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 towneri CIP 107472, 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_KB8496907437011824786,701RefSeq:NZ_KB849690
NZ_KB8496895885491227603,874RefSeq:NZ_KB849689
NZ_KB8496885695392010587,353RefSeq:NZ_KB849688
NZ_KB849691342314208367,899RefSeq:NZ_KB849691
NZ_KB849695212200210225,517RefSeq:NZ_KB849695
NZ_KB84968313312139149,847RefSeq:NZ_KB849683
NZ_KB84967944402248,648RefSeq:NZ_KB849679
NZ_KB84968521210023,356RefSeq:NZ_KB849685
NZ_KB84968427251123,299RefSeq:NZ_KB849684
NZ_KB84969915150017,499RefSeq:NZ_KB849699
NZ_KB8497001292114,140RefSeq:NZ_KB849700
31 Undisplayed Contigs/Replicons9186615104,221
Total:2,8132,620861072,952,354
Ortholog data available?Yes
Database Contents
Genes2,803
Pathways229
Enzymatic Reactions1,121
Transport Reactions56
Polypeptides2,650
Protein Complexes28
Enzymes631
Transporters198
Compounds829
Transcription Units2,055
tRNAs61
Protein Features3,259
GO Terms15
Database Version29.0
Sequence SourceGCF_000368785.1
Synonyms Acinetobacter towneri CIP 107472
Acinetobacter towneri CIP 107472 = DSM 14962
Acinetobacter towneri DSM 14962
Acinetobacter towneri DSM 14962 = CIP 107472
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter towneri
Acinetobacter towneri DSM 14962 = CIP 107472
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN01087853
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1120929
EnvironmentActivated sludge plant
Geographic LocationAustralia
Collection Date1988
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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