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 Actinomyces radingae DSM 9169, 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 I2,1392,04659342,430,293RefSeq:NZ_LT629792
Ortholog data available?Yes
Database Contents
Genes2,140
Pathways154
Enzymatic Reactions841
Transport Reactions42
Polypeptides2,046
Protein Complexes19
Enzymes439
Transporters214
Compounds684
Transcription Units1,307
tRNAs48
Protein Features2,466
GO Terms8,518
Database Version29.0
Synonyms ATCC 51856
Actinomyces radingae Wust et al. 1995 emend Vandamme et al. 1998
CCUG 32394
CCUG 34270
CIP 105358
DSM 9169
LMG 15960
strain APL1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Actinomycetales
Actinomycetaceae
Actinomyces
Actinomyces radingae
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN04489714
NCBI BioProjectPRJNA224116
NCBI-Taxonomy131110

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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