HHsearch alignment for GI: 254781112 and conserved domain: cd00134
>cd00134 PBPb Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD.
Probab=100.00 E-value=4e-41 Score=273.99 Aligned_cols=215 Identities=35% Similarity=0.572 Sum_probs=190.7
Q ss_pred EEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCCH-HCCCCHHHHHHHCC
Q ss_conf 89996289987248704699848898852167899762998555668988988643103221100-00367567542002
Q gi|254781112|r 43 LRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFETAVSGLITGLDTNRYDVLV-NVAITPERQKKYDF 121 (274)
Q Consensus 43 l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~lg~~~~~~~~~~~~~~~~l~~g~~D~~~-~~~~t~eR~~~~~f 121 (274)
T Consensus 1 l~Vg~~~~~pP~~~~--~~~G~~~G~~~dl~~~i~~~lg~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~~t~~R~~~~~f 78 (218)
T cd00134 1 LTVGTAGTYPPFSFR--DANGELTGFDVDLAKAIAKELGVKVKFVEVDWDGLITALKSGKVDLIAAGMTITPERAKQVDF 78 (218)
T ss_pred CEEEECCCCCCCEEE--CCCCCEEEEHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHCCCCCEEEEEECCCHHHHCCCCC
T ss_conf 989948998990689--999978883999999999996996699975889999998579977688850258566141455
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCHHHHHHHCC--CCCCEEECCHHHHHHHHHHHHHHCCCCCHHHH
Q ss_conf 3332222222221112222111112334320231010122332013--45421336855777755443210036655899
Q gi|254781112|r 122 SIPYIAHRVLLVVRSDQQDIRSFKDLTDKTVAQILGTDLSRFAKEL--KSHLVFSHNFEQSLQLLLSKRTDATMIPDIPF 199 (274)
Q Consensus 122 s~p~~~~~~~~~~~~~~~~~~~~~dL~g~~V~~~~g~~~~~~l~~~--~~~~~~~~~~~~~~~~l~~grvD~~~~~~~~~ 199 (274)
T Consensus 79 s~p~~~~~~~~~~~~~~-~~~~~~dl~g~~i~v~~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~l~~G~vD~~v~~~~~~ 157 (218)
T cd00134 79 SDPYYKSGQVILVKKGS-PIKSVKDLKGKKVAVQKGSTAEKYLKKALPEAKVVSYDDNAEALAALENGRADAVIVDEIAL 157 (218)
T ss_pred CCCEECCCEEEEEECCC-CCCCHHHHCCCEEEEECCCHHHHHHHHHHCCCEEEEECCHHHHHHHHHCCCCEEEEECHHHH
T ss_conf 76444157079998689-99998997796267958988999999731575499969999999999859946999769999
Q ss_pred HHHHHHCCCCCCCEEECCCCCCCCCEEEEEECCCHHHHHHHHHHHHHHHHCCHHHHHHHHHC
Q ss_conf 99998458766732623677687707999818998999999999999997985999998767
Q gi|254781112|r 200 FNFLERRPHDGNLFKIADRMKDNSAVAFMMRKGNNKLTRSINEILCAIHLDGTYKKIFDRYF 261 (274)
Q Consensus 200 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~L~~~in~~l~~l~~~G~~~~I~~kw~ 261 (274)
T Consensus 158 ~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~l~~~~n~~l~~l~~~G~~~~I~~kwf 218 (218)
T cd00134 158 AALLKKHPPEL-KIVGPSIDLEPLGFGVAVGKDNKELLDAVNKALKELRADGELKKISKKWF 218 (218)
T ss_pred HHHHHHCCCCC-EEECCCCCCCCEEEEEEECCCCHHHHHHHHHHHHHHHHCHHHHHHHHCCC
T ss_conf 99998679981-99635667673489999749999999999999999986829999984569