Database Authors
Pallavi Subhraveti1, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 15-Feb-2020 from the annotated genome of Acinetobacter ursingii CIP 107286, 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 24.0) [Karp16, Karp11] using MetaCyc version 23.5 [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_KB8497171,3961,32541301,511,393RefSeq:NZ_KB849717
NZ_KB849716566541421609,654RefSeq:NZ_KB849716
NZ_KB849715327307137360,620RefSeq:NZ_KB849715
NZ_KB84971131529988344,355RefSeq:NZ_KB849711
NZ_KB84971929728566328,735RefSeq:NZ_KB849719
NZ_KB84971019718494182,855RefSeq:NZ_KB849710
NZ_KB8497181059609106,882RefSeq:NZ_KB849718
NZ_KB849713805902176,759RefSeq:NZ_KB849713
NZ_KB8497121010008,890RefSeq:NZ_KB849712
NZ_KB84971455005,596RefSeq:NZ_KB849714
Total:3,2983,111811063,535,739
Ortholog data available?Yes
Database Contents
Genes3,297
Pathways256
Enzymatic Reactions1,240
Transport Reactions80
Polypeptides3,116
Protein Complexes34
Enzymes700
Transporters300
Compounds922
Transcription Units2,275
tRNAs64
Protein Features3,887
GO Terms17
Database Version29.0
Sequence SourceGCF_000368825.1
Synonyms Acinetobacter ursingii CIP 107286
Acinetobacter ursingii CIP 107286 = DSM 16037
Acinetobacter ursingii DSM 16037
Acinetobacter ursingii LMG 19575
Acinetobacter ursingii LUH 3792
Acinetobacter ursingii NIPH 137
Acinetobacter ursingii DSM 16037 = CIP 107286
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter ursingii
Acinetobacter ursingii DSM 16037 = CIP 107286
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN01087837
NCBI BioProjectPRJNA224116
NCBI-Taxonomy981336
Environmentblood
Geographic LocationCzech Republic
Collection Date1993
HostHomo sapiens
Human Microbiome Body Siteblood
Annotation ProviderNCBI RefSeq
Annotation Date2019-11-25
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.10
Annotation CommentBest-placed reference protein set; GeneMarkS-2+
NCBI Genome Typerepresentative

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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