Database Authors
Pallavi Subhraveti1, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 15-Feb-2020 from the annotated genome of Actinomadura atramentaria SF2197, 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 24.0) [Karp16, Karp11] using MetaCyc version 23.5 [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_KB907208763747610759,081RefSeq:NZ_KB907208
NZ_KB907209671651911728,992RefSeq:NZ_KB907209
NZ_KB90721062660989642,211RefSeq:NZ_KB907210
NZ_KB90721155955135603,365RefSeq:NZ_KB907211
NZ_KB907212416395912449,998RefSeq:NZ_KB907212
NZ_KB90721340138759422,996RefSeq:NZ_KB907213
NZ_KB90721435934559403,986RefSeq:NZ_KB907214
NZ_KB90721533432527360,162RefSeq:NZ_KB907215
NZ_KB90721623723142243,688RefSeq:NZ_KB907216
NZ_KB90721721821413232,667RefSeq:NZ_KB907217
NZ_KB90721821320166230,294RefSeq:NZ_KB907218
NZ_KB90721920019910219,854RefSeq:NZ_KB907219
NZ_KB90722018918603206,390RefSeq:NZ_KB907220
NZ_KB90722115915252185,116RefSeq:NZ_KB907221
NZ_KB90722215114812182,005RefSeq:NZ_KB907222
NZ_KB90722314213525159,859RefSeq:NZ_KB907223
NZ_KB90722413813701155,270RefSeq:NZ_KB907224
NZ_KB90722514313922145,836RefSeq:NZ_KB907225
NZ_KB90722611411004118,316RefSeq:NZ_KB907226
NZ_KB90722710510221117,481RefSeq:NZ_KB907227
NZ_KB90722831263226,305RefSeq:NZ_KB907228
NZ_KB90722925240119,506RefSeq:NZ_KB907229
NZ_KB90723115150014,144RefSeq:NZ_KB907231
14 Undisplayed Contigs/Replicons71701683,057
Total:6,2866,099751126,710,579
Ortholog data available?Yes
Database Contents
Genes6,283
Pathways234
Enzymatic Reactions1,152
Transport Reactions47
Polypeptides6,102
Protein Complexes44
Enzymes875
Transporters395
Compounds927
Transcription Units4,326
tRNAs63
Protein Features6,733
Database Version29.0
Sequence SourceGCF_000381885.1
Synonyms Actinomadura atramentaria SF2197
Actinomadura atramentaria DSM 43919
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Streptosporangiales
Thermomonosporaceae
Actinomadura
Actinomadura atramentaria
Actinomadura atramentaria DSM 43919
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02441315
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1120936
EnvironmentSoil
Geographic LocationJapan
Latitude/Longitude34.8743 N 138.324 E
Collection Date1981-08
Relationship to Oxygenaerobe
Temperature Rangemesophile
Annotation ProviderNCBI
Annotation Date2017-04-15
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline
Annotation Pipeline Version4.1
Annotation CommentBest-placed reference protein set; GeneMarkS+
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.