HHsearch alignment for GI: 254780711 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=96.03  E-value=0.01  Score=40.95  Aligned_cols=198  Identities=22%  Similarity=0.304  Sum_probs=124.6

Q ss_pred             HHHHCCCCCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHCCCCCCCCC
Q ss_conf             98718774210002588418996234433346889999999986148950782054221004779999851034742223
Q gi|254780711|r   83 VEVLGKESIELDLNAPSPLVIMLVGLQGSGKTTTTAKIAYHLKTLKKKKILMASLDVHRPAAQEQLRYLGEQIQVDTLEV  162 (461)
Q Consensus        83 ~~lLg~~~~~l~~~~~~p~vIllvGl~GsGKTTT~aKLA~~~~~~~~~kV~lv~~Dt~R~aA~eQL~~~a~~~~v~~~~~  162 (461)
T Consensus        75 VdFLK~P~kf~~LGaKIPKGVLLvGPPGTGKT--------LLAK------Av-----------------AGEA~VPFF~i  123 (505)
T TIGR01241        75 VDFLKNPSKFTKLGAKIPKGVLLVGPPGTGKT--------LLAK------AV-----------------AGEAGVPFFSI  123 (505)
T ss_pred             HHHCCCCHHHHHCCCCCCCCEEEECCCCCCHH--------HHHH------HH-----------------HCCCCCCCEEE
T ss_conf             42226963798727889871473178784246--------7887------52-----------------02588962474


Q ss_pred             CCCCHHHH--------HHHHHHHHHHHCCCCEEEEE---CCCCCC--------CHH---HHHHHHHHHHHHCCCCCCCCC
Q ss_conf             32103689--------99999999974158869983---344222--------112---468999999851385110003
Q gi|254780711|r  163 IPEQSPEK--------IAIRATQSARDGGYDAVILD---TAGRNH--------IND---SLMQEISEIKSLTNPHEILLV  220 (461)
Q Consensus       163 ~~~~dp~~--------i~~~a~~~a~~~~~D~iiiD---TaGR~~--------~d~---~lm~El~~i~~~~~p~e~~lV  220 (461)
T Consensus       124 -SGSdFVEMFVGVGASRVRDLFeqAK~nAPCIIFIDEIDAVGr~RGaG~lGGGnDEREQTLNQLLVEMDGF~-~~~gvIv  201 (505)
T TIGR01241       124 -SGSDFVEMFVGVGASRVRDLFEQAKKNAPCIIFIDEIDAVGRQRGAGELGGGNDEREQTLNQLLVEMDGFG-TNTGVIV  201 (505)
T ss_pred             -CCCCEEECCCCCCCEEHHHHHHHHHHHCCCEEEEECHHHCCCCCCCCCCCCCCCHHHHHHHHHHEECCCCC-CCCCEEE
T ss_conf             -07610111205640001445799997189705640100003335643667654135543323313317858-9885799


Q ss_pred             CCHHCCHHHHHHH----HHHHHHCCCCCEEEEECCCCCCCCHHHHHHHHHCCCHHHEECCCCCCCCCCCCHHHHHHHHHC
Q ss_conf             1011122568888----988763584407764115766330367778884787302615867232100136889987735
Q gi|254780711|r  221 ADALTGQDAVHLA----RNFDKIVDLTGIILTRMDGDGRGGAALSMRTVTGKPIKAIGTGEKINDLENFFPDRIANRILG  296 (461)
Q Consensus       221 ~da~~Gq~a~~~a----~~F~~~~~i~giIlTKlD~~akgG~als~~~~~~~PI~fig~GE~~~dle~F~p~~~~~riLG  296 (461)
T Consensus       202 ~AATNRPDvLD~ALLRPGRFDRQ-----v~V~~PD--~~GR~~IL~VH~~~~kLa-----------~~vdL~~~Ar~TPG  263 (505)
T TIGR01241       202 IAATNRPDVLDPALLRPGRFDRQ-----VVVDLPD--IKGREEILKVHAKNKKLA-----------PDVDLKAVARRTPG  263 (505)
T ss_pred             EEECCCCCCCCCCCCCCCCCCCE-----EECCCCC--HHHHHHHHHHHHCCCCCC-----------CCCCHHHHHHHCCC
T ss_conf             85048841165100687874451-----3458887--467899999985488997-----------02477999701568


Q ss_pred             C--CCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHH
Q ss_conf             8--6278899987421126789988865310463799999999998
Q gi|254780711|r  297 M--GDVVSLVEKAARNLNEKQAALTAKKIAKGKFDLEDLAEQFRQT  340 (461)
Q Consensus       297 m--gD~~~l~e~~~~~~d~~~~~~l~~k~~~g~F~l~Df~~Ql~~i  340 (461)
T Consensus       264 fSGADLaNl~N---------EAALlAAR~n~~~i~~~~~eeA~Drv  300 (505)
T TIGR01241       264 FSGADLANLLN---------EAALLAARKNKTEITMNDIEEAVDRV  300 (505)
T ss_pred             CCHHHHHHHHH---------HHHHHHHHCCCCEECHHHHHHHHHHH
T ss_conf             76788999999---------99999861798656288898787765