HHsearch alignment for GI: 254780700 and conserved domain: TIGR00225

>TIGR00225 prc C-terminal processing peptidase; InterPro: IPR004447 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 MEROPS peptidase family S41 (clan SM), subfamily S41A (C-terminal processing peptidase). It is a family of C-terminal peptidases with different substrates in different species, including processing of D1 protein of the photosystem II reaction centre in higher plants, and cleavage of a peptide of 11 residues from the precursor form of penicillin-binding protein in Escherichia coli.; GO: 0008236 serine-type peptidase activity, 0006508 proteolysis.
Probab=96.09  E-value=0.0092  Score=36.24  Aligned_cols=70  Identities=24%  Similarity=0.368  Sum_probs=53.2

Q ss_conf             113201111121134671167888752431-----478743--10122203566752010120478---16651255655
Q Consensus       307 GvlV~~V~~~sPA~~AGLk~GDvI~~ing~-----~I~~~~--~l~~~i~~~~~G~~v~l~v~R~g---~~~~~~V~l~~  376 (489)
T Consensus        67 ~~~~~~~~~g~p~~~~g~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~-~~g~~g~~~~~~~~~~g~g~~~~~~~~~~~~  145 (361)
T ss_conf             378862146773112046666406861676664102220125788997-5077786168998427778753026787511

Q ss_pred             C
Q ss_conf             8
Q gi|254780700|r  377 S  377 (489)
Q Consensus       377 ~  377 (489)
T Consensus       146 ~  146 (361)
T TIGR00225       146 D  146 (361)
T ss_pred             H
T ss_conf             0