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 15-Oct-2019 from the annotated genome of Klebsiella pneumoniae KPC2, 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 23.0) [Karp, 2016; Karp, 2011] using MetaCyc version 23.1 [Caspi, 2019]. 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 15,3225,1971251025,399,983RefSeq:NZ_LR130548
2210210034207,198RefSeq:NZ_LR130549
357570443,380RefSeq:NZ_LR130550
416160213,841RefSeq:NZ_LR130551
Total:5,7475,4801251425,664,402
Ortholog data available?Yes
Database Contents
Genes5,747
Pathways396
Enzymatic Reactions1,862
Transport Reactions201
Polypeptides5,482
Protein Complexes140
Enzymes1,241
Transporters759
Compounds1,481
Transcription Units3,675
tRNAs88
Protein Features7,075
GO Terms3,751
Database Version29.1
Synonyms Klebsiella aerogenes (Kruse) Taylor et al. 1956
Bacillus pneumoniae
Bacterium pneumoniae crouposae
Hyalococcus pneumoniae
Klebsiella pneumoniae aerogenes
Klebsiella sp. 2N3
Klebsiella sp. C1(2016)
Klebsiella sp. M-AI-2
Klebsiella sp. PB12
Klebsiella sp. RCE-7
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadota
Gammaproteobacteria
Enterobacterales
Enterobacteriaceae
Klebsiella/Raoultella group
Klebsiella
Klebsiella pneumoniae
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMEA5128438
NCBI BioProjectPRJNA224116
NCBI-Taxonomy573
HostHomo sapiens
Annotation ProviderNCBI RefSeq
Annotation Date2019-02-7
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline
Annotation Pipeline Version4.7
Annotation CommentBest-placed reference protein set; GeneMarkS-2+

References

Caspi R, Billington R, Keseler IM, Kothari A, Krummenacker M, Midford PE, Ong WK, Paley S, Subhraveti P, Karp PD (2019). "The MetaCyc database of metabolic pathways and enzymes-a 2019 update." Nucleic Acids Res. PMID: 31586394

Karp PD, Latendresse M, Caspi R (2011). "The pathway tools pathway prediction algorithm." Stand Genomic Sci 5(3);424-9. PMID: 22675592

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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