Database Authors
Pallavi Subhraveti1, Peter Midford1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 8-Mar-2022 from the annotated genome of Burkholderia gladioli KACC 11889, 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 26.0) [Karp16, Karp11] using MetaCyc version 26.0 [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
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
Chromosome 14,1444,073711174,668,350RefSeq:NZ_CP022005
Chromosome 23,1663,15115733,922,845RefSeq:NZ_CP022006
pls1195195025210,524RefSeq:NZ_CP022007
pls2272701026,639RefSeq:NZ_CP022008
pls3212101626,479RefSeq:NZ_CP022009
Total:7,7947,467862418,854,837
Ortholog data available?No
Database Contents
Genes7,553
Pathways374
Enzymatic Reactions1,812
Transport Reactions95
Polypeptides7,467
Protein Complexes7
Enzymes1,315
Transporters1,010
Compounds1,323
Transcription Units5,429
tRNAs67
Protein Features9,531
GO Annotations5,218
Database Version29.6
Sequence SourceGCF_002208175.1
Synonyms Burkholderia gladioli gladioli
Burkholderia gladioli subsp. gladioli
Phytomonas marginata
Pseudomonas gladioli gladioli
Burkholderia gladioli pv. gladioli
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadati
Pseudomonadota
Betaproteobacteria
Burkholderiales
Burkholderiaceae
Burkholderia
Burkholderia gladioli
Burkholderia gladioli pv. gladioli
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN07253176
NCBI BioProjectPRJNA224116
NCBI-Taxonomy32009
Environmentgladiolus
Geographic LocationSouth Korea
Collection Date2015
Annotation ProviderNCBI RefSeq
Annotation Date2021-12-20
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.3
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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