Treponema pallidum
Gene Image Map

 Treponema pallidum database overview  
The Treponema pallidum circular genome of 1.138 Mb was sequenced in 1998 by teams at The Institute for Genomic Research (TIGR) and the University of Texas at Houston, working under the aegis of the STD Branch, NIAID/NIH. The key publication describing this newly sequenced genome is "Complete Genome Sequence of Treponema pallidum, the Syphilis Spirochete" by C.M. Fraser, S.J. Norris, G.M. Weinstock and colleagues, Science 281:375-388, 1998. Approximately 300 additional references pertaining to Treponema species can be extracted from the Molecular Subset of MEDLINE (T.pallidum References).

The core information in this relational database is the table of annotated records for each gene. TP0001 through TP1041 (with some minor exceptions) identify the gene records for T.pallidum. To these records analyses and links are appended, and from these, tables and graphics are dynamically derived. For a general perspective of the genome, go to the Gene Image Map and browse blocks of coordinates. Caution: The entire 1,138,006 base pair genome can be viewed at one time, however this large file can cause some machines to freeze. For a text discussion of the proteome and how it was annotated, go to the T.pallidum Properties file. Finally, browsing is facilitated by the Functional Classes, EC table, and Biochemical Pathways summaries. For precise inquiries on the other hand, the user should start with the Search capabilities and the tables associated with those.

User Defined Database Searches
Gene Image Map
Basic Search
Intermediate Search
Advanced SQL Search
Sequence Search

Predefined Database Searches
Genomic Island Table
Definition Search
Functional Classes Search
EC Table
Biochemical Pathways
PDB Table
Repeat Search
       Repeat Table - Tandem
       Repeat Table - All

Specialized Analysis
Base Composition Analysis
BLAST Taxonomy Analysis

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

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