Database Authors
Pallavi Subhraveti1, Peter Midford1, Anamika Kothari1, Ron Caspi1, Peter D Karp1
1SRI International
Summary This Pathway/Genome Database (PGDB) was generated on 01-June-2022 from the annotated genome of Bacteroides thetaiotaomicron VPI-5482, 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 26.0) [Karp16, Karp11] using MetaCyc version 26.0 [Caspi19]. 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
NC_0046634,7294,64287986,260,361RefSeq:NC_004663
p548238380033,038RefSeq:NC_004703
Total:4,8654,68087986,293,399
Ortholog data available?No
Database Contents
Genes4,767
Pathways212
Enzymatic Reactions1,133
Transport Reactions62
Polypeptides4,680
Protein Complexes51
Enzymes772
Transporters369
Compounds824
Transcription Units2,927
tRNAs70
Growth Media1
Protein Features8,033
GO Annotations338
Gene Essentiality Datasets1
Database Version29.6
Sequence SourceGCF_000011065.1
Synonyms Bacteroides thetaiotaomicron strain VPI-5482
Bacteroides thetaiotaomicron str. VPI-5482
Bacteroides thetaiotaomicron VPI-5482
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Pseudomonadati
FCB group
Bacteroidota/Chlorobiota group
Bacteroidota
Bacteroidia
Bacteroidales
Bacteroidaceae
Bacteroides
Bacteroides thetaiotaomicron
Bacteroides thetaiotaomicron VPI-5482
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMN02604314
NCBI BioProjectPRJNA224116
NCBI-Taxonomy226186
Annotation ProviderNCBI RefSeq
Annotation Date2022-02-8
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version6.0
Annotation CommentBest-placed reference protein set; GeneMarkS-2+

References

Caspi19: 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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