HHsearch alignment for GI: 254780810 and conserved domain: TIGR00763

>TIGR00763 lon ATP-dependent protease La; InterPro: IPR004815 Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases . Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) , . 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 signature defines the bacterial and eukaryotic lon proteases, which are ATP-dependent serine peptidases belonging to the MEROPS peptidase family S16 (lon protease family, clan SF). This family of sequences does not include the archaeal lon homologs, IPR004663 from INTERPRO. In the eukaryotes the majority of the proteins are located in the mitochondrial matrix , . In yeast, Pim1, is located in the mitochondrial matrix, is required for mitochondrial function, is constitutively expressed but is increased after thermal stress, suggesting that Pim1 may play a role in the heat shock response .; GO: 0004176 ATP-dependent peptidase activity, 0005524 ATP binding, 0006510 ATP-dependent proteolysis.
Probab=96.33  E-value=0.0025  Score=41.02  Aligned_cols=267  Identities=22%  Similarity=0.241  Sum_probs=150.4

Q ss_pred             CHHHHHHHHH--HCCCCCCCCCCHHHHHHHHHHHHHHCCCEEEEE------------EEEEEECCCCEEEEECCCCCCCC
Q ss_conf             9899999999--838988576667899999998752058748999------------99854047702675045486666
Q gi|254780810|r   13 SPTKLLAFAE--SLEIENANVMRKQELMFSILKVLSGRDVEIIGE------------GVIEVLQDGFGFLRSPDANYLAG   78 (423)
Q Consensus        13 ~l~EL~eiAk--elgIe~~~~l~K~eLI~~Il~~~~~~~g~~~~e------------GvLEIl~dGyGFLR~~~~~yl~~   78 (423)
T Consensus       312 L~EQLKaIkkyhELG~~~---d~~~~~~~~~~~kle~~~e~~P~~~~k~~~~El~kL~~l~~~SsE~~v~R----nYL--  382 (941)
T TIGR00763       312 LREQLKAIKKYHELGIEK---DDKDELIEKLKEKLEELKEFLPEEVKKVIEKELTKLELLEPSSSEFTVTR----NYL--  382 (941)
T ss_pred             HHHHHHHHHHHHHCCCCC---CCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCCCCHHHHH----HHH--
T ss_conf             888999988875258999---86478999999998740574774689999999987505883353046799----999--


Q ss_pred             CCCCEEECCCCCCCCCCCCCEEEEEEEECCCCCCCCCCEEECCCC--CCCHHHHHCCCCHHHCCCCCCCCCCCCCCCCCC
Q ss_conf             556046010000122125987999886246888763000222255--688788512443000200011223432477865
Q gi|254780810|r   79 PDDIYVSPSQIKSFSLKTGDTVEGSIRAPREGERYFALLKVNAIN--FDVPERVRNKIHFDNLTPLYPDKRFNMELNNPE  156 (423)
Q Consensus        79 ~~DiyVs~slir~f~Lr~GD~V~g~~r~~~~~~~~~~L~rV~~vn--G~~~d~~~~~~~f~~l~p~~p~~~i~le~~~~~  156 (423)
T Consensus       383 --Dwl~~-----------------------lP---W~--~-~S~~f~n~Dl~~A~~~LD~DHYGL~~VK~RIlEYlAV~q  431 (941)
T TIGR00763       383 --DWLTD-----------------------LP---WG--K-YSKEFDNLDLKRAKEILDEDHYGLKKVKERILEYLAVQQ  431 (941)
T ss_pred             --HHHHH-----------------------CC---CC--C-CCCHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHH
T ss_conf             --99983-----------------------77---22--1-470266521899999831678888773034135888989


Q ss_pred             CCCHHHHHHHHHHHHHCCC-CEEEECCCCCCHHHHHHHHHHHHHHCCCCCEEEEEECCCCHHHHHHHHHHHCCEEEECCC
Q ss_conf             3213688899886551023-122204877878999999999986118864699995087878999999840342782366
Q gi|254780810|r  157 NKDISSRVIDLIAPIGKGQ-RSLIVAPPRTGKTILLQNIAHSIKKNHPECYLIVLLIDERPEEVTDMQRSVQGEVISSTF  235 (423)
Q Consensus       157 p~~~~~~~id~~~pig~gq-r~~i~~~~~~gkt~ll~~ia~~~~~~~~~v~~i~~ligEr~~ev~e~~~~~~~~vv~st~  235 (423)
T Consensus       432 llemrrkkkPkL~~~~~GpqIlClvGPPGVGKTSlg~SIA~ALnRkF---vR~--SlGG~-~DeAEIrGHRRTYvGA---  502 (941)
T TIGR00763       432 LLEMRRKKKPKLRGKMKGPQILCLVGPPGVGKTSLGKSIAKALNRKF---VRF--SLGGV-RDEAEIRGHRRTYVGA---  502 (941)
T ss_pred             HHHHHHHCCCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHCCEE---EEE--EECCC-EEHHHCCCCCCCCCCC---
T ss_conf             99876403644477888876787207269542227899999968804---999--52672-2031127864320346---


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECHHHHH--HHHHCCCCCCCCCCCCCCCHHHH-H--------------
Q ss_conf             788889999999999999999977992899981638987--76200136677767775202466-5--------------
Q gi|254780810|r  236 DESAARHVQVAEMVIAKAKCLVEYGLDVVILLDSITRLC--RAYNVLMPSSGKILTGGVDANAL-Q--------------  298 (423)
Q Consensus       236 d~~~~~~~~~a~~a~~~a~~~~e~G~dVll~~DslTR~A--rA~~~~~~~~g~~~~gg~~~~~l-~--------------  298 (423)
T Consensus       503 --MPGriiQ~----lk~~-----~t~NPl~LlDEIDK~~~~~~~------------~GDPaSALLEvLDPEQN~~F~DHY  559 (941)
T TIGR00763       503 --MPGRIIQG----LKKA-----KTKNPLILLDEIDKIGLKSSF------------RGDPASALLEVLDPEQNNAFSDHY  559 (941)
T ss_pred             --CHHHHHHH----HHHC-----CCCCCEEEEEEEEEECCCCCC------------CCCHHHHHHHHCCHHHCCCCCCCC
T ss_conf             --72578999----8760-----415880686202200167886------------556378886412864360425530


Q ss_pred             ------HCHHH--HHCCCCCCCCCCCEEEEEEEECCCCCC-----CCHHHHHHHHCCCCEEEEEHHHHHCCCCCC
Q ss_conf             ------04687--522577777785001211201267655-----413889885226607898087884799974
Q gi|254780810|r  299 ------RPKRF--FGAARNIKEGGSLTIIGTALVDTGSRM-----DEVIFEEFKGTGNSEIVLERKIADKRIFPA  360 (423)
Q Consensus       299 ------~~~~~--~~~ar~~~~~Gs~T~~~t~lvetg~~~-----d~~i~~~~~~~~d~~i~L~r~la~~~~~PA  360 (423)
T Consensus       560 ldvp~DLS~V~CyFi~TA-----N~~d~IP~PLLD---RMEvI~lsGY~~~EK~~IA~~yLi-P~~~~~~GL~~~  625 (941)
T TIGR00763       560 LDVPFDLSKVLCYFIATA-----NSIDTIPRPLLD---RMEVIELSGYTEEEKLEIAKKYLI-PKALEDHGLKPD  625 (941)
T ss_pred             CCCCCCHHHHHHHEEECC-----CCCCCCCCCCCC---CEEEEECCCCCHHHHHHHHHHCCH-HHHHHHHCCCCC
T ss_conf             023400420021000244-----757677722137---402452388876789999985471-367987088813