>TIGR02771 TraF_Ti conjugative transfer signal peptidase TraF; InterPro: IPR014139 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 entry contains the conjugative transfer signal peptidase (TraF), which belongs to MEROPS peptidase family S26, subfamily S26C (TraF signal peptidase, clan SF). It is found in operons that encode elements of conjugative transfer systems. This family is homologous to a broader family of signal (leader) peptidases such as LepB. This family is present in both Ti-type and I-type conjugative systems ..

Probab=99.73  E-value=2.2e-17  Score=129.26  Aligned_cols=107  Identities=34%  Similarity=0.576  Sum_probs=81.9

Q ss_pred             CCCCCCCCEEEEECC-CCCHH-------------------HEEEEEEEECHHHEEECCCCEEECCCCCCCCCCCCCEEEC
Q ss_conf             555334704664014-42003-------------------1000000304234320077324535312245446400221
Q gi|254780939|r   82 NNQPRRGDVVVFRYP-KDPSI-------------------DYVKRVIGLPGDRISLEKGIIYINGAPVVRHMEGYFSYHY  141 (248)
Q Consensus        82 ~~~p~RGDIVVF~~P-~d~~~-------------------~yVKRvIGlPGDtV~i~~~~l~INg~~i~~~~~~~~~~~~  141 (248)
T Consensus        47 ~~~v~~G~yV~fcpPe~~~~~~~A~~RGY~~~G~C~GGf~pl~K~v~~l~Gd~v~~~~~~v~iNg~~~~~~~~~~~D---  123 (183)
T TIGR02771        47 SKPVERGDYVVFCPPEDNAVFEEARERGYLREGLCPGGFGPLLKRVLGLPGDRVTVRADVVAINGKLLPYSKPLATD---  123 (183)
T ss_pred             CCCCCCCCEEEEECCCCCHHHHHHHHCCCCCCCCCCCCHHHHHHEEECCCCCEEEEECCEEEECCEECCCCCEEECC---
T ss_conf             26877787789835986678740545143357888986001202321278955886068888878677987311007---


Q ss_pred             CCCCCEEEEEECCCCCCCCCCCEEECCCCCCCCCC-C-EEECCCC--EEEEEECCCC-CCCCCCCCCCCCCCHHHEEEEE
Q ss_conf             47862012210221467850002212455788745-3-0232446--4999717887-7764453653026088825338
Q gi|254780939|r  142 KEDWSSNVPIFQEKLSNGVLYNVLSQDFLAPSSNI-S-EFLVPKG--HYFMMGDNRD-KSKDSRWVEVGFVPEENLVGRA  216 (248)
Q Consensus       142 ~~~~~~~~~~~~e~l~~~~~~~~~~~~~~~~~~~~-~-~~~VP~g--~yfvlGDNRd-nS~DSR~~~~G~Vp~~~IvGka  216 (248)
T Consensus       124 ---------------~~GR~--------l---~p~k~s~~~~p~G~~~~~~v~~~~~a~SFDSRYA~fG~i~~~q~~~~~  177 (183)
T TIGR02771       124 ---------------SEGRP--------L---PPLKASEGVVPPGEAEFLVVSDTSPATSFDSRYAEFGPISREQVIGRV  177 (183)
T ss_pred             ---------------CCCCC--------C---CCCCCCCCEECCCCCEEEEEECCCCCCCCCHHHHCCCCEECCCEEEEE
T ss_conf             ---------------88888--------8---765788853028862178985088987610011024772000505877


Q ss_pred             E
Q ss_conf             9
Q gi|254780939|r  217 S  217 (248)
Q Consensus       217 ~  217 (248)
T Consensus       178 ~  178 (183)
T TIGR02771       178 K  178 (183)
T ss_pred             E
T ss_conf             1