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_2008-15-45, 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_AMHL0100011627626871274,379RefSeq:NZ_AMHL01000116
NZ_AMHL0100008725024604241,065RefSeq:NZ_AMHL01000087
NZ_AMHL0100002421721403225,467RefSeq:NZ_AMHL01000024
NZ_AMHL0100006517416824187,685RefSeq:NZ_AMHL01000065
NZ_AMHL0100007515815512177,001RefSeq:NZ_AMHL01000075
NZ_AMHL0100007613012064138,875RefSeq:NZ_AMHL01000076
NZ_AMHL0100009713712971138,245RefSeq:NZ_AMHL01000097
NZ_AMHL0100012912711953129,781RefSeq:NZ_AMHL01000129
NZ_AMHL0100008811010622119,379RefSeq:NZ_AMHL01000088
NZ_AMHL010000441009901108,104RefSeq:NZ_AMHL01000044
NZ_AMHL0100009812712601104,197RefSeq:NZ_AMHL01000098
NZ_AMHL01000074989602102,496RefSeq:NZ_AMHL01000074
NZ_AMHL0100008677720584,811RefSeq:NZ_AMHL01000086
NZ_AMHL0100008075740183,014RefSeq:NZ_AMHL01000080
NZ_AMHL0100011775730282,061RefSeq:NZ_AMHL01000117
NZ_AMHL0100006049444168,962RefSeq:NZ_AMHL01000060
NZ_AMHL0100004991900167,064RefSeq:NZ_AMHL01000049
NZ_AMHL0100004057541263,513RefSeq:NZ_AMHL01000040
NZ_AMHL0100006364604063,026RefSeq:NZ_AMHL01000063
NZ_AMHL0100005358571060,116RefSeq:NZ_AMHL01000053
NZ_AMHL0100010953520158,077RefSeq:NZ_AMHL01000109
NZ_AMHL0100011451500156,815RefSeq:NZ_AMHL01000114
NZ_AMHL0100006953510256,725RefSeq:NZ_AMHL01000069
NZ_AMHL0100003352510156,473RefSeq:NZ_AMHL01000033
NZ_AMHL0100005745450053,585RefSeq:NZ_AMHL01000057
NZ_AMHL0100011841370453,213RefSeq:NZ_AMHL01000118
NZ_AMHL0100003148443152,426RefSeq:NZ_AMHL01000031
NZ_AMHL0100010754520250,703RefSeq:NZ_AMHL01000107
NZ_AMHL0100007849470250,372RefSeq:NZ_AMHL01000078
NZ_AMHL0100014043410245,359RefSeq:NZ_AMHL01000140
NZ_AMHL0100010037360143,297RefSeq:NZ_AMHL01000100
NZ_AMHL0100010239380141,883RefSeq:NZ_AMHL01000102
NZ_AMHL0100009548461140,771RefSeq:NZ_AMHL01000095
NZ_AMHL0100009434320238,944RefSeq:NZ_AMHL01000094
NZ_AMHL0100007329280137,650RefSeq:NZ_AMHL01000073
NZ_AMHL0100000637360135,220RefSeq:NZ_AMHL01000006
NZ_AMHL0100012733320133,930RefSeq:NZ_AMHL01000127
NZ_AMHL0100006229290032,953RefSeq:NZ_AMHL01000062
NZ_AMHL0100002929280132,872RefSeq:NZ_AMHL01000029
NZ_AMHL0100013129290031,796RefSeq:NZ_AMHL01000131
NZ_AMHL0100011031300131,696RefSeq:NZ_AMHL01000110
NZ_AMHL0100012228260228,265RefSeq:NZ_AMHL01000122
NZ_AMHL0100009232300227,913RefSeq:NZ_AMHL01000092
NZ_AMHL0100001029280127,703RefSeq:NZ_AMHL01000010
NZ_AMHL0100006129271127,188RefSeq:NZ_AMHL01000061
NZ_AMHL0100004125230226,088RefSeq:NZ_AMHL01000041
NZ_AMHL0100011227260125,569RefSeq:NZ_AMHL01000112
NZ_AMHL0100013433320124,091RefSeq:NZ_AMHL01000134
NZ_AMHL0100009127221423,799RefSeq:NZ_AMHL01000091
NZ_AMHL0100000225231123,636RefSeq:NZ_AMHL01000002
NZ_AMHL0100008920190120,813RefSeq:NZ_AMHL01000089
NZ_AMHL0100007226260020,448RefSeq:NZ_AMHL01000072
NZ_AMHL0100013921190219,832RefSeq:NZ_AMHL01000139
NZ_AMHL0100013013120118,506RefSeq:NZ_AMHL01000130
NZ_AMHL0100012417140316,448RefSeq:NZ_AMHL01000124
NZ_AMHL0100008325231115,980RefSeq:NZ_AMHL01000083
NZ_AMHL0100013215140115,824RefSeq:NZ_AMHL01000132
NZ_AMHL0100003212120014,944RefSeq:NZ_AMHL01000032
NZ_AMHL0100008515150014,651RefSeq:NZ_AMHL01000085
NZ_AMHL0100001812120014,052RefSeq:NZ_AMHL01000018
NZ_AMHL010000031283112,479RefSeq:NZ_AMHL01000003
NZ_AMHL0100010616160011,078RefSeq:NZ_AMHL01000106
NZ_AMHL010000111414009,520RefSeq:NZ_AMHL01000011
NZ_AMHL010000521310039,481RefSeq:NZ_AMHL01000052
NZ_AMHL010000681211016,574RefSeq:NZ_AMHL01000068
75 Undisplayed Contigs/Replicons180171938191,850
Total:4,0303,837601334,100,733
Ortholog data available?Yes
Database Contents
Genes4,030
Pathways259
Enzymatic Reactions1,303
Transport Reactions112
Polypeptides3,870
Protein Complexes53
Enzymes815
Transporters367
Compounds1,060
Transcription Units2,787
tRNAs54
GO Terms2,260
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii AB_2008-15-45
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02471271
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1221256
Environmentbronchoalveolar lavage
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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