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_TG27343, 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_AMIS01000109416397127426,710RefSeq:NZ_AMIS01000109
NZ_AMIS0100016325424068272,310RefSeq:NZ_AMIS01000163
NZ_AMIS0100001023723322261,950RefSeq:NZ_AMIS01000010
NZ_AMIS0100017719919216210,594RefSeq:NZ_AMIS01000177
NZ_AMIS0100004921420716204,500RefSeq:NZ_AMIS01000049
NZ_AMIS0100006416315805164,282RefSeq:NZ_AMIS01000064
NZ_AMIS0100009915114506157,845RefSeq:NZ_AMIS01000099
NZ_AMIS0100003213712953142,181RefSeq:NZ_AMIS01000032
NZ_AMIS0100006112312012117,723RefSeq:NZ_AMIS01000061
NZ_AMIS010000291009253102,490RefSeq:NZ_AMIS01000029
NZ_AMIS01000173989440100,740RefSeq:NZ_AMIS01000173
NZ_AMIS0100005098970197,195RefSeq:NZ_AMIS01000050
NZ_AMIS0100001191861488,534RefSeq:NZ_AMIS01000011
NZ_AMIS0100008684781587,231RefSeq:NZ_AMIS01000086
NZ_AMIS0100012781760587,051RefSeq:NZ_AMIS01000127
NZ_AMIS0100015282765182,709RefSeq:NZ_AMIS01000152
NZ_AMIS0100006070661374,711RefSeq:NZ_AMIS01000060
NZ_AMIS0100018274682467,306RefSeq:NZ_AMIS01000182
NZ_AMIS0100006761570465,430RefSeq:NZ_AMIS01000067
NZ_AMIS0100006563620163,812RefSeq:NZ_AMIS01000065
NZ_AMIS0100007361524561,045RefSeq:NZ_AMIS01000073
NZ_AMIS0100005484830158,348RefSeq:NZ_AMIS01000054
NZ_AMIS0100016648443151,310RefSeq:NZ_AMIS01000166
NZ_AMIS0100012148450350,435RefSeq:NZ_AMIS01000121
NZ_AMIS0100009646440250,144RefSeq:NZ_AMIS01000096
NZ_AMIS0100010054500449,463RefSeq:NZ_AMIS01000100
NZ_AMIS0100008145441048,710RefSeq:NZ_AMIS01000081
NZ_AMIS0100015738370144,783RefSeq:NZ_AMIS01000157
NZ_AMIS0100012640380244,036RefSeq:NZ_AMIS01000126
NZ_AMIS0100011045431140,325RefSeq:NZ_AMIS01000110
NZ_AMIS0100006645441039,766RefSeq:NZ_AMIS01000066
NZ_AMIS0100009838360236,960RefSeq:NZ_AMIS01000098
NZ_AMIS0100011736330336,957RefSeq:NZ_AMIS01000117
NZ_AMIS0100011336340236,273RefSeq:NZ_AMIS01000113
NZ_AMIS0100008835350034,865RefSeq:NZ_AMIS01000088
NZ_AMIS0100012528270132,413RefSeq:NZ_AMIS01000125
NZ_AMIS0100008239390027,759RefSeq:NZ_AMIS01000082
NZ_AMIS0100011929280126,535RefSeq:NZ_AMIS01000119
NZ_AMIS0100014316141124,386RefSeq:NZ_AMIS01000143
NZ_AMIS0100013322183121,651RefSeq:NZ_AMIS01000133
NZ_AMIS0100004223230018,856RefSeq:NZ_AMIS01000042
NZ_AMIS0100013517142117,705RefSeq:NZ_AMIS01000135
NZ_AMIS0100010516140216,129RefSeq:NZ_AMIS01000105
NZ_AMIS0100014814130111,650RefSeq:NZ_AMIS01000148
NZ_AMIS0100018121210010,919RefSeq:NZ_AMIS01000181
NZ_AMIS010001471717008,087RefSeq:NZ_AMIS01000147
NZ_AMIS01000009109017,909RefSeq:NZ_AMIS01000009
135 Undisplayed Contigs/Replicons182176692228,442
Total:4,0213,748692044,011,165
Ortholog data available?Yes
Database Contents
Genes4,021
Pathways253
Enzymatic Reactions1,266
Transport Reactions102
Polypeptides3,797
Protein Complexes52
Enzymes762
Transporters333
Compounds1,032
Transcription Units2,760
tRNAs61
GO Terms1,968
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii AB_TG27343
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02471285
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1221288
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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