Table 4

Transmembrane topologies of VraT/LiaF homologuesa

Organism (strain)GenBank accession no.Locus tagaa positions of TM helicespsi BLAST e value (% identity)
Staphylococcus aureus (Mu50)NP_372410.1SAV188610–27, 32–49, 56–73, 78–95, 102–119Query
Staphylococcus haemolyticus JCSC1435YP_252984.1SH106910–28, 33–51, 66–908e−139 (81)
Staphylococcus epidermidis (M23864:W1)ZP_04817379HMPREF0793_024710–28, 33–51, 66–906e−135 (86)
Staphylococcus simiae CCM 7213ZP_09147023SS7213T_0874710–28, 33–51, 64–883e−135 (91)
Staphylococcus lugdunensis HKU09-01YP_003471302.1SLGD_0104310–28, 33–51, 66–902e−132 (82)
Staphylococcus warneri L37603ZP_04679015.1STAWA0001_060110–28, 33–51, 66–902e−128 (86)
Staphylococcus pseudintermediusYP_004149802SPSINT_163810–28, 33–51, 64–887e−121 (69)
Listeria monocytogenes serotype 4b strain F2365YP_013641LMOf2365_10410–34, 55–796e−17 (30)
Enterococcus faecium TX1330ZP_03980568.1HMPREF0352_046121–45, 66–903e−12 (26)
Streptococcus pneumoniaeNP_357936spr03426–23, 30–46, 53–774e−10 (27)
Bacillus anthracis (Ames)NP_843911.1BA_145522–46, 61–855e−09 (25)
Bacillus subtilis subsp. spizizenii TU-B-10YP_004878824GYO_36166–30, 57–812e−06 (25)
  • a Topologies were determined using the HMMTOP server (http://www.enzim.hu/hmmtop/) for prediction of transmembrane helices and membrane topology using hidden Markov models. The proteins listed here were a subset of those identified by psi BLAST analysis using the S. aureus VraT protein sequence as the query. All proteins with significant alignment belong to the cell wall-active response family, including LiaF from Bacillus spp., and contain a conserved domain in the carboxy terminus (DUF154). S. aureus has a unique membrane topology compared with other Staphylococcus species and all other members from this family (DUF154).