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 Acidovorax facilis , 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_CAIGKB01000000157255886621,144RefSeq:NZ_CAIGKB010000001
NZ_CAIGKB010000002362345143394,769RefSeq:NZ_CAIGKB010000002
NZ_CAIGKB01000000327827431309,500RefSeq:NZ_CAIGKB010000003
NZ_CAIGKB010000004248234113264,204RefSeq:NZ_CAIGKB010000004
NZ_CAIGKB01000000524423662239,229RefSeq:NZ_CAIGKB010000005
NZ_CAIGKB01000000622521537230,777RefSeq:NZ_CAIGKB010000006
NZ_CAIGKB01000000719919207221,554RefSeq:NZ_CAIGKB010000007
NZ_CAIGKB01000000819018910193,518RefSeq:NZ_CAIGKB010000008
NZ_CAIGKB01000000917216615190,917RefSeq:NZ_CAIGKB010000009
NZ_CAIGKB01000001016015352180,189RefSeq:NZ_CAIGKB010000010
NZ_CAIGKB01000001116516500172,528RefSeq:NZ_CAIGKB010000011
NZ_CAIGKB01000001213112911142,406RefSeq:NZ_CAIGKB010000012
NZ_CAIGKB01000001312412202141,704RefSeq:NZ_CAIGKB010000013
NZ_CAIGKB01000001411911612134,847RefSeq:NZ_CAIGKB010000014
NZ_CAIGKB01000001512212200133,083RefSeq:NZ_CAIGKB010000015
NZ_CAIGKB01000001611010523117,660RefSeq:NZ_CAIGKB010000016
NZ_CAIGKB01000001710810611112,233RefSeq:NZ_CAIGKB010000017
NZ_CAIGKB010000018969501102,795RefSeq:NZ_CAIGKB010000018
NZ_CAIGKB01000001911210606100,843RefSeq:NZ_CAIGKB010000019
NZ_CAIGKB01000002088841396,508RefSeq:NZ_CAIGKB010000020
NZ_CAIGKB01000002180800096,288RefSeq:NZ_CAIGKB010000021
NZ_CAIGKB01000002281780378,099RefSeq:NZ_CAIGKB010000022
NZ_CAIGKB01000002373721064,544RefSeq:NZ_CAIGKB010000023
NZ_CAIGKB01000002448470156,202RefSeq:NZ_CAIGKB010000024
NZ_CAIGKB01000002544430155,619RefSeq:NZ_CAIGKB010000025
NZ_CAIGKB01000002648480050,730RefSeq:NZ_CAIGKB010000026
NZ_CAIGKB01000002736350146,013RefSeq:NZ_CAIGKB010000027
NZ_CAIGKB01000002841410044,772RefSeq:NZ_CAIGKB010000028
NZ_CAIGKB01000002943390444,221RefSeq:NZ_CAIGKB010000029
NZ_CAIGKB01000003044420244,044RefSeq:NZ_CAIGKB010000030
NZ_CAIGKB01000003144440042,535RefSeq:NZ_CAIGKB010000031
NZ_CAIGKB01000003227240334,109RefSeq:NZ_CAIGKB010000032
NZ_CAIGKB01000003327270032,084RefSeq:NZ_CAIGKB010000033
NZ_CAIGKB01000003423230024,118RefSeq:NZ_CAIGKB010000034
NZ_CAIGKB01000003516110514,490RefSeq:NZ_CAIGKB010000035
NZ_CAIGKB01000003617170013,681RefSeq:NZ_CAIGKB010000036
NZ_CAIGKB01000003715150013,587RefSeq:NZ_CAIGKB010000037
NZ_CAIGKB01000003815150013,196RefSeq:NZ_CAIGKB010000038
28 Undisplayed Contigs/Replicons9792510113,883
Total:4,6544,50554954,982,623
Ortholog data available?No
Database Contents
Genes4,654
Pathways299
Enzymatic Reactions1,499
Transport Reactions75
Polypeptides4,531
Protein Complexes66
Enzymes954
Transporters503
Compounds1,166
Transcription Units2,954
tRNAs48
Protein Features5,954
GO Terms3
Database Version29.0
Sequence SourceGCF_903797705.1
Synonyms Acidivorax facilis
Hydrogenomonas facilis
Pseudomonas facilis
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Betaproteobacteria
Burkholderiales
Comamonadaceae
Acidovorax
Acidovorax facilis
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMEA6854749
NCBI BioProjectPRJNA224116
NCBI-Taxonomy12917
Annotation ProviderNCBI RefSeq
Annotation Date2020-08-11
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.12
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

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