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 Mycobacterium lepraemurium Hawaii, 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_CP0212383,9552,589511,3154,050,523RefSeq:NZ_CP021238
Ortholog data available?Yes
Database Contents
Genes3,955
Pathways241
Enzymatic Reactions1,328
Transport Reactions7
Polypeptides2,591
Protein Complexes24
Enzymes612
Transporters151
Compounds1,103
Transcription Units2,570
tRNAs45
Protein Features3,240
Database Version29.0
Synonyms Bacillus der Rattenlepra
Mycobacterium leprae murium
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Mycobacteriales
Mycobacteriaceae
Mycobacterium
Mycobacterium avium complex (MAC)
Mycobacterium lepraemurium
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN06841017
NCBI BioProjectPRJNA224116
NCBI-Taxonomy64667
EnvironmentBalb/c mice spleen and liver
Geographic LocationMexico
Latitude/Longitude19.27 N 99.1 W
Collection Date2015
HostRattus sp.
Annotation ProviderNCBI RefSeq
Annotation Date2019-01-14
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline
Annotation Pipeline Version4.7
Annotation CommentBest-placed reference protein set; GeneMarkS-2+
NCBI Genome Typerepresentative

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

Report Errors or Provide Feedback
Page generated by Pathway Tools version 29.0 (software by SRI International) on Sat Aug 2, 2025, BIOCYC18.