Database Authors
Pallavi Subhraveti1, Quang Ong1, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 27-Feb-2018 from the annotated genome of Acidovorax wautersii DSM 27981, 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 22.0) [Karp16, Karp11] using MetaCyc version 21.5 [Caspi18]. 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 Institutess of Health.
Genome
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_FONX01000001523506125612,921RefSeq:NZ_FONX01000001
NZ_FONX0100000246846107532,756RefSeq:NZ_FONX01000002
NZ_FONX0100000340639925454,836RefSeq:NZ_FONX01000003
NZ_FONX01000004395379610420,673RefSeq:NZ_FONX01000004
NZ_FONX0100000532531258375,043RefSeq:NZ_FONX01000005
NZ_FONX0100000628027226282,850RefSeq:NZ_FONX01000006
NZ_FONX0100000719218714228,250RefSeq:NZ_FONX01000007
NZ_FONX0100000818618114217,420RefSeq:NZ_FONX01000008
NZ_FONX0100000917317111197,571RefSeq:NZ_FONX01000009
NZ_FONX0100001015214705182,061RefSeq:NZ_FONX01000010
NZ_FONX0100001117516546174,921RefSeq:NZ_FONX01000011
NZ_FONX0100001215415301174,804RefSeq:NZ_FONX01000012
NZ_FONX0100001314714412173,017RefSeq:NZ_FONX01000013
NZ_FONX0100001415514834167,237RefSeq:NZ_FONX01000014
NZ_FONX0100001514314012142,734RefSeq:NZ_FONX01000015
NZ_FONX0100001610910603117,622RefSeq:NZ_FONX01000016
NZ_FONX01000017878601101,312RefSeq:NZ_FONX01000017
NZ_FONX0100001875722188,810RefSeq:NZ_FONX01000018
NZ_FONX0100001966612379,785RefSeq:NZ_FONX01000019
NZ_FONX0100002081771379,254RefSeq:NZ_FONX01000020
NZ_FONX0100002169671177,959RefSeq:NZ_FONX01000021
NZ_FONX0100002271691174,051RefSeq:NZ_FONX01000022
NZ_FONX0100002367670073,147RefSeq:NZ_FONX01000023
NZ_FONX0100002443410256,152RefSeq:NZ_FONX01000024
NZ_FONX0100002533301236,117RefSeq:NZ_FONX01000025
NZ_FONX0100002614130119,838RefSeq:NZ_FONX01000026
NZ_FONX0100002716150117,577RefSeq:NZ_FONX01000027
NZ_FONX0100002817170015,862RefSeq:NZ_FONX01000028
NZ_FONX0100002915120315,136RefSeq:NZ_FONX01000029
NZ_FONX0100003120200013,965RefSeq:NZ_FONX01000031
NZ_FONX0100003212120011,676RefSeq:NZ_FONX01000032
NZ_FONX010000341212008,858RefSeq:NZ_FONX01000034
23 Undisplayed Contigs/Replicons8376714111,371
Total:4,7784,618541065,335,586
Ortholog data available?Yes
Database Contents
Genes4,779
Pathways239
Enzymatic Reactions1,448
Transport Reactions88
Polypeptides4,629
Protein Complexes33
Enzymes913
Transporters579
Compounds1,220
Transcription Units3,266
tRNAs49
Protein Features5,879
GO Terms19,518
Database Version29.0
Synonyms CCUG 62584
LMG 26971
strain NF 1078
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Betaproteobacteria
Burkholderiales
Comamonadaceae
Acidovorax
Acidovorax wautersii
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN04489711
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1177982
NCBI Genome Typerepresentative

References

Caspi18: Caspi R, Billington R, Fulcher CA, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Midford PE, Ong Q, Ong WK, Paley S, Subhraveti P, Karp PD (2018). "The MetaCyc database of metabolic pathways and enzymes." Nucleic Acids Res 46(D1);D633-D639. PMID: 29059334

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

Report Errors or Provide Feedback
Page generated by Pathway Tools version 29.0 (software by SRI International) on Mon Jun 30, 2025, BIOCYC18A.