>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=99.42 E-value=1.4e-12 Score=109.47 Aligned_cols=231 Identities=25% Similarity=0.367 Sum_probs=133.3 Q ss_pred CHHHHHHHHHHHHHHHHHH------------CCCCCCEEEECCCCCHHHHHHHHHHHHHHCCCCCHHHHEEEEEEEEHHH Q ss_conf 1122217899999999862------------2677874896676411668999999998548988345201445540467 Q gi|254780163|r 203 VDILVGRHEEINRTIQILC------------RRSKNNPLYVGDPGVGKTAIAEGFAKQIVDGMVPDILLGARIFSLDMGN 270 (798) Q Consensus 203 LDPVIGRd~EI~riiqIL~------------RR~KNn~~lvG~~gvGktaive~la~~i~~~~vp~~l~~~~i~~ld~~~ 270 (798) 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 HHCCCCCCCHHHHHHHHHHHHHCCCCCEEEEECCHHHH---HCCCCCCCCCCC-H---HHHHHHH----HCCCCEEEEEE Q ss_conf 53063431237899999998720389839997361663---015544434477-7---8888766----30266038873 Q gi|254780163|r 271 LIAGTRYRGDFEERIKKIVKEIESYANAILYIDEIHTL---VGAGSASGISVD-A---SNLLKPA----LSSGAVRCIGS 339 (798) Q Consensus 271 l~ag~~~rg~fe~r~~~~~~~~~~~~~~ilfideih~l---igag~~~g~~~d-~---an~lkP~----L~rg~~~~Iga 339 (798) T Consensus 128 FVE--MFVGVGASRVRDLFeqAK~nAPCIIFIDEIDAVGr~RGaG~lGGGn-DEREQTLNQLLVEMDGF~~~~gvIv~AA 204 (505) T TIGR01241 128 FVE--MFVGVGASRVRDLFEQAKKNAPCIIFIDEIDAVGRQRGAGELGGGN-DEREQTLNQLLVEMDGFGTNTGVIVIAA 204 (505) T ss_pred EEE--CCCCCCCEEHHHHHHHHHHHCCCEEEEECHHHCCCCCCCCCCCCCC-CHHHHHHHHHHEECCCCCCCCCEEEEEE T ss_conf 011--1205640001445799997189705640100003335643667654-1355433233133178589885799850 Q ss_pred CC-HHHHHHHHHCCHHHHH--HCEE-EEECCCCHHHHHHHHHHHHHHHHHHCCCEECCHHH-HHHHHHHHHHCCCCCCHH Q ss_conf 04-8999998520111432--0014-43068786899999986127665410351211178-999998654201555646 Q gi|254780163|r 340 TT-YSEYRQFFEKDKALVR--RFQK-IDVSEPSIEDAIEIVKGIKPYFEEHHQLRYSKEAI-RAAVQLSVRHFTSRKLPD 414 (798) Q Consensus 340 tT-~~ey~~~~e~d~al~r--rF~~-i~v~ep~~~~~~~iL~~~~~~ye~~h~v~~~~~al-~~av~ls~ryi~~r~lPd 414 (798) T Consensus 205 TNRPD------vLD~ALLRPGRFDRQv~V~~PD~~GR~~IL~VH~------~~~kLa~~vdL~~~Ar~TPGf-SGADL-- 269 (505) T TIGR01241 205 TNRPD------VLDPALLRPGRFDRQVVVDLPDIKGREEILKVHA------KNKKLAPDVDLKAVARRTPGF-SGADL-- 269 (505) T ss_pred CCCCC------CCCCCCCCCCCCCCEEECCCCCHHHHHHHHHHHH------CCCCCCCCCCHHHHHHHCCCC-CHHHH-- T ss_conf 48841------1651006878744513458887467899999985------488997024779997015687-67889-- Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCHHHHHCCHHHH Q ss_conf 79889986533332114432211365789998663102453101110011233 Q gi|254780163|r 415 KAIDVIDEAGASQILQPLSKRRKFITEKDIKKTIASMNRSIHTTSFSRDDDSV 467 (798) Q Consensus 415 kAidllDea~a~~~~~~~~~~~~~~~~~~i~~~~~~~~~gip~~~~~~~~~~~ 467 (798) T Consensus 270 --aNl~NEA----ALlAAR~n~~~i~~~~~eeA~Drv~~G~ekKsr~is~~eK 316 (505) T TIGR01241 270 --ANLLNEA----ALLAARKNKTEITMNDIEEAVDRVIAGLEKKSRVISEKEK 316 (505) T ss_pred --HHHHHHH----HHHHHHCCCCEECHHHHHHHHHHHHCCCCCCCCCCCHHHC T ss_conf --9999999----9998617986562888987877652276678853267774

HHsearch alignment for GI: 254780163 and conserved domain: TIGR01241