HHsearch alignment for GI: 254780828 and conserved domain: cd03752

>cd03752 proteasome_alpha_type_4 proteasome_alpha_type_4. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.
Probab=99.97  E-value=2.6e-29  Score=203.16  Aligned_cols=171  Identities=21%  Similarity=0.112  Sum_probs=145.4

Q ss_pred             CCEEEEEEEECCEEEEEECCCCCCCCEEEECCCEEEEEECCCEEEEEECCHHHHHHHHHHHHHHHHHHHCC--CCCCCHH
Q ss_conf             37179999979979998136545053677445105798159759997313058899999999999998536--6563067
Q gi|254780828|r   14 HATTILTVRKDGVVVIAGDGQVSLGQTVMKANARKVRRLGKGNIIAGFAGSSADAFTLLERLEKKLEQYPN--QLLRSSV   91 (190)
Q Consensus        14 ~GTTivgi~~~dgVviAaDtR~S~G~~v~sr~~~KI~~i~d~~~~~g~ag~a~d~~~~~~~~~~~~~~~~~--~~~~~~~   91 (190)
T Consensus        28 ~G~T~Vgik~kdgVVlaadkr~~s~l~~~~~~~~Ki~~I~~~ig~~-~sG~~~D~~~lv~~~r~~a~~~~~~~g~~i~v~  106 (213)
T cd03752          28 HAGTCLGILAKDGIVLAAEKKVTSKLLDQSFSSEKIYKIDDHIACA-VAGITSDANILINYARLIAQRYLYSYQEPIPVE  106 (213)
T ss_pred             CCCCEEEEEECCEEEEEEECCCCCCCCCCCCCCCCEEEECCCEEEE-EECCCHHHHHHHHHHHHHHHHHHHHHCCCCHHH
T ss_conf             4797899997999999996136776642777632089953876899-722554889999999999999999809964299


Q ss_pred             HHHHHHHHHH-------HHHHCCCE--EEECCC-CCCEEEEECCCCCEECCCEEEEECCHHHHHHHHHHHHCCCCCHHH-
Q ss_conf             9999997611-------22201310--451378-764699805863114132799606423457889852078999899-
Q gi|254780828|r   92 ELAKDWRMDK-------YLRNLEAM--ILIADK-TITLVITGMGDVLEPENGVMAIGSGGSYALSAARALMSTQNSAEE-  160 (190)
Q Consensus        92 ~~~~~~~~~~-------y~~~~~~~--~~~~~~-~~~~~~~~d~~g~~~~~~~~a~GSGs~~A~g~Le~~y~~~~sa~e-  160 (190)
T Consensus       107 ~la~~ls~~~q~~t~~~~~RP~gvs~ii~G~D~~~g~~Ly~~dpsG~~~~~~a~aiGsgs~~a~~~LEk~y~~~mt~eea  186 (213)
T cd03752         107 QLVQRLCDIKQGYTQYGGLRPFGVSFLYAGWDKHYGFQLYQSDPSGNYSGWKATAIGNNNQAAQSLLKQDYKDDMTLEEA  186 (213)
T ss_pred             HHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEECCCCCEEEEECCCCCEEEEEEEEECCCCHHHHHHHHHHCCCCCCHHHH
T ss_conf             99999999999873545625533489999880799946999889866872228980786499999998754489999999


Q ss_pred             --HHHHHHHHHHCCCEEECCCEEEEEE
Q ss_conf             --9999999754011022595699999
Q gi|254780828|r  161 --IARKAMSIAADICVYTNHNIVLETL  185 (190)
Q Consensus       161 --la~~Al~~A~erDvyTgd~i~i~~i  185 (190)
T Consensus       187 i~lai~al~~~~~~~~~~~~~iei~vi  213 (213)
T cd03752         187 LALAVKVLSKTMDSTKLTSEKLEFATL  213 (213)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCEEEEEC
T ss_conf             999999999997043688885799979