HHsearch alignment for GI: 254780588 and conserved domain: cd00394

>cd00394 Clp_protease_like Caseinolytic protease (ClpP) is an ATP-dependent protease. Clp protease (caseinolytic protease; ClpP; endopeptidase Clp; Peptidase S14; ATP-dependent protease, ClpAP)-like enzymes are highly conserved serine proteases and belong to the ClpP/Crotonase superfamily. Included in this family are Clp proteases that are involved in a number of cellular processes such as degradation of misfolded proteins, regulation of short-lived proteins and housekeeping removal of dysfunctional proteins. They are also implicated in the control of cell growth, targeting DNA-binding protein from starved cells. The functional Clp protease is comprised of two components: a proteolytic component and one of several regulatory ATPase components, both of which are required for effective levels of protease activity in the presence of ATP. Active site consists of the triad Ser, His and Asp, preferring hydrophobic or non-polar residues at P1 or P1' positions. The protease exists as a tetradec
Probab=98.62  E-value=2.7e-07  Score=72.84  Aligned_cols=91  Identities=18%  Similarity=0.183  Sum_probs=72.7

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHCC--CCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCCCC
Q ss_conf             67768368999999999999719--9489999535324677843002799999998886237998899996167777542
Q gi|254780588|r  129 FGSPRPEGYRKAVRLMEMADRFK--IPVISFIDTAGAYPGVDAEARGQGEAIARATEMCLKLQVPILSIIIGEGGSGGAM  206 (317)
Q Consensus       129 ~G~~~p~g~rKa~r~~~~A~~f~--lPiv~lvDtpGa~~g~~aE~~G~~~aia~~l~~~~~~~vP~i~vv~geg~sGGA~  206 (317)
T Consensus         5 ~g~I~~~~a~~iv~~L~~l~~~~~~k~I~l~InSpGG~v-------~~~~~i~d---~i~~~~~~v~t~~~g~aaS~g~~   74 (161)
T cd00394           5 NGVIEDVSADQLAAQIRFAEADNSVKAIVLEVNTPGGRV-------DAGMNIVD---ALQASRKPVIAYVGGQAASAGYY   74 (161)
T ss_pred             CCEECHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCH-------HHHHHHHH---HHHHCCCCEEEECCCCEEEHHHH
T ss_conf             655578999999999999983899997899998999888-------99999999---99961999999668737760456


Q ss_pred             CCCCCCCEEEECCCCEEEECHHH
Q ss_conf             11332000220467401215544
Q gi|254780588|r  207 GIAAANFVYMLEHAIYSVISPEG  229 (317)
Q Consensus       207 a~~~~d~v~m~~~s~ysvisPEg  229 (317)
T Consensus        75 i~~a~~~~~~~p~s~v~~h~~~~   97 (161)
T cd00394          75 IATAANKIVMAPGTRVGSHGPIG   97 (161)
T ss_pred             HHHCCCCCCCCCCCEEEEECCCC
T ss_conf             65158853308874045525621