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 johnsonii SH046, 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_GG7049641,01193824491,096,329RefSeq:NZ_GG704964
NZ_GG7049656365991621686,327RefSeq:NZ_GG704965
NZ_GG7049664173931311466,230RefSeq:NZ_GG704966
NZ_GG70496729128416304,625RefSeq:NZ_GG704967
NZ_GG704968246224715254,051RefSeq:NZ_GG704968
NZ_GG704969183171210226,351RefSeq:NZ_GG704969
NZ_GG704970958807107,532RefSeq:NZ_GG704970
NZ_GG70497191891199,730RefSeq:NZ_GG704971
NZ_GG70497262590371,565RefSeq:NZ_GG704972
NZ_GG70497361540765,785RefSeq:NZ_GG704973
NZ_GG70497485850063,978RefSeq:NZ_GG704974
NZ_GG70497566573663,688RefSeq:NZ_GG704975
NZ_GG70497654480652,496RefSeq:NZ_GG704976
NZ_GG70497734294135,936RefSeq:NZ_GG704977
NZ_GG70497820200020,656RefSeq:NZ_GG704978
NZ_GG70497914140013,170RefSeq:NZ_GG704979
31 Undisplayed Contigs/Replicons474441061,561
Total:3,4243,196751533,690,010
Ortholog data available?Yes
Database Contents
Genes3,423
Pathways262
Enzymatic Reactions1,312
Transport Reactions56
Polypeptides3,283
Protein Complexes71
Enzymes727
Transporters279
Compounds966
Transcription Units2,455
tRNAs69
Protein Features3,846
GO Terms245
Database Version29.0
Sequence SourceGCF_000162055.1
Synonyms Acinetobacter johnsonii strain SH046
Acinetobacter johnsonii str. SH046
Acinetobacter johnsonii SH046
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter johnsonii
Acinetobacter johnsonii SH046
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02463729
NCBI BioProjectPRJNA224116
NCBI-Taxonomy575586
Environmentbiological product [ENVO:02000043]
HostHomo sapiens
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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