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 populi PBJ7, 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_NEXX010000011,2391,20423121,322,962RefSeq:NZ_NEXX01000001
NZ_NEXX010000025765421420646,435RefSeq:NZ_NEXX01000002
NZ_NEXX0100000340740241438,898RefSeq:NZ_NEXX01000003
NZ_NEXX0100000433032082339,843RefSeq:NZ_NEXX01000004
NZ_NEXX01000005277261115303,124RefSeq:NZ_NEXX01000005
NZ_NEXX01000006272256124299,369RefSeq:NZ_NEXX01000006
NZ_NEXX0100000719718773203,265RefSeq:NZ_NEXX01000007
NZ_NEXX0100000876751082,990RefSeq:NZ_NEXX01000008
NZ_NEXX0100000917170024,277RefSeq:NZ_NEXX01000009
NZ_NEXX01000011540112,061RefSeq:NZ_NEXX01000011
NZ_NEXX010000101313007,462RefSeq:NZ_NEXX01000010
NZ_NEXX0100001244006,016RefSeq:NZ_NEXX01000012
Total:3,4133,28570583,686,702
Ortholog data available?Yes
Database Contents
Genes3,413
Pathways270
Enzymatic Reactions1,370
Transport Reactions56
Polypeptides3,293
Protein Complexes73
Enzymes731
Transporters311
Compounds1,022
Transcription Units2,300
tRNAs60
Protein Features4,182
GO Terms275
Database Version29.0
Sequence SourceGCF_002174125.1
Synonyms Acinetobacter sp. 05d10-3-4
Acinetobacter sp. 07d10-4-10
Acinetobacter sp. 16D10-4-5
Acinetobacter sp. BQ4-2
Acinetobacter sp. PBJ7
Acinetobacter sp. PZ2
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter populi
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN06891249
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1582270
EnvironmentBark canker
Geographic LocationChina
Collection Date2011-07
HostPopulus x canadensis
Annotation ProviderNCBI RefSeq
Annotation Date2022-04-19
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version6.1
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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