HHsearch alignment for GI: 254780700 and conserved domain: TIGR02037

>TIGR02037 degP_htrA_DO protease Do; InterPro: IPR011782 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 serine peptidases belonging to MEROPS peptidase family S1, subfamily S1C (protease Do, clan PA(S)). They are variously designated DegP, DegQ, heat shock protein HtrA, MucD and protease DO. The ortholog in Pseudomonas aeruginosa is designated MucD and is found in an operon that controls mucoid phenotype. This family also includes the DegQ (HhoA) paralog in Escherichia coli which can rescue a DegP mutant, but not the smaller DegS paralog, which cannot. Members of this family are located in the periplasm and have separable functions as both protease and chaperone. Members have a trypsin domain and two copies of a PDZ domain. This protein protects bacteria from thermal and other stresses and may be important for the survival of bacterial pathogens . The chaperone function is dominant at low temperatures, whereas the proteolytic activity is turned on at elevated temperatures .; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis.
Probab=99.39  E-value=5.8e-14  Score=107.66  Aligned_cols=299  Identities=21%  Similarity=0.283  Sum_probs=167.8

Q ss_pred             CCCCCCCCCCCCCCCCHHHHHH-HHCCCCC----CCCCC-----CCCC----CCCCCCCEEE--EEECCCCEEEECHHCC
Q ss_conf             5555445567888770025445-5301357----76666-----7544----5552234027--8975996298510104
Q gi|254780700|r   66 QMFNAYGFGNLPEDHPLKNYFR-KDFHKFF----SGEEP-----ILSD----TVERLMFGSG--FFITDDGYILTSNHIV  129 (489)
Q Consensus        66 ~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~----~~~~~-----~~~~----~~~~~~~GsG--~ii~~~G~ilTn~hvv  129 (489)
T Consensus        39 ~~~~g~~fddf~Fd~~F~~FFg~~~~p~~~~~~~~~~~~~~g~~~~~~~~LGSGvIi~~d~Gk~YilTNn-HVv~gA~~I  117 (484)
T TIGR02037        39 ENPGGSPFDDFEFDEFFDQFFGDDEMPNQPGGREFPQPEFVGERERKVRGLGSGVIISADKGKFYILTNN-HVVDGADEI  117 (484)
T ss_pred             CCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCEEEECCCCEEEEEECC-EEECCCCEE
T ss_conf             7777785556668741056648887888888888885200376403776414418984789869998754-363685379


Q ss_pred             C----CCCEEEEEC--CCCEEEEECCCCCCCC-CCEEEEEEECCCCCC----CCCCCCCCCCCCCCEEE-----EECCC-
Q ss_conf             7----871437962--8980674011123344-432899960676676----55655673111241467-----52366-
Q gi|254780700|r  130 E----DGASFSVIL--SDDTELPAKLVGTDAL-FDLAVLKVQSDRKFI----PVEFEDANNIRVGEAVF-----TIGNP-  192 (489)
Q Consensus       130 ~----~a~~i~V~~--~dg~~~~a~vvg~D~~-~DlAvlki~~~~~~~----~~~lg~s~~~~~G~~v~-----aiG~P-  192 (489)
T Consensus       118 ~V~L~DgrefkAklvG~D~-~~D~AvlKi~~~D~~Lp~~~~GDSD~LrVGd~V~AIGNPFG-Nlg~TVT~GIVSAlgRs~  195 (484)
T TIGR02037       118 TVTLSDGREFKAKLVGKDP-RTDIAVLKIEAKDKKLPVVKLGDSDKLRVGDWVLAIGNPFG-NLGQTVTSGIVSALGRSG  195 (484)
T ss_pred             EEEECCCCEEEEEEECCCC-CEEEEEEEEECCCCCCCEEEECCCCCCEECCEEEEEECCCC-CCCCEEEEEEEEEECCCC
T ss_conf             9994599485568866677-21389999827889745677348555224349999327742-458425788998321688


Q ss_pred             CCCC------CC---C-------------------CCCCCCCCC----------------------------CCCCCCCC
Q ss_conf             5531------11---1-------------------258744311----------------------------22334434
Q gi|254780700|r  193 FRLR------GT---V-------------------SAGIVSALD----------------------------RDIPDRPG  216 (489)
Q Consensus       193 ~g~~------~t---v-------------------t~GiiSa~~----------------------------R~~~~~~~  216 (489)
T Consensus       196 ~~~~~y~~FIQTDAAINpGNSGGPLvN~~GEvIGINTaI~S~sGG~~GIGFAIP~n~a~~v~~ql~~~G~V~RG~L---G  272 (484)
T TIGR02037       196 LGIGDYENFIQTDAAINPGNSGGPLVNLRGEVIGINTAIYSPSGGNVGIGFAIPSNMAKNVVDQLIEGGKVQRGWL---G  272 (484)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCEECCHHHHHHHHHHHHHHHHHHCCEEEECEE---E
T ss_conf             8877747650224233747887753567853888888876178881010102126889999999983892870215---1


Q ss_pred             CE-EEE---E---------------EEEECCC--------CCCEEEECCCEEEEEECCCCCCCCCCCCCCCCCCCCCCC-
Q ss_conf             20-233---2---------------3320134--------770354034303555123445532222223211233211-
Q gi|254780700|r  217 TF-TQI---D---------------APINQGN--------SGGPCFNALGHVIGVNAMIVTSGQFHMGVGLIIPLSIIK-  268 (489)
Q Consensus       217 ~~-iqt---D---------------a~InpGn--------SGGpl~n~~G~viGint~i~~~~g~~~GigfaIP~~~~~-  268 (489)
T Consensus       273 V~~~q~~~~d~A~~lGl~~~~GALV~~V~~gSPA~kAGlk~GDvI~~~nGk~i~~~~~L~~~i-~~~~pG~~~~L~i~R~  351 (484)
T TIGR02037       273 VTQIQEITSDLAKSLGLEKQEGALVAQVLPGSPAEKAGLKAGDVILSVNGKKIKSFADLRRAI-GTLKPGKKVTLTILRK  351 (484)
T ss_pred             EEECCCCCHHHHHHHCCCCCCCEEEEEECCCCCHHCCCCCCCCEEEEECCEEECCHHHHHHHH-HCCCCCCEEEEEEEEC
T ss_conf             010775797999970888536558885448970100675326689985886405879998987-4058987799999978


Q ss_pred             -------CCCCCC--------C-----CCCC-----CCCCCCCCCCCCCHHHHHHHCCC-CC-CCCEEEECCCCCCCCCC
Q ss_conf             -------001000--------0-----2333-----33343320003421667644176-44-44113201111121134
Q gi|254780700|r  269 -------KAIPSL--------I-----SKGR-----VDHGWFGIMTQNLTQELAIPLGL-RG-TKGSLITAVVKESPADK  321 (489)
Q Consensus       269 -------~i~~~l--------~-----~~g~-----v~rg~lGv~~~~v~~~la~~lgl-~~-~~GvlV~~V~~~sPA~~  321 (489)
T Consensus       352 Gk~~~~~V~l~~Ld~~~a~~~~~~~~~~~~~~~~~~~~~~~~Gl~v~~L~~~~~~~l~~~~~~~~Gv~V~~v~~~s~Aa~  431 (484)
T TIGR02037       352 GKEKTITVTLGELDEKTASAAPEEKASSERSTEPGVGRLGFPGLSVANLTPEIAKKLLNLAGVSKGVVVTKVVSGSPAAR  431 (484)
T ss_pred             CEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCHHHHHHHCCCCCCCCCEEEEEECCCCHHHH
T ss_conf             86888999981078500256645555554322653455322501623799899998713226777489997338888997


Q ss_pred             CCCHHHHHHHHHCCCCCCCCCCEEEEECCCCCCCC--EEEEECCCCCEEEEC
Q ss_conf             67116788875243147874310122203566752--010120478166512
Q gi|254780700|r  322 AGMKVGDVICMLDGRIIKSHQDFVWQIASRSPKEQ--VKISLCKEGSKHSVA  371 (489)
Q Consensus       322 AGLk~GDvI~~ing~~I~~~~~l~~~i~~~~~G~~--v~l~v~R~g~~~~~~  371 (489)
T Consensus       432 ~Gl~~GDvI~~vN~~~V~s~~e~~~~l~~~~k~~~k~~~L~i~Rg~~~~~~~  483 (484)
T TIGR02037       432 AGLQPGDVILSVNQQPVSSVAELNKVLARAKKGGRKKVALLIERGGATIFVT  483 (484)
T ss_pred             CCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEEEEEECCEEEEEE
T ss_conf             1787661899508801467899999999732887047999999878068976