HHsearch alignment for GI: 254780274 and conserved domain: TIGR01250
>TIGR01250 pro_imino_pep_2 proline-specific peptidases; InterPro: IPR005945 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 group of serine peptidase belong to MEROPS peptidase family S33 (clan SC). They are proline iminopeptidase (Prolyl aminopeptidase, 3.4.11.5 from EC), which catalyzes the removal of the N-terminal proline from peptides. This family represents one of two related families of proline iminopeptidase containing the alpha/beta fold. The fine specificities of the various members, including both the range of short peptides from which proline can be removed and whether other amino acids such as alanine can be also removed, may vary among members. One of the members of this family is the tricorn protease (TRI) interacting factor 1 from Thermoplasma acidophilum. Factor 1 (F1) is a 33.5 kDa serine peptidase of the alpha/beta-hydrolase family. Tricorn generates small peptides, which are cleaved by F1 to yield single amino acids , . ; GO: 0016804 prolyl aminopeptidase activity, 0005737 cytoplasm.
Probab=99.92 E-value=4.9e-24 Score=178.74 Aligned_cols=270 Identities=13% Similarity=0.087 Sum_probs=147.9
Q ss_pred EEEEEEECCC-CCCCEEEEEECCCCCCHH-HHHHHHHHHHH-CCCEEEEECCHHHCCCCCCCCCC--C-CCCCHHHHHHH
Q ss_conf 9999973488-999679999886878988-89999999998-69899995860208855367876--6-65563999999
Q gi|254780274|r 15 KSVHSYNQTH-KTPRAIILACQSIEENIE-DYNDFREYFAE-ENVAVYIYSYRNTIKTTSDYLRD--Y-PKNTSDTTIVC 88 (317)
Q Consensus 15 ~~~~~~~~~~-~~p~~~vl~~HG~~~~~~-~~~~~~~~l~~-~G~~V~a~D~rG~G~s~~~~~~~--~-~~~~~~~~~~~ 88 (317)
T Consensus 11 Gg~~~~~~~~~~g~~~~Ll~lHGGPG~~H~Yl~~l~~~~~~~~G~~V~~YDQLGcg~Sd~Pd~s~PE~~~kl~t~d~fV~ 90 (302)
T TIGR01250 11 GGYVLFTKTGGEGEKIKLLVLHGGPGSSHEYLENLKELLKEDLGREVIMYDQLGCGYSDQPDDSDPEIAEKLWTIDYFVD 90 (302)
T ss_pred CCEEEEEEECCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHH
T ss_conf 86899987317898921899708898874237999999764078279998324577778588877312345420002389
Q ss_pred HHHHHHHHHHHHCCCCE--EEEEECCCCHHHHHHHHHHC-CHHHHEHEECCCCCCCCCCCHHHHHHH-HHHHHHHCCCCC
Q ss_conf 99999999998559955--99993387228999999968-323213202277777544101566888-777753056321
Q gi|254780274|r 89 DVMKLRTLISEKHGNTS--VLLFGYSLGTIIALSTLLKY-PQKFSGIALWNLDLCFEKYSCMLMTLL-LKIEKFFKGSDT 164 (317)
Q Consensus 89 d~~~~~~~~~~~~~~~~--v~lvGhS~GG~ia~~~a~~~-p~~v~~lvl~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~ 164 (317)
T Consensus 91 E~e~vR~----~L~l~~~nfyllG~SWGG~LA~~Yal~Yh~~~lkglI~ss~~~s~pey~~~~~r~~~~~Lp~~~~~~i~ 166 (302)
T TIGR01250 91 ELEEVRE----KLGLDKKNFYLLGHSWGGLLAQEYALKYHGQHLKGLIISSMLDSAPEYVKELNRLRDKKLPPEVREAIK 166 (302)
T ss_pred HHHHHHH----HHCCCCCCEEEEECCHHHHHHHHHHHHHCCCCCEEEEEECCCCCHHHHHHHHHHHHHHCCCHHHHHHHH
T ss_conf 9999999----855786527897026789999999997378982699985565672478999998776328998999999
Q ss_pred HHHHHHHHHHHHHCCCCCCCC--CCCCCCCCHHHHHHHHHCCCCCCH-HHHHHHHHHHH--------HHHHHHHHH-CCC
Q ss_conf 023433311111001110012--334457446888876421157897-89999999998--------500023331-035
Q gi|254780274|r 165 PSRLMRHLTTDLWNRNNQNWK--NFLKDHSVKKNSQNYILDSNHIPI-SVWLEFMSMAT--------DISSRGSFN-PLS 232 (317)
Q Consensus 165 ~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~--------~~~~~~~~~-~~~ 232 (317)
T Consensus 167 ~~E~~g~~~~~~Y~~~v~~~~~~~~~~~~~~~P~~l~---~~~~~~~n~~vY~~m~GpnEF~~~Gda~L~dWD~~D~L~~ 243 (302)
T TIGR01250 167 RCEASGDYDDPEYQEAVEVFYYQHLICRLRKWPEALK---RLKSGMRNTEVYNIMQGPNEFTITGDANLKDWDITDKLSE 243 (302)
T ss_pred HHHCCCCCCCHHHHHHHHHHCCCEEEECCCCCHHHHH---HHHHCCCHHHHHHHHCCCCCCEEECCCEEEECCHHCCHHH
T ss_conf 9742689889899999986220124204677547899---9873155036677442895653513643430201031543
Q ss_pred CCCCEEEEEECCCCCCCCCHHHHHHHHHHHHHCCCCCCEEEEECCCCCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf 688479997268887467579999999999857899828998259831656569898999999999998
Q gi|254780274|r 233 RFIPFCLIGGGNVSSKIEDLTQTYKLTTRLQNEEFYDISLMSLPPTMHSNDPHNVFPPPAIKKLRNWIV 301 (317)
Q Consensus 233 ~~~Pvlli~G~~D~~~~~~~~~~~~~~~~l~~~~~~~~~l~~~pg~~H~~~l~e~~~~~~~~~i~~Wl~ 301 (317)
T Consensus 244 I~vPTLlt~G~~D~~~-p--~~~~~m~~~-----i~~Srl~~f~~g~H~~m~e--~~~~y~~~l~~Fl~ 302 (302)
T TIGR01250 244 IKVPTLLTVGEFDTMT-P--EAAREMQEL-----IAKSRLVVFPDGSHMTMIE--EPEVYFKLLSDFLR 302 (302)
T ss_pred CCCCCEEEEECCCCCC-H--HHHHHHHHH-----CCCCEEEECCCCCCCCCCC--CHHHHHHHHHHHHC
T ss_conf 5876003342046578-8--999999876-----0787389847885137534--83889999998709