Database Authors
Pallavi Subhraveti1, Peter Midford, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 15-Feb-2019 from the annotated genome of Acinetobacter nosocomialis Ab22222, 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 23.0 [Caspi18]. 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 Institutess of Health.
Genome
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_JH9304511,4001,29752511,420,788RefSeq:NZ_JH930451
NZ_JH930445955919729985,704RefSeq:NZ_JH930445
NZ_JH930447603571527631,145RefSeq:NZ_JH930447
NZ_JH9304445024771015505,891RefSeq:NZ_JH930444
NZ_JH93044322121074210,457RefSeq:NZ_JH930443
NZ_JH93045086794393,513RefSeq:NZ_JH930450
NZ_JH930449503801236,934RefSeq:NZ_JH930449
NZ_JH93044838350333,121RefSeq:NZ_JH930448
NZ_JH93044630230725,175RefSeq:NZ_JH930446
NZ_JH93045333260723,275RefSeq:NZ_JH930453
15 Undisplayed Contigs/Replicons414101249,808
Total:3,9713,716851704,015,811
Ortholog data available?Yes
Database Contents
Genes3,971
Pathways247
Enzymatic Reactions1,435
Transport Reactions87
Polypeptides3,724
Protein Complexes41
Enzymes755
Transporters366
Compounds1,165
Transcription Units2,778
tRNAs68
GO Terms740
Database Version29.0
Synonyms Acinetobacter nosocomialis str. Ab22222
Acinetobacter nosocomialis strain Ab22222
Acinetobacter nosocomialis Ab22222
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter calcoaceticus/baumannii complex
Acinetobacter nosocomialis
Acinetobacter nosocomialis Ab22222
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02596916
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1183155
Annotation ProviderNCBI
Annotation Date2017-03-30
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline
Annotation Pipeline Version4.1
Annotation CommentBest-placed reference protein set; GeneMarkS+

References

Caspi18: Caspi R, Billington R, Fulcher CA, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Midford PE, Ong Q, Ong WK, Paley S, Subhraveti P, Karp PD (2018). "The MetaCyc database of metabolic pathways and enzymes." Nucleic Acids Res 46(D1);D633-D639. PMID: 29059334

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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