Database Authors
Pallavi Subhraveti1, Peter Midford1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 01-June-2022 from the annotated genome of Mycobacterium marseillense FLAC0026, 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 26.0) [Karp et al., 2016; Karp et al., 2011] using MetaCyc version 26.0 [Caspi et al., 2020]. 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_CP0231474,9124,78950735,266,037RefSeq:NZ_CP023147
pFLAC002620200019,605RefSeq:NZ_CP023148
Total:4,9324,80950735,285,642
Ortholog data available?Yes
Database Contents
Genes4,932
Pathways289
Enzymatic Reactions1,667
Transport Reactions26
Polypeptides4,809
Protein Complexes68
Enzymes931
Transporters237
Compounds1,096
Transcription Units3,129
tRNAs44
Protein Features6,108
Database Version29.0
Sequence SourceGCF_002285715.1
Synonyms Mycobacterium sp. 1165549.7
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Mycobacteriales
Mycobacteriaceae
Mycobacterium
Mycobacterium avium complex (MAC)
Mycobacterium marseillense
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN07528776
NCBI BioProjectPRJNA224116
NCBI-Taxonomy701042
Geographic LocationUSA
Collection Date2013
HostHomo sapiens
Annotation ProviderNCBI RefSeq
Annotation Date2022-04-10
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version6.1
Annotation CommentBest-placed reference protein set; GeneMarkS-2+

References

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

Karp PD, Latendresse M, Caspi R (2011). "The pathway tools pathway prediction algorithm." Stand Genomic Sci 5(3);424-9. PMID: 22675592

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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