>TIGR01241 FtsH_fam ATP-dependent metallopeptidase HflB; InterPro: IPR005936 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 group of metallopeptidases belong to MEROPS peptidase family M41 (FtsH endopeptidase family, clan MA(E)). The predicted active site residues for members of this family and thermolysin, the type example for clan MA, occur in the motif HEXXH. FtsH is a membrane-anchored ATP-dependent protease that degrades misfolded or misassembled membrane proteins as well as a subset of cytoplasmic regulatory proteins. FtsH is a 647-residue protein of 70 kDa, with two putative transmembrane segments towards its N terminus which anchor the protein to the membrane, giving rise to a periplasmic domain of 70 residues and a cytoplasmic segment of 520 residues containing the ATPase and protease domains . ; GO: 0004222 metalloendopeptidase activity, 0030163 protein catabolic process, 0016020 membrane.

Probab=98.91  E-value=2.4e-08  Score=71.27  Aligned_cols=184  Identities=18%  Similarity=0.237  Sum_probs=125.2

Q ss_pred             HHHHHHHHHCC------CCCEEEEECCCCCCHHHHHHHHHHHHCCCCHHHHH----------------HHHHHHHHHHHH
Q ss_conf             99999851016------78849998787778688999999862762013567----------------644454666666
Q gi|254780567|r   52 AVRLIDSWPSW------PSRVVILVGPSGSGKSCLANIWSDKSRSTRFSNIA----------------KSLDSILIDTRK  109 (246)
Q Consensus        52 A~~~i~~~~~~------~~~~l~i~G~~GsGKTHLl~a~~~~~~~~~~~~~~----------------~~~~~~~~~~~~  109 (246)
T Consensus        74 iVdFLK~P~kf~~LGaKIPKGVLLvGPPGTGKTLLAKAvAGEA~VPFF~iSGSdFVEMFVGVGASRVRDLFeqAK~nAPC  153 (505)
T TIGR01241        74 IVDFLKNPSKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAGVPFFSISGSDFVEMFVGVGASRVRDLFEQAKKNAPC  153 (505)
T ss_pred             HHHHCCCCHHHHHCCCCCCCCEEEECCCCCCHHHHHHHHHCCCCCCCEEECCCCEEECCCCCCCEEHHHHHHHHHHHCCC
T ss_conf             34222696379872788987147317878424678875202588962474076101112056400014457999971897


Q ss_pred             HHHHHHHHCCCC-----------C--CHHHHHH---HHHHHCCCCCEEEEECCCCCCHHHHHHHHH-HHHHHCCEEEECC
Q ss_conf             533433210037-----------6--1033545---554311234215640354320022345667-8852122245078
Q gi|254780567|r  110 PVLLEDIDLLDF-----------N--DTQLFHI---INSIHQYDSSLLMTARTFPVSWGVCLPDLC-SRLKAATVVKISL  172 (246)
Q Consensus       110 ~i~iddi~~~~~-----------~--ee~lf~l---~n~~~~~~~~iilts~~~p~~~~~~l~DL~-SRl~~g~~~~I~~  172 (246)
T Consensus       154 IIFIDEIDAVGr~RGaG~lGGGnDEREQTLNQLLVEMDGF~~~~gvIv~AATNRPDvLD~AL--LRPGRFD--RQv~V~~  229 (505)
T TIGR01241       154 IIFIDEIDAVGRQRGAGELGGGNDEREQTLNQLLVEMDGFGTNTGVIVIAATNRPDVLDPAL--LRPGRFD--RQVVVDL  229 (505)
T ss_pred             EEEEECHHHCCCCCCCCCCCCCCCHHHHHHHHHHEECCCCCCCCCEEEEEECCCCCCCCCCC--CCCCCCC--CEEECCC
T ss_conf             05640100003335643667654135543323313317858988579985048841165100--6878744--5134588


Q ss_pred             CCHHHHHHHHHHHHHHCCCCCCHHH-HHHHHHCCC-CCHHHHHHHHHHHHHHH-HHHCCCCCHHHHHHHHHH
Q ss_conf             8978999999998666289798899-999994066-79899999999999999-984778788999999986
Q gi|254780567|r  173 PDDDFLEKVIVKMFADRQIFIDKKL-AAYIVQRME-RSLVFAEKLVDKMDNLA-LSRGMGITRSLAAEVLKE  241 (246)
Q Consensus       173 pdde~~~~il~k~~~~r~i~l~~~v-~~yl~~r~~-Rs~~~l~~~l~~Ld~~s-l~~kr~ITi~lvk~vL~~  241 (246)
T Consensus       230 PD~~GR~~IL~VH~~~--~kLa~~vdL~~~Ar~TPGfSGADLaNl~NEAALlAAR~n~~~i~~~~~eeA~Dr  299 (505)
T TIGR01241       230 PDIKGREEILKVHAKN--KKLAPDVDLKAVARRTPGFSGADLANLLNEAALLAARKNKTEITMNDIEEAVDR  299 (505)
T ss_pred             CCHHHHHHHHHHHHCC--CCCCCCCCHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCEECHHHHHHHHHH
T ss_conf             8746789999998548--899702477999701568767889999999999986179865628889878776