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 Ligilactobacillus ruminis SPM0211, as obtained from RefSeq (annotation date: 27-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_AFOJ01000002608583258604,702RefSeq:NZ_AFOJ01000002
NZ_AFOJ01000006352350211404,421RefSeq:NZ_AFOJ01000006
NZ_AFOJ01000007395388713389,608RefSeq:NZ_AFOJ01000007
NZ_AFOJ0100000519619523212,023RefSeq:NZ_AFOJ01000005
NZ_AFOJ0100000312512502150,533RefSeq:NZ_AFOJ01000003
NZ_AFOJ0100000411811802133,751RefSeq:NZ_AFOJ01000004
NZ_AFOJ0100000812111474114,676RefSeq:NZ_AFOJ01000008
NZ_AFOJ0100000111198135104,511RefSeq:NZ_AFOJ01000001
NZ_AFOJ0100000931247130,269RefSeq:NZ_AFOJ01000009
NZ_AFOJ0100001022220023,046RefSeq:NZ_AFOJ01000010
NZ_AFOJ0100001110203,206RefSeq:NZ_AFOJ01000011
NZ_AFOJ0100001200101,481RefSeq:NZ_AFOJ01000012
Total:2,1292,01766492,172,227
Ortholog data available?Yes
Database Contents
Genes2,080
Pathways154
Enzymatic Reactions969
Transport Reactions36
Polypeptides2,023
Protein Complexes61
Enzymes466
Transporters193
Compounds905
Transcription Units1,347
tRNAs58
GO Annotations3,392
Database Version29.6
Sequence SourceGCF_000217755.1
Synonyms Lactobacillus ruminis SPM0211
Lactobacillus ruminis strain SPM0211
Lactobacillus ruminis str. SPM0211
Ligilactobacillus ruminis SPM0211
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Bacillati
Bacillota
Bacilli
Lactobacillales
Lactobacillaceae
Ligilactobacillus
Ligilactobacillus ruminis
Ligilactobacillus ruminis SPM0211
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02470898
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1040964
Annotation ProviderNCBI RefSeq
Annotation Date2025-01-27
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

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Page generated by Pathway Tools version 29.5 (software by SRI International) on Fri Apr 3, 2026, BIOCYC16.