HHsearch alignment for GI: 254781112 and conserved domain: TIGR01096

>TIGR01096 3A0103s03R lysine-arginine-ornithine-binding periplasmic protein; InterPro: IPR005768 Bacterial high affinity transport systems are involved in active transport of solutes across the cytoplasmic membrane. The protein components of these traffic systems include one or two transmembrane protein components, one or two membrane-associated ATP-binding proteins (ABC transporters; see IPR003439 from INTERPRO) and a high affinity periplasmic solute-binding protein. The later are thought to bind the substrate in the vicinity of the inner membrane, and to transfer it to a complex of inner membrane proteins for concentration into the cytoplasm. In Gram-positive bacteria which are surrounded by a single membrane and have therefore no periplasmic region the equivalent proteins are bound to the membrane via an N-terminal lipid anchor. These homolog proteins do not play an integral role in the transport process per se, but probably serve as receptors to trigger or initiate translocation of the solute through the membrane by binding to external sites of the integral membrane proteins of the efflux system. In addition at least some solute-binding proteins function in the initiation of sensory transduction pathways. On the basis of sequence similarities, the vast majority of these solute-binding proteins can be grouped into eight families of clusters, which generally correlate with the nature of the solute bound. Family 3 groups together specific amino acids and opine-binding periplasmic proteins and a periplasmic homolog with catalytic activity. ; GO: 0005215 transporter activity, 0006810 transport, 0030288 outer membrane-bounded periplasmic space.
Probab=100.00  E-value=2.9e-44  Score=293.35  Aligned_cols=232  Identities=30%  Similarity=0.484  Sum_probs=208.3

Q ss_pred             HHHHHCHHHHHHCCCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHCC-------CCCCCCCCCHHHHHHHHHC
Q ss_conf             998417887885895899962899872487046998488988521678997629-------9855566898898864310
Q gi|254781112|r   28 YYFVIYPFRTEDQSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLN-------LKVEFFETAVSGLITGLDT  100 (274)
Q Consensus        28 ~~~~~~~~~~~~~~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~lg-------~~~~~~~~~~~~~~~~l~~  100 (274)
T Consensus        14 ~~~~a~~~a~~~~~~v~~gt~~~y~PF~~~--~a~G~~~GFDvDl~~alc~~~~gD~GWdh~~c~~~~~~~~~liPsL~~   91 (333)
T TIGR01096        14 ASSAATAAAAKEKGSVRIGTETAYPPFEFK--DADGKLVGFDVDLANALCKEMKGDPGWDHAKCKFVEQAFDGLIPSLKA   91 (333)
T ss_pred             HHHHCCHHHHHHCCCEEEEECCCCCCCCCC--CCCCCEEEHHHHHHHHHHHHHCCCCCCCCCEEEEECCCHHHHHHHHHC
T ss_conf             986215688852880799865787986551--889545632678999999984589996431488842756652025453


Q ss_pred             CCCCCC-H-HCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCC-----------------------CC-CCCEEE
Q ss_conf             322110-0-003675675420023332222222221112222111112-----------------------33-432023
Q gi|254781112|r  101 NRYDVL-V-NVAITPERQKKYDFSIPYIAHRVLLVVRSDQQDIRSFKD-----------------------LT-DKTVAQ  154 (274)
Q Consensus       101 g~~D~~-~-~~~~t~eR~~~~~fs~p~~~~~~~~~~~~~~~~~~~~~d-----------------------L~-g~~V~~  154 (274)
T Consensus        92 k~~Dai~an~~~It~~R~~~i~F~~~yy~~~~~f~v~~~~~~~~~~~~~E~~~Ld~~A~~~K~~~d~~~~~L~nG~~~gV  171 (333)
T TIGR01096        92 KKVDAIMANAMSITDERQKQIDFSDPYYATGAGFVVKKDSDLAKTLEDGENYSLDNQADAAKKEIDDVTKFLKNGKKVGV  171 (333)
T ss_pred             CCEEEEEECCCCCCHHHHHHHCCCCCCCCCCCEEEEECCCCCCCCHHHHCCCCCCCCCHHHHHHHHHHHHHHHCCCEEEE
T ss_conf             80689972665546656632114430000443022224887543145330367200037989989989998527548986


Q ss_pred             ECCCHHHHHHHCC------CCCCEEECCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCEEEC----CC-----C
Q ss_conf             1010122332013------4542133685577775544321003665589999998458766732623----67-----7
Q gi|254781112|r  155 ILGTDLSRFAKEL------KSHLVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLFKIA----DR-----M  219 (274)
Q Consensus       155 ~~g~~~~~~l~~~------~~~~~~~~~~~~~~~~l~~grvD~~~~~~~~~~~~~~~~~~~~~~~~~~----~~-----~  219 (274)
T Consensus       172 ~~GTT~~~~~~~~~~~~Nl~v~~~~Y~~~~~~~~dL~~GR~Da~~~D~~~l~~~~~~~~~gkd~~~~g~~~~~~PLGP~~  251 (333)
T TIGR01096       172 QSGTTHEQYLKDEFKPKNLGVDIVEYDSYDNANMDLKAGRIDAVLADASVLAEGFLKPPNGKDLKFVGPKVTDEPLGPVK  251 (333)
T ss_pred             CCCCCHHHHHHHHCCCCCCEEEEEEECCHHHHHHHHHCCCCEEEECCHHHHHHHHHCCCCCCCEEECCCCCCCCCCCCCC
T ss_conf             26884899998624433742666640886799999757962177436588888873789888637728322688989855


Q ss_pred             CCCCC------------------EEEEEEC-------------------CC---HHHHHHHHHHHHHHHHCCHHHHHHHH
Q ss_conf             68770------------------7999818-------------------99---89999999999999979859999987
Q gi|254781112|r  220 KDNSA------------------VAFMMRK-------------------GN---NKLTRSINEILCAIHLDGTYKKIFDR  259 (274)
Q Consensus       220 ~~~~~------------------~~~~~~k-------------------~~---~~L~~~in~~l~~l~~~G~~~~I~~k  259 (274)
T Consensus       252 ~FG~g~W~DiV~W~~YAL~~A~E~Gig~rk~de~~~s~Np~i~r~lg~~~Dt~G~eL~~~~n~Al~~~~adGtY~~i~~k  331 (333)
T TIGR01096       252 YFGDGYWFDIVRWSAYALVAAEEVGIGLRKVDEVKASTNPEIKRLLGSEGDTIGKELKAKFNKALKAIRADGTYQKISKK  331 (333)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCCCCHHHHHCCCCCCHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHH
T ss_conf             57888300121446677763443212534558885188830232204556512189999999999999865874688865


Q ss_pred             HC
Q ss_conf             67
Q gi|254781112|r  260 YF  261 (274)
Q Consensus       260 w~  261 (274)
T Consensus       332 wf  333 (333)
T TIGR01096       332 WF  333 (333)
T ss_pred             CC
T ss_conf             19