Strain SK36 of Streptococcus sanguinis (formerly Streptococcus sanguis) is found to have a genome of approximately 2.39 Mb encoding approximately 2300 proteins. The key publication reporting this work is Xu, Alves, Kitten et al., Journal of Bacteriology 189: 3166-3175, 2007. Dr. Todd Kitten of Virginia Commenwealth University has been helpful in the foundational curation of this database. Approximately 25 recent references pertaining to S. sanguinis have been extracted from a 2002-2007 molecular subset of PubMed (S. sanguinis references). If we have overlooked any pertinent refernce, please inform us.

S. sanguinis is reported to inhibit the growth of periodontopathic bacteria such as S. mutans. One study proposes that a bacteriocin (sanguicin) of approximately 65 Kd is responsible for this effect (Deng et al., 2004). The coding sequence for this proposed bacteriocin has not been identified, however a BLAST comparison of mutacin and SMB proteins against S. sanguinis reveals similarities with ABC-related elements, a subtilisin-like protein and a Dfp-like protein. We have yet toidentify some genomic islands that could encode bacteriocin-related proteins.

Xu et al. make note of a 70 kb region that may have arisen through horizontal gene transmission (HGT) (SSA_0463 to SSA_0541). This stretch is not obviously similar to other strep sequences (see below) but is similar to Listeria and Lactobaccili sequences and clearly encodes genes related to cobalamin and degradation of ethanolamine and propanediol. The authors also identify nearly 200 other SSA genes as potential HGT elements (see Comments herein).

Sanguinis infection is regarded to be a major cause of endocarditis. Paik et al. (2005) identified a handful of virulence factors that are, for the most part, housekeeping genes: fimA, sloC, purB, etc. The records for these are annotated herein.

The core information for the database is a table of 2274 predicted open reading frames. Each gene record is identified by a gene id, SSA_0001-SSA_2394. Two definitions may be provided for each gene: an Oralgen determined Definition derives from extensive BLAST analyses against S. mutans, S. agalactiae and S. thermophilus. Tri-directional and bi-directional best hit relationships (bets) coupled with co-annotation to attain consistency across these genome databases, yields what we designate a Species (plural) Definition. A detailed description of this methodology is forthcoming. The second definition is that provided by GenBank. In the absence of a reciprocal best hit relationship among the above-named streps, the Oralgen-derived Definition field will be empty (this informs the user that a pre-defined bet relationship to mutans, agalactiae or thermophilus genomes was not found). These records may have manual annotation that casts light upon their specious nature.

Basic summaries of specific information are available below in the Predefined Database Searches which contain links to the complete gene record.

For a general perspective of the genome, we recommend you go to the Gene Image Map and browse blocks of coordinates. Caution: The entire 2.39 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. We encourage anyone with questions or suggestions to contact us at oralgen_db@lanl.gov

User Defined Database Searches
Basic Search
Intermediate Search
Advanced Search
Sequence Search
Protein Motif Search
Repeat Search
DNA/RNA Motif 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
Phylotenetic Fingerprints
ABC Transporters
Base Composition Analysis

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