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 Clostridium sp. SY8519 SY8519, 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 [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_0157372,5492,48069422,835,737RefSeq:NC_015737
Ortholog data available?Yes
Database Contents
Genes2,549
Pathways179
Enzymatic Reactions977
Transport Reactions48
Polypeptides2,480
Protein Complexes27
Enzymes564
Transporters216
Compounds729
Transcription Units1,576
tRNAs53
Protein Features3,368
Database Version29.6
Sequence SourceGCF_000270305.1
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Bacillati
Bacillota
Clostridia
Eubacteriales
Clostridiaceae
Clostridium
unclassified Clostridium
Clostridium sp. SY8519
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
BIOSAMPLESAMD00060994
NCBI BioProjectPRJNA224116
NCBI-Taxonomy1042156
EnvironmentAdult Human Intestine
Annotation ProviderNCBI RefSeq
Annotation Date2020-12-13
Annotation PipelineNCBI Prokaryotic Genome Annotation Pipeline (PGAP)
Annotation Pipeline Version5.0
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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