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