Database Authors
Carol A Fulcher1, Anamika Kothari1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 11-Oct-2016 by the PathoLogic [Karp10, Karp11, Caspi14] component of Pathway Tools software version 20.5 and MetaCyc version 20.1. The PGDB, which integrates the biochemical reaction network and metabolic pathways of the organism with its genome, was improved by limited manual curation.

The primary data source for this dataset was the whole genome shotgun sequencing project for Prevotella copri DSM 18205 derived from NCBI Reference Sequence: NZ_ACBX00000000.2.

Genome
ContigTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
NZ_GG7038527256872315866,821RefSeq:NZ_GG703852
NZ_GG703853412395512493,568RefSeq:NZ_GG703853
NZ_GG70385433531997442,348RefSeq:NZ_GG703854
NZ_GG70385526124579294,362RefSeq:NZ_GG703855
NZ_GG70385616916072204,356RefSeq:NZ_GG703856
NZ_GG70385714513816193,190RefSeq:NZ_GG703857
NZ_GG70385815214813158,202RefSeq:NZ_GG703858
NZ_GG70385914413482155,952RefSeq:NZ_GG703859
NZ_GG703860979115121,916RefSeq:NZ_GG703860
NZ_GG70386110310102117,994RefSeq:NZ_GG703861
NZ_GG70386260552396,518RefSeq:NZ_GG703862
NZ_GG70386372693091,171RefSeq:NZ_GG703863
NZ_GG70386476730378,236RefSeq:NZ_GG703864
NZ_GG70386543390455,594RefSeq:NZ_GG703865
NZ_GG70386637360139,668RefSeq:NZ_GG703866
NZ_GG70386726220426,861RefSeq:NZ_GG703867
NZ_GG70386827178222,009RefSeq:NZ_GG703868
NZ_GG70386918170116,436RefSeq:NZ_GG703869
9 Undisplayed Contigs/Replicons34315437,271
Total:2,9422,77780853,512,473
Ortholog data available?Yes
Database Contents
Genes2,936
Pathways176
Enzymatic Reactions1,020
Transport Reactions44
Polypeptides2,782
Protein Complexes14
Enzymes746
Transporters170
Compounds832
Transcription Units2,099
tRNAs62
Growth Media19
Protein Features3,362
GO Terms16,257
Database Version29.0
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
FCB group
Bacteroidota/Chlorobiota group
Bacteroidota
Bacteroidia
Bacteroidales
Prevotellaceae
Prevotella
Prevotella copri
Prevotella copri DSM 18205
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
NCBI BioProjectPRJNA224116
NCBI-Taxonomy537011
Environmentbiological product [ENVO:02000043]
Relationship to Oxygenanaerobe
Temperature Rangemesophile
HostHomo sapiens
Copyright SRI International 2016. All Rights Reserved.

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

Report Errors or Provide Feedback
Page generated by Pathway Tools version 29.0 (software by SRI International) on Mon Jun 30, 2025, BIOCYC14.