The ABC (ATP binding cassette) transporter is one of the active transport systems of the cell, which is widespread in archaea, eubacteria, and eukaryotes (Higgins 1992). It is also known as the periplasmic binding protein-dependent transport system in Gram-negative bacteria and the binding-lipoprotein-dependent transport system in Gram-positive bacteria. The transporter shows a common global organization with three types of molecular components. Typically, it consists of two integral membrane proteins (permeases) each having six transmembrane segments, two peripheral membrane proteins that bind and hydrolyze ATP, and a periplasmic (or lipoprotein) substrate-binding protein. The ATP-binding protein component is the most conserved, the membrane protein component is somewhat less conserved, and the substrate-binding protein component is most divergent (Tam and Saier 1993; Saurin and Dassa 1994) in terms of the sequence similarity. The ABC transporters form the largest group of paralogous genes in bacterial and archaeal genomes (Tatusov et al. 1996), and the genes for the three components frequently form an operon (Higgins 1992).

Importers and exporters represent the ABC transporters. ABC transporters include nucleotide binding domains (NBD1 and NBD2), transmembrane spanning domains (MSD1 and MSD2) and solute binding proteins (SBP1 and SBP2). In the case of exporters, the SBP domains are absent. Also inherent to the ABC transporters is the conserved organizational nature of the genes involved.

Orthologous groups were examined to get an understanding of gene organization, and orthologous groups were used in similarity searches. The gene organization data comes from a larger data set that contains Blastp data of eight complete genomes. Each genome was used as a query against each other genome. The set of genomes includes the genomes of the known bacterial STDs.
 

Methods Pattern search approach Gene cluster analysis Chlamydia trachomatis Data table NBD Amino Acid Alignment NBD Organization Plasma membrane Organization	Orthologous Groups Orthologous group subfamily   Mycoplasma genitalium Data table NBD Amino Acid Alignment NBD Organization Plasma membrane Organization
Treponema pallidum Data table NBD Amino Acid Alignment NBD Organization Plasma membrane Organization	Ureaplasma urealyticum Data table NBD Amino Acid Alignment NBD Organization Plasma membrane Organization
Haemophilus ducreyi Data table NBD Amino Acid Alignment NBD Organization Plasma membrane Organization	Porphyromonas gingivalis Data table NBD Amino Acid Alignment NBD Organization Plasma membrane Organization
Neisseria gonorrhoeae Data table NBD Amino Acid Alignment NBD Organization Plasma membrane Organization	Streptococcus mutans Data table NBD Amino Acid Alignment NBD Organization Plasma membrane Organization
Streptococcus agalactiae Data table NBD Amino Acid Alignment NBD Organization Plasma membrane Organization	Fusobacterium nucleatum nucleatum Data table NBD Amino Acid Alignment NBD Organization Plasma membrane Organization
Treponema denticola Data table NBD Amino Acid Alignment NBD Organization	Actinobacillus actinomycetemcomitans Data Table NBD Amino Acid Alignment NBD Organization Plasma Membrane Organization
Cytophaga hutchinsonii Data table NBD Amino Acid Alignment NBD Organization	Prevotella intermedia Data table NBD Amino Acid Alignment NBD Organization Plasma Membrane Organization

This analysis was prepared by Gary Xie, Thomas Brettin and Staff. Please direct questions concerning this analysis to Gary Xie.