The 2.03 Mb genome of Streptococcus mutans UA159, a serotype C strain, was sequenced in 2002 by teams at the University of Oklahoma Health Sciences Center, Department of Microbiology and Immunology, and the University of Oklahoma, Department of Chemistry and Biochemistry, working under the aegis of the National Institute of Dental and Craniofacial Research (NIDCR) within the National Institutes of Health. The key publication describing this newly sequenced genome is "Genome sequence of Streptococcus mutans UA159, a cariogenic dental pathogen" by Ajdic D, McShan WM, McLaughlin RE, Savic G, Chang J, Carson MB, Primeaux C, Tian R, Kenton S, Jia H, Lin S, Qian Y, Li S, Zh H, Najar F, Lai H, White J, Roe BA and Ferretti JJ, PNAS 99:14434-14439 (PMID: 12397186). Approximately 250 additional and recent references pertaining to S. mutans have been extracted from a 2000-2006 molecular subset of PubMed. If we have overlooked any pertinent reference, please inform us (S. mutans references). Dr. Dragana Ajdic has been especially helpful in the foundational curation of this database.

Two S. mutans related plasmids, pUA140 and pLM7, have been included in this section. To access the gene records for these, use the Gene Image Map. A publication concerning these plasmids is Zou et al., 2001 (PMID: 11591133).

The core information in this database is the table of annotated records, one for each of the 1966 (1963 in the Ajdic paper) predicted open reading frames. Each gene record is identified by a gene id, SMu0001-SMu1964. Basic summaries of specific information are available below in the Predefined Database Searches and contain links to the complete gene record. A table cross-referencing the gene ids used in this database and the gene ids found in the GenBank record can be used to resolve differences in naming conventions (ID cross-reference).

For a general perspective of the genome, we recommend you go to the Gene Image Map and browse blocks of coordinates. Caution: The entire 2.03 Mb genome can be viewed at one time, however this large file can cause some machines to freeze. Browsing and searching are also facilitated by the Functional Classes, EC Table, and Biochemical Pathways summaries. For precise inquiries on the other hand, start with the search capabilities and their associated tables. Fuller analyses of the proteome are underway, for example a table of proteins found in S. mutans and not in S. pneumoniae, S. pyogenes and S. agalactiae is presented in the Streptococcus proteome comparison section of the database. Finally, we would encourage anyone with questions or suggestions to contact us at std_db@lanl.gov.

A special section concerning bacteriocin operons and genes has been added (Bacteriocins) and records for such -- not characteristic of the UA159 genome (although see below) -- have been added. These new records have IDs MI0001 - MI0015, MII0001 - MII0007, MIII0001 - MIII0008 and Smb0001 - Smb0007. Some bacteriocin-like genes have been located on two potential genetic islands in S. mutans UA159 (Genomic Island Table).

Note: Genome sequence of S. mutansUA159 was recently updated in Genbank and gene coordinates of S. mutans UA159 in our database is updated (Nov 21, 2007) to reflect this change. A few gene records were removed or merged in this update. See below.

SMu0925: Deleted
SMu1408: Merged with SMu1407 (Annotated as sensor histidine kinase)
SMu1449: Merged with SMu1450 (Annotated as carbonic anhydrase (carbonate dehydratase))

User Defined Database Searches
Basic Search
Intermediate Search
Sequence Search
Protein Motif Search
Repeat Search

Predefined Database Searches
Genomic Island Table
Secondary Structure Table
Definition Table
Functional Classes Table
EC Table
PDB Table
Metabolic Pathways
Repeat Table
Codon Usage Table

Specialized Analysis
Bacteriocins
Sorbose PTS Genomic Island
Insertion Sequences
ABC Transporters
Base Composition Analysis

RNA Tables and Maps
Transfer RNA Table
Ribosomal RNA Table
Transfer & Ribosomal RNA Map