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 temperans KY4, 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_JXYQ0100000824023406263,914RefSeq:NZ_JXYQ01000008
NZ_JXYQ0100000216015406173,231RefSeq:NZ_JXYQ01000002
NZ_JXYQ0100003214013802165,504RefSeq:NZ_JXYQ01000032
NZ_JXYQ0100001215915405165,476RefSeq:NZ_JXYQ01000012
NZ_JXYQ0100001914513708164,574RefSeq:NZ_JXYQ01000019
NZ_JXYQ0100000912412211144,719RefSeq:NZ_JXYQ01000009
NZ_JXYQ0100001712311940136,224RefSeq:NZ_JXYQ01000017
NZ_JXYQ0100003011911702124,898RefSeq:NZ_JXYQ01000030
NZ_JXYQ0100000310610204123,993RefSeq:NZ_JXYQ01000003
NZ_JXYQ0100005311311012116,159RefSeq:NZ_JXYQ01000053
NZ_JXYQ01000037838102115,328RefSeq:NZ_JXYQ01000037
NZ_JXYQ01000022949103109,255RefSeq:NZ_JXYQ01000022
NZ_JXYQ01000023100946095,812RefSeq:NZ_JXYQ01000023
NZ_JXYQ0100001184792392,792RefSeq:NZ_JXYQ01000011
NZ_JXYQ0100000589860392,516RefSeq:NZ_JXYQ01000005
NZ_JXYQ0100002183810292,311RefSeq:NZ_JXYQ01000021
NZ_JXYQ0100006684831090,180RefSeq:NZ_JXYQ01000066
NZ_JXYQ0100005171700184,180RefSeq:NZ_JXYQ01000051
NZ_JXYQ0100003673711177,906RefSeq:NZ_JXYQ01000036
NZ_JXYQ0100006068641376,355RefSeq:NZ_JXYQ01000060
NZ_JXYQ0100004168621574,008RefSeq:NZ_JXYQ01000041
NZ_JXYQ0100006867631370,749RefSeq:NZ_JXYQ01000068
NZ_JXYQ0100004367651169,281RefSeq:NZ_JXYQ01000043
NZ_JXYQ0100007255540167,729RefSeq:NZ_JXYQ01000072
NZ_JXYQ0100002955540166,002RefSeq:NZ_JXYQ01000029
NZ_JXYQ0100000462600264,509RefSeq:NZ_JXYQ01000004
NZ_JXYQ0100002462610161,826RefSeq:NZ_JXYQ01000024
NZ_JXYQ0100001042420053,702RefSeq:NZ_JXYQ01000010
NZ_JXYQ0100004047450252,328RefSeq:NZ_JXYQ01000040
NZ_JXYQ0100002845431152,068RefSeq:NZ_JXYQ01000028
NZ_JXYQ0100003349462151,542RefSeq:NZ_JXYQ01000033
NZ_JXYQ0100007045421247,580RefSeq:NZ_JXYQ01000070
NZ_JXYQ0100006947442147,239RefSeq:NZ_JXYQ01000069
NZ_JXYQ0100005041400146,602RefSeq:NZ_JXYQ01000050
NZ_JXYQ0100005647450246,195RefSeq:NZ_JXYQ01000056
NZ_JXYQ0100001345420345,919RefSeq:NZ_JXYQ01000013
NZ_JXYQ0100009038360244,488RefSeq:NZ_JXYQ01000090
NZ_JXYQ0100003832320043,410RefSeq:NZ_JXYQ01000038
NZ_JXYQ0100006146441141,471RefSeq:NZ_JXYQ01000061
NZ_JXYQ0100003939330640,991RefSeq:NZ_JXYQ01000039
NZ_JXYQ0100008236285340,556RefSeq:NZ_JXYQ01000082
NZ_JXYQ0100004247461040,057RefSeq:NZ_JXYQ01000042
NZ_JXYQ0100000139361239,808RefSeq:NZ_JXYQ01000001
NZ_JXYQ0100004923230035,778RefSeq:NZ_JXYQ01000049
NZ_JXYQ0100007345440135,208RefSeq:NZ_JXYQ01000073
NZ_JXYQ0100007831280334,443RefSeq:NZ_JXYQ01000078
NZ_JXYQ0100006231280334,386RefSeq:NZ_JXYQ01000062
NZ_JXYQ0100004633303033,034RefSeq:NZ_JXYQ01000046
NZ_JXYQ0100008937330432,428RefSeq:NZ_JXYQ01000089
NZ_JXYQ0100001823230031,159RefSeq:NZ_JXYQ01000018
NZ_JXYQ0100006331310030,613RefSeq:NZ_JXYQ01000063
NZ_JXYQ0100001621200130,097RefSeq:NZ_JXYQ01000016
NZ_JXYQ0100000723221024,788RefSeq:NZ_JXYQ01000007
NZ_JXYQ0100003528250324,106RefSeq:NZ_JXYQ01000035
NZ_JXYQ0100009315150023,259RefSeq:NZ_JXYQ01000093
NZ_JXYQ0100007425250021,400RefSeq:NZ_JXYQ01000074
NZ_JXYQ0100005818171020,328RefSeq:NZ_JXYQ01000058
NZ_JXYQ0100002511100120,263RefSeq:NZ_JXYQ01000025
NZ_JXYQ0100002018180018,593RefSeq:NZ_JXYQ01000020
NZ_JXYQ0100005915140116,829RefSeq:NZ_JXYQ01000059
NZ_JXYQ0100004716160016,269RefSeq:NZ_JXYQ01000047
NZ_JXYQ0100004413120116,037RefSeq:NZ_JXYQ01000044
NZ_JXYQ0100005216160015,811RefSeq:NZ_JXYQ01000052
NZ_JXYQ0100007714120215,538RefSeq:NZ_JXYQ01000077
NZ_JXYQ0100004514130115,170RefSeq:NZ_JXYQ01000045
NZ_JXYQ0100003112110114,404RefSeq:NZ_JXYQ01000031
NZ_JXYQ010000541310309,917RefSeq:NZ_JXYQ01000054
74 Undisplayed Contigs/Replicons143137826192,539
Total:4,0763,883501434,475,784
Ortholog data available?No
Database Contents
Genes4,074
Pathways271
Enzymatic Reactions1,388
Transport Reactions74
Polypeptides3,946
Protein Complexes50
Enzymes840
Transporters453
Compounds1,040
Transcription Units2,821
tRNAs43
Protein Features5,072
GO Terms16,365
Database Version29.0
Sequence SourceGCF_000935585.1
Synonyms Acidivorax temperans
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Betaproteobacteria
Burkholderiales
Comamonadaceae
Acidovorax
Acidovorax temperans
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN03265417
NCBI BioProjectPRJNA224116
NCBI-Taxonomy80878
Environmentlake water
Geographic LocationMalaysia
Collection Date2014-04
Annotation ProviderNCBI RefSeq
Annotation Date2020-04-8
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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