HHsearch alignment for GI: 254780627 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=94.28  E-value=0.029  Score=36.07  Aligned_cols=175  Identities=19%  Similarity=0.254  Sum_probs=110.4

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCCCEEEEEHHHHH---------HHHHHHHHCCCHHHHHHHHHHCCHHHHHHHH
Q ss_conf             8986278888579999999999863068816864698889---------9999998619889999997403102054444
Q gi|254780627|r  199 LFIHASVGLGKTHLLQAIANASIKRQPNLRVVYLTAEYFM---------WRFASAIRDNCALNLKDSLRNIDLLLIDDMQ  269 (502)
Q Consensus       199 Lfi~G~~GlGKTHLl~ai~~~~~~~~~~~~v~y~~~e~F~---------~~~~~a~~~~~~~~fr~~~r~~DvLliDDiq  269 (502)
T Consensus       453 lClvGPPGVGKTSlg~SIA~ALnRkF-----vR~SlGG~~DeAEIrGHRRTYvGAMPGriiQ~lk~~~t~NPl~LlDEID  527 (941)
T TIGR00763       453 LCLVGPPGVGKTSLGKSIAKALNRKF-----VRFSLGGVRDEAEIRGHRRTYVGAMPGRIIQGLKKAKTKNPLILLDEID  527 (941)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHCCEE-----EEEEECCCEEHHHCCCCCCCCCCCCHHHHHHHHHHCCCCCCEEEEEEEE
T ss_conf             87207269542227899999968804-----9995267220311278643203467257899987604158806862022


Q ss_pred             HHC--C----C-C-HHHHHH-----HHHHH-----HHHCCCEE-EEECCCCHHHHCCCCHHHHHHHHCCEEEEECCCCHH
Q ss_conf             531--7----5-0-699999-----99999-----88569879-996487567613630345765302115775158889
Q gi|254780627|r  270 FLQ--G----K-L-IQHEFC-----HLLNS-----LLDSAKQV-VAAADRPPSELESLDPRIRSRLQGGVSVPLGLHDYE  330 (502)
Q Consensus       270 fl~--g----k-~-tqee~f-----~~~n~-----l~~~gkqi-v~tsd~~P~~l~~l~~rL~SR~~~Gl~~~i~~Pd~e  330 (502)
T Consensus       528 K~~~~~~~~GDPaSALLEvLDPEQN~~F~DHYldvp~DLS~V~CyFi~T--AN~~d~IP~PLLDRME---vI~lsGY~~~  602 (941)
T TIGR00763       528 KIGLKSSFRGDPASALLEVLDPEQNNAFSDHYLDVPFDLSKVLCYFIAT--ANSIDTIPRPLLDRME---VIELSGYTEE  602 (941)
T ss_pred             EECCCCCCCCCHHHHHHHHCCHHHCCCCCCCCCCCCCCHHHHHHHEEEC--CCCCCCCCCCCCCCEE---EEECCCCCHH
T ss_conf             0016788655637888641286436042553002340042002100024--4757677722137402---4523888767


Q ss_pred             HHHHHHHHHHHH-----HHHHCCCCCCCHHHHHHHHHHCCC--CHHHHHHHHHHHHHHHH
Q ss_conf             999999999988-----643116897898999999850278--88999999999999863
Q gi|254780627|r  331 MRFSILKNRLAI-----SQKEDPKLNINEEVLMHVARTVTT--SGRELDGAFNQLVFRHS  383 (502)
Q Consensus       331 ~r~~Il~~k~~~-----~~~~~~~~~l~~~v~~~la~~~~~--~vR~Legal~~l~~~~~  383 (502)
T Consensus       603 EK~~IA~~yLiP~~~~~~GL~~~~l~~~d~al~~lI~~YtREaGVRNL~r~I~~i~RK~A  662 (941)
T TIGR00763       603 EKLEIAKKYLIPKALEDHGLKPDELKISDEALLLLIKYYTREAGVRNLERQIEKICRKAA  662 (941)
T ss_pred             HHHHHHHHCCHHHHHHHHCCCCCCEEECHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHH
T ss_conf             899999854713679870888132212689999999875132021338999999999999