HHsearch alignment for GI: 254780334 and conserved domain: cd03224

>cd03224 ABC_TM1139_LivF_branched LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a heterodimer of six-helix TM domains (LivM and LivH), and one of two alternative soluble periplasmic substrate binding proteins (LivK or LivJ). ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules.
Probab=97.77  E-value=0.0011  Score=46.49  Aligned_cols=136  Identities=22%  Similarity=0.325  Sum_probs=71.9

Q ss_pred             CCCCCCEEEEECCCCCCHHHHHHHHHHHHHCCCCCEEEEECCCCHH-HHHHHHHH-CCCCCCCHHEECCC----------
Q ss_conf             8578708999549875188999999999850398199998646304-78888752-01577510000347----------
Q gi|254780334|r   86 GFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEEAIG-QIRLRAQR-LNTINSSVYIAIET----------  153 (479)
Q Consensus        86 Gl~~Gs~~Li~G~PGvGKSTL~Lqia~~~a~~g~~vlYvS~EEs~~-Qi~~Ra~R-l~~~~~~i~~~~e~----------  153 (479)
T Consensus        22 ~v~~Gei~~liG~nGaGKSTLl~~i~Gl~~p~~G~-I~~~G~~i~~~~~~~~~~~gi~~v~Q~~~l~~~ltv~enl~~~~  100 (222)
T cd03224          22 TVPEGEIVALLGRNGAGKTTLLKTIMGLLPPRSGS-IRFDGRDITGLPPHERARAGIGYVPEGRRIFPELTVEENLLLGA  100 (222)
T ss_pred             EECCCCEEEEECCCCCCHHHHHHHHHCCCCCCCEE-EEECCEECCCCCHHHHHHCCEEEECCCCCCCCCCCHHHHHHHHH
T ss_conf             98899899999999985999999997798899609-99999999999999999759389635665688990999999987


Q ss_pred             ----------CHHHH---------------------------HHHHHHCCCCCEEEECHHHHHHHHHHCCCCCCHHHHHH
Q ss_conf             ----------88999---------------------------99997316982899721687665420445563679999
Q gi|254780334|r  154 ----------NVEDI---------------------------IATLITNEKPDLVIIDSIQTLWSQTAESSPGTVIQVRT  196 (479)
Q Consensus       154 ----------~l~~i---------------------------l~~~i~~~~~~~vVIDSIQtl~~~~~~s~~GsvsQvre  196 (479)
T Consensus       101 ~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~~LSgG~~Qrv~iAraL-~~~P~lllLDEPt~----gLD-----~~~~~~  170 (222)
T cd03224         101 YARRRAKRKARLERVYELFPRLKERRKQLAGTLSGGEQQMLAIARAL-MSRPKLLLLDEPSE----GLA-----PKIVEE  170 (222)
T ss_pred             HHCCCHHHHHHHHHHHHHHHHHHHHHHCCHHHCCHHHHHHHHHHHHH-HCCCCEEEEECCCC----CCC-----HHHHHH
T ss_conf             63581359999999998866379987484544899999999999999-64999999938654----799-----999999


Q ss_pred             HHHHHHHHHHHCCCEEEEEEEECCCCCCCCHHHHHHHHHEEEEEE
Q ss_conf             999999975307978999863036654331145787753027851
Q gi|254780334|r  197 SVQAMIQYAKKNGVAMVLVGHVTKEGQIAGPRVIEHMVDAVLYFE  241 (479)
Q Consensus       197 ~~~~L~~~AK~~~i~vilighvTK~G~iAGp~~LeH~VD~vl~~e  241 (479)
T Consensus       171 i~~~l~~l-~~~g~tii~vtHd--------l~~~~~~~Drv~vl~  206 (222)
T cd03224         171 IFEAIREL-RDEGVTILLVEQN--------ARFALEIADRAYVLE  206 (222)
T ss_pred             HHHHHHHH-HHCCCEEEEECCC--------HHHHHHHCCEEEEEE
T ss_conf             99999999-9569999999085--------899999699999997