Database Authors
Pallavi Subhraveti1, Peter Midford1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 01-June-2022 from the annotated genome of Acinetobacter lactucae OTEC-02, 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
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_CP0200153,7543,58795723,981,712RefSeq:NZ_CP020015
Ortholog data available?Yes
Database Contents
Genes3,754
Pathways295
Enzymatic Reactions1,462
Transport Reactions69
Polypeptides3,587
Protein Complexes77
Enzymes814
Transporters374
Compounds1,111
Transcription Units2,573
tRNAs73
Protein Features4,554
GO Terms416
Database Version29.0
Sequence SourceGCF_002076935.1
Synonyms Acinetobacter dijkshoorniae
Acinetobacter genomosp. NB14
Acinetobacter sp. JVAP01
Acinetobacter sp. LUH 08258
Acinetobacter sp. LUH 09464
Acinetobacter sp. LUH 10297
Acinetobacter sp. LUH 13623
Acinetobacter sp. NRRL B-41902
Acinetobacter sp. NRRL B-41903
Acinetobacter sp. NRRL B-41916
Acinetobacter sp. NRRL B-41918
Acinetobacter sp. R10-JV221
Acinetobacter sp. R10-JV222
Acinetobacter sp. R10-JV463
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter lactucae
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN06215789
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1785128
EnvironmentSoil
Geographic LocationMexico
Collection Date2005-03-21
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+

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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