADHA01000321
NZ_ADHA0100013512120010,090RefSeq:NZ_ADHA01000135
NZ_ADHA010001411110019,245RefSeq:NZ_ADHA01000141
NZ_ADHA010000601210118,735RefSeq:NZ_ADHA01000060
961 Undisplayed Contigs/Replicons1,9211,906204772,426,327
Total:3,7493,190255343,765,368
Ortholog data available?Yes
Database Contents
Genes3,744
Pathways260
Enzymatic Reactions1,279
Transport Reactions104
Polypeptides3,440
Protein Complexes48
Enzymes757
Transporters339
Compounds1,036
Transcription Units2,919
tRNAs15
GO Terms2,047
Database Version29.0
Synonyms Acinetobacter baumannii str. AB058
Acinetobacter baumannii strain AB058
Acinetobacter baumannii AB058
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii AB058
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02469415
NCBI BioProjectPRJNA224116
NCBI-Taxonomy710095
Environmentpatient at Walter Reed Army Medical Center with a bloodstream infection
Geographic LocationUSA
Collection Date2003
HostHomo sapiens
Annotation ProviderNCBI
Annotation Date2017-11-15
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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