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 brisouii CIP 110357, 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_KI5307622,1662,07169262,252,752RefSeq:NZ_KI530762
NZ_KI530763464445172494,839RefSeq:NZ_KI530763
NZ_KI530764156136020182,937RefSeq:NZ_KI530764
NZ_KI53076588810786,482RefSeq:NZ_KI530765
NZ_KI53076654449156,509RefSeq:NZ_KI530766
NZ_KI53076751510039,901RefSeq:NZ_KI530767
NZ_KI53076833294035,092RefSeq:NZ_KI530768
Total:3,0122,85799563,148,512
Ortholog data available?Yes
Database Contents
Genes3,012
Pathways243
Enzymatic Reactions1,195
Transport Reactions69
Polypeptides2,863
Protein Complexes39
Enzymes708
Transporters264
Compounds915
Transcription Units1,970
tRNAs76
Protein Features3,609
GO Terms9
Database Version29.0
Sequence SourceGCF_000488275.1
Synonyms Acinetobacter brisouii DSM 18516
Acinetobacter brisouii CIP 110357
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter brisouii
Acinetobacter brisouii CIP 110357
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02335354
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1341683
Collection Date2011-12-31/2010-12-31
Annotation ProviderNCBI RefSeq
Annotation Date2019-12-6
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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