Database Authors
Pallavi Subhraveti1, Peter Midford1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 8-Mar-2022 from the annotated genome of Acinetobacter ursingii NIPH 706, 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 26.0) [Karp16, Karp11] using MetaCyc version 26.0 [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_KB8502611,8941,81243391,982,894RefSeq:NZ_KB850261
NZ_KB8502607186891811729,300RefSeq:NZ_KB850260
NZ_KB850259493457288535,105RefSeq:NZ_KB850259
NZ_KB850266126107019135,215RefSeq:NZ_KB850266
NZ_KB85026457552061,655RefSeq:NZ_KB850264
NZ_KB8502631313009,682RefSeq:NZ_KB850263
14 Undisplayed Contigs/Replicons55550356,194
Total:3,3593,18891803,510,045
Ortholog data available?Yes
Database Contents
Genes3,355
Pathways263
Enzymatic Reactions1,331
Transport Reactions62
Polypeptides3,196
Protein Complexes5
Enzymes762
Transporters336
Compounds956
Transcription Units2,295
tRNAs68
Protein Features3,926
GO Terms261
Database Version29.0
Sequence SourceGCF_000369885.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter ursingii
Acinetobacter ursingii NIPH 706
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN01087838
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1217716
Environmentblood
Geographic LocationCzech Republic
Collection Date1997
HostHomo sapiens
Annotation ProviderNCBI RefSeq
Annotation Date2021-11-7
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.3
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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