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 cattleyae DSM 17101, 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_FNJL0100000131230516330,615RefSeq:NZ_FNJL01000001
NZ_FNJL01000002244227512275,647RefSeq:NZ_FNJL01000002
NZ_FNJL01000003240226212257,627RefSeq:NZ_FNJL01000003
NZ_FNJL01000004238224014247,993RefSeq:NZ_FNJL01000004
NZ_FNJL01000005215203210236,249RefSeq:NZ_FNJL01000005
NZ_FNJL0100000617817305196,151RefSeq:NZ_FNJL01000006
NZ_FNJL0100000716515546193,384RefSeq:NZ_FNJL01000007
NZ_FNJL0100000819418419189,437RefSeq:NZ_FNJL01000008
NZ_FNJL01000009168155112179,038RefSeq:NZ_FNJL01000009
NZ_FNJL0100001020218868175,561RefSeq:NZ_FNJL01000010
NZ_FNJL0100001116215615169,736RefSeq:NZ_FNJL01000011
NZ_FNJL0100001214313508168,888RefSeq:NZ_FNJL01000012
NZ_FNJL01000013155140312167,570RefSeq:NZ_FNJL01000013
NZ_FNJL0100001413412914143,183RefSeq:NZ_FNJL01000014
NZ_FNJL0100001512712007141,076RefSeq:NZ_FNJL01000015
NZ_FNJL0100001611511203114,632RefSeq:NZ_FNJL01000016
NZ_FNJL0100001711210507113,806RefSeq:NZ_FNJL01000017
NZ_FNJL01000018787305113,233RefSeq:NZ_FNJL01000018
NZ_FNJL0100001910110001111,013RefSeq:NZ_FNJL01000019
NZ_FNJL01000020918425104,039RefSeq:NZ_FNJL01000020
NZ_FNJL01000021999423102,125RefSeq:NZ_FNJL01000021
NZ_FNJL0100002294851897,684RefSeq:NZ_FNJL01000022
NZ_FNJL0100002383790495,702RefSeq:NZ_FNJL01000023
NZ_FNJL0100002478730595,241RefSeq:NZ_FNJL01000024
NZ_FNJL0100002578722488,246RefSeq:NZ_FNJL01000025
NZ_FNJL0100002676730382,401RefSeq:NZ_FNJL01000026
NZ_FNJL0100002770681178,377RefSeq:NZ_FNJL01000027
NZ_FNJL0100002873720177,508RefSeq:NZ_FNJL01000028
NZ_FNJL0100002970660477,174RefSeq:NZ_FNJL01000029
NZ_FNJL0100003082781376,438RefSeq:NZ_FNJL01000030
NZ_FNJL0100003156521371,478RefSeq:NZ_FNJL01000031
NZ_FNJL0100003255474466,633RefSeq:NZ_FNJL01000032
NZ_FNJL0100003359550465,206RefSeq:NZ_FNJL01000033
NZ_FNJL0100003453500362,720RefSeq:NZ_FNJL01000034
NZ_FNJL0100003552510152,110RefSeq:NZ_FNJL01000035
NZ_FNJL0100003656540250,566RefSeq:NZ_FNJL01000036
NZ_FNJL0100003738360245,974RefSeq:NZ_FNJL01000037
NZ_FNJL0100003848402641,224RefSeq:NZ_FNJL01000038
NZ_FNJL0100003936320440,243RefSeq:NZ_FNJL01000039
NZ_FNJL0100004031300140,149RefSeq:NZ_FNJL01000040
NZ_FNJL0100004132300238,546RefSeq:NZ_FNJL01000041
NZ_FNJL0100004235350037,141RefSeq:NZ_FNJL01000042
NZ_FNJL0100004331290235,344RefSeq:NZ_FNJL01000043
NZ_FNJL0100004427231332,308RefSeq:NZ_FNJL01000044
NZ_FNJL0100004536270931,137RefSeq:NZ_FNJL01000045
NZ_FNJL0100004623220126,550RefSeq:NZ_FNJL01000046
NZ_FNJL0100004718170124,955RefSeq:NZ_FNJL01000047
NZ_FNJL0100004821180324,524RefSeq:NZ_FNJL01000048
NZ_FNJL0100004919170222,738RefSeq:NZ_FNJL01000049
NZ_FNJL0100005016150120,576RefSeq:NZ_FNJL01000050
NZ_FNJL0100005121210020,284RefSeq:NZ_FNJL01000051
NZ_FNJL0100005216140217,016RefSeq:NZ_FNJL01000052
NZ_FNJL0100005613110211,458RefSeq:NZ_FNJL01000056
NZ_FNJL0100005714100410,959RefSeq:NZ_FNJL01000057
NZ_FNJL01000063129038,809RefSeq:NZ_FNJL01000063
38 Undisplayed Contigs/Replicons132127532210,823
Total:5,1594,826492845,609,245
Ortholog data available?No
Database Contents
Genes5,159
Pathways299
Enzymatic Reactions1,484
Transport Reactions80
Polypeptides4,919
Protein Complexes68
Enzymes989
Transporters594
Compounds1,132
Transcription Units3,439
tRNAs42
Protein Features6,102
GO Terms2
Database Version29.0
Sequence SourceGCF_900104515.1
Synonyms Acidivorax cattleyae
Acidovorax avenae subsp. cattleyae
Bacterium cattleyae
Pseudomonas cattleyae
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Betaproteobacteria
Burkholderiales
Comamonadaceae
Acidovorax
Acidovorax cattleyae
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN04489708
NCBI BioProjectPRJNA224116
NCBI-Taxonomy80868
Annotation ProviderNCBI RefSeq
Annotation Date2020-04-2
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.11
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

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