>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-09  Score=94.85  Aligned_cols=160  Identities=27%  Similarity=0.491  Sum_probs=105.4

Q ss_pred             CCCCCCHHHHHHHHHHHH------------CCCCCCCEEEECCCCCCHHHHHHHHHHHHHCCCCCHHHCCCEEEEEEHHH
Q ss_conf             533333578999999963------------36777866895288740777999999987348998444574378873135
Q gi|254780877|r  177 LDPVIGRDDEMRRAIQVL------------SRRTKNNPVLIGDPGVGKTAIIEGLASRIINGDIPESLKGKRLMALDMGA  244 (853)
Q Consensus       177 LDPVIGRe~EI~~~~~iL------------~r~~k~n~~lvGe~GvGKtaive~la~~i~~~~vp~~l~~~~i~~ld~~~  244 (853)
T Consensus        58 F~DVAG~dEAKeEl~EiVdFLK~P~kf~~LGaKIPKGVLLvGPPGTGKTLLAKAvAG---EA~VP-------FF~iSGSd  127 (505)
T TIGR01241        58 FKDVAGIDEAKEELVEIVDFLKNPSKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAG---EAGVP-------FFSISGSD  127 (505)
T ss_pred             ECCCCCCHHHHHHHHHHHHHCCCCHHHHHCCCCCCCCEEEECCCCCCHHHHHHHHHC---CCCCC-------CEEECCCC
T ss_conf             234445323334333134222696379872788987147317878424678875202---58896-------24740761


Q ss_pred             HHCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCHHHH---CCCCCCCCCCCH-HHHHHHHH-------CCCCEEEEEE
Q ss_conf             421745420245458999999860799769996362773---026665543358-88876531-------2466048997
Q gi|254780877|r  245 LIAGAKFRGEFEERLKSLLCEIRSEDGEIILFIDELHVL---VGAGKTDGAMDA-SNLLKPSL-------ARGELHCIGA  313 (853)
Q Consensus       245 l~ag~~~rg~~e~r~~~i~~~~~~~~~~~ilfide~h~~---~gaG~~~g~~Da-an~LKP~L-------arG~l~~Iga  313 (853)
T Consensus       128 FVE--MFVGVGASRVRDLFeqAK~n-APCIIFIDEIDAVGr~RGaG~lGGGnDEREQTLNQLLVEMDGF~~~~gvIv~AA  204 (505)
T TIGR01241       128 FVE--MFVGVGASRVRDLFEQAKKN-APCIIFIDEIDAVGRQRGAGELGGGNDEREQTLNQLLVEMDGFGTNTGVIVIAA  204 (505)
T ss_pred             EEE--CCCCCCCEEHHHHHHHHHHH-CCCEEEEECHHHCCCCCCCCCCCCCCCHHHHHHHHHHEECCCCCCCCCEEEEEE
T ss_conf             011--12056400014457999971-897056401000033356436676541355433233133178589885799850


Q ss_pred             EC-HHHHHHHHHCCHHHHH--CCCE-EECCCCCHHHHHHHHHHHHH
Q ss_conf             44-8999997300111320--2311-11157776789999999789
Q gi|254780877|r  314 TT-LDEYRKYIEKDPALAR--RFQS-LLVGEPTVTDTISILRGLKE  355 (853)
Q Consensus       314 TT-~~Eyrk~iEkD~Al~R--RFq~-i~V~Eps~~~t~~iL~gl~~  355 (853)
T Consensus       205 TNRPDv------LD~ALLRPGRFDRQv~V~~PD~~GR~~IL~VH~~  244 (505)
T TIGR01241       205 TNRPDV------LDPALLRPGRFDRQVVVDLPDIKGREEILKVHAK  244 (505)
T ss_pred             CCCCCC------CCCCCCCCCCCCCEEECCCCCHHHHHHHHHHHHC
T ss_conf             488411------6510068787445134588874678999999854