Database Authors
Pallavi Subhraveti1, Anamika Kothari1, Peter Midford1, Ron Caspi1, Lisa Moore1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 03-Nov-2025 from the annotated genome of Klebsiella pneumoniae DSM 30104, as obtained from RefSeq (annotation date: 07-JAN-2025). The PGDB was created computationally by the PathoLogic component of the Pathway Tools software (version 29.5) [Karp11, Karp16] using MetaCyc version 29.5 [Caspi20]. It has not undergone any manual curation or review, and may contain errors.
Genome
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_AJJI010000141,0581,03226201,148,365RefSeq:NZ_AJJI01000014
NZ_AJJI010000156696571211684,971RefSeq:NZ_AJJI01000015
NZ_AJJI01000010529526335548,693RefSeq:NZ_AJJI01000010
NZ_AJJI01000007414400146459,638RefSeq:NZ_AJJI01000007
NZ_AJJI01000008384381318402,975RefSeq:NZ_AJJI01000008
NZ_AJJI01000011367359822384,283RefSeq:NZ_AJJI01000011
NZ_AJJI0100000334033643370,018RefSeq:NZ_AJJI01000003
NZ_AJJI01000001307303414334,673RefSeq:NZ_AJJI01000001
NZ_AJJI0100000524724434250,850RefSeq:NZ_AJJI01000005
NZ_AJJI01000017183172111190,809RefSeq:NZ_AJJI01000017
pKPt3686809103,907RefSeq:NZ_AJJI01000025
NZ_AJJI01000016969602100,746RefSeq:NZ_AJJI01000016
NZ_AJJI0100000677770390,673RefSeq:NZ_AJJI01000006
pKPt4929201788,770RefSeq:NZ_AJJI01000026
NZ_AJJI0100000472684072,389RefSeq:NZ_AJJI01000004
pKPt5454501446,267RefSeq:NZ_AJJI01000027
NZ_AJJI0100001841347044,702RefSeq:NZ_AJJI01000018
NZ_AJJI0100000232311539,305RefSeq:NZ_AJJI01000002
NZ_AJJI0100000931310234,671RefSeq:NZ_AJJI01000009
pKPt2181801632,275RefSeq:NZ_AJJI01000024
NZ_AJJI0100001235350130,552RefSeq:NZ_AJJI01000012
NZ_AJJI0100002016160213,285RefSeq:NZ_AJJI01000020
NZ_AJJI0100001311110212,618RefSeq:NZ_AJJI01000013
NZ_AJJI0100002220200111,024RefSeq:NZ_AJJI01000022
pKPt199016,592RefSeq:NZ_AJJI01000023
NZ_AJJI0100002166036,331RefSeq:NZ_AJJI01000021
NZ_AJJI0100001910102,965RefSeq:NZ_AJJI01000019
Total:5,3805,0671012125,512,347
Ortholog data available?Yes
Database Contents
Genes5,168
Pathways473
Enzymatic Reactions2,286
Transport Reactions301
Polypeptides5,197
Protein Complexes196
Enzymes1,365
Transporters709
Compounds1,829
Transcription Units3,607
tRNAs77
Protein Features3
GO Annotations7,287
Database Version29.6
Sequence SourceGCF_000281755.1
Synonyms Klebsiella pneumoniae subsp. pneumoniae DSM 30104
Klebsiella pneumoniae subsp. pneumoniae JCM 1662
Klebsiella pneumoniae subsp. pneumoniae NBRC 14940
Klebsiella pneumoniae subsp. pneumoniae strain DSM 30104
Klebsiella pneumoniae subsp. pneumoniae str. DSM 30104
Klebsiella pneumoniae subsp. pneumoniae DSM 30104 = JCM 1662 = NBRC 14940
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadati
Pseudomonadota
Gammaproteobacteria
Enterobacterales
Enterobacteriaceae
Klebsiella/Raoultella group
Klebsiella
Klebsiella pneumoniae complex
Klebsiella pneumoniae
Klebsiella pneumoniae pneumoniae
Klebsiella pneumoniae pneumoniae DSM 30104 = JCM 1662 = NBRC 14940
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02470063
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1162296
Environmentblood
HostHomo sapiens
Annotation ProviderNCBI RefSeq
Annotation Date2025-01-5
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version6.9
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

Report Errors or Provide Feedback
Page generated by Pathway Tools version 29.5 (software by SRI International) on Wed May 13, 2026, BIOCYC19.