Database Authors
Biswarup Sen, Feng Chia University, Taiwan.
Summary This Pathway/Genome Database (PGDB) for Clostridium saccharoperbutylacetonicum N1-4(HMT) was created on Aug 30, 2013 using the PathoLogic component of the Pathway Tools software version 17.0 [Karp11, Karp19] and the MetaCyc reference database version 17.0 [Caspi20]. The annotated genome file was retrieved from the RefSeq resource on Aug 04, 2013.

The PGDB, which integrates the biochemical reaction network and metabolic pathways of the organism with its genome, was improved by limited manual curation.

Genome
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
Chromosome5,8205,71510506,530,257RefSeq:NC_020291
Plasmid10610600136,188RefSeq:NC_020292
Total:5,9265,82110506,666,445
Ortholog data available?Yes
Database Contents
Genes5,926
Pathways382
Enzymatic Reactions1,661
Transport Reactions22
Polypeptides5,821
Protein Complexes0
Enzymes1,466
Transporters616
Compounds1,085
Transcription Units4,173
tRNAs70
Protein Features7,323
Database Version29.0
Synonyms Clostridium saccharoperbutylacetonicum N1-4(HMT)
Clostridium saccharoperbutylacetonicum ATCC 27021
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Terrabacteria group
Bacillota
Clostridia
Eubacteriales
Clostridiaceae
Clostridium
Clostridium saccharoperbutylacetonicum
Clostridium saccharoperbutylacetonicum N1-4
Clostridium saccharoperbutylacetonicum N1-4(HMT)
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
NCBI-Taxonomy931276
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

Karp19: Karp PD, Midford PE, Billington R, Kothari A, Krummenacker M, Latendresse M, Ong WK, Subhraveti P, Caspi R, Fulcher C, Keseler IM, Paley SM (2019). "Pathway Tools version 23.0 update: software for pathway/genome informatics and systems biology." Brief Bioinform. PMID: 31813964

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