HHsearch alignment for GI: 254780820 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=95.28  E-value=0.077  Score=34.78  Aligned_cols=91  Identities=21%  Similarity=0.307  Sum_probs=64.1

Q ss_pred             HHCCCCCHHHHHHHHHHHHHHHHHC--CCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCEE
Q ss_conf             3185357789999999999998628--96899976888776521246777788999999998629988998567642011
Q gi|254780820|r  131 FIGGSIGIAAGEAIVKSCERAIAEK--CPLVMFTASGGARMQEGILSLMQLPRTTIAINMLKDAGLPYIVVLTNPTTGGV  208 (284)
Q Consensus       131 F~GGSmG~~~geki~~a~e~A~~~~--~PlI~~~~SGGaRMqEG~~sL~qMakt~~a~~~l~~~~lP~I~vl~~pt~GGv  208 (284)
T Consensus         3 ~l~g~I~~~~a~~iv~~L~~l~~~~~~k~I~l~InSpGG~----v~~~~~---i~d~i---~~~~~~v~t~~~g~aaS~-   71 (161)
T cd00394           3 FINGVIEDVSADQLAAQIRFAEADNSVKAIVLEVNTPGGR----VDAGMN---IVDAL---QASRKPVIAYVGGQAASA-   71 (161)
T ss_pred             EECCEECHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCC----HHHHHH---HHHHH---HHCCCCEEEECCCCEEEH-
T ss_conf             9665557899999999999998389999789999899988----899999---99999---961999999668737760-


Q ss_pred             EEEE-CCCCCEEEEECCCEEECCCHH
Q ss_conf             1120-146852555314211023278
Q gi|254780820|r  209 TASY-AMLGDIHLAEPGAEIGFAGRR  233 (284)
Q Consensus       209 ~AS~-a~lgDiiiaep~a~igFaG~r  233 (284)
T Consensus        72 -g~~i~~a~~~~~~~p~s~v~~h~~~   96 (161)
T cd00394          72 -GYYIATAANKIVMAPGTRVGSHGPI   96 (161)
T ss_pred             -HHHHHHCCCCCCCCCCCEEEEECCC
T ss_conf             -4566515885330887404552562