Database Authors
Pallavi Subhraveti1, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 15-Feb-2020 from the annotated genome of Acinetobacter gyllenbergii NIPH 230, 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 24.0) [Karp16, Karp11] using MetaCyc version 23.5 [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_KI5306991,7331,585151331,921,223RefSeq:NZ_KI530699
NZ_KI5307041,2661,18230541,337,924RefSeq:NZ_KI530704
NZ_KI5307057907571716826,606RefSeq:NZ_KI530705
NZ_KI530706250236410288,897RefSeq:NZ_KI530706
NZ_KI53070713513122144,588RefSeq:NZ_KI530707
NZ_KI53070815150010,895RefSeq:NZ_KI530708
7 Undisplayed Contigs/Replicons12120621,213
Total:4,2073,918682214,551,346
Ortholog data available?Yes
Database Contents
Genes4,207
Pathways249
Enzymatic Reactions1,298
Transport Reactions82
Polypeptides4,042
Protein Complexes38
Enzymes771
Transporters381
Compounds988
Transcription Units3,076
tRNAs53
Protein Features4,558
GO Terms42
Database Version29.0
Sequence SourceGCF_000488195.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter gyllenbergii
Acinetobacter gyllenbergii NIPH 230
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN01828185
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1217658
EnvironmentVagina
Geographic LocationCzech Republic
Collection Date1994-12-31/1993-12-31
HostHomo sapiens
Human Microbiome Body Siteurogenital-tract
Annotation ProviderNCBI RefSeq
Annotation Date2019-12-6
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.10
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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