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 AA-014, 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_AMGA010000546256041011658,514RefSeq:NZ_AMGA01000054
NZ_AMGA01000036429409164441,506RefSeq:NZ_AMGA01000036
NZ_AMGA0100000226425725287,645RefSeq:NZ_AMGA01000002
NZ_AMGA0100002727026712279,858RefSeq:NZ_AMGA01000027
NZ_AMGA0100004522922405253,393RefSeq:NZ_AMGA01000045
NZ_AMGA0100004820720016229,634RefSeq:NZ_AMGA01000048
NZ_AMGA0100004119718953222,999RefSeq:NZ_AMGA01000041
NZ_AMGA01000028191176132199,146RefSeq:NZ_AMGA01000028
NZ_AMGA0100005016115173173,127RefSeq:NZ_AMGA01000050
NZ_AMGA01000015165150114169,358RefSeq:NZ_AMGA01000015
NZ_AMGA0100000912912135136,935RefSeq:NZ_AMGA01000009
NZ_AMGA0100001693829295,289RefSeq:NZ_AMGA01000016
NZ_AMGA0100001376750194,862RefSeq:NZ_AMGA01000013
NZ_AMGA0100005680752378,135RefSeq:NZ_AMGA01000056
NZ_AMGA0100004258550364,299RefSeq:NZ_AMGA01000042
NZ_AMGA0100005862574163,236RefSeq:NZ_AMGA01000058
NZ_AMGA0100000345430257,212RefSeq:NZ_AMGA01000003
NZ_AMGA0100000754495056,113RefSeq:NZ_AMGA01000007
NZ_AMGA0100001753510253,829RefSeq:NZ_AMGA01000017
NZ_AMGA0100001942400244,727RefSeq:NZ_AMGA01000019
NZ_AMGA0100002133285032,318RefSeq:NZ_AMGA01000021
NZ_AMGA0100000124231024,205RefSeq:NZ_AMGA01000001
NZ_AMGA0100001423185023,276RefSeq:NZ_AMGA01000014
NZ_AMGA0100003817170019,857RefSeq:NZ_AMGA01000038
NZ_AMGA0100006120190112,746RefSeq:NZ_AMGA01000061
NZ_AMGA010000531211017,689RefSeq:NZ_AMGA01000053
NZ_AMGA010000441514017,241RefSeq:NZ_AMGA01000044
NZ_AMGA010000391312016,812RefSeq:NZ_AMGA01000039
NZ_AMGA010000511313006,322RefSeq:NZ_AMGA01000051
32 Undisplayed Contigs/Replicons414102657,649
Total:3,6673,471100963,857,932
Ortholog data available?Yes
Database Contents
Genes3,667
Pathways279
Enzymatic Reactions1,330
Transport Reactions38
Polypeptides3,493
Protein Complexes44
Enzymes776
Transporters362
Compounds1,047
Transcription Units2,546
tRNAs75
GO Terms1,338
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter baumannii
Acinetobacter baumannii AA-014
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN00761248
NCBI BioProjectPRJNA224116
NCBI-Taxonomy903937
Environmentwound
Geographic LocationIraq
Collection Date2008-10-1
HostHomo sapiens
Annotation ProviderNCBI
Annotation Date2017-03-15
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline
Annotation Pipeline Version4.1
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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