HHsearch alignment for GI: 254780829 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=469.80  Aligned_cols=358  Identities=14%  Similarity=0.097  Sum_probs=326.8

Q ss_pred             CEECHHHHHHHHHHHHHHHHHHHCCCCCCCCC----CCCCCEEEECCCCCCHHHHHHHHHHHHCCCEEEEECCCEEECCC
Q ss_conf             30486899999999998778864086444466----56686699679888689999999997078779714341012122
Q gi|254780829|r   19 YIIGQQDAKRAVAIALRNRWRRQQLPADLRDE----LMPKNILLVGPTGVGKTAISRRLARLAGAPFIKVEVTKFTEIGY   94 (437)
Q Consensus        19 ~VvGQ~~AKk~lavav~nhy~R~~~~~~~~~e----~~psNiLLiGPtGtGKTlLAktLA~~l~VPF~~~daT~ftE~gy   94 (437)
T Consensus        60 DVAG~dEAKeEl~EiV------dFLK~P~kf~~LGaKIPKGVLLvGPPGTGKTLLAKAvAGEA~VPFF~iSGSdFVEMF-  132 (505)
T TIGR01241        60 DVAGIDEAKEELVEIV------DFLKNPSKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAGVPFFSISGSDFVEMF-  132 (505)
T ss_pred             CCCCCHHHHHHHHHHH------HHCCCCHHHHHCCCCCCCCEEEECCCCCCHHHHHHHHHCCCCCCCEEECCCCEEECC-
T ss_conf             4445323334333134------222696379872788987147317878424678875202588962474076101112-


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHCCCCCCCHHHHHHHHHHHHCCCCCCEEEEEECCCC
Q ss_conf             343101346788876521278998565498888688875555-3114321100466898898616888854998753554
Q gi|254780829|r   95 VGRNVEQIIRDLVDVAINIVRESRRDEVREQASINAEERILD-ALVGKTATSNTREVFRKKLRDGEISDKEIDIEVADTS  173 (437)
Q Consensus        95 vG~DVes~i~~l~~~a~~~~~~a~~~i~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~i~~~~~~  173 (437)
T Consensus       133 ----VGVGASRVRDLFeqAK~nAPCIIFIDEIDAVGr~RGaG~lGGGnDEREQTLNQLLVEMDGF~~~~gvIv~AATNRP  208 (505)
T TIGR01241       133 ----VGVGASRVRDLFEQAKKNAPCIIFIDEIDAVGRQRGAGELGGGNDEREQTLNQLLVEMDGFGTNTGVIVIAATNRP  208 (505)
T ss_pred             ----CCCCCEEHHHHHHHHHHHCCCEEEEECHHHCCCCCCCCCCCCCCCHHHHHHHHHHEECCCCCCCCCEEEEEECCCC
T ss_conf             ----0564000144579999718970564010000333564366765413554332331331785898857998504884


Q ss_pred             CCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCEEEEEHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             55443346676663210001101001354322100000102355332788863031011123678887532221002221
Q gi|254780829|r  174 SDISNFDIPGGASVGILNLSELFSKVMGSGRKKKIRMSVQKCYPELMRDESDRLIDMDTVHRDSIQMVENYGIVFLDEFD  253 (437)
Q Consensus       174 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~f~~~~~  253 (437)
T Consensus       209 DvLD~A--LLRPGRFDRQv~V~~PD~~GR~~IL~VH~~~~kLa~~vdL~~~Ar~TPGfSGADLaNl~NEAALlAAR~n~~  286 (505)
T TIGR01241       209 DVLDPA--LLRPGRFDRQVVVDLPDIKGREEILKVHAKNKKLAPDVDLKAVARRTPGFSGADLANLLNEAALLAARKNKT  286 (505)
T ss_pred             CCCCCC--CCCCCCCCCEEECCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCC
T ss_conf             116510--068787445134588874678999999854889970247799970156876788999999999998617986


Q ss_pred             HHCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHCCCCCCCCCCCCCCCC-CCCCEEEEECC-CCCH
Q ss_conf             001357665654332101223432046652211246664202466401675422112125543-34512688615-5424
Q gi|254780829|r  254 KIVARDSGNGIGVSREGVQRDLLPLVEGSSVSTKYGSINTDHILFIASGAFHVSRPADLLPEI-QGRFPVRVHLK-SLNK  331 (437)
Q Consensus       254 ki~~~~~~~~~~~~~~g~~~~~~~~~e~~~v~~~~~~~~~~~~~~i~~~~~~~~k~~glipE~-~GR~p~~v~l~-~L~~  331 (437)
T Consensus       287 ~i~~~~~eeA~Drv~~G~ekKsr~is~~eK~~vAYHEaGHAl~G~~~~~~DpV~KvTIIPRG~~AlG~t~~lP~~~D~~l  366 (505)
T TIGR01241       287 EITMNDIEEAVDRVIAGLEKKSRVISEKEKKIVAYHEAGHALVGLLLKDADPVHKVTIIPRGQGALGYTQFLPEEGDKYL  366 (505)
T ss_pred             EECHHHHHHHHHHHHCCCCCCCCCCCHHHCCEEEEECHHHHHHHHHCCCCCCCCCEEECCCCCCCCCCEEECCCCCCCCC
T ss_conf             56288898787765227667885326777422201115789999735344752325631478441551683677444100


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHC--CCEEEECHHH---HHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHCC
Q ss_conf             6788876434688999999998751--9689984249---9999999998404001237246799999986776212
Q gi|254780829|r  332 SDFRLILTDTESNLILQYKELMKTE--GIILDFTEDS---IDALADVAVNLNSTVGDIGARRLQTVMERVLEDISFS  403 (437)
Q Consensus       332 ~~l~~IL~epk~~l~~q~~~lf~~~--~v~L~ft~~A---l~~IA~~A~~~~t~~~~~GAR~LrtI~E~~l~d~~fe  403 (437)
T Consensus       367 ~~k~~L~~~i~~~lGGRaAEe~~fG~~~v----ttGA~nD~~~AT~iAr~MVT---~~G-------MS~klG~v~~~  429 (505)
T TIGR01241       367 YTKKQLLAKIAVLLGGRAAEEIIFGEEEV----TTGASNDLKQATNIARAMVT---EWG-------MSEKLGPVAYG  429 (505)
T ss_pred             CCHHHHHHHHHHHHHHHHEEEEECCCCCC----CCCCCHHHHHHHHHHHHHCC---CCC-------CCCCCCCCEEC
T ss_conf             36889999999873203100223078873----23621158999999997315---336-------74200451220