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 radioresistens TG02010, 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_AMJJ01000003450434142496,770RefSeq:NZ_AMJJ01000003
NZ_AMJJ0100000430229282328,885RefSeq:NZ_AMJJ01000004
NZ_AMJJ0100000221721115229,725RefSeq:NZ_AMJJ01000002
NZ_AMJJ0100000116015163182,427RefSeq:NZ_AMJJ01000001
NZ_AMJJ01000008162150102170,915RefSeq:NZ_AMJJ01000008
NZ_AMJJ0100000917217011168,132RefSeq:NZ_AMJJ01000009
NZ_AMJJ0100001017517122167,897RefSeq:NZ_AMJJ01000010
NZ_AMJJ0100000611410941130,813RefSeq:NZ_AMJJ01000006
NZ_AMJJ0100000514313841128,385RefSeq:NZ_AMJJ01000005
NZ_AMJJ010000071079782115,515RefSeq:NZ_AMJJ01000007
NZ_AMJJ0100001280791086,707RefSeq:NZ_AMJJ01000012
NZ_AMJJ0100003784794183,727RefSeq:NZ_AMJJ01000037
NZ_AMJJ0100001153520173,730RefSeq:NZ_AMJJ01000011
NZ_AMJJ0100001366640270,415RefSeq:NZ_AMJJ01000013
NZ_AMJJ0100001465631166,525RefSeq:NZ_AMJJ01000014
NZ_AMJJ0100001559590058,150RefSeq:NZ_AMJJ01000015
NZ_AMJJ0100003847442155,307RefSeq:NZ_AMJJ01000038
NZ_AMJJ0100001656515053,818RefSeq:NZ_AMJJ01000016
NZ_AMJJ0100001737361046,297RefSeq:NZ_AMJJ01000017
NZ_AMJJ0100001938361142,926RefSeq:NZ_AMJJ01000019
NZ_AMJJ0100001835340142,390RefSeq:NZ_AMJJ01000018
NZ_AMJJ0100002030300037,759RefSeq:NZ_AMJJ01000020
NZ_AMJJ0100002637360137,272RefSeq:NZ_AMJJ01000026
NZ_AMJJ0100002130291033,138RefSeq:NZ_AMJJ01000021
NZ_AMJJ0100002234331031,089RefSeq:NZ_AMJJ01000022
NZ_AMJJ0100002331301027,783RefSeq:NZ_AMJJ01000023
NZ_AMJJ0100002421210025,817RefSeq:NZ_AMJJ01000024
NZ_AMJJ0100002822220017,998RefSeq:NZ_AMJJ01000028
NZ_AMJJ0100002912120010,713RefSeq:NZ_AMJJ01000029
9 Undisplayed Contigs/Replicons32269242,823
Total:2,8762,75985323,063,848
Ortholog data available?Yes
Database Contents
Genes2,868
Pathways257
Enzymatic Reactions1,238
Transport Reactions72
Polypeptides2,767
Protein Complexes46
Enzymes702
Transporters268
Compounds921
Transcription Units1,965
tRNAs66
Protein Features3,461
GO Terms13
Database Version29.0
Sequence SourceGCF_000301795.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Moraxellales
Moraxellaceae
Acinetobacter
Acinetobacter radioresistens
Acinetobacter radioresistens TG02010
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02471290
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1221310
Environmentblood
HostHomo sapiens
Annotation ProviderNCBI RefSeq
Annotation Date2020-05-16
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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