BsubCyc Update History

This document summarizes the history of updates to BsubCyc.

Release Notes for BsubCyc Version 28.0

Released on April 2, 2024.

For this release we performed significant manual curation of the BsubCyc database. Many gene names and functions were updated to reflect data published in Bremer et al 2023. The B. subtilis genome contains 54 riboswitches that were previously entered as genes. The riboswitches have been re-curated and now appear as DNA sites. Their display reflects their interaction with a small molecule.

Four new pathways have been added:

Two pathways have been revised: Several existing pathways have been removed from the database. Many enzymes were curated from the literature and received text summaries, including the twin-arginine pre-protein translocation (TAT) systems; the type VIIb secretion system; the Sec holo-translocon; the potassium transporters KtrAB, KtrCD, KimA, and KhtSTU; the manganese transporters MneP and MneS and the transcriptional regulator for manganese transport MntR; the catalases KatA, KatE and KatX; the branched-chain α-keto acid dehydrogenase system; isocitrate dehydrogenase; autolysin LytD, cyclic nucleotide monophosphate phosphodiesterase PdeB; and the citrate synthases CitA and CitZ.

In addition, a subset of the transcriptional regulatory data captured in DBTBS (Sierro et al 2008) was imported from an XML file provided by K. Nakai and Y. Makita, and 958 new intrinsic terminators were added based on a dataset in Mandell et al 2022. Features like riboswitches and transcription terminators are visible in the genome browser.

Release Notes for BsubCyc Version 25.0

Released on May 19, 2021.

BsubCyc currently contains references to 223 papers published in 2020 and 58 papers published in 2021.

For this release, we have curated 151 gene products that encode transmembrane transporters or transporter components. Curation included the creation of 14 new transporter protein complexes. 17 additional, not transport-related proteins were fully curated.

We have added a new signal transduction pathway for the PsdSR two-component signal transduction system.

Release Notes for BsubCyc Version 22.0

Released on April 24, 2018.

We added 211 new literature citations covering more than 230 genes in BsubCyc.

New curation includes:

Release Notes for BsubCyc Version 21.5

Released on November 28, 2017.

We have imported or updated four pathways in BsubCyc:

Additional fully curated enzymes include BioW, LytG, IolU, StoA, and SpoVD.

We computed Pfam domain membership for all proteins; domain assignments can be accessed in the "Protein Features" tab.

684 gene products in BsubCyc have at least one GO term assignment with experimental evidence; BsubCyc curators have assigned 714 experimental GO terms to B. subtilis gene products.

BsubCyc now cites 270 publications from 2016 and 226 publications from 2017.

Release Notes for BsubCyc Version 19.1

Released on June 21, 2015.

BsubCyc now cites 307 publications from 2014 and 109 publications from 2015.

Release Notes for BsubCyc Version 19.0

Released on March 20, 2015.

Release Notes for BsubCyc Version 18.5

Released on November 7, 2014.

Release Notes for BsubCyc Version 18.1

Released on June 23, 2014.

Release Notes for BsubCyc Version 18.0

Released on March 24, 2014.

The computational GO term assigments have been updated with new data from UniProt.

BsubCyc now cites 334 publications from 2013 and 23 publications from 2014.

Release Notes for BsubCyc Version 17.6

Released on December 17, 2013.

BsubCyc now cites 303 publications from 2013.

Release Notes for BsubCyc Version 17.5

Released on October 11, 2013.

BsubCyc now cites 241 publications from 2013.

Release Notes for BsubCyc Version 17.1

Released on June 11, 2013.

BsubCyc now cites 134 publications from 2013.

Release Notes for BsubCyc Version 17.0

Released on March 28, 2013.

BsubCyc now cites 266 publications from 2012 and 50 publications from 2013.

Release Notes for BsubCyc Version 16.5

Released on November 14, 2012.

BsubCyc has been updated to add protein feature information from UniProt. In addition, we have added links to the Bacillus Genetic Stock Center from the gene/protein pages of many of the genes for which null mutant strains are available at the BGSC.

BsubCyc now cites 232 publications from 2012.

Release Notes for BsubCyc Version 16.1

Released on July 5, 2012.

BsubCyc now cites 328 publications from 2011 and 102 publications from 2012.

Release Notes for BsubCyc Version 16.0

Released on February 20, 2012.

We have added transcription units for all "single-gene directons" to BsubCyc. Single-gene directons are genes that are encoded on the opposite strand compared to both the upstream and downstream neighboring genes, and thus have to be transcribed as single-gene transcription units.

BsubCyc now cites 323 publications from 2011 and 10 publications from 2012.

Release Notes for BsubCyc Version 15.5

Released on October 21, 2011.

The last few months have seen a large number of publications where the functions of previously unknown genes have been identified. Short summaries of several function updates can be found on the main BsubCyc website.

BsubCyc now cites 221 publications from 2011 and 223 publications from 2010.

Release Notes for BsubCyc Version 15.1

Released on June 8, 2011.

Citations to recently published research articles are regularly being added to the genes/proteins that were studied. BsubCyc now contains 1935 literature references, including 119 references to papers published in 2011.

The final missing enzyme in the biosynthesis of queuosine, a base that replaces guanine in the wobble position of a subset of tRNAs, has been identified. Two new pathways, preQ0 biosynthesis and queuosine biosynthesis, show the series of biochemical steps that lead to the final modified tRNA product.

Release Notes for BsubCyc Version 15.0

Released on March 18, 2011.

In this release, we have corrected the accidental deletion of a number of Gene Ontology terms that had been imported from UniProt. BsubCyc should now contain the full complement of GO terms from UniProt, as well as GO terms with experimental evidence codes that were assigned based on recent publications.

Release Notes for BsubCyc Version 14.6

Released on December 3, 2010.

The major update for this release is the addition of Gene Ontology terms from UniProt. More than 29,000 GO term assignments, largely with computational evidence, were added to genes/proteins in BsubCyc. GO terms can be used to search for gene products with related function, involved in the same process, or residing in the same subcellular location.

Release Notes for BsubCyc Version 14.5

Released on October 1, 2010.

This is a minor release with a small number of changes; references to recent literature were added to a number of gene products.

Release Notes for BsubCyc Version 14.2

Released on August 20, 2010.

This is a minor release with a small number of changes:

Release Notes for BsubCyc Version 14.1

Released on June 16, 2010.

Two major improvements to BsubCyc are included in this release:

Release Notes for BsubCyc Version 14.0

Released on March 18, 2010.

This is the first release of the BsubCyc model-organism database for Bacillus subtilis. The database was built using the Pathway Tools software and is based on the sequence and annotation of the B. subtilis genome in Genbank record AL009126.3 GI:225184640, produced by the Genoscope group (Antoine Danchin), October 1, 2009. This Genbank record reflects the corrected nucleotide sequence and revised genome annotation published in Barbe et al. (2009).

Further improvements to the automatically-built database were made as follows:

We plan to further enhance the utility of BsubCyc by incorporating the following information in future releases: