Database Authors
Pallavi Subhraveti1, Peter Midford1, Ingrid Keseler1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 13-Mar-2021 from the annotated genome of Prevotella scopos W2052, 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 25.0) [Karp16, Karp11] using MetaCyc version 24.5 [Caspi20]. 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 Institutes of Health.
Genome
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
Chromosome 11,4471,39750561,859,892RefSeq:NZ_CP016204
Chromosome 21,0301,01614601,436,518RefSeq:NZ_CP016205
unnamed11010007,335RefSeq:NZ_CP016206
Total:2,6032,423641163,303,745
Ortholog data available?Yes
Database Contents
Genes2,487
Pathways159
Enzymatic Reactions836
Transport Reactions29
Polypeptides2,430
Protein Complexes14
Enzymes504
Transporters152
Compounds595
Transcription Units1,829
tRNAs49
Protein Features2,906
Database Version29.6
Sequence SourceGCF_001683355.1
Synonyms Prevotella scopos CCUG 57945
Prevotella scopos DSM 22613
Prevotella scopos W2052
Prevotella scopos JCM 17725
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadati
FCB group
Bacteroidota/Chlorobiota group
Bacteroidota
Bacteroidia
Bacteroidales
Prevotellaceae
Prevotella
Prevotella scopos
Prevotella scopos JCM 17725
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN03897722
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1236518
EnvironmentDental implant
Geographic LocationUnited Kingdom
Latitude/Longitude51.48 N 3.18 W
Collection Date1988
HostHomo sapiens
Annotation ProviderNCBI RefSeq
Annotation Date2020-06-5
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version4.11
Annotation CommentBest-placed reference protein set; GeneMarkS-2+
NCBI Genome Typerepresentative

References

Caspi20: Caspi R, Billington R, Keseler IM, Kothari A, Krummenacker M, Midford PE, Ong WK, Paley S, Subhraveti P, Karp PD (2020). "The MetaCyc database of metabolic pathways and enzymes - a 2019 update." Nucleic Acids Res 48(D1);D445-D453. PMID: 31586394

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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