HHsearch alignment for GI: 254780829 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=99.26  E-value=1.8e-10  Score=87.29  Aligned_cols=245  Identities=21%  Similarity=0.284  Sum_probs=145.1

Q ss_pred             HHHHHHCEECHHHHHHH----HHHHHHHHHHHHCCCCCCCCCCCCC-CEEEECCCCCCHHHHHHHHHHHHCCCEEEEECC
Q ss_conf             99862030486899999----9999987788640864444665668-669967988868999999999707877971434
Q gi|254780829|r   13 VSELDRYIIGQQDAKRA----VAIALRNRWRRQQLPADLRDELMPK-NILLVGPTGVGKTAISRRLARLAGAPFIKVEVT   87 (437)
Q Consensus        13 ~~~Ld~~VvGQ~~AKk~----lavav~nhy~R~~~~~~~~~e~~ps-NiLLiGPtGtGKTlLAktLA~~l~VPF~~~daT   87 (437)
T Consensus       406 ~~~LD~DHYGL~~VK~RIlEYlAV~qllemrrkkk-PkL~~~~~GpqIlClvGPPGVGKTSlg~SIA~ALnRkFvR~Sl-  483 (941)
T TIGR00763       406 KEILDEDHYGLKKVKERILEYLAVQQLLEMRRKKK-PKLRGKMKGPQILCLVGPPGVGKTSLGKSIAKALNRKFVRFSL-  483 (941)
T ss_pred             HHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCC-CCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHCCEEEEEEE-
T ss_conf             99831678888773034135888989998764036-4447788887678720726954222789999996880499952-


Q ss_pred             CEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHCCCCCCEEEE
Q ss_conf             10121223431013467888765212789985654988886888755553114321100466898898616888854998
Q gi|254780829|r   88 KFTEIGYVGRNVEQIIRDLVDVAINIVRESRRDEVREQASINAEERILDALVGKTATSNTREVFRKKLRDGEISDKEIDI  167 (437)
Q Consensus        88 ~ftE~gyvG~DVes~i~~l~~~a~~~~~~a~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~i~i  167 (437)
T Consensus       484 -----G------------------G~~DeA------------------------------------------------EI  492 (941)
T TIGR00763       484 -----G------------------GVRDEA------------------------------------------------EI  492 (941)
T ss_pred             -----C------------------CCEEHH------------------------------------------------HC
T ss_conf             -----6------------------722031------------------------------------------------12


Q ss_pred             EECCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCEEEEEHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             75355455443346676663210001101001354322100000102355332788863031011123678887532221
Q gi|254780829|r  168 EVADTSSDISNFDIPGGASVGILNLSELFSKVMGSGRKKKIRMSVQKCYPELMRDESDRLIDMDTVHRDSIQMVENYGIV  247 (437)
Q Consensus       168 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~  247 (437)
T Consensus       493 --------------------------------------rGHRRTYvGAMPGriiQ~lk~-------------~~t~NPl~  521 (941)
T TIGR00763       493 --------------------------------------RGHRRTYVGAMPGRIIQGLKK-------------AKTKNPLI  521 (941)
T ss_pred             --------------------------------------CCCCCCCCCCCHHHHHHHHHH-------------CCCCCCEE
T ss_conf             --------------------------------------786432034672578999876-------------04158806


Q ss_pred             HCCCCCHHC-CCCCCCCCCCCCCCHHHHHH-HCCCCCCCCC--CCC--CCCCCHHH--HHHCCCCCCCCCCCCCCCCCCC
Q ss_conf             002221001-35766565433210122343-2046652211--246--66420246--6401675422112125543345
Q gi|254780829|r  248 FLDEFDKIV-ARDSGNGIGVSREGVQRDLL-PLVEGSSVST--KYG--SINTDHIL--FIASGAFHVSRPADLLPEIQGR  319 (437)
Q Consensus       248 f~~~~~ki~-~~~~~~~~~~~~~g~~~~~~-~~~e~~~v~~--~~~--~~~~~~~~--~i~~~~~~~~k~~glipE~~GR  319 (437)
T Consensus       522 LlDEIDK~~~~~~~~G--DPa-----SALLEvLDPEQN~~F~DHYldvp~DLS~V~CyFi~TAN~-----~d~IP~PLLD  589 (941)
T TIGR00763       522 LLDEIDKIGLKSSFRG--DPA-----SALLEVLDPEQNNAFSDHYLDVPFDLSKVLCYFIATANS-----IDTIPRPLLD  589 (941)
T ss_pred             EEEEEEEECCCCCCCC--CHH-----HHHHHHCCHHHCCCCCCCCCCCCCCHHHHHHHEEECCCC-----CCCCCCCCCC
T ss_conf             8620220016788655--637-----888641286436042553002340042002100024475-----7677722137


Q ss_pred             CEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEECHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHH
Q ss_conf             12688615542467888764346889999999987519689984249999999999840400123724679999998677
Q gi|254780829|r  320 FPVRVHLKSLNKSDFRLILTDTESNLILQYKELMKTEGIILDFTEDSIDALADVAVNLNSTVGDIGARRLQTVMERVLED  399 (437)
Q Consensus       320 ~p~~v~l~~L~~~~l~~IL~epk~~l~~q~~~lf~~~~v~L~ft~~Al~~IA~~A~~~~t~~~~~GAR~LrtI~E~~l~d  399 (437)
T Consensus       590 RMEvI~lsGY~~~EK~~IA---~~yLiP~~~~~~GL~~~~l~~~d~al~~lI~~Yt-R-----EaGVRNL~r~I~~i~RK  660 (941)
T TIGR00763       590 RMEVIELSGYTEEEKLEIA---KKYLIPKALEDHGLKPDELKISDEALLLLIKYYT-R-----EAGVRNLERQIEKICRK  660 (941)
T ss_pred             CEEEEECCCCCHHHHHHHH---HHCCHHHHHHHHCCCCCCEEECHHHHHHHHHHHH-H-----HHCCHHHHHHHHHHHHH
T ss_conf             4024523888767899999---8547136798708881322126899999998751-3-----20213389999999999


Q ss_pred             HHC
Q ss_conf             621
Q gi|254780829|r  400 ISF  402 (437)
Q Consensus       400 ~~f  402 (437)
T Consensus       661 ~A~  663 (941)
T TIGR00763       661 AAV  663 (941)
T ss_pred             HHH
T ss_conf             999