HHsearch alignment for GI: 254780272 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=100.00  E-value=0  Score=399.35  Aligned_cols=192  Identities=63%  Similarity=1.040  Sum_probs=188.8

Q ss_pred             CCCCCEEEEECCCCCCCCCHHHHHHCCCEEEECCCCCHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHH
Q ss_conf             24575797665998401220034514677998783189899999999999741157697699993687614678999999
Q gi|254780272|r   16 LGLVPMVVEQTNRGERSYDIYSRLLKERIVFVTGQIEDHMATLICAQLLFLEAENPQKEISLYINSPGGVVTAGMAIYDT   95 (216)
Q Consensus        16 ~~~~p~~~e~~~~~~~~~Di~s~L~~~Riifl~g~I~~~~a~~iia~Ll~L~~~~~~k~I~l~INSpGG~v~~glaIyD~   95 (216)
T Consensus         1 ~~~~P~v~e~~~~~~r~~diysrll~~r~~~l~~~~~d~~a~~~vaqllfl~~e~~~k~i~ly~nsPGG~~~aG~~iydt   80 (192)
T TIGR00493         1 MSLIPTVIEQTGRGERAFDIYSRLLKERIIFLSGEVEDEVANLIVAQLLFLEAEDPEKDIYLYINSPGGSITAGLAIYDT   80 (192)
T ss_pred             CCCCCCEEECCCCCCHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCEEHHHHHHHHH
T ss_conf             97454001125665404788999987555332020013578899999887513687551588983688500144688877


Q ss_pred             HHHCCCCEEEEEECCCCCCCCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             86448734899831556652000024677714554415664412566665554128999999999999999999987199
Q gi|254780272|r   96 MQFIKPPISTFCMGQAASMGSLLLSAGEKGMRFALPNARILLHQPSGGFSGQASDIERHAQDIVKIKRRLNEIYVKNCGK  175 (216)
Q Consensus        96 i~~i~~~V~Ti~~G~aaS~aslIl~aG~~g~R~~~pns~iMiHqps~~~~G~~~di~~~a~el~~~~~~l~~i~a~~Tg~  175 (216)
T Consensus        81 m~~i~P~v~t~C~G~aasmGafll~~G~~Gkr~~l~~~~~mihqPlGG~~Gqa~~i~i~a~~il~~~~~~~~~l~~~~G~  160 (192)
T TIGR00493        81 MQFIKPDVSTICIGQAASMGAFLLAAGAKGKRAALPNSRIMIHQPLGGAQGQASDIEIQAKEILKLKKLLNEILAEHTGQ  160 (192)
T ss_pred             HHHHCCCHHEEEHHHHHHHHHHHHHCCCCCCHHCCCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             87516322000010166677898743765310002434057864778866540134566899999999999999874073


Q ss_pred             CHHHHHHHHCCCCCCCHHHHHHCCCCCEEECC
Q ss_conf             98999997245858888999975886446045
Q gi|254780272|r  176 TYEEVEKTLDRDHIMSASEACDWGVVDKVLMS  207 (216)
Q Consensus       176 ~~e~i~~~~~rD~~lsa~EA~eyGliD~Ii~~  207 (216)
T Consensus       161 ~~e~~~~d~~rd~f~~a~~a~~yGl~d~~l~~  192 (192)
T TIGR00493       161 SLEKIEKDTERDFFMSAEEAKEYGLIDKVLTR  192 (192)
T ss_pred             HHHHHHHHHHHHHHHCHHHHHHCCHHHHHHCC
T ss_conf             16788765422221022556530307888419