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 27-Aug-2025 from the annotated genome of Rhizobium leguminosarum BIHB 1148, as obtained from RefSeq (annotation date: 11-JUN-2025). The PGDB was created computationally by the PathoLogic component of the Pathway Tools software (version 29.5) [Karp11, Karp16] using MetaCyc version 29.1 [Caspi19]. It has not undergone any manual curation or review, and may contain errors.
Genome
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_CP0225644,2704,210601304,418,978RefSeq:NZ_CP022564
pSK01878878057976,232RefSeq:NZ_CP022565
pSK02499499014549,819RefSeq:NZ_CP022566
pSK03380377315407,945RefSeq:NZ_CP022567
pSK04314314010326,874RefSeq:NZ_CP022568
pSK05222222010264,815RefSeq:NZ_CP022569
pSK0616160312,967RefSeq:NZ_CP022570
Total:6,8186,516632396,957,630
Ortholog data available?No
Database Contents
Genes6,579
Pathways386
Enzymatic Reactions1,962
Transport Reactions93
Polypeptides6,523
Protein Complexes295
Enzymes1,266
Transporters652
Compounds1,706
Transcription Units4,744
tRNAs50
Protein Features8,192
GO Annotations11,050
Database Version29.6
Sequence SourceGCF_002240185.1
Synonyms Rhizobium leguminosarum symbiovar viciae
Rhizobium leguminosarum bv. viciae
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadati
Pseudomonadota
Alphaproteobacteria
Hyphomicrobiales
Rhizobiaceae
Rhizobium/Agrobacterium group
Rhizobium
Rhizobium leguminosarum
Rhizobium leguminosarum bv. viciae
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN04849238
NCBI BioProjectPRJNA224116
NCBI-Taxonomy387
EnvironmentPisum sativum root-nodule
Latitude/Longitude32.16 N 78.04 E
Altitude (m)3990.0
Collection Date2005-09
Annotation ProviderNCBI RefSeq
Annotation Date2025-06-11
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version6.10
Annotation CommentBest-placed reference protein set; GeneMarkS-2+

References

Caspi19: 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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Page generated by Pathway Tools version 29.5 (software by SRI International) on Wed Jun 10, 2026, BIOCYC17.