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 Acidovorax sp. Leaf160 Leaf160, 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_LMOV0100002359658169671,218RefSeq:NZ_LMOV01000023
NZ_LMOV010000126095811711670,038RefSeq:NZ_LMOV01000012
NZ_LMOV0100000140339238487,298RefSeq:NZ_LMOV01000001
NZ_LMOV0100002433332094377,020RefSeq:NZ_LMOV01000024
NZ_LMOV0100002825524717295,544RefSeq:NZ_LMOV01000028
NZ_LMOV0100002525124074272,239RefSeq:NZ_LMOV01000025
NZ_LMOV0100002622121605255,491RefSeq:NZ_LMOV01000026
NZ_LMOV0100000221620547222,060RefSeq:NZ_LMOV01000002
NZ_LMOV0100002717217002205,616RefSeq:NZ_LMOV01000027
NZ_LMOV0100002918317517194,502RefSeq:NZ_LMOV01000029
NZ_LMOV0100000313713313155,155RefSeq:NZ_LMOV01000003
NZ_LMOV0100000483810294,838RefSeq:NZ_LMOV01000004
NZ_LMOV0100000577770092,165RefSeq:NZ_LMOV01000005
NZ_LMOV0100000676751090,037RefSeq:NZ_LMOV01000006
NZ_LMOV0100000789821685,254RefSeq:NZ_LMOV01000007
NZ_LMOV0100000873700378,756RefSeq:NZ_LMOV01000008
NZ_LMOV0100000969681074,800RefSeq:NZ_LMOV01000009
NZ_LMOV0100001066650171,543RefSeq:NZ_LMOV01000010
NZ_LMOV0100001150472156,129RefSeq:NZ_LMOV01000011
NZ_LMOV0100001349480151,396RefSeq:NZ_LMOV01000013
NZ_LMOV0100001444440049,262RefSeq:NZ_LMOV01000014
NZ_LMOV0100001549481046,903RefSeq:NZ_LMOV01000015
NZ_LMOV0100001633310240,170RefSeq:NZ_LMOV01000016
NZ_LMOV0100001730300036,211RefSeq:NZ_LMOV01000017
NZ_LMOV0100001818170122,521RefSeq:NZ_LMOV01000018
NZ_LMOV0100001913130013,869RefSeq:NZ_LMOV01000019
NZ_LMOV0100002042024,035RefSeq:NZ_LMOV01000020
NZ_LMOV0100002121012,718RefSeq:NZ_LMOV01000021
NZ_LMOV0100002240311,109RefSeq:NZ_LMOV01000022
Total:4,2054,05958884,717,897
Ortholog data available?No
Database Contents
Genes4,204
Pathways280
Enzymatic Reactions1,452
Transport Reactions84
Polypeptides4,068
Protein Complexes53
Enzymes868
Transporters536
Compounds1,110
Transcription Units2,888
tRNAs51
Protein Features5,450
GO Terms17,445
Database Version29.0
Sequence SourceGCF_001424265.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Betaproteobacteria
Burkholderiales
Comamonadaceae
Acidovorax
Acidovorax sp. Leaf160
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN04151660
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1736280
Environmentnatural site
Geographic LocationSwitzerland
Latitude/Longitude47.48168 N 8.217547 E
Collection Date2013-10
HostArabidopsis thaliana
Annotation ProviderNCBI RefSeq
Annotation Date2020-02-7
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.11
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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