HHsearch alignment for GI: 254780464 and conserved domain: TIGR02110
>TIGR02110 PQQ_syn_pqqF coenzyme PQQ biosynthesis protein PqqF; InterPro: IPR011844 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 family of metallopeptidases belong to MEROPS peptidase family M16, subfamily M16A (clan ME). In the subset of species that make coenzyme PQQ (pyrrolo-quinoline-quinone), this peptidase is found in the PQQ biosynthesis region and is thought to act as a protease on PqqA (IPR011725 from INTERPRO), a probable peptide precursor of the coenzyme. PQQ is required for some glucose dehydrogenases and alcohol dehydrogenases .; GO: 0008234 cysteine-type peptidase activity, 0008270 zinc ion binding, 0018189 pyrroloquinoline quinone biosynthetic process.
Probab=95.06 E-value=0.063 Score=31.91 Aligned_cols=223 Identities=13% Similarity=0.119 Sum_probs=114.7
Q ss_pred HCCEEEEEECCCEEEEEEECCCCCCCCCHHHHHHHHHCCCCCCCHHHHHHHHH-HHHHHHCCCCCCCCCHHHCCCCCCCC
Q ss_conf 08767997532237999612665652100122232210356620011245567-66665113321110000001222222
Q gi|254780464|r 71 VGGDINAYTSLEHTSYHAWVLKEHVPLALEIIGDMLSNSSFNPSDIERERNVV-LEEIGMSEDDSWDFLDARFSEMVWKD 149 (424)
Q Consensus 71 ~G~~~na~t~~d~~~~~~~~~~~~~~~~l~ll~~~~~~p~~~~~~~~~ek~~v-~~e~~~~~~~p~~~~~~~~~~~~f~~ 149 (424)
T Consensus 509 AGv~~~~~~~g~~W~L~L~gp~~~~~A~~~~~l~~l~~a---~P~~~~~~~~~ssaer---~as~p~i~IRQLL~aL-p~ 581 (737)
T TIGR02110 509 AGVELEFEALGEDWQLKLNGPRSPMRAVVSLALALLALA---APSLAQEAARLSSAER---RASAPSIPIRQLLAAL-PE 581 (737)
T ss_pred CCCCCEEEEECCCHHHHHCCCCCCCCHHHHHHHHHHHCC---CCCHHCCCHHHHHHHH---CCCCCCCHHHHHHHHH-HH
T ss_conf 483311121164212220487977727899999997268---8720215201004442---1577761689999960-10
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCC-CCCCCEEEE
Q ss_conf 2222222210344200016677642011245663000002545512211221101235877778866422-332210233
Q gi|254780464|r 150 QIIGRPILGKPETISSFTPEKIISFVSRNYTADRMYVVCVGAVDHEFCVSQVESYFNVCSVAKIKESMKP-AVYVGGEYI 228 (424)
Q Consensus 150 ~~~~~~~~g~~~~i~~lt~~~l~~f~~~~y~p~n~~l~i~Gd~~~~~~~~~i~~~f~~~~~~~~~~~~~p-~~~~~~~~~ 228 (424)
T Consensus 582 ~l~~-------~~~A~~d~e~L~~~W~~arw-~~l~~~l~a~~~~a~~~a~-~--~~p~T--a~~~~~~P~Par~g~~~~ 648 (737)
T TIGR02110 582 RLLK-------SKPAQVDDEDLQALWLAARW-DSLALALPAAVQLALSVAL-Q--LSPGT--ADVERPTPLPARLGRGWE 648 (737)
T ss_pred CCCC-------CCCCCCCCHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHH-H--CCCCC--CCCCCCCCCCCCCCCCEE
T ss_conf 2577-------77788981789999999756-5667666899999987776-4--68887--876777888688888604
Q ss_pred E-CCCCCCCEEEECCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHH-CCCCEEEEEECCCC
Q ss_conf 0-368432102301000013521135689987776248765322220002686210133322210-12201344425830
Q gi|254780464|r 229 Q-KRDLAEEHMMLGFNGCAYQSRDFYLTNILASILGDGMSSRLFQEVREKRGLCYSISAHHENFS-DNGVLYIASATAKE 306 (424)
Q Consensus 229 ~-~~~~~~~~i~~~~~~~~~~~~d~~al~ll~~iLg~g~sSrL~~~lRe~~glaY~v~s~~~~~~-~~g~~~i~~~~~~~ 306 (424)
T Consensus 649 ~la~~gge~ALLlF~PlP~a~~a~eAAwRLLA~l~e----~~F~qRLRVElQlGY~Vf~~~r~va~R~GLL-fa~QSP~~ 723 (737)
T TIGR02110 649 ELAVDGGESALLLFCPLPTADVASEAAWRLLAQLLE----PPFFQRLRVELQLGYAVFSRYRRVADRDGLL-FAVQSPDA 723 (737)
T ss_pred ECCCCCCCCEEEEECCCCCCCCHHHHHHHHHHHHHC----CHHHHHHHHHHHHHHHHHHHHHHCCCCCCHH-HCCCCCCC
T ss_conf 445687765276431788998453799999998716----3100122477788677764233203654011-10458300
Q ss_pred HHHHHHHHHHHH
Q ss_conf 247778778999
Q gi|254780464|r 307 NIMALTSSIVEV 318 (424)
Q Consensus 307 ~~~~~~~~i~~~ 318 (424)
T Consensus 724 ~~~~LL~H~~~F 735 (737)
T TIGR02110 724 SAAELLQHIKTF 735 (737)
T ss_pred HHHHHHHHHHHH
T ss_conf 089999999986