Summary This Pathway/Genome Database (PGDB) was generated by the PathoLogic [Karp10, Karp11, Caspi14] component of Pathway Tools software version 22.0 and MetaCyc version 22.0 on 22-May-2018 14:57:55.
Genome
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_GL6369341,7591,567461462,137,113RefSeq:NZ_GL636934
NZ_GL636935520462850636,035RefSeq:NZ_GL636935
41 Undisplayed Contigs/Replicons191903043,958
Total:2,3282,048542262,817,106
Ortholog data available?Yes
Database Contents
Genes2,329
Pathways152
Enzymatic Reactions793
Transport Reactions47
Polypeptides2,122
Protein Complexes24
Enzymes420
Transporters237
Compounds697
Transcription Units1,604
tRNAs49
Protein Features2,376
GO Terms9,432
Database Version29.0
Synonyms Actinomyces sp. oral taxon 178 str. F0338
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Actinomycetota
Actinomycetes
Actinomycetales
Actinomycetaceae
Actinomyces
Actinomyces sp. oral taxon 178
Actinomyces sp. oral taxon 178 F0338
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN00210764
NCBI BioProjectPRJNA224116
NCBI-Taxonomy888051
Environmentoral
HostHomo sapiens
Human Microbiome Body Siteoral

References

Caspi14: Caspi R, Altman T, Billington R, Dreher K, Foerster H, Fulcher CA, Holland TA, Keseler IM, Kothari A, Kubo A, Krummenacker M, Latendresse M, Mueller LA, Ong Q, Paley S, Subhraveti P, Weaver DS, Weerasinghe D, Zhang P, Karp PD (2014). "The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases." Nucleic Acids Res. 42(1):D459-D471. PMID: 24225315

Karp10: Karp PD, Paley SM, Krummenacker M, Latendresse M, Dale JM, Lee TJ, Kaipa P, Gilham F, Spaulding A, Popescu L, Altman T, Paulsen I, Keseler IM, Caspi R (2010). "Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology." Brief Bioinform 11(1);40-79. PMID: 19955237

Karp11: Karp PD, Latendresse M, Caspi R (2011). "The pathway tools pathway prediction algorithm." Stand Genomic Sci 5(3);424-9. PMID: 22675592

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