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MtbRvCyc Release Note History

Version 10.1 -- May, 2006

Ongoing updating of this database was assumed in 2006 by Drs. Shubhada Godbole and Richard Scheuermann of UT Southwestern Medical Center/BioHealthBase BRC under contract from the NIH NIAID.

Significant curation of transport proteins was performed for this release.

Version 7.6 -- November 4, 2003

  • In this release, we have made putative functional assignments to 78 genes in MtbRvCyc. These functional assignments were made to fill pathway holes in the database. A pathway hole occurs when a reaction in a pathway does not have an assigned enzyme. The putative enzymes that fill these pathway holes were identified using a prediction program developed by Green and Karp (Green, 2003). Each enzymatic reaction linked to an enzyme by this program is identified by the evidence code "Computational Evidence: EV-COMP-HINF-FN-FROM-SEQ". The evidence code indicates the source of information as computationally-derived from sequence analysis with human review. The gene product field of the corresponding enzyme has also been updated to include the functional description of the reaction to which it has been linked. In total, 17 pathways were completed by filling these 78 pathway holes. A list of the remaining pathway holes may be found in the Missing Reactions Report.

  • We have added links between equivalent genes and proteins in our MtbRvCyc and MtbCDCCyc PGDBs. The links were inferred based on the all-vs-all sequence comparisons in the TIGR CMR database. These links allow easy navigation between equivalent genes in the two M. tuberculosis strains.

    The links appear on gene pages and protein pages in these two PGDBs. The link relationships are termed "orthologs" or "homologs" according to the following definitions.

    3544 protein ortholog pairs, 3544 gene ortholog pairs, 323 protein homolog pairs, and 323 gene homolog pairs were added to each of the two PGDBs.

    ortholog pairs
    A pair of genes in MtbRvCyc and MtbCDCCyc where each polypeptide product is each other's strongest BLAST sequence match and the length of the match extends over at least 90% of each polypeptide.
    homolog pairs
    A pair of genes where each gene of the pair has no ortholog in the other organism and the P-value of the BLAST sequence match between the two polypeptide products is less than 0.00001.

Version 7.0

Released on February 28, 2003.

2509 predicted transcription units (operons) were added to MtbRvCyc. They were predicted using a prediction program developed by Romero and Karp (Bioinformatics, 2004). When a predicted transcription unit exists for a gene, it will be displayed at the bottom of a gene page.

Version 6.5

Released on August 30, 2002

  • Added Mycothiol Metabolism Superpathway

Version 6.0

Released on February 15, 2002.

  • First release of MtbRvCyc.