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 sp. RUH 2624 RUH2624, 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_KI3919393,1222,96859953,295,382RefSeq:NZ_KI391939
NZ_KI3919404584301612484,040RefSeq:NZ_KI391940
NZ_KI3919411048501993,246RefSeq:NZ_KI391941
NZ_KI39194258474761,599RefSeq:NZ_KI391942
NZ_KI3919431111008,170RefSeq:NZ_KI391943
NZ_KI39194465015,295RefSeq:NZ_KI391944
NZ_KI39194542023,753RefSeq:NZ_KI391945
NZ_KI39194611001,149RefSeq:NZ_KI391946
Total:3,7643,549791363,952,634
Ortholog data available?Yes
Database Contents
Genes3,762
Pathways285
Enzymatic Reactions1,402
Transport Reactions66
Polypeptides3,569
Protein Complexes70
Enzymes782
Transporters353
Compounds1,050
Transcription Units2,616
tRNAs64
Protein Features4,421
GO Terms1,083
Database Version29.0
Sequence SourceGCF_000162375.2
Synonyms Acinetobacter genomosp. 13TU strain RUH2624
Acinetobacter genomosp. 13TU str. RUH2624
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
unclassified Acinetobacter
Acinetobacter sp. RUH 2624
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02463742
NCBI BioProjectPRJNA224116
NCBI-Taxonomy575564
Environmentbiological product [ENVO:02000043]
HostHomo sapiens
Human Microbiome Body Sitenot-specified
Annotation ProviderNCBI RefSeq
Annotation Date2021-10-31
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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