Database Authors
Pallavi Subhraveti1, Peter Midford1, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 13-Mar-2021 from the annotated genome of Acinetobacter towneri 5-2Ac02, 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 25.0) [Karp16, Karp11] using MetaCyc version 24.5 [Caspi20]. 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 Institutes of Health.
Genome
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_MKQS010000013963571623432,187RefSeq:NZ_MKQS01000001
NZ_MKQS010000053242991213337,792RefSeq:NZ_MKQS01000005
NZ_MKQS010000071791541114176,330RefSeq:NZ_MKQS01000007
NZ_MKQS0100000915214345155,494RefSeq:NZ_MKQS01000009
NZ_MKQS0100001112411653134,959RefSeq:NZ_MKQS01000011
NZ_MKQS0100004911010514112,172RefSeq:NZ_MKQS01000049
NZ_MKQS0100001312011523111,938RefSeq:NZ_MKQS01000013
NZ_MKQS01000012938472103,832RefSeq:NZ_MKQS01000012
NZ_MKQS010000031029417103,724RefSeq:NZ_MKQS01000003
NZ_MKQS0100000281741691,856RefSeq:NZ_MKQS01000002
NZ_MKQS0100006489814488,185RefSeq:NZ_MKQS01000064
NZ_MKQS0100001577722382,010RefSeq:NZ_MKQS01000015
NZ_MKQS0100001467640370,632RefSeq:NZ_MKQS01000014
NZ_MKQS0100001659571161,935RefSeq:NZ_MKQS01000016
NZ_MKQS01000008584601260,698RefSeq:NZ_MKQS01000008
NZ_MKQS01000004625001258,020RefSeq:NZ_MKQS01000004
NZ_MKQS0100001744431052,329RefSeq:NZ_MKQS01000017
NZ_MKQS0100001842362446,244RefSeq:NZ_MKQS01000018
NZ_MKQS0100001936342043,267RefSeq:NZ_MKQS01000019
NZ_MKQS0100002038370142,394RefSeq:NZ_MKQS01000020
NZ_MKQS0100002143410242,159RefSeq:NZ_MKQS01000021
NZ_MKQS0100002242400241,491RefSeq:NZ_MKQS01000022
NZ_MKQS0100000644339239,861RefSeq:NZ_MKQS01000006
NZ_MKQS0100002342390338,977RefSeq:NZ_MKQS01000023
NZ_MKQS0100002432300238,534RefSeq:NZ_MKQS01000024
NZ_MKQS0100002530300035,003RefSeq:NZ_MKQS01000025
NZ_MKQS01000026372701033,441RefSeq:NZ_MKQS01000026
NZ_MKQS0100002726240231,003RefSeq:NZ_MKQS01000027
NZ_MKQS0100002828260228,979RefSeq:NZ_MKQS01000028
NZ_MKQS0100002926195224,938RefSeq:NZ_MKQS01000029
NZ_MKQS0100003027251123,878RefSeq:NZ_MKQS01000030
NZ_MKQS0100003121181219,880RefSeq:NZ_MKQS01000031
NZ_MKQS0100003218170117,423RefSeq:NZ_MKQS01000032
NZ_MKQS0100003321120915,843RefSeq:NZ_MKQS01000033
NZ_MKQS0100003511110012,358RefSeq:NZ_MKQS01000035
NZ_MKQS0100003611100111,579RefSeq:NZ_MKQS01000036
NZ_MKQS010000381080210,435RefSeq:NZ_MKQS01000038
NZ_MKQS01000044109015,287RefSeq:NZ_MKQS01000044
29 Undisplayed Contigs/Replicons80711529114,380
Total:2,8472,5511031932,951,447
Ortholog data available?Yes
Database Contents
Genes2,831
Pathways217
Enzymatic Reactions1,122
Transport Reactions64
Polypeptides2,638
Protein Complexes29
Enzymes713
Transporters202
Compounds827
Transcription Units2,091
tRNAs74
Protein Features3,172
GO Terms23
Database Version29.0
Sequence SourceGCF_001758345.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter towneri
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN05860603
NCBI BioProjectPRJNA224116
NCBI-Taxonomy202956
EnvironmentAir sample from hospital environment
Geographic LocationBrazil
Latitude/Longitude23.128235 S 42.70313 W
Collection Date2012-05
Annotation ProviderNCBI RefSeq
Annotation Date2021-01-24
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.0
Annotation CommentBest-placed reference protein set; GeneMarkS-2+

References

Caspi20: Caspi R, Billington R, Keseler IM, Kothari A, Krummenacker M, Midford PE, Ong WK, Paley S, Subhraveti P, Karp PD (2020). "The MetaCyc database of metabolic pathways and enzymes - a 2019 update." Nucleic Acids Res 48(D1);D445-D453. PMID: 31586394

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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