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 12-July-2021 from the annotated genome of Acinetobacter vivianii CCM 8642, 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 25.0 [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_BMDR0100000173873233775,832RefSeq:NZ_BMDR01000001
NZ_BMDR010000025655421310605,511RefSeq:NZ_BMDR01000002
NZ_BMDR01000003487473122510,599RefSeq:NZ_BMDR01000003
NZ_BMDR01000004419404114470,925RefSeq:NZ_BMDR01000004
NZ_BMDR0100000537136434399,380RefSeq:NZ_BMDR01000005
NZ_BMDR0100000621420761227,652RefSeq:NZ_BMDR01000006
NZ_BMDR01000007216203112226,277RefSeq:NZ_BMDR01000007
NZ_BMDR0100000815715520163,301RefSeq:NZ_BMDR01000008
NZ_BMDR0100000910710412119,099RefSeq:NZ_BMDR01000009
NZ_BMDR01000010908901102,934RefSeq:NZ_BMDR01000010
NZ_BMDR0100001187870095,934RefSeq:NZ_BMDR01000011
NZ_BMDR0100001284794188,595RefSeq:NZ_BMDR01000012
NZ_BMDR0100001352474158,106RefSeq:NZ_BMDR01000013
NZ_BMDR0100001455550054,647RefSeq:NZ_BMDR01000014
NZ_BMDR0100001545450039,067RefSeq:NZ_BMDR01000015
NZ_BMDR0100001619160323,261RefSeq:NZ_BMDR01000016
10 Undisplayed Contigs/Replicons12112934,450
Total:3,7283,61372433,995,570
Ortholog data available?Yes
Database Contents
Genes3,726
Pathways276
Enzymatic Reactions1,335
Transport Reactions80
Polypeptides3,634
Protein Complexes49
Enzymes768
Transporters381
Compounds1,014
Transcription Units2,605
tRNAs63
Protein Features4,414
GO Terms12
Database Version29.0
Sequence SourceGCF_014635885.1
Synonyms Acinetobacter genomosp. 20
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter vivianii
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMD00244885
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1776742
Annotation ProviderNCBI RefSeq
Annotation Date2020-11-22
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.13
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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