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 bohemicus ANC 3994, 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_KB8491641,1351,08820271,223,481RefSeq:NZ_KB849164
NZ_KB8491768367893017881,473RefSeq:NZ_KB849176
NZ_KB849175479448256509,045RefSeq:NZ_KB849175
NZ_KB849168356344120387,769RefSeq:NZ_KB849168
NZ_KB84916715814279169,760RefSeq:NZ_KB849167
NZ_KB84916615514195168,321RefSeq:NZ_KB849166
NZ_KB84916510991117134,741RefSeq:NZ_KB849165
NZ_KB84917012411761130,098RefSeq:NZ_KB849170
NZ_KB84916917160114,952RefSeq:NZ_KB849169
NZ_KB84917111110010,267RefSeq:NZ_KB849171
NZ_KB84917255007,760RefSeq:NZ_KB849172
NZ_KB84917387017,187RefSeq:NZ_KB849173
NZ_KB84916353026,420RefSeq:NZ_KB849163
NZ_KB84917453026,420RefSeq:NZ_KB849174
Total:3,4033,205110883,657,694
Ortholog data available?Yes
Database Contents
Genes3,403
Pathways265
Enzymatic Reactions1,265
Transport Reactions60
Polypeptides3,210
Protein Complexes38
Enzymes709
Transporters267
Compounds940
Transcription Units2,376
tRNAs82
Protein Features3,906
GO Terms8
Database Version29.0
Sequence SourceGCF_000367925.1
Synonyms Acinetobacter sp. ANC 3994
Acinetobacter bohemicus ANC 3994
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter bohemicus
Acinetobacter bohemicus ANC 3994
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN01828192
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1217715
Geographic LocationCzech Republic
Collection Date2011
Annotation ProviderNCBI RefSeq
Annotation Date2019-11-25
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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