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 rudis CIP 110305, 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_KE3403531,0611,0248291,165,160RefSeq:NZ_KE340353
NZ_KE3403526506131423765,256RefSeq:NZ_KE340352
NZ_KE340355664629269758,841RefSeq:NZ_KE340355
NZ_KE340348607581206645,532RefSeq:NZ_KE340348
NZ_KE340354339323106374,289RefSeq:NZ_KE340354
NZ_KE34035132431194350,374RefSeq:NZ_KE340351
NZ_KE34035011001,602RefSeq:NZ_KE340350
NZ_KE34035721011,546RefSeq:NZ_KE340357
NZ_KE34035611001,418RefSeq:NZ_KE340356
NZ_KE34035800001,340RefSeq:NZ_KE340358
NZ_KE34034911001,336RefSeq:NZ_KE340349
Total:3,6503,48587784,066,694
Ortholog data available?Yes
Database Contents
Genes3,650
Pathways275
Enzymatic Reactions1,356
Transport Reactions59
Polypeptides3,516
Protein Complexes4
Enzymes801
Transporters400
Compounds1,015
Transcription Units2,585
tRNAs70
Protein Features4,291
GO Terms290
Database Version29.0
Sequence SourceGCF_000413895.1
Synonyms Acinetobacter rudis G30
Acinetobacter rudis strain CIP 110305
Acinetobacter rudis str. CIP 110305
Acinetobacter sp. G30
Acinetobacter rudis CIP 110305
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter rudis
Acinetobacter rudis CIP 110305
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN01087851
NCBI BioProjectPRJNA224116
NCBI-Taxonomy421052
EnvironmentRaw milk
Geographic LocationIsrael
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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Page generated by Pathway Tools version 29.0 (software by SRI International) on Mon Jun 30, 2025, BIOCYC18A.