Summary This Pathway/Genome Database (PGDB) was generated by the PathoLogic [Karp16, Karp11] component of Pathway Tools software version 24.5 and MetaCyc [Caspi18] version 24.1 on 02-Jun-2020 16:00:59.
Genome
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
GEN-EL16694802,0211,86293662,385,164NCBI Assembly:GCF_000196555.1
Ortholog data available?Yes
Database Contents
Genes2,021
Pathways195
Enzymatic Reactions830
Transport Reactions48
Polypeptides1,862
Protein Complexes44
Enzymes468
Transporters201
Compounds643
Transcription Units1,543
tRNAs77
Protein Features2,359
GO Terms3
Database Version29.0
Synonyms Bifidobacterium longum subsp. longum strain JCM 1217
Bifidobacterium longum subsp. longum str. JCM 1217
Bifidobacterium longum subsp. longum JCM 1217
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Bifidobacteriales
Bifidobacteriaceae
Bifidobacterium
Bifidobacterium longum
Bifidobacterium longum longum
Bifidobacterium longum longum JCM 1217
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMD00060951
NCBI BioProjectPRJNA224116
NCBI-Taxonomy565042
Annotation ProviderNCBI RefSeq
Annotation Date2020-02-14
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.11
Annotation CommentBest-placed reference protein set; GeneMarkS-2+

References

Caspi18: Caspi R, Billington R, Fulcher CA, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Midford PE, Ong Q, Ong WK, Paley S, Subhraveti P, Karp PD (2018). "The MetaCyc database of metabolic pathways and enzymes." Nucleic Acids Res 46(D1);D633-D639. PMID: 29059334

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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Page generated by Pathway Tools version 29.0 (software by SRI International) on Mon Jun 30, 2025, BIOCYC14.