Database Authors
Pallavi Subhraveti1, Quang Ong1, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 27-Feb-2018 from the annotated genome of Actinoplanes derwentensis DSM 43941, 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 22.0) [Karp16, Karp11] using MetaCyc version 21.5 [Caspi18]. 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 Institutess of Health.
Genome
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
Chromosome I9,4979,0799232610,654,181RefSeq:NZ_LT629758
Ortholog data available?Yes
Database Contents
Genes9,498
Pathways244
Enzymatic Reactions1,477
Transport Reactions77
Polypeptides9,079
Protein Complexes48
Enzymes1,282
Transporters719
Compounds1,276
Transcription Units6,483
tRNAs75
Protein Features10,175
GO Terms25,344
Database Version29.0
Synonyms ATCC 49798
Actinoplanes derwentensis Goodfellow et al. 1990
DSM 43941
IFO 14935
JCM 7556
NBRC 14935
NCIB 12875
NCIMB 12875
NRRL B-16692
strain LA 107
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Micromonosporales
Micromonosporaceae
Actinoplanes
Actinoplanes derwentensis
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN04489716
NCBI BioProjectPRJNA224116
NCBI-Taxonomy113562
NCBI Genome Typerepresentative

References

Caspi18: Caspi R, Billington R, Fulcher CA, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Midford PE, Ong Q, Ong WK, Paley S, Subhraveti P, Karp PD (2018). "The MetaCyc database of metabolic pathways and enzymes." Nucleic Acids Res 46(D1);D633-D639. PMID: 29059334

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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