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 AB056, 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_ADGZ0100010846450147,323RefSeq:NZ_ADGZ01000108
NZ_ADGZ0100005242410146,247RefSeq:NZ_ADGZ01000052
NZ_ADGZ0100016338380043,632RefSeq:NZ_ADGZ01000163
NZ_ADGZ0100005536360041,765RefSeq:NZ_ADGZ01000055
NZ_ADGZ0100002941410038,501RefSeq:NZ_ADGZ01000029
NZ_ADGZ0100005027270033,385RefSeq:NZ_ADGZ01000050
NZ_ADGZ0100001728270131,057RefSeq:NZ_ADGZ01000017
NZ_ADGZ0100017029290030,721RefSeq:NZ_ADGZ01000170
NZ_ADGZ0100019424230130,345RefSeq:NZ_ADGZ01000194
NZ_ADGZ0100005620200029,649RefSeq:NZ_ADGZ01000056
NZ_ADGZ0100017327250228,981RefSeq:NZ_ADGZ01000173
NZ_ADGZ0100004028270128,935RefSeq:NZ_ADGZ01000040
NZ_ADGZ0100016726250128,566RefSeq:NZ_ADGZ01000167
NZ_ADGZ0100017731290226,761RefSeq:NZ_ADGZ01000177
NZ_ADGZ0100000922220026,461RefSeq:NZ_ADGZ01000009
NZ_ADGZ0100010728280026,371RefSeq:NZ_ADGZ01000107
NZ_ADGZ0100003738380026,120RefSeq:NZ_ADGZ01000037
NZ_ADGZ0100015123210225,445RefSeq:NZ_ADGZ01000151
NZ_ADGZ0100005923210225,277RefSeq:NZ_ADGZ01000059
NZ_ADGZ0100002227251124,757RefSeq:NZ_ADGZ01000022
NZ_ADGZ0100003320200023,876RefSeq:NZ_ADGZ01000033
NZ_ADGZ0100003122210123,048RefSeq:NZ_ADGZ01000031
NZ_ADGZ0100015320190122,938RefSeq:NZ_ADGZ01000153
NZ_ADGZ0100004623221022,849RefSeq:NZ_ADGZ01000046
NZ_ADGZ0100006021201022,736RefSeq:NZ_ADGZ01000060
NZ_ADGZ0100006621210022,657RefSeq:NZ_ADGZ01000066
NZ_ADGZ0100004824240022,169RefSeq:NZ_ADGZ01000048
NZ_ADGZ0100001520200022,108RefSeq:NZ_ADGZ01000015
NZ_ADGZ0100011617170021,392RefSeq:NZ_ADGZ01000116
NZ_ADGZ0100003619180121,265RefSeq:NZ_ADGZ01000036
NZ_ADGZ0100001317160120,640RefSeq:NZ_ADGZ01000013
NZ_ADGZ0100009120180220,453RefSeq:NZ_ADGZ01000091
NZ_ADGZ0100013317170020,438RefSeq:NZ_ADGZ01000133
NZ_ADGZ0100004520180219,584RefSeq:NZ_ADGZ01000045
NZ_ADGZ0100003515140119,374RefSeq:NZ_ADGZ01000035
NZ_ADGZ0100011917160119,152RefSeq:NZ_ADGZ01000119
NZ_ADGZ0100007619190018,998RefSeq:NZ_ADGZ01000076
NZ_ADGZ0100026716150118,929RefSeq:NZ_ADGZ01000267
NZ_ADGZ0100004917160118,915RefSeq:NZ_ADGZ01000049
NZ_ADGZ0100004418180018,664RefSeq:NZ_ADGZ01000044
NZ_ADGZ0100019311110018,475RefSeq:NZ_ADGZ01000193
NZ_ADGZ0100039613130018,297RefSeq:NZ_ADGZ01000396
NZ_ADGZ0100018822200218,212RefSeq:NZ_ADGZ01000188
NZ_ADGZ0100000417150218,108RefSeq:NZ_ADGZ01000004
NZ_ADGZ0100010620190117,716RefSeq:NZ_ADGZ01000106
NZ_ADGZ0100012414130117,553RefSeq:NZ_ADGZ01000124
NZ_ADGZ0100005717170017,507RefSeq:NZ_ADGZ01000057
NZ_ADGZ0100009320200017,310RefSeq:NZ_ADGZ01000093
NZ_ADGZ0100003215140117,212RefSeq:NZ_ADGZ01000032
NZ_ADGZ0100015216160017,047RefSeq:NZ_ADGZ01000152
NZ_ADGZ0100006316130316,681RefSeq:NZ_ADGZ01000063
NZ_ADGZ0100012617160116,399RefSeq:NZ_ADGZ01000126
NZ_ADGZ0100016917150216,296RefSeq:NZ_ADGZ01000169
NZ_ADGZ0100013013110216,146RefSeq:NZ_ADGZ01000130
NZ_ADGZ0100019115140116,123RefSeq:NZ_ADGZ01000191
NZ_ADGZ0100008218170116,086RefSeq:NZ_ADGZ01000082
NZ_ADGZ0100018315140115,881RefSeq:NZ_ADGZ01000183
NZ_ADGZ0100009416150115,587RefSeq:NZ_ADGZ01000094
NZ_ADGZ0100009216150115,543RefSeq:NZ_ADGZ01000092
NZ_ADGZ0100024814130115,189RefSeq:NZ_ADGZ01000248
NZ_ADGZ0100005814140015,040RefSeq:NZ_ADGZ01000058
NZ_ADGZ0100026014140014,721RefSeq:NZ_ADGZ01000260
NZ_ADGZ0100011113120114,610RefSeq:NZ_ADGZ01000111
NZ_ADGZ0100003013111114,487RefSeq:NZ_ADGZ01000030
NZ_ADGZ0100002016140214,250RefSeq:NZ_ADGZ01000020
NZ_ADGZ0100018012110114,159RefSeq:NZ_ADGZ01000180
NZ_ADGZ0100014915141014,140RefSeq:NZ_ADGZ01000149
NZ_ADGZ0100006517170013,978RefSeq:NZ_ADGZ01000065
NZ_ADGZ0100016811101013,957RefSeq:NZ_ADGZ01000168
NZ_ADGZ0100012514140013,950RefSeq:NZ_ADGZ01000125
NZ_ADGZ0100010911110013,877RefSeq:NZ_ADGZ01000109
NZ_ADGZ010001281290313,844RefSeq:NZ_ADGZ01000128
NZ_ADGZ0100027413120113,117RefSeq:NZ_ADGZ01000274
NZ_ADGZ0100014715140113,102RefSeq:NZ_ADGZ01000147
NZ_ADGZ0100019514130113,101RefSeq:NZ_ADGZ01000195
NZ_ADGZ0100020613130012,896RefSeq:NZ_ADGZ01000206
NZ_ADGZ0100007014130112,778RefSeq:NZ_ADGZ01000070
NZ_ADGZ0100014114120212,754RefSeq:NZ_ADGZ01000141
NZ_ADGZ0100005313130012,729RefSeq:NZ_ADGZ01000053
NZ_ADGZ0100008912120012,673RefSeq:NZ_ADGZ01000089
NZ_ADGZ0100002714130112,495RefSeq:NZ_ADGZ01000027
NZ_ADGZ0100039212100212,455RefSeq:NZ_ADGZ01000392
NZ_ADGZ0100008818170112,386RefSeq:NZ_ADGZ01000088
NZ_ADGZ0100028719190012,341RefSeq:NZ_ADGZ01000287
NZ_ADGZ0100009511110012,323RefSeq:NZ_ADGZ01000095
NZ_ADGZ0100020413121012,226RefSeq:NZ_ADGZ01000204
NZ_ADGZ0100020013130012,171RefSeq:NZ_ADGZ01000200
NZ_ADGZ0100025913120112,137RefSeq:NZ_ADGZ01000259
NZ_ADGZ0100007515150011,885RefSeq:NZ_ADGZ01000075
NZ_ADGZ0100037313130011,810RefSeq:NZ_ADGZ01000373
NZ_ADGZ0100014613120110,616RefSeq:NZ_ADGZ01000146
NZ_ADGZ010005381110109,232RefSeq:NZ_ADGZ01000538
NZ_ADGZ010001101110019,217RefSeq:NZ_ADGZ01000110
NZ_ADGZ010001871514019,046RefSeq:NZ_ADGZ01000187
865 Undisplayed Contigs/Replicons1,5781,565174792,011,899
Total:3,8313,257255493,844,254
Ortholog data available?Yes
Database Contents
Genes3,827
Pathways267
Enzymatic Reactions1,346
Transport Reactions107
Polypeptides3,485
Protein Complexes51
Enzymes765
Transporters337
Compounds1,049
Transcription Units2,965
tRNAs17
GO Terms2,061
Database Version29.0
Synonyms Acinetobacter baumannii str. AB056
Acinetobacter baumannii strain AB056
Acinetobacter baumannii AB056
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii AB056
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02469414
NCBI BioProjectPRJNA224116
NCBI-Taxonomy710094
Environmentpatient at Walter Reed Army Medical Center with a bloodstream infection
Geographic LocationUSA
Collection Date2004
HostHomo sapiens
Annotation ProviderNCBI
Annotation Date2017-11-16
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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