HHsearch alignment for GI: 254780444 and conserved domain: TIGR02227

>TIGR02227 sigpep_I_bact signal peptidase I; InterPro: IPR000223 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 S26A. At least 3 eubacterial leader peptidases are known: murein prelipoprotein peptidase, which cleaves the leader peptide from a component of the bacterial outer membrane; type IV prepilin leader peptidase; and the serine-dependent leader peptidase 1, which has the more general role of cleaving the leader peptide from a variety of secreted proteins and proteins directed to the periplasm and periplasmic membrane . Leader peptidase 1 is similar to the eukaryotic signal peptidase, although the bacterial protein is monomeric, while the eukaryotic protein is multimeric . Mitochondria contain a similar two-subunit serine protease that removes leader peptides from nuclear- and mitochondrial-encoded proteins, which localise in the inner mitochondrial space . The catalytic residues of a number of these peptides have been identified as a serine/lysine dyad .; GO: 0008236 serine-type peptidase activity, 0006508 proteolysis, 0016020 membrane.
Probab=98.42  E-value=1.3e-06  Score=62.93  Aligned_cols=60  Identities=23%  Similarity=0.369  Sum_probs=51.7

Q ss_pred             EE-EEECCCCCCCCCCCCCEEEEEC-----------------CCCCCCCCEEEEEEEC--CC-EEEEEEEEECCCEEEEE
Q ss_conf             99-9962833242148786899936-----------------8974058889999717--96-89999999779879999
Q gi|254780444|r  138 TR-HKTQDTSMLPLYRKGDILILNS-----------------AIQVNCGDRLLIKPRT--GD-IVAKVLISRRGRSIDLM  196 (223)
Q Consensus       138 ~~-l~V~GDSM~P~i~~Gd~vlVd~-----------------~~~~~~g~~v~~~~~~--~~-~~iKrl~~~~~~~~~l~  196 (223)
T Consensus        21 ~~~~~v~g~SM~PTL~~gD~~lv~K~~y~r~~lp~~~~~~~~~~~~~rgDivVF~~~~~~~~~~yiKRviglPGD~v~~~  100 (203)
T TIGR02227        21 FPVYKVPGGSMEPTLKEGDRILVNKFAYGRLKLPFTHKLLFKTSDPKRGDIVVFKAPDDPDNRIYIKRVIGLPGDKVEIK  100 (203)
T ss_pred             EEEEEECCCCCCHHHCCCCEEEEEEECCCEEEEECCEEEEEEECCCEECCEEEEECCCCCCCCEEEEEEEECCCCEEEEE
T ss_conf             78898088975532237988999981264456302100035605750040899953899889616789996588889998


Q ss_pred             E
Q ss_conf             6
Q gi|254780444|r  197 S  197 (223)
Q Consensus       197 s  197 (223)
T Consensus       101 ~  101 (203)
T TIGR02227       101 D  101 (203)
T ss_pred             E
T ss_conf             0