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 Actinoplanes globisporus DSM 43857, 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_KB9032941,3411,2944431,541,790RefSeq:NZ_KB903294
NZ_KB903295513502110573,240RefSeq:NZ_KB903295
NZ_KB90330644644033449,222RefSeq:NZ_KB903306
NZ_KB90331739538519436,137RefSeq:NZ_KB903317
NZ_KB90332836535717419,172RefSeq:NZ_KB903328
NZ_KB903339366356010402,945RefSeq:NZ_KB903339
NZ_KB90335036135515373,546RefSeq:NZ_KB903350
NZ_KB90335630930225346,848RefSeq:NZ_KB903356
NZ_KB90335729829503344,305RefSeq:NZ_KB903357
NZ_KB90335829128506309,041RefSeq:NZ_KB903358
NZ_KB90329626826602307,609RefSeq:NZ_KB903296
NZ_KB90329724123335274,805RefSeq:NZ_KB903297
NZ_KB903298234224010249,270RefSeq:NZ_KB903298
NZ_KB90329921921702238,266RefSeq:NZ_KB903299
NZ_KB90330019919513234,194RefSeq:NZ_KB903300
NZ_KB90330120720502225,465RefSeq:NZ_KB903301
NZ_KB90330219118704223,114RefSeq:NZ_KB903302
NZ_KB90330318217903213,292RefSeq:NZ_KB903303
NZ_KB90330419318418207,889RefSeq:NZ_KB903304
NZ_KB90330518217624195,538RefSeq:NZ_KB903305
NZ_KB90330717016514178,555RefSeq:NZ_KB903307
NZ_KB90330815615213177,427RefSeq:NZ_KB903308
NZ_KB90330918117542170,788RefSeq:NZ_KB903309
NZ_KB90331016716025167,343RefSeq:NZ_KB903310
NZ_KB90331115014226159,412RefSeq:NZ_KB903311
NZ_KB90331213612439153,040RefSeq:NZ_KB903312
NZ_KB90331314313922149,866RefSeq:NZ_KB903313
NZ_KB90331413012703144,523RefSeq:NZ_KB903314
NZ_KB90331513213002139,181RefSeq:NZ_KB903315
NZ_KB90331613412734136,721RefSeq:NZ_KB903316
NZ_KB90331813512591134,522RefSeq:NZ_KB903318
NZ_KB90331912612141133,079RefSeq:NZ_KB903319
NZ_KB90332012912513130,752RefSeq:NZ_KB903320
NZ_KB903321999612115,938RefSeq:NZ_KB903321
NZ_KB90332210810800114,221RefSeq:NZ_KB903322
NZ_KB903323938814106,355RefSeq:NZ_KB903323
NZ_KB90332410710214105,503RefSeq:NZ_KB903324
NZ_KB90332580770391,733RefSeq:NZ_KB903325
NZ_KB90332686831291,561RefSeq:NZ_KB903326
NZ_KB90332756560089,843RefSeq:NZ_KB903327
NZ_KB90332970690178,979RefSeq:NZ_KB903329
NZ_KB90333066640274,762RefSeq:NZ_KB903330
NZ_KB90333166613272,709RefSeq:NZ_KB903331
NZ_KB90333274712170,044RefSeq:NZ_KB903332
NZ_KB90333372710169,612RefSeq:NZ_KB903333
NZ_KB90333455540156,317RefSeq:NZ_KB903334
NZ_KB90333554503154,811RefSeq:NZ_KB903335
NZ_KB90333652501148,871RefSeq:NZ_KB903336
NZ_KB90333745414039,878RefSeq:NZ_KB903337
NZ_KB90333821200131,828RefSeq:NZ_KB903338
NZ_KB90334020180227,299RefSeq:NZ_KB903340
NZ_KB90334123211126,942RefSeq:NZ_KB903341
NZ_KB90334223220125,895RefSeq:NZ_KB903342
NZ_KB90334311110014,268RefSeq:NZ_KB903343
NZ_KB90334413120112,371RefSeq:NZ_KB903344
10 Undisplayed Contigs/Replicons14142527,870
Total:10,0059,7087222510,988,507
Ortholog data available?Yes
Database Contents
Genes9,999
Pathways280
Enzymatic Reactions1,435
Transport Reactions69
Polypeptides9,724
Protein Complexes89
Enzymes1,198
Transporters849
Compounds1,125
Transcription Units6,584
tRNAs59
Protein Features11,397
Database Version29.0
Sequence SourceGCF_000379645.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Micromonosporales
Micromonosporaceae
Actinoplanes
Actinoplanes globisporus
Actinoplanes globisporus DSM 43857
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02256449
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1120949
EnvironmentSoil
Geographic LocationItaly
Latitude/Longitude45.73 N 8.98 E
Temperature Rangemesophile
Annotation ProviderNCBI
Annotation Date2017-05-17
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline
Annotation Pipeline Version4.2
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

Report Errors or Provide Feedback
Page generated by Pathway Tools version 29.0 (software by SRI International) on Mon Jun 30, 2025, BIOCYC18A.