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 nectaris CIP 110549, 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_KI5307121,2341,19823131,252,772RefSeq:NZ_KI530712
NZ_KI530723453431184485,463RefSeq:NZ_KI530723
NZ_KI530734292276160289,024RefSeq:NZ_KI530734
NZ_KI530735276265101287,426RefSeq:NZ_KI530735
NZ_KI530736949202110,877RefSeq:NZ_KI530736
NZ_KI53073755521264,961RefSeq:NZ_KI530737
NZ_KI53073852484057,476RefSeq:NZ_KI530738
NZ_KI53073938330534,549RefSeq:NZ_KI530739
NZ_KI53071322147118,233RefSeq:NZ_KI530713
NZ_KI53071415130212,797RefSeq:NZ_KI530714
19 Undisplayed Contigs/Replicons28281555,360
Total:2,5652,45080352,668,938
Ortholog data available?Yes
Database Contents
Genes2,560
Pathways201
Enzymatic Reactions1,021
Transport Reactions60
Polypeptides2,470
Protein Complexes34
Enzymes594
Transporters239
Compounds774
Transcription Units1,708
tRNAs66
Protein Features3,116
GO Terms7
Database Version29.0
Sequence SourceGCF_000488215.1
Synonyms Acinetobacter nectaris SAP 763.2
Acinetobacter nectaris CIP 110549
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter nectaris
Acinetobacter nectaris CIP 110549
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02335355
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1392540
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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