HHsearch alignment for GI: 254780747 and conserved domain: TIGR00493

>TIGR00493 clpP ATP-dependent Clp protease, proteolytic subunit ClpP; InterPro: IPR001907 Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases . Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) , . Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. This group of serine peptidases belong to the MEROPS peptidase family S14 (ClpP endopeptidase family, clan SK). ClpP is an ATP-dependent protease that cleaves a number of proteins, such as casein and albumin . It exists as a heterodimer of ATP-binding regulatory A and catalytic P subunits, both of which are required for effective levels of protease activity in the presence of ATP , although the P subunit alone does possess some catalytic activity. This family of sequences represent the P subunit. Proteases highly similar to ClpP have been found to be encoded in the genome of bacteria, metazoa, some viruses and in the chloroplast of plants. A number of the proteins in this family are classified as non-peptidase homologues as they have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for catalytic activity. ; GO: 0008462 endopeptidase Clp activity, 0006508 proteolysis.
Probab=98.36  E-value=1.6e-06  Score=61.07  Aligned_cols=154  Identities=23%  Similarity=0.297  Sum_probs=99.1

Q ss_pred             EEEEEEECCH--HHHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCCCCCCCC
Q ss_conf             9976662386--99999999986189987999975888888899999999999841478679960332332232100011
Q gi|254780747|r   41 IAIRGQIEDS--QELIERIERISRDDSATALIVSLSSPGGSAYAGEAIFRAIQKVKNRKPVITEVHEMAASAGYLISCAS  118 (293)
Q Consensus        41 i~i~G~I~~~--~~l~~~l~~a~~d~~ik~ivL~i~SpGG~~~~~~~i~~ai~~~k~~kpvva~~~~~~~S~~Y~iAs~a  118 (293)
T Consensus        30 ~~l~~~~~d~~a~~~vaqllfl~~e~~~k~i~ly~nsPGG~~~aG~~iydtm~~i~P--~v~t~C~G~aasmGafll~~G  107 (192)
T TIGR00493        30 IFLSGEVEDEVANLIVAQLLFLEAEDPEKDIYLYINSPGGSITAGLAIYDTMQFIKP--DVSTICIGQAASMGAFLLAAG  107 (192)
T ss_pred             HHHCCCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCEEHHHHHHHHHHHHHCC--CHHEEEHHHHHHHHHHHHHCC
T ss_conf             332020013578899999887513687551588983688500144688877875163--220000101666778987437


Q ss_pred             C--CCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHCCEEEEECCCCCCCCCCCC--CCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             1--00013013534555653021024567774204225531552112346667--8999988777776666677899998
Q gi|254780747|r  119 N--IIVAAETSLVGSIGVLFQYPYVKPFLDKLGVSIKSVKSSPMKAEPSPFSE--VNPKAVQMMQDVVDSSYHWFVRLVS  194 (293)
Q Consensus       119 d--~I~a~p~s~vGsiGv~~~~~~~~~ll~k~gi~~~~~~~g~~K~~~~p~~~--~s~e~~~~~~~~l~~~~~~f~~~Va  194 (293)
T Consensus       108 ~~Gkr~~l~~~~~m------i--------------------------hqPlGG~~Gqa~~i~i~a~~il~~~~~~~~~l~  155 (192)
T TIGR00493       108 AKGKRAALPNSRIM------I--------------------------HQPLGGAQGQASDIEIQAKEILKLKKLLNEILA  155 (192)
T ss_pred             CCCCHHCCCCCEEE------E--------------------------ECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             65310002434057------8--------------------------647788665401345668999999999999998


Q ss_pred             HCCCCCHHHHHHHHC-CCCCCHHHHHHCCCCCCCC
Q ss_conf             514999889988734-9823788998779806238
Q gi|254780747|r  195 ESRNIPYDKTLVLSD-GRIWTGAEAKKVGLIDVVG  228 (293)
Q Consensus       195 ~~R~~~~~~~~~~~~-g~~~~~~~A~~~GLvD~ig  228 (293)
T Consensus       156 ~~~G~~~e~~~~d~~rd~f~~a~~a~~yGl~d~~l  190 (192)
T TIGR00493       156 EHTGQSLEKIEKDTERDFFMSAEEAKEYGLIDKVL  190 (192)
T ss_pred             HHHCCHHHHHHHHHHHHHHHCHHHHHHCCHHHHHH
T ss_conf             74073167887654222210225565303078884