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 01-June-2020 from the annotated genome of Acinetobacter defluvii WCHA30, 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 24.5) [Karp16, Karp11] using MetaCyc version 24.1 [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_CP0293973,2183,029103863,353,930RefSeq:NZ_CP029397
pOXA58_010030355315040355,358RefSeq:NZ_CP029396
p1_01003096940276,885RefSeq:NZ_CP029389
p2_01003099007,173RefSeq:NZ_CP029390
p3_01003077005,017RefSeq:NZ_CP029391
p4_01003066004,761RefSeq:NZ_CP029392
p5_01003032014,700RefSeq:NZ_CP029393
p6_01003033003,063RefSeq:NZ_CP029394
p7_01003011001,381RefSeq:NZ_CP029395
Total:3,6983,4661031293,812,268
Ortholog data available?Yes
Database Contents
Genes3,698
Pathways252
Enzymatic Reactions1,236
Transport Reactions75
Polypeptides3,468
Protein Complexes36
Enzymes718
Transporters272
Compounds920
Transcription Units2,612
tRNAs78
Protein Features3,848
GO Terms39
Database Version29.0
Sequence SourceGCF_001704615.3
Synonyms Acinetobacter sp. WCHA30
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter defluvii
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN05356262
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1871111
Environmentsewage
Geographic LocationChina
Collection Date2015-10-31
Annotation ProviderNCBI RefSeq
Annotation Date2020-05-22
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.11
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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