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 15-Oct-2019 from the annotated genome of Acinetobacter lwoffii NCTC5866, 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 23.1 [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
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
Chromosome 23,1362,941114813,264,872RefSeq:NZ_LR215977
Chromosome 1268197071230,808RefSeq:NZ_LR215976
Total:3,4043,1381141523,495,680
Ortholog data available?Yes
Database Contents
Genes3,404
Pathways191
Enzymatic Reactions1,193
Transport Reactions6
Polypeptides3,140
Protein Complexes22
Enzymes605
Transporters253
Compounds1,001
Transcription Units2,361
tRNAs89
Protein Features3,832
GO Terms24
Database Version29.0
Synonyms Acinetobacter genomosp. 8
Acinetobacter genomosp. 9
Acinetobacter genomospecies 8
Acinetobacter genomospecies 9
Moraxella lwoffi
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter lwoffii
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMEA3881066
NCBI BioProjectPRJNA224116
NCBI-Taxonomy28090
Environmentnot available: to be reported later
Collection Date1900/1939
Health/Disease Statenot available: to be reported later
Annotation ProviderNCBI RefSeq
Annotation Date2019-02-28
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline
Annotation Pipeline Version4.7
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 (2019). "The MetaCyc database of metabolic pathways and enzymes-a 2019 update." Nucleic Acids Res. 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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