HHsearch alignment for GI: 254780545 and conserved domain: TIGR01241

>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=100.00  E-value=0  Score=1683.78  Aligned_cols=497  Identities=61%  Similarity=0.968  Sum_probs=488.9

Q ss_pred             HHHHHHHHHHH-HHHHHHHHHHHHHHCCCC-CCC-C-CCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             89999999999-999999999999851677-887-7-7676632100001124225698898528899999999987433
Q gi|254780545|r   94 GLLSYLGSWFP-LVLVVLVWMFLMRQIQGG-GAR-G-AMGFGKSKAKLLSGNVGSVTFKDVAGVDEAKEDLQEIVDFLCD  169 (647)
Q Consensus        94 ~~~~iL~~~LP-liLli~i~~fl~rr~~gG-g~~-~-~msfGKSkAk~~~~~~~~v~f~dv~g~~~~k~~~~~~v~~l~~  169 (647)
T Consensus         1 ~~~~~l~~~~P~iL~l~g~~~~f~R~~~G~lGG~~~g~f~fGKS~Ak~~~~~~~kv~F~DVAG~dEAKeEl~EiVdFLK~   80 (505)
T TIGR01241         1 SLLGFLFSLLPPILLLIGLFFLFRRQMQGGLGGKGRGAFSFGKSKAKLLNEEKPKVTFKDVAGIDEAKEELVEIVDFLKN   80 (505)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHCCCCCCEEECCCCCCHHHHHHHHHHHHHCCC
T ss_conf             95777999999999999999999997226788877652565337898730589813223444532333433313422269


Q ss_pred             HHHHHHHHCCCCCCEEECCCCCHHHHHHHHHHHCCCCCCEECCCHHHHHHHHHHCCHHHHHHHHHHHHHHCCHHEEHHHH
Q ss_conf             56766420123331100378742588899997424699702058578864442033245999999998737801206323
Q gi|254780545|r  170 PQKFKRLGGRIPHGVLLVGPPGTGKTLLARAVAGEANVPFFTISGSDFVELFVGVGASRVRDMFEQAKNNSPCIVFVDEI  249 (647)
Q Consensus       170 ~~~~~~~g~~~p~g~ll~GppGtGKTlla~a~a~e~~~~f~~~~~s~~~~~~~g~g~~~vr~lf~~a~~~~p~iifiDei  249 (647)
T Consensus        81 P~kf~~LGaKIPKGVLLvGPPGTGKTLLAKAvAGEA~VPFF~iSGSdFVEMFVGVGASRVRDLFeqAK~nAPCIIFIDEI  160 (505)
T TIGR01241        81 PSKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAGVPFFSISGSDFVEMFVGVGASRVRDLFEQAKKNAPCIIFIDEI  160 (505)
T ss_pred             CHHHHHCCCCCCCCEEEECCCCCCHHHHHHHHHCCCCCCCEEECCCCEEECCCCCCCEEHHHHHHHHHHHCCCEEEEECH
T ss_conf             63798727889871473178784246788752025889624740761011120564000144579999718970564010


Q ss_pred             HHHHCCCCCC-CCCCCHHHHHHHHHHHHHHCCCCCCCCEEEEEECCCCCCCCHHHCCCCCCCCEEEECHHHHHHHHHHHH
Q ss_conf             5641445578-988626889889989985303235778299996298100883331656423141000134788999999
Q gi|254780545|r  250 DAVGRHRGIG-LGGGNDEREQTLNQLLVEMDGFESSEGVILIAATNRPDVLDAALLRPGRFDRQITVPNPDIVGREHILM  328 (647)
Q Consensus       250 da~~~~r~~~-~~~~~~e~~~~ln~ll~~mdg~~~~~~v~vi~aTn~~~~lD~al~RpgRfd~~i~~~~P~~~~r~~i~~  328 (647)
T Consensus       161 DAVGr~RGaG~lGGGnDEREQTLNQLLVEMDGF~~~~gvIv~AATNRPDvLD~ALLRPGRFDRQv~V~~PD~~GR~~IL~  240 (505)
T TIGR01241       161 DAVGRQRGAGELGGGNDEREQTLNQLLVEMDGFGTNTGVIVIAATNRPDVLDPALLRPGRFDRQVVVDLPDIKGREEILK  240 (505)
T ss_pred             HHCCCCCCCCCCCCCCCHHHHHHHHHHEECCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCEEECCCCCHHHHHHHHH
T ss_conf             00033356436676541355433233133178589885799850488411651006878744513458887467899999


Q ss_pred             HHHCCCCCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHH
Q ss_conf             98548877732110245441203798999999999876455320242104568999750136865567666866778999
Q gi|254780545|r  329 VHSRNVPLAPNVILKTIARGTPGFSGADLRNLVNEAALMAARRNRRLVTMQEFEDAKDKILMGAERRSTAMTEEEKKITA  408 (647)
Q Consensus       329 ~~~~~~~~~~~~d~~~la~~t~g~sgAdi~~~~~eAa~~a~r~~~~~i~~~dl~~A~~rv~~G~ek~~~~~~~~ek~~vA  408 (647)
T Consensus       241 VH~~~~kLa~~vdL~~~Ar~TPGfSGADLaNl~NEAALlAAR~n~~~i~~~~~eeA~Drv~~G~ekKsr~is~~eK~~vA  320 (505)
T TIGR01241       241 VHAKNKKLAPDVDLKAVARRTPGFSGADLANLLNEAALLAARKNKTEITMNDIEEAVDRVIAGLEKKSRVISEKEKKIVA  320 (505)
T ss_pred             HHHCCCCCCCCCCHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCEECHHHHHHHHHHHHCCCCCCCCCCCHHHCCEEE
T ss_conf             98548899702477999701568767889999999999986179865628889878776522766788532677742220


Q ss_pred             HHHHHHHHHHHHCCCCCCHHHHHHHCCCC-CCCCEEEEHHH-HHHCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCC
Q ss_conf             99999999998505877323432201455-56405640024-43226899999999999878988888613687565233
Q gi|254780545|r  409 YHEAGHAVVACHVPKADPLHKATIIPRGR-ALGMVMQLPEA-DRHSTTYVWMTSRLTILMGGRVAEEFTFGEDNVTSGAM  486 (647)
Q Consensus       409 yHEAGHAlva~~l~~~~~v~kVTIipRg~-alG~t~~~p~~-d~~~~tk~~l~~~i~v~LgGRaAEei~fG~~~ittGAs  486 (647)
T Consensus       321 YHEaGHAl~G~~~~~~DpV~KvTIIPRG~~AlG~t~~lP~~~D~~l~~k~~L~~~i~~~lGGRaAEe~~fG~~~vttGA~  400 (505)
T TIGR01241       321 YHEAGHALVGLLLKDADPVHKVTIIPRGQGALGYTQFLPEEGDKYLYTKKQLLAKIAVLLGGRAAEEIIFGEEEVTTGAS  400 (505)
T ss_pred             EECHHHHHHHHHCCCCCCCCCEEECCCCCCCCCCEEECCCCCCCCCCCHHHHHHHHHHHHHHHHEEEEECCCCCCCCCCC
T ss_conf             11157899997353447523256314784415516836774441003688999999987320310022307887323621


Q ss_pred             CCHHHHHHHHHHHHHHCCCCCCCCCEEEC-CCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             55899999999998624888766733404-78767434565677678788999999999999999999999999999899
Q gi|254780545|r  487 SDIEYATKLARVMVTQFGFSNLLGKVSYE-EGQQEALLSHPVSRPRSISEETAQKIDKEVFRLIEEAYQKAKSIIQEKND  565 (647)
Q Consensus       487 ~DL~~AT~iA~~mV~~~GMs~~lG~i~~~-~~~~~~~lg~~~~~~~~~s~~t~~~Id~Ev~~il~~ay~~a~~iL~~n~~  565 (647)
T Consensus       401 nD~~~AT~iAr~MVT~~GMS~klG~v~~~~~~~~~~flg~~~~~~~~~Se~tA~~ID~EV~~i~~~~Y~~A~~iL~e~~~  480 (505)
T TIGR01241       401 NDLKQATNIARAMVTEWGMSEKLGPVAYGQSDGGEVFLGRGFAKAKEYSEETAREIDEEVKRIIEEAYKRAKQILTENRD  480 (505)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCCCCCCEECCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             15899999999731533674200451220234677679876544412218899999999999999999999999986488


Q ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHH
Q ss_conf             9999999998885499999999972
Q gi|254780545|r  566 NFVAIAEALLEYETLSGKEIASLIR  590 (647)
Q Consensus       566 ~l~~la~~Lle~EtL~~~ei~~il~  590 (647)
T Consensus       481 ~L~~~a~~Ll~~ETi~~~~~~~l~~  505 (505)
T TIGR01241       481 ELELLAKELLEKETITREEIKELLA  505 (505)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHC
T ss_conf             9999999888763588689999819