HHsearch alignment for GI: 254780700 and conserved domain: TIGR02038

>TIGR02038 protease_degS periplasmic serine peptidase DegS; InterPro: IPR011783 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 family consists of the periplasmic serine protease DegS (HhoB). They belong to MEROPS peptidase family S1, subfamily S1C (protease Do, clan PA(S)). They are a shorter paralogs of protease Do (HtrA, DegP) and DegQ (HhoA). They are found in Escherichia coli and several of the gammaproteobacteria. DegS contains a trypsin domain and a single copy of PDZ domain (in contrast to DegP with two copies). A critical role of this DegS is to sense stress by detecting misfolded proteins in the periplasm. DegS then cleaves the periplasmic domain of RseA, a transmembrane protein and inhibitor of sigmaE, activating the sigmaE-driven expression of periplasmic proteases/chaperones , , .; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis.
Probab=98.49  E-value=4.3e-07  Score=63.85  Aligned_cols=78  Identities=19%  Similarity=0.208  Sum_probs=62.2

Q ss_conf             54698728965715------200799960688978982999888999889999389999999999886259956999997
Q Consensus       394 lGl~v~~l~~~~~~------~~gi~vv~v~~~s~Aa~~GL~~GDiIl~VNg~~V~s~~dl~~iL~~~k~~~~~~VLL~V~  467 (489)
T Consensus       264 ~Gv~G~~I~s~~~~~lg~~~l~Givv~~vdPnGPAA~Ag~l~~Dvilk~dg~~~~g~~~~md~vA~~~PG~--~v~~tvl  341 (358)
T ss_conf             50287036626664078752240788534898767650677155789867953675655455543179997--7899997

Q ss_pred             ECCCCC
Q ss_conf             177643
Q gi|254780700|r  468 YDPDMQ  473 (489)
Q Consensus       468 r~~~~~  473 (489)
T Consensus       342 R~Gk~l  347 (358)
T TIGR02038       342 RKGKQL  347 (358)
T ss_pred             CCCCEE
T ss_conf             069678