HHsearch alignment for GI: 254780444 and conserved domain: TIGR02228

>TIGR02228 sigpep_I_arch signal peptidase I; InterPro: IPR001733 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 S26 (signal peptidase I family, clan SF), subfamily S26B. Eukaryotic microsomal signal peptidase is involved in the removal of signal peptides from secretory proteins as they pass into the endoplasmic reticulum lumen . The peptidase is more complex than its mitochondrial and bacterial counterparts, containing a number of subunits, ranging from two in the chicken oviduct peptidase, to five in the dog pancreas protein . They share sequence similarity with the bacterial leader peptidases (family S26A), although activity here is mediated by a serine/histidine dyad rather than a serine/lysine dyad . Archaeal signal peptidases also belong to this group. ; GO: 0008233 peptidase activity, 0006465 signal peptide processing, 0006508 proteolysis, 0016020 membrane.
Probab=97.18  E-value=0.0016  Score=42.94  Aligned_cols=75  Identities=20%  Similarity=0.302  Sum_probs=52.2

Q ss_conf             62833242148786899936---89740588899997179----689999999------77987999--968589887--
Q Consensus       142 V~GDSM~P~i~~Gd~vlVd~---~~~~~~g~~v~~~~~~~----~~~iKrl~~------~~~~~~~l--~s~Np~y~~--  204 (223)
T Consensus        42 VlSgSMEP~f~~Gd~~~~~~~~~~~~~~~GDvI~y~~~~~~WyG~~v~HRv~~~~yiyi~~~~~~~fiTKGDnN~~pDqr  121 (175)
T ss_conf             98554306252130999804217666301567999246995235389999998899999659878999425678655842

Q ss_pred             -E-EECHHHEEEEEEE
Q ss_conf             -5-8547865999779
Q gi|254780444|r  205 -D-TVEMSDIEWIARI  218 (223)
Q Consensus       205 -~-~i~~~~i~iigrV  218 (223)
T Consensus       122 v~~p~~~~--NviG~~  135 (175)
T TIGR02228       122 VIEPVPSE--NVIGKY  135 (175)
T ss_pred             EEEEECCC--CEEEEE
T ss_conf             35001158--547650