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