Database Authors
Pallavi Subhraveti1, Peter Midford1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 8-Mar-2022 from the annotated genome of Actinomadura rubteroloni RB29, 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) [Karp16, Karp11] using MetaCyc version 26.0 [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
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_MTBP010000012,3082,25735162,582,138RefSeq:NZ_MTBP01000001
NZ_MTBP010000021,9651,93024112,134,329RefSeq:NZ_MTBP01000002
NZ_MTBP01000003591572712659,230RefSeq:NZ_MTBP01000003
NZ_MTBP0100000447947342542,245RefSeq:NZ_MTBP01000004
NZ_MTBP0100000527026910339,793RefSeq:NZ_MTBP01000005
NZ_MTBP0100000619619312205,762RefSeq:NZ_MTBP01000006
NZ_MTBP0100000730305,640RefSeq:NZ_MTBP01000007
Total:5,8125,69475436,469,137
Ortholog data available?No
Database Contents
Genes5,804
Pathways251
Enzymatic Reactions1,342
Transport Reactions47
Polypeptides5,694
Protein Complexes122
Enzymes886
Transporters332
Compounds1,052
Transcription Units3,966
tRNAs59
Protein Features7,158
GO Terms327
Database Version29.0
Sequence SourceGCF_002911665.1
Synonyms Actinomadura sp. RB29
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Streptosporangiales
Thermomonosporaceae
Actinomadura
Actinomadura rubteroloni
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN06127924
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1926885
Environmenttermite gut
Geographic LocationSouth Africa
Collection Date2015-01
HostTermitoidae
Annotation ProviderNCBI RefSeq
Annotation Date2021-03-19
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.1
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 (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 29.0 (software by SRI International) on Mon Jun 30, 2025, BIOCYC18A.