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 25-Oct-2020 from the annotated genome of Acinetobacter harbinensis HITLi 7, 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 24.5) [Karp16, Karp11] using MetaCyc version 24.1 [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_JXBK010000012,4362,28887612,633,214RefSeq:NZ_JXBK01000001
NZ_JXBK01000002136117019160,606RefSeq:NZ_JXBK01000002
NZ_JXBK01000003683503368,563RefSeq:NZ_JXBK01000003
NZ_JXBK0100000421200118,370RefSeq:NZ_JXBK01000004
NZ_JXBK0100000522200218,368RefSeq:NZ_JXBK01000005
NZ_JXBK010000060000664RefSeq:NZ_JXBK01000006
Total:2,6832,480871162,899,785
Ortholog data available?Yes
Database Contents
Genes2,683
Pathways228
Enzymatic Reactions1,149
Transport Reactions61
Polypeptides2,490
Protein Complexes29
Enzymes629
Transporters227
Compounds845
Transcription Units1,862
tRNAs75
Protein Features3,127
GO Terms4
Database Version29.0
Sequence SourceGCF_000816495.1
Synonyms Acinetobacter sp. HITLi 7
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter harbinensis
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN03274949
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1353941
Environmentriver water
Geographic LocationChina
Collection Date2012-01-13
Annotation ProviderNCBI RefSeq
Annotation Date2020-05-17
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.11
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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