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 13-Mar-2021 from the annotated genome of Acinetobacter bereziniae HPC229, 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 25.0) [Karp16, Karp11] using MetaCyc version 24.5 [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_LKDJ020000014,1563,895701914,435,219RefSeq:NZ_LKDJ02000001
pAbe229-114115103012114,007RefSeq:NZ_CM012183
pNDM22950440644,560RefSeq:NZ_CM012324
pAbe229-1516160015,389RefSeq:NZ_CM012184
pAbe229-91313009,154RefSeq:NZ_CM012186
10 Undisplayed Contigs/Replicons29290228,855
Total:4,3814,100702114,647,184
Ortholog data available?Yes
Database Contents
Genes4,381
Pathways260
Enzymatic Reactions1,280
Transport Reactions80
Polypeptides4,120
Protein Complexes42
Enzymes795
Transporters367
Compounds955
Transcription Units3,178
tRNAs62
Protein Features4,709
GO Terms53
Database Version29.0
Sequence SourceGCF_001500155.2
Synonyms Acinetobacter genomic species 10
Acinetobacter genomosp. 10
Acinetobacter genomospecies 10
Acinetobacter genospecies 10
Acinetobacter sp. TDB-2008a
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter bereziniae
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN04115377
NCBI BioProjectPRJNA224116
NCBI-Taxonomy106648
Environmentblood
Geographic LocationArgentina
Collection Date2014-06
HostHomo sapiens
Annotation ProviderNCBI RefSeq
Annotation Date2021-01-26
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.0
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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