Database Authors
Pallavi Subhraveti1, Peter Midford1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 01-June-2022 from the annotated genome of Acidovorax valerianellae DSM 16619, 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 26.0) [Karp16, Karp11] using MetaCyc version 26.0 [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_FMZC0100000156154696615,681RefSeq:NZ_FMZC01000001
NZ_FMZC01000002514496711573,506RefSeq:NZ_FMZC01000002
NZ_FMZC0100000349848594541,712RefSeq:NZ_FMZC01000003
NZ_FMZC0100000444844701487,634RefSeq:NZ_FMZC01000004
NZ_FMZC0100000524123704288,807RefSeq:NZ_FMZC01000005
NZ_FMZC0100000622121623235,924RefSeq:NZ_FMZC01000006
NZ_FMZC0100000722522302225,364RefSeq:NZ_FMZC01000007
NZ_FMZC0100000820519915216,876RefSeq:NZ_FMZC01000008
NZ_FMZC0100000917016802203,301RefSeq:NZ_FMZC01000009
NZ_FMZC01000010181167104201,292RefSeq:NZ_FMZC01000010
NZ_FMZC0100001117917414198,627RefSeq:NZ_FMZC01000011
NZ_FMZC0100001216215732187,877RefSeq:NZ_FMZC01000012
NZ_FMZC0100001315715313153,864RefSeq:NZ_FMZC01000013
NZ_FMZC0100001413213200141,539RefSeq:NZ_FMZC01000014
NZ_FMZC010000151019812106,022RefSeq:NZ_FMZC01000015
NZ_FMZC0100001681782192,309RefSeq:NZ_FMZC01000016
NZ_FMZC0100001786820490,125RefSeq:NZ_FMZC01000017
NZ_FMZC0100001885850083,915RefSeq:NZ_FMZC01000018
NZ_FMZC0100001960590171,669RefSeq:NZ_FMZC01000019
NZ_FMZC0100002059580168,552RefSeq:NZ_FMZC01000020
NZ_FMZC0100002166660065,829RefSeq:NZ_FMZC01000021
NZ_FMZC0100002254511262,721RefSeq:NZ_FMZC01000022
NZ_FMZC0100002365630262,021RefSeq:NZ_FMZC01000023
NZ_FMZC0100002432320043,253RefSeq:NZ_FMZC01000024
NZ_FMZC0100002533321038,650RefSeq:NZ_FMZC01000025
NZ_FMZC0100002627260134,072RefSeq:NZ_FMZC01000026
NZ_FMZC0100002743420130,865RefSeq:NZ_FMZC01000027
NZ_FMZC0100002821200126,045RefSeq:NZ_FMZC01000028
NZ_FMZC0100002921172224,610RefSeq:NZ_FMZC01000029
NZ_FMZC0100003012110113,611RefSeq:NZ_FMZC01000030
24 Undisplayed Contigs/Replicons322751170,803
Total:4,7834,64755815,257,076
Ortholog data available?Yes
Database Contents
Genes4,783
Pathways281
Enzymatic Reactions1,484
Transport Reactions44
Polypeptides4,694
Protein Complexes116
Enzymes887
Transporters444
Compounds1,114
Transcription Units3,272
tRNAs47
Protein Features5,888
GO Terms421
Database Version29.0
Sequence SourceGCF_900102625.1
Synonyms Acidivorax valerianellae
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Betaproteobacteria
Burkholderiales
Comamonadaceae
Acidovorax
Acidovorax valerianellae
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN05192589
NCBI BioProjectPRJNA224116
NCBI-Taxonomy187868
Annotation ProviderNCBI RefSeq
Annotation Date2022-04-18
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version6.1
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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