HHsearch alignment for GI: 254780217 and conserved domain: TIGR00764

>TIGR00764 lon_rel ATP-dependent protease, putative; InterPro: IPR004663 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 signature defines the archaeal lon protease homologs, which are ATP-dependent serine peptidases belonging to the MEROPS peptidase family S16 (lon protease family, clan SF). Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein conserved region.; GO: 0004176 ATP-dependent peptidase activity, 0005524 ATP binding, 0030163 protein catabolic process.
Probab=94.94  E-value=0.043  Score=36.51  Aligned_cols=52  Identities=23%  Similarity=0.363  Sum_probs=45.6

Q ss_pred             CCCCCHHHHCCHHHHHHHHHHHHHCCCCCEEEEECCCCCCCHHHHHHHHHHHHHC
Q ss_conf             5587565610929999999999982889816631179898889999999999817
Q gi|254780217|r    6 FDPVYNQRLFGHEDIEKFLSQYYCSGRMHHALLFEGEQGIGKATLGFRYAGHVLQ   60 (347)
Q Consensus         6 ~~p~~~~~i~G~~~~~~~L~~~~~~~~l~ha~Lf~Gp~GiGK~~~A~~~A~~llc   60 (347)
T Consensus        13 p~p~l~d~~~g~~~~~~~~~~~~~~~~--~-~~l~g~pg~g~~~~~~~~~~~l~~   64 (662)
T TIGR00764        13 PEPRLIDQVIGQEEAVEVIKKAAKQKR--N-VLLLGEPGVGKSMLAKAVAELLPD   64 (662)
T ss_pred             CCHHHHHHHHCCHHHHHHHHHHHHHCC--C-EEEECCCCCCHHHHHHHHHHHCCC
T ss_conf             641456666140468899998754103--3-578617775457888888874133