HHsearch alignment for GI: 254781037 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=92.81  E-value=0.85  Score=25.49  Aligned_cols=147  Identities=16%  Similarity=0.214  Sum_probs=78.2

Q ss_pred             HHHHHHHCCCCEEEEECCCCCCCCCCCCCEEEEECCCCCCCEEEEECCC---CCCCCCCCCCEEECCCC-CHHHHHHHHH
Q ss_conf             9999987098369974034321110122101222365683105665243---24332456732204753-0288899842
Q gi|254781037|r   67 EIEKKLISGEIDCAVHSAKDMPTKLLKGLQISAYLPREDIRDVFISHTA---QSLKDLALHSVIGTSSL-RRKALLLRWR  142 (307)
Q Consensus        67 ele~aLl~g~iDiAVHSlKDlP~~~~~~l~i~a~~~R~d~rD~lv~~~~---~~l~~lp~~a~IGTsS~-RR~aql~~~~  142 (307)
T Consensus        49 ~~~~~l~~g~~D~~~~~~~~t~~R-~~~~~fs~-p~~~~-~~~~~~~~~~~~~~~~dl~-g~~i~v~~g~~~~~~l~~~~  124 (218)
T cd00134          49 GLITALKSGKVDLIAAGMTITPER-AKQVDFSD-PYYKS-GQVILVKKGSPIKSVKDLK-GKKVAVQKGSTAEKYLKKAL  124 (218)
T ss_pred             HHHHHHHCCCCCEEEEEECCCHHH-HCCCCCCC-CEECC-CEEEEEECCCCCCCHHHHC-CCEEEEECCCHHHHHHHHHH
T ss_conf             999998579977688850258566-14145576-44415-7079998689999989977-96267958988999999731


Q ss_pred             CCCCCHHHCCCHHHHHHHHHCCCCCEEEEEHHHHHHCCCCCC-CCCCCCHHHCCCCCCCCEEEEEEECCCCHHHHHHHHH
Q ss_conf             377310330767999998637876556301454542162112-2233686673585432078999852761245567762
Q gi|254781037|r  143 SDISVIDFRGKIETRLNKLNNNKAHAILLAYAGIKRLKKEKV-IKEILNIEDFPPSPGQGAICIETHVNNPKAQELVKVI  221 (307)
Q Consensus       143 p~l~~~~iRGNv~TRl~Kl~~g~~DaiilA~Agl~RL~l~~~-i~~~l~~~~~~PA~gQGaIaIe~r~~d~~i~~il~~I  221 (307)
T Consensus       125 ~~~~~~~~~-~~~~~~~~l~~G~vD~~v~~~~~~~~~~~~~~~~~~~~~~~-~--~~~~~~~~~~~~~~~~~l---~~~~  197 (218)
T cd00134         125 PEAKVVSYD-DNAEALAALENGRADAVIVDEIALAALLKKHPPELKIVGPS-I--DLEPLGFGVAVGKDNKEL---LDAV  197 (218)
T ss_pred             CCCEEEEEC-CHHHHHHHHHCCCCEEEEECHHHHHHHHHHCCCCCEEECCC-C--CCCCEEEEEEECCCCHHH---HHHH
T ss_conf             575499969-99999999985994699976999999998679981996356-6--767348999974999999---9999


Q ss_pred             CCH
Q ss_conf             397
Q gi|254781037|r  222 NHE  224 (307)
Q Consensus       222 nd~  224 (307)
T Consensus       198 n~~  200 (218)
T cd00134         198 NKA  200 (218)
T ss_pred             HHH
T ss_conf             999