HHsearch alignment for GI: 254781026 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=98.91  E-value=1.9e-09  Score=76.27  Aligned_cols=123  Identities=24%  Similarity=0.379  Sum_probs=77.2

Q ss_pred             CCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHCEEECCCCCCCCCCCCCCCEEECCCCCCCHHHCCCCCCCCCHHHHHH-
Q ss_conf             9777860599999998874889897885323000000278887565311120203775210011023434568279982-
Q gi|254781026|r    1 MIGPPGARKSMLASCLPSILLPLSLEESLEVSMIYSISGHSSHEYSFIQNRPFRSPHHSVTIAALIGGGLQVLPGEDSL-   79 (186)
Q Consensus         1 l~GpPG~GKS~lar~l~~iLP~l~~~e~le~~~i~s~~g~~~~~~~~~~~~p~~~~~~~~~~~~l~gg~~~~~pG~i~l-   79 (186)
T Consensus       455 lvGPPGVGKTSlg~SIA~ALnR---------kFvR~SlGG~~DeAEIrGHRR-----------TYv----GAMPGriiQ~  510 (941)
T TIGR00763       455 LVGPPGVGKTSLGKSIAKALNR---------KFVRFSLGGVRDEAEIRGHRR-----------TYV----GAMPGRIIQG  510 (941)
T ss_pred             EECCCCCCHHHHHHHHHHHHCC---------EEEEEEECCCEEHHHCCCCCC-----------CCC----CCCHHHHHHH
T ss_conf             2072695422278999999688---------049995267220311278643-----------203----4672578999


Q ss_pred             -----CCCCEEEEECHHHCC--HHHH----HHHHHHHHCCCE---EEHHCCEEEEECCCEE--EEEECCCCCCCCCCCCC
Q ss_conf             -----799889980387859--8899----999999971952---3010030789847015--67522746588788988
Q gi|254781026|r   80 -----AHNGVLFLDEIPEFS--PQTL----NALRQPLETGEC---IIARANRKISYPSRIQ--LIAAMNPCRCGMSNKDE  143 (186)
Q Consensus        80 -----Ah~GVLflDE~~e~~--~~~l----~~L~~~le~g~v---~i~R~g~~~~~Pa~f~--Lvaa~NPcpcG~~~~~~  143 (186)
T Consensus       511 lk~~~t~NPl~LlDEIDK~~~~~~~~GDPaSALLEvLDPEQN~~F~DHYldvp~DL-S~V~CyFi~TAN~~---------  580 (941)
T TIGR00763       511 LKKAKTKNPLILLDEIDKIGLKSSFRGDPASALLEVLDPEQNNAFSDHYLDVPFDL-SKVLCYFIATANSI---------  580 (941)
T ss_pred             HHHCCCCCCEEEEEEEEEECCCCCCCCCHHHHHHHHCCHHHCCCCCCCCCCCCCCH-HHHHHHEEECCCCC---------
T ss_conf             87604158806862022001678865563788864128643604255300234004-20021000244757---------


Q ss_pred             CCCCCCHHHHHHHHHHCCHHHHHCCCEE
Q ss_conf             7643899999999851224321004259
Q gi|254781026|r  144 NVCIRGPRCATEYQARISGPLMDRIDIR  171 (186)
Q Consensus       144 ~~c~c~~~~~~~Y~~rls~plldR~Dl~  171 (186)
T Consensus       581 --------------d~IP~PLLDRMEvI  594 (941)
T TIGR00763       581 --------------DTIPRPLLDRMEVI  594 (941)
T ss_pred             --------------CCCCCCCCCCEEEE
T ss_conf             --------------67772213740245