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 15-Oct-2019 from the annotated genome of Acinetobacter sp. WCHA60 WCHAW010062, 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 23.0) [Karp16, Karp11] using MetaCyc version 23.1 [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_CP0331333,8913,691107934,056,085RefSeq:NZ_CP033133
pOXA23_010062322288034311,749RefSeq:NZ_CP033130
pOXA58_01006255470859,191RefSeq:NZ_CP033131
p1_01006257480950,181RefSeq:NZ_CP033119
p2_01006241410028,438RefSeq:NZ_CP033122
p3_01006221180316,135RefSeq:NZ_CP033123
p4_01006218180015,012RefSeq:NZ_CP033124
p5_01006213130012,698RefSeq:NZ_CP033125
p6_01006214140012,655RefSeq:NZ_CP033126
pOXA653_0100621212008,773RefSeq:NZ_CP033132
p7_01006288007,351RefSeq:NZ_CP033127
p8_01006244005,594RefSeq:NZ_CP033128
p9_01006277004,890RefSeq:NZ_CP033129
p10_01006244004,283RefSeq:NZ_CP033118
p11_01006244003,984RefSeq:NZ_CP033120
p12_01006233002,121RefSeq:NZ_CP033121
Total:4,4744,2201071474,599,140
Ortholog data available?Yes
Database Contents
Genes4,474
Pathways227
Enzymatic Reactions1,453
Transport Reactions9
Polypeptides4,221
Protein Complexes22
Enzymes679
Transporters333
Compounds1,174
Transcription Units3,249
tRNAs81
Protein Features4,638
GO Terms38
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter sp. WCHA60
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN07138954
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1879050
EnvironmentSewage
Geographic LocationChina
Collection Date2015-10-31
Annotation ProviderNCBI RefSeq
Annotation Date2018-10-31
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline
Annotation Pipeline Version4.6
Annotation CommentBest-placed reference protein set; GeneMarkS+

References

Caspi20: Caspi R, Billington R, Keseler IM, Kothari A, Krummenacker M, Midford PE, Ong WK, Paley S, Subhraveti P, Karp PD (2019). "The MetaCyc database of metabolic pathways and enzymes-a 2019 update." Nucleic Acids Res. 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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