HHsearch alignment for GI: 254780899 and conserved domain: TIGR00501

>TIGR00501 met_pdase_II methionine aminopeptidase, type II; InterPro: IPR002468 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 M24 (clan MG), subfamily M24A. Methionine aminopeptidase (3.4.11.18 from EC) (MAP) is responsible for the removal of the amino-terminal (initiator) methionine from nascent eukaryotic cytosolic and cytoplasmic prokaryotic proteins if the penultimate amino acid is small and uncharged. All MAP studied to date are monomeric proteins that require cobalt ions for activity. Two subfamilies of MAP enzymes are known to exist , . While being evolutionary related, they only share a limited amount of sequence similarity mostly clustered around the residues shown, in the Escherichia coli MAP , to be involved in cobalt-binding. The first family consists of enzymes from prokaryotes as well as eukaryotic MAP-1, while the second group (IPR002467 from INTERPRO) is made up of archaeal MAP and eukaryotic MAP-2 and includes proteins which do not seem to be MAP, but that are clearly evolutionary related such as mouse proliferation-associated protein 1 and fission yeast curved DNA-binding protein. ; GO: 0004239 methionyl aminopeptidase activity, 0006508 proteolysis.
Probab=100.00  E-value=4.7e-38  Score=274.30  Aligned_cols=236  Identities=24%  Similarity=0.383  Sum_probs=201.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHC-CCC-------CCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             99999999999999999999997579988999999999999985-983-------0344332444553234464211121
Q gi|254780899|r   18 EELENIRSACNVVARCLDSLTPIIKPGTTTEEIDDFVLKFGMEN-NAI-------PATLNYRGYKKSCCTSINHVICHGI   89 (273)
Q Consensus        18 ~EI~~~R~A~~i~~~~~~~~~~~i~~G~se~el~~~~~~~~~~~-g~~-------~~~~~~~~f~~~~~~s~N~~~~H~~   89 (273)
T Consensus         6 E~~nD~~aGakI~~~vr~ea~~~I~PG~klleva~fvEnri~e~tGa~nllameDPksqG-iAFP~--n~S~N~~AAHfT   82 (327)
T TIGR00501         6 EKLNDIEAGAKIVSKVRREAADRIVPGVKLLEVAEFVENRIRELTGAENLLAMEDPKSQG-IAFPC--NISINEVAAHFT   82 (327)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCHHHCCCCCCCC-CCCCC--CCCHHCCCCCCC
T ss_conf             446777744799999999998526788612122121210121220641001103863255-22556--751213010168


Q ss_pred             C---CCCCCCCCEEEEEEEEEEEEEECCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHH
Q ss_conf             2---2220013405799787665300023111233344443210367787765432211001121221048999999986
Q gi|254780899|r   90 P---SNKQLREGDIVNVDVTYVVNGWHGDSSRMYPVGKIKRAAERILQVTYESLYKGIAAVKLNANIEDIGKAIQRYAHS  166 (273)
Q Consensus        90 p---~d~~l~~GD~v~iD~g~~~~GY~~D~~RT~~~G~~~~~~~~l~~~~~~a~~~~i~~ikpG~~~~ei~~a~~~~~~~  166 (273)
T Consensus        83 p~~gD~~~~k~~DvvKlD~GahvdGyIaD~A~TV~l~~~ddky~~L~~A~~dAl~~~i~~~~~~v~v~eiG~~I~e~i~s  162 (327)
T TIGR00501        83 PKAGDETVFKDGDVVKLDLGAHVDGYIADTAITVDLGDQDDKYKELVKAAKDALYTAIKEIRAGVEVGEIGKAIEEVIES  162 (327)
T ss_pred             CCCCCCCCCCCCCEEEEEECCEECCEEEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCCEEECCCHHHHHHHCC
T ss_conf             68888631277876887522066557870478850688701589999999999887775006981260020776653221


Q ss_pred             ---------CCCEECCCCCCCCCCCC-CCCCCEEEECCCCCCCCCCEECCCCEEEECCEEECCCCCCEECC---------
Q ss_conf             ---------29601047521233221-13540365315645456645116737883111443777625646---------
Q gi|254780899|r  167 ---------ERYSVVEVFCGHGIGKS-FHEKPEILHFYDPLYPSVGTFQEGMVFTIEPMLNVGGSSAKVLS---------  227 (273)
Q Consensus       167 ---------~g~~~~~~~~GHgiGl~-~hE~P~i~~~~~~~~~~~~~le~GMV~aiEP~i~~~~~~~~~~~---------  227 (273)
T Consensus       163 yeveinGetYg~kP~~NL~GHs~~rY~~H~G~SiPn~~~---~~~~~leeG~~~AIEpFAt~G~G~V~~~~~~~iY~~l~  239 (327)
T TIGR00501       163 YEVEINGETYGVKPISNLTGHSMARYLLHAGLSIPNVKE---RDTTKLEEGDVVAIEPFATDGVGLVTDGGEVEIYKFLA  239 (327)
T ss_pred             EEEEECCCCCCCCCCCCCCCCCCCHHHHCCCCCCEEEEC---CCCCEEECCCEEEECCCCCCCEEEEECCCCCHHHHHHC
T ss_conf             357765720143342227356400154358950003427---98745102578884366768745651288610122105


Q ss_pred             -------------------------------------------------------CCCEEEE-CCCCEEEEEEEEEEECC
Q ss_conf             -------------------------------------------------------8866883-37871678442189847
Q gi|254780899|r  228 -------------------------------------------------------DGWTAVT-RDRSLSAQYEHTIGITK  251 (273)
Q Consensus       228 -------------------------------------------------------d~w~~~~-~~g~~~~~~Ed~vlVT~  251 (273)
T Consensus       240 ~DrpvrPtL~~Ar~lL~~i~~nY~~LPFA~RwL~~~~~~Kr~~~~l~~L~r~~~~~~YPvL~e~~G~~vaQ~EHTilv~~  319 (327)
T TIGR00501       240 EDRPVRPTLKSARKLLKKIEENYKTLPFAKRWLEKLEDEKRLRLALNKLIREGVIYDYPVLKEKSGGLVAQWEHTILVEE  319 (327)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEEEEEEEEC
T ss_conf             68896733589999876786640788247889752333026899999988733334788752478874523245889964


Q ss_pred             CCCEECCC
Q ss_conf             98576526
Q gi|254780899|r  252 AGCEIFTL  259 (273)
Q Consensus       252 ~G~E~LT~  259 (273)
T Consensus       320 ~g~~v~tk  327 (327)
T TIGR00501       320 DGVEVTTK  327 (327)
T ss_pred             CCEEEEEC
T ss_conf             83468509