HHsearch alignment for GI: 254781093 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=99.61  E-value=1e-13  Score=102.64  Aligned_cols=190  Identities=18%  Similarity=0.302  Sum_probs=126.9

Q ss_pred             ECCCCCEEEEEEECCCCCC-CCEEEEECCCCCCCCCCCCHHHHHHHHHHHH-CCCEEEEEEECCCCCCCCCCCCCCHHH-
Q ss_conf             6589961879996688877-8799995789988889989999999999997-398499985315588767785210238-
Q gi|254781093|r    6 FNGPSGRLEGRYQPSTNPN-APIALILHPHPRFGGTMNDNIVYQLFYLFQQ-RGFVSLRFNFRGIGRSEGEFDYGDGEL-   82 (225)
Q Consensus         6 i~g~~G~l~~~~~~~~~~~-~~~vv~~Hp~p~~GG~~~~~~~~~la~~l~~-~G~~vl~fd~RG~G~S~G~~~~g~~E~-   82 (225)
T Consensus         7 ~~~~Gg~--~~~~~~~~~g~~~~Ll~lHGGP--G~~H--~Yl~~l~~~~~~~~G~~V~~YDQLGcg~Sd~-Pd~s~PE~~   79 (302)
T TIGR01250         7 ITVDGGY--VLFTKTGGEGEKIKLLVLHGGP--GSSH--EYLENLKELLKEDLGREVIMYDQLGCGYSDQ-PDDSDPEIA   79 (302)
T ss_pred             EEECCCE--EEEEEECCCCCCCEEEEEECCC--CCCH--HHHHHHHHHHHHCCCCEEEEEECCCCCCCCC-CCCCCCHHH
T ss_conf             7206868--9998731789892189970889--8874--2379999997640782799983245777785-888773123


Q ss_pred             HHH---HHHHHH---HHHH-CCCCCCEEEEEECHHHHHHHHHHHCC-C-CHHEEEECCCCCCC-----------------
Q ss_conf             999---998999---9862-35467405888720368787645038-6-21330122757443-----------------
Q gi|254781093|r   83 SDA---AAALDW---VQSL-NPESKSCWIAGYSFGAWISMQLLMRR-P-EINGFISVAPQPKS-----------------  136 (225)
Q Consensus        83 ~D~---~aa~~~---l~~~-~~~~~~i~l~G~S~Gg~val~~a~~~-p-~i~~~v~isp~~~~-----------------  136 (225)
T Consensus        80 ~kl~t~d~fV~E~e~vR~~L~l~~~nfyllG~SWGG~LA~~Yal~Yh~~~lkglI~ss~~~s~pey~~~~~r~~~~~Lp~  159 (302)
T TIGR01250        80 EKLWTIDYFVDELEEVREKLGLDKKNFYLLGHSWGGLLAQEYALKYHGQHLKGLIISSMLDSAPEYVKELNRLRDKKLPP  159 (302)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCEEEEECCHHHHHHHHHHHHHCCCCCEEEEEECCCCCHHHHHHHHHHHHHHCCCH
T ss_conf             45420002389999999985578652789702678999999999737898269998556567247899999877632899


Q ss_pred             ---------------------------------------------------------------------------CCC-C
Q ss_conf             ---------------------------------------------------------------------------332-2
Q gi|254781093|r  137 ---------------------------------------------------------------------------YDF-S  140 (225)
Q Consensus       137 ---------------------------------------------------------------------------~~~-~  140 (225)
T Consensus       160 ~~~~~i~~~E~~g~~~~~~Y~~~v~~~~~~~~~~~~~~~P~~l~~~~~~~~n~~vY~~m~GpnEF~~~Gda~L~dWD~~D  239 (302)
T TIGR01250       160 EVREAIKRCEASGDYDDPEYQEAVEVFYYQHLICRLRKWPEALKRLKSGMRNTEVYNIMQGPNEFTITGDANLKDWDITD  239 (302)
T ss_pred             HHHHHHHHHHCCCCCCCHHHHHHHHHHCCCEEEECCCCCHHHHHHHHHCCCHHHHHHHHCCCCCCEEECCCEEEECCHHC
T ss_conf             89999999742689889899999986220124204677547899987315503667744289565351364343020103


Q ss_pred             CCCCCCCCEEEEECCCCCCCCHHHHHHHHHHHHHCCCCCEEEEEECCCCCC-CCCCHHHHHHHHHHHHH
Q ss_conf             234334773776168655028999999999986077996079997879847-55858999999999999
Q gi|254781093|r  141 FLAPCPSSGLIINGSNDTVATTSDVKDLVNKLMNQKGISITHKVIPDANHF-FIGKVDELINECAHYLD  208 (225)
Q Consensus       141 ~l~~~~~p~LiIhG~~D~~vp~~~~~~~~~~l~~~~~~~~~~~~i~ga~H~-f~~~~~~l~~~i~~fl~  208 (225)
T Consensus       240 ~L~~I~vPTLlt~G~~D~~~-p~~~~~m~~~i~~Sr-----l~~f~~g~H~~m~e~~~~y~~~l~~Fl~  302 (302)
T TIGR01250       240 KLSEIKVPTLLTVGEFDTMT-PEAAREMQELIAKSR-----LVVFPDGSHMTMIEEPEVYFKLLSDFLR  302 (302)
T ss_pred             CHHHCCCCCEEEEECCCCCC-HHHHHHHHHHCCCCE-----EEECCCCCCCCCCCCHHHHHHHHHHHHC
T ss_conf             15435876003342046578-899999987607873-----8984788513753483889999998709