Database Authors
Dan Weaver1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 06-Feb-2015 from the annotated genome of [Eubacterium rectale] ATCC 33656 by the PathoLogic [Karp10, Dale10, Caspi14] component of Pathway Tools software version 19.0 and MetaCyc version 19.1.

The PGDB, which integrates the biochemical reaction network and metabolic pathways of the organism with its genome, has undergone significant curation of its metabolic network in the course of metabolic model construction.

Genome
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
GEN-EL11988523,6973,6217603,449,685RefSeq:NC_012781.1
Ortholog data available?Yes
Database Contents
Genes3,697
Pathways229
Enzymatic Reactions1,089
Transport Reactions26
Polypeptides3,622
Protein Complexes0
Enzymes633
Transporters184
Compounds767
tRNAs57
Protein Features3,862
GO Terms14,153
Database Version29.0
Synonyms [Eubacterium rectale] ATCC 33656
Eubacterium rectale str. ATCC 33656
Eubacterium rectale strain ATCC 33656
Eubacterium rectale ATCC 33656
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Bacillota
Clostridia
Lachnospirales
Lachnospiraceae
Agathobacter
Agathobacter rectalis
[Eubacterium rectale] ATCC 33656
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
NCBI BioProjectPRJNA59169
NCBI-Taxonomy515619

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

Dale10: Dale JM, Popescu L, Karp PD (2010). "Machine learning methods for metabolic pathway prediction." BMC Bioinformatics 11;15. PMID: 20064214

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

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