Database Authors
Pallavi Subhraveti1, Anamika Kothari1, Peter Midford1, Ron Caspi1, Lisa Moore1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 01-Nov-2024 from the annotated genome of Acidovorax sp. NO-1 NO-1, as obtained from RefSeq (annotation date: 02-AUG-2023). The PGDB was created computationally by the PathoLogic component of the Pathway Tools software (version 28.5) [Karp11, Karp16] using MetaCyc version 28.1 [Caspi20]. It has not undergone any manual curation or review, and may contain errors.
Genome
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_AGTS0100007832230868339,177RefSeq:NZ_AGTS01000078
NZ_AGTS0100007719618529203,983RefSeq:NZ_AGTS01000077
NZ_AGTS0100007519018604200,506RefSeq:NZ_AGTS01000075
NZ_AGTS0100010017517203180,639RefSeq:NZ_AGTS01000100
NZ_AGTS0100008316215705179,265RefSeq:NZ_AGTS01000083
NZ_AGTS0100007113713502162,627RefSeq:NZ_AGTS01000071
NZ_AGTS0100014513613114145,757RefSeq:NZ_AGTS01000145
NZ_AGTS0100014312311832139,447RefSeq:NZ_AGTS01000143
NZ_AGTS0100003613512924136,828RefSeq:NZ_AGTS01000036
NZ_AGTS0100010112511762135,943RefSeq:NZ_AGTS01000101
NZ_AGTS0100004911010604121,961RefSeq:NZ_AGTS01000049
NZ_AGTS010000021019911115,081RefSeq:NZ_AGTS01000002
NZ_AGTS0100010511711511114,663RefSeq:NZ_AGTS01000105
NZ_AGTS0100007210210002108,498RefSeq:NZ_AGTS01000072
NZ_AGTS010000631019623104,595RefSeq:NZ_AGTS01000063
NZ_AGTS01000012918605104,237RefSeq:NZ_AGTS01000012
NZ_AGTS01000090989602104,191RefSeq:NZ_AGTS01000090
NZ_AGTS01000137101981299,736RefSeq:NZ_AGTS01000137
NZ_AGTS0100004783821096,026RefSeq:NZ_AGTS01000047
NZ_AGTS0100010271661482,459RefSeq:NZ_AGTS01000102
NZ_AGTS0100004675710480,742RefSeq:NZ_AGTS01000046
NZ_AGTS0100015964600479,612RefSeq:NZ_AGTS01000159
NZ_AGTS0100014757570078,194RefSeq:NZ_AGTS01000147
NZ_AGTS0100015173700374,564RefSeq:NZ_AGTS01000151
NZ_AGTS0100014073656273,980RefSeq:NZ_AGTS01000140
NZ_AGTS0100005557541267,892RefSeq:NZ_AGTS01000055
NZ_AGTS0100009463610262,163RefSeq:NZ_AGTS01000094
NZ_AGTS0100002954520262,146RefSeq:NZ_AGTS01000029
NZ_AGTS0100007459560359,655RefSeq:NZ_AGTS01000074
NZ_AGTS0100005259580158,443RefSeq:NZ_AGTS01000052
NZ_AGTS0100001950490157,037RefSeq:NZ_AGTS01000019
NZ_AGTS0100008847470053,237RefSeq:NZ_AGTS01000088
NZ_AGTS0100014943412051,780RefSeq:NZ_AGTS01000149
NZ_AGTS0100000845450051,357RefSeq:NZ_AGTS01000008
NZ_AGTS0100016041410050,288RefSeq:NZ_AGTS01000160
NZ_AGTS0100007942400248,496RefSeq:NZ_AGTS01000079
NZ_AGTS0100007645430247,321RefSeq:NZ_AGTS01000076
NZ_AGTS0100004446422246,250RefSeq:NZ_AGTS01000044
NZ_AGTS0100009935341043,917RefSeq:NZ_AGTS01000099
NZ_AGTS0100003341401043,546RefSeq:NZ_AGTS01000033
NZ_AGTS0100014839350443,447RefSeq:NZ_AGTS01000148
NZ_AGTS0100008945422142,435RefSeq:NZ_AGTS01000089
NZ_AGTS0100008636360040,294RefSeq:NZ_AGTS01000086
NZ_AGTS0100003239351338,895RefSeq:NZ_AGTS01000032
NZ_AGTS0100009337360138,339RefSeq:NZ_AGTS01000093
NZ_AGTS0100001744430138,108RefSeq:NZ_AGTS01000017
NZ_AGTS0100008030280232,475RefSeq:NZ_AGTS01000080
NZ_AGTS0100006126260031,942RefSeq:NZ_AGTS01000061
NZ_AGTS0100014431300131,226RefSeq:NZ_AGTS01000144
NZ_AGTS0100015628260228,408RefSeq:NZ_AGTS01000156
NZ_AGTS0100003827260128,019RefSeq:NZ_AGTS01000038
NZ_AGTS0100003122220027,172RefSeq:NZ_AGTS01000031
NZ_AGTS0100005322200225,483RefSeq:NZ_AGTS01000053
NZ_AGTS0100011129254024,846RefSeq:NZ_AGTS01000111
NZ_AGTS0100015021200123,542RefSeq:NZ_AGTS01000150
NZ_AGTS0100008728250323,187RefSeq:NZ_AGTS01000087
NZ_AGTS0100004322200221,095RefSeq:NZ_AGTS01000043
NZ_AGTS0100010921200119,316RefSeq:NZ_AGTS01000109
NZ_AGTS0100009219190018,961RefSeq:NZ_AGTS01000092
NZ_AGTS0100003419170218,199RefSeq:NZ_AGTS01000034
NZ_AGTS0100002813130017,856RefSeq:NZ_AGTS01000028
NZ_AGTS0100000315150017,854RefSeq:NZ_AGTS01000003
NZ_AGTS0100002018180017,618RefSeq:NZ_AGTS01000020
NZ_AGTS0100004516140216,379RefSeq:NZ_AGTS01000045
NZ_AGTS0100006716150116,259RefSeq:NZ_AGTS01000067
NZ_AGTS0100010721190213,991RefSeq:NZ_AGTS01000107
NZ_AGTS0100016113130013,722RefSeq:NZ_AGTS01000161
NZ_AGTS0100014613100312,986RefSeq:NZ_AGTS01000146
NZ_AGTS0100004013130012,642RefSeq:NZ_AGTS01000040
92 Undisplayed Contigs/Replicons164159531210,801
Total:4,6634,448521635,011,736
Ortholog data available?No
Database Contents
Genes4,663
Pathways325
Enzymatic Reactions1,813
Transport Reactions77
Polypeptides4,542
Protein Complexes116
Enzymes991
Transporters452
Compounds1,590
Transcription Units3,332
tRNAs46
Protein Features5,990
GO Terms5,728
Database Version29.0
Sequence SourceGCF_000238595.1
Synonyms Acidovorax sp. NO1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Betaproteobacteria
Burkholderiales
Comamonadaceae
Acidovorax
unclassified Acidovorax
Acidovorax sp. NO-1
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02471019
NCBI BioProjectPRJNA224116
NCBI-Taxonomy512030
Annotation ProviderNCBI RefSeq
Annotation Date2023-08-2
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version6.5
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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