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 NB5306, 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) [Karp16, Karp11] using MetaCyc version 23.1 [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
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_CP0347605,2845,0591231025,261,911RefSeq:NZ_CP034760
unnamed21048102381,092RefSeq:NZ_CP034761
unnamed385036,141RefSeq:NZ_CP034762
unnamed466004,976RefSeq:NZ_CP034763
unnamed555003,674RefSeq:NZ_CP034764
unnamed677002,927RefSeq:NZ_CP034765
Total:5,4145,1631231285,360,721
Ortholog data available?Yes
Database Contents
Genes5,414
Pathways363
Enzymatic Reactions1,815
Transport Reactions42
Polypeptides5,164
Protein Complexes68
Enzymes1,185
Transporters840
Compounds1,440
Transcription Units3,494
tRNAs87
Protein Features6,745
GO Terms3,394
Database Version29.0
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)
BIOSAMPLESAMN10662038
NCBI BioProjectPRJNA224116
NCBI-Taxonomy573
Environmentblood
Geographic LocationChina
Latitude/Longitude30.0 N 120.0 E
Collection Date2014-09-24
HostHomo sapiens
Human Microbiome Body Siteblood
Annotation ProviderNCBI RefSeq
Annotation Date2019-01-12
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline
Annotation Pipeline Version4.7
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 (2019). "The MetaCyc database of metabolic pathways and enzymes - a 2019 update." Nucleic Acids Res. 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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