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. Root217 Root217, 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_LMIH010000129209035121,029,633RefSeq:NZ_LMIH01000012
NZ_LMIH0100000660059307645,645RefSeq:NZ_LMIH01000006
NZ_LMIH01000005500485105553,360RefSeq:NZ_LMIH01000005
NZ_LMIH0100004141139759454,048RefSeq:NZ_LMIH01000041
NZ_LMIH0100002334533564370,770RefSeq:NZ_LMIH01000023
NZ_LMIH0100001631731304337,792RefSeq:NZ_LMIH01000016
NZ_LMIH0100002429629114307,252RefSeq:NZ_LMIH01000024
NZ_LMIH0100001022722412258,851RefSeq:NZ_LMIH01000010
NZ_LMIH0100004518618402202,605RefSeq:NZ_LMIH01000045
NZ_LMIH0100001318618006201,128RefSeq:NZ_LMIH01000013
NZ_LMIH0100001816615916194,110RefSeq:NZ_LMIH01000018
NZ_LMIH0100003418318021189,516RefSeq:NZ_LMIH01000034
NZ_LMIH0100000314413806173,612RefSeq:NZ_LMIH01000003
NZ_LMIH0100001115214318170,227RefSeq:NZ_LMIH01000011
NZ_LMIH0100002713012703158,772RefSeq:NZ_LMIH01000027
NZ_LMIH0100004213913801147,744RefSeq:NZ_LMIH01000042
NZ_LMIH0100001414113704146,724RefSeq:NZ_LMIH01000014
NZ_LMIH0100002814013802143,076RefSeq:NZ_LMIH01000028
NZ_LMIH0100000811010550116,243RefSeq:NZ_LMIH01000008
NZ_LMIH01000044979502105,353RefSeq:NZ_LMIH01000044
NZ_LMIH0100001510410112104,163RefSeq:NZ_LMIH01000015
NZ_LMIH0100002982790399,999RefSeq:NZ_LMIH01000029
NZ_LMIH0100000799932496,962RefSeq:NZ_LMIH01000007
NZ_LMIH010000011171131393,617RefSeq:NZ_LMIH01000001
NZ_LMIH0100001961600163,477RefSeq:NZ_LMIH01000019
NZ_LMIH0100000949490055,451RefSeq:NZ_LMIH01000009
NZ_LMIH0100004048453044,297RefSeq:NZ_LMIH01000040
NZ_LMIH0100002054474338,623RefSeq:NZ_LMIH01000020
NZ_LMIH0100000236360037,089RefSeq:NZ_LMIH01000002
NZ_LMIH0100002536360036,625RefSeq:NZ_LMIH01000025
NZ_LMIH0100004329261233,111RefSeq:NZ_LMIH01000043
NZ_LMIH0100003926240230,609RefSeq:NZ_LMIH01000039
NZ_LMIH0100000425240125,893RefSeq:NZ_LMIH01000004
NZ_LMIH0100002627240322,483RefSeq:NZ_LMIH01000026
NZ_LMIH0100003813130020,001RefSeq:NZ_LMIH01000038
NZ_LMIH0100001716150114,637RefSeq:NZ_LMIH01000017
9 Undisplayed Contigs/Replicons15105732,833
Total:6,2346,060541206,756,331
Ortholog data available?No
Database Contents
Genes6,234
Pathways301
Enzymatic Reactions1,514
Transport Reactions78
Polypeptides6,106
Protein Complexes78
Enzymes1,061
Transporters765
Compounds1,135
Transcription Units4,163
tRNAs48
Protein Features7,672
GO Terms22,166
Database Version29.0
Sequence SourceGCF_001428645.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Betaproteobacteria
Burkholderiales
Comamonadaceae
Acidovorax
Acidovorax sp. Root217
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN04155761
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1736492
Environmentgreenhouse
Geographic LocationGermany
Latitude/Longitude50.958 N 6.856 E
Collection Date2013
HostArabidopsis thaliana
Annotation ProviderNCBI RefSeq
Annotation Date2020-02-18
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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