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=100.00  E-value=0  Score=635.10  Aligned_cols=310  Identities=30%  Similarity=0.534  Sum_probs=284.6

Q ss_pred             CCCCCHHHHHHHHCCCEEEEEEEEEEEECCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCEEEE
Q ss_conf             55589889999848950899999998722555555445567888770025445530135776666754455522340278
Q gi|254780700|r   35 PSSVDLPPVIARVSPSIVSVMVEPKKKVSVEQMFNAYGFGNLPEDHPLKNYFRKDFHKFFSGEEPILSDTVERLMFGSGF  114 (489)
Q Consensus        35 ~~~~~~~~~~~~~~paVV~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~GsG~  114 (489)
T Consensus        42 ~~~~SF~~AVR~AAPAVVNvYnr~~~~~r~~----------------------------------ndnd~L~i~~LGSGV   87 (358)
T TIGR02038        42 EVEISFNKAVRRAAPAVVNVYNRSLSENRSL----------------------------------NDNDQLSIQGLGSGV   87 (358)
T ss_pred             CHHHHHHHHHHHCCCCEEEEEECCCCCCCCC----------------------------------CCCCCCEECCCCCEE
T ss_conf             2456688642330786487752574436786----------------------------------756651461256557


Q ss_pred             EECCCCEEEECHHCCCCCCEEEEECCCCEEEEECCCCCCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCEEEEECCCCC
Q ss_conf             97599629851010478714379628980674011123344432899960676676556556731112414675236655
Q gi|254780700|r  115 FITDDGYILTSNHIVEDGASFSVILSDDTELPAKLVGTDALFDLAVLKVQSDRKFIPVEFEDANNIRVGEAVFTIGNPFR  194 (489)
Q Consensus       115 ii~~~G~ilTn~hvv~~a~~i~V~~~dg~~~~a~vvg~D~~~DlAvlki~~~~~~~~~~lg~s~~~~~G~~v~aiG~P~g  194 (489)
T Consensus        88 Ims~~GYIlTN~Hvi~~ADqIvVALQdGr~f~A~lVG~D~~TDLAVLki~a~nGLptiP~N~~~~p~vGDVVLAIGNPYN  167 (358)
T TIGR02038        88 IMSKEGYILTNKHVIKKADQIVVALQDGRVFEAELVGSDSLTDLAVLKIEADNGLPTIPVNADRQPHVGDVVLAIGNPYN  167 (358)
T ss_pred             EECCCCCEEECHHHHHCCCEEEEEECCCCEEEEEEECCCCCCCEEEEEEEECCCCCCCCCCCCCCCCCCCEEEECCCCCC
T ss_conf             97288745133575404483998713893577676357775451688995169885112077886850437872368851


Q ss_pred             CCCCCCCCCCCCCCCCCC---CCCCCEEEEEEEEECCCCCCEEEECCCEEEEEECCCCCCC---CCCCCCCCCCCCCCCC
Q ss_conf             311112587443112233---4434202332332013477035403430355512344553---2222223211233211
Q gi|254780700|r  195 LRGTVSAGIVSALDRDIP---DRPGTFTQIDAPINQGNSGGPCFNALGHVIGVNAMIVTSG---QFHMGVGLIIPLSIIK  268 (489)
Q Consensus       195 ~~~tvt~GiiSa~~R~~~---~~~~~~iqtDa~InpGnSGGpl~n~~G~viGint~i~~~~---g~~~GigfaIP~~~~~  268 (489)
T Consensus       168 LGQtitqGIISAtGR~~~G~s~Grq~FlQTDAaIN~GNSGGALvnt~GeLvGInT~sf~~~~~G~~~~Gi~FAIP~~LA~  247 (358)
T TIGR02038       168 LGQTITQGIISATGRNGLGSSVGRQNFLQTDAAINAGNSGGALVNTAGELVGINTLSFQKAADGEEAEGINFAIPIKLAS  247 (358)
T ss_pred             CCCCEEEEEEEEECCCCCCCCCCCHHHHHHHHHHHCCCCCCEEECCCCCEEEEEHHHHCCCCCCCCCCCCCEECCHHHHH
T ss_conf             45311111224330011468531024442018770889653002268652210101001457877655563104178999


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCEEEECCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCEEEEE
Q ss_conf             00100002333333433200034216676441764444113201111121134671167888752431478743101222
Q gi|254780700|r  269 KAIPSLISKGRVDHGWFGIMTQNLTQELAIPLGLRGTKGSLITAVVKESPADKAGMKVGDVICMLDGRIIKSHQDFVWQI  348 (489)
Q Consensus       269 ~i~~~l~~~g~v~rg~lGv~~~~v~~~la~~lgl~~~~GvlV~~V~~~sPA~~AGLk~GDvI~~ing~~I~~~~~l~~~i  348 (489)
T Consensus       248 ~im~Kli~dGRVIRGy~Gv~G~~I~s~~~~~lg~~~l~Givv~~vdPnGPAA~Ag~l~~Dvilk~dg~~~~g~~~~md~v  327 (358)
T TIGR02038       248 KIMDKLIRDGRVIRGYIGVDGEDINSLVAQGLGLEDLRGIVVTGVDPNGPAARAGILVRDVILKVDGKEVIGAEELMDRV  327 (358)
T ss_pred             HHHHHHHHCCCEEEEEEECCCCCCCHHHHHHCCCCCCCEEEEECCCCCCHHHHHCCCCCCEEEEECCCCCCCHHHHHHHH
T ss_conf             99998863797896875028703662666407875224078853489876765067715578986795367565545554


Q ss_pred             CCCCCCCCEEEEECCCCCEEEECCCCCCCC
Q ss_conf             035667520101204781665125565587
Q gi|254780700|r  349 ASRSPKEQVKISLCKEGSKHSVAVVLGSSP  378 (489)
Q Consensus       349 ~~~~~G~~v~l~v~R~g~~~~~~V~l~~~p  378 (489)
T Consensus       328 A~~~PG~~v~~tvlR~Gk~l~LpV~I~E~~  357 (358)
T TIGR02038       328 AETRPGSKVLVTVLRKGKQLELPVTIDEKP  357 (358)
T ss_pred             HCCCCCCEEEEEEECCCCEEEEEEEEECCC
T ss_conf             317999778999970696787007850015