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 13-Mar-2021 from the annotated genome of Acinetobacter haemolyticus TJS01, 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 25.0) [Karp16, Karp11] using MetaCyc version 24.5 [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
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_CP0188713,3093,107971053,442,728RefSeq:NZ_CP018871
pAHTJS1483801056,602RefSeq:NZ_CP018872
pAHTJS2453401139,508RefSeq:NZ_CP018873
Total:3,4023,179971263,538,838
Ortholog data available?Yes
Database Contents
Genes3,402
Pathways245
Enzymatic Reactions1,249
Transport Reactions78
Polypeptides3,179
Protein Complexes36
Enzymes729
Transporters282
Compounds921
Transcription Units2,336
tRNAs75
Protein Features4,007
GO Terms21
Database Version29.0
Sequence SourceGCF_001932555.1
Synonyms Achromobacter haemolyticus
Acinetobacter genomosp. 4
Acinetobacter genomospecies 4
Acinetobacter haematolyticus
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter haemolyticus
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN06166709
NCBI BioProjectPRJNA224116
NCBI-Taxonomy29430
Geographic LocationChina
Collection Date2012
HostHomo sapiens
Annotation ProviderNCBI RefSeq
Annotation Date2021-02-1
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.0
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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