>TIGR00054 TIGR00054 membrane-associated zinc metalloprotease, putative; InterPro: IPR004387 Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site . The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases . 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 contains putative zinc metallopeptidases belonging to MEROPS peptidase family M50 (S2P protease family, clan MM). The N-terminal region of contains a perfectly conserved motif HEXGH, where the Glu is the active site and the His residues coordinate the metal cation. The family of bacterial and plant proteins also includes a region that hits the PDZ domain (IPR001478 from INTERPRO), found in a number of proteins targeted to the membrane by binding to a peptide ligand . The family includes EcfE, which is a homolog of human site-2 protease (S2P), a membrane-bound zinc metalloprotease involved in regulated intramembrane proteolysis. In Escherichia coli EcfE activates the sigma(E) pathway of stress response through a site-2 cleavage of anti-sigma(E), RseA.; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis, 0016021 integral to membrane.

Probab=99.41  E-value=1.8e-13  Score=104.45  Aligned_cols=157  Identities=19%  Similarity=0.251  Sum_probs=112.2

Q ss_pred             CCCEEEECCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCEEEEECCCCCCCCEEEEECC----CCCEEEECCCCCCCCCC
Q ss_conf             44113201111121134671167888752431478743101222035667520101204----78166512556558763
Q gi|254780700|r  305 TKGSLITAVVKESPADKAGMKVGDVICMLDGRIIKSHQDFVWQIASRSPKEQVKISLCK----EGSKHSVAVVLGSSPTA  380 (489)
Q Consensus       305 ~~GvlV~~V~~~sPA~~AGLk~GDvI~~ing~~I~~~~~l~~~i~~~~~G~~v~l~v~R----~g~~~~~~V~l~~~p~~  380 (489)
T Consensus       134 ~~~~vi~~~~~~S~a~~a~~~~Gd~il~~~~~~~~~f~~~~~~~~~~~~g~~-~~~I~~~PF~S~~e~~~~L~L~~~~~~  212 (463)
T TIGR00054       134 EVGPVIEELDKNSIALEAGIEPGDEILSVNGKKIPGFKDVRKQIADIVAGEP-MVEILAAPFNSDIEREVKLDLRNWTFE  212 (463)
T ss_pred             CCCCCCCCCCHHHHHHHHCCCCCCEEEEECCCCCCCCHHHHHHHHHHHCCCC-CCEEEECCCCCCCHHHCCCCCEEEEEE
T ss_conf             1366456554457998711689847874077667880889999999751785-415776577754112000033123862


Q ss_pred             CCCCCCCCCCCCCCCEEEEECCHHHCCEEEEEEEEECCCCHHHHCCCCCCCEEEEECCEECCCHHHHHHHHHHHHHCCCC
Q ss_conf             10000124654525469872896571520079996068897898299988899988999938999999999988625995
Q gi|254780700|r  381 KNDMHLEVGDKELLGMVLQDINDGNKKLVRIVALNPNREREVEAKGIQKGMTIVSVNTHEVSCIKDVERLIGKAKEKKRD  460 (489)
Q Consensus       381 ~~~~~~~~~~~~~lGl~v~~l~~~~~~~~gi~vv~v~~~s~Aa~~GL~~GDiIl~VNg~~V~s~~dl~~iL~~~k~~~~~  460 (489)
T Consensus       213 ~~~------~~~~~~lgl~~~~P----~ie~vl~~~~~N~~A~~AGLk~GD~I~~i~g~~l~~w~d~v~~v~~---np~~  279 (463)
T TIGR00054       213 VEK------EDAVEQLGLKPRGP----KIEPVLSDVTPNSPAEKAGLKEGDKIISIDGEKLKSWRDFVSLVKE---NPGK  279 (463)
T ss_pred             CCC------CCHHHHCCCCCCCC----CCEEEECCCCCCCHHHHCCCCCCCEEEEECCCCCCCHHHHHHHHHH---CCCC
T ss_conf             112------55255414424787----2012331267885377534656888985568123442458999986---8995


Q ss_pred             EEEEEEEECCCCCCC
Q ss_conf             699999717764334
Q gi|254780700|r  461 SVLLQIKYDPDMQSG  475 (489)
Q Consensus       461 ~VLL~V~r~~~~~~~  475 (489)
T Consensus       280 ~~~i~v~R~G~~l~~  294 (463)
T TIGR00054       280 SLEIKVERNGETLSI  294 (463)
T ss_pred             EEEEEEEECCCEEEE
T ss_conf             699999727814634