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