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