HHsearch alignment for GI: 254780444 and conserved domain: TIGR00498

>TIGR00498 lexA LexA repressor; InterPro: IPR006200 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 group of proteins are serine peptidases belong to MEROPS peptidase S24 (LexA family, clan SF). The family contains the LexA proteins. LexA represses around 20 genes of the cellular SOS response to DNA damage in Escherichia coli . Damage to cellular DNA results in inactivation of LexA, allowing transcription of the genes involved in DNA repair. In E. coli, this derepression of the DNA repair system is mediated by RecA, which binds to LexA upon interaction with single-stranded DNA. This results in inactivation of LexA by proteolytic self cleavage, disrupting the DNA-binding capabilities of LexA. LexA consists of around 200 amino acids, of which the first 90 form the DNA-binding domain. The remaining residues form the protease domain, Ser-119 and Lys-156 being the active residues. The crystal structures of the wild type and several mutant forms of LexA reveal two distinct conformations: one compatible with cleavage, and the other in which the cleavage site is approximately 20 A from the catalytic centre. It is suggested that recA activates the self-cleavage of LexA and related proteins through selective stabilisation of the cleavable conformation .; GO: 0008992 repressor LexA activity, 0006508 proteolysis.
Probab=98.63  E-value=2.1e-07  Score=67.99  Aligned_cols=207  Identities=16%  Similarity=0.203  Sum_probs=124.8

Q ss_pred             CCCCC--HHHHHHHHHHHHHHCCCCH--HHHHHHHCCCHHH-HHH-HHHCCCCCCC-CCCCHHHHHHHHHHCCCCCCCCC
Q ss_conf             97755--8999999999999649998--8999982899879-889-9751578875-57798999998732187521000
Q gi|254780444|r    1 MTSFS--HKKIWEAIDRMAERHNLTP--SGLARKAGLDPTS-FNK-SKRFGIEGRN-RWPSTESIFKILAATNETICQLL   73 (223)
Q Consensus         1 ~~~~~--~~~i~~~i~~l~~~~gls~--~~lA~~~Gv~~~t-i~~-~~~~~~~g~~-r~p~~~~l~kia~~~~v~~~~l~   73 (223)
T Consensus         1 ~~~l~~~~~~~~~~~~~~~~~~g~pp~~~~~~~~~~~~~~~~~~~~l~~l~~~g~~~~~~~~~~~~~~~~~~~~~~~~gp   80 (227)
T TIGR00498         1 LKPLTERQREVLDLLKAHIESTGYPPSVREIARALGLTSPSAAEEHLKALERKGYIERDPGKPRALRILDNEEEDEPEGP   80 (227)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCCHHHHHHHHHHHHCCCEEECCCCCCEEEECCCCCHHHCCCH
T ss_conf             94024788999999998765148870178898873355730478898887644741223775311211011000000230


Q ss_pred             CCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCEEEEEECCCCCCC-CCC
Q ss_conf             0111124445442212202431011345222111254446403564372113545420036855999962833242-148
Q gi|254780444|r   74 DLPFSDGRTTEKKEKEIPLLYFPPSGSGGFFDSGVFPTGNKWNTVGVPEIRSPHNGIYAIQTQDTRHKTQDTSMLP-LYR  152 (223)
Q Consensus        74 ~~~~~~~~~~~~~~~~ip~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~l~V~GDSM~P-~i~  152 (223)
T Consensus        81 ~~~~~~~~~~~p~p~~~p~~g~~~~g~p~~~------~~~~~~~~~~~~~~------~~~~~~~~~l~~~g~~~~~~~~~  148 (227)
T TIGR00498        81 AVLTEVAGDVLPEPTFVPLIGRVAAGEPLLA------EEHLEDYFPLPESL------LKPPGAVFLLKVLGDSLVDAGIL  148 (227)
T ss_pred             HHHHHHHHHHCCCCCHHHHHHCCCCCCCHHH------HHHHHHHHCCCHHH------CCCCCCEEEEEECCCHHHHHHHC
T ss_conf             5677766531377420011100025762011------33223332044223------27875225665414202232211


Q ss_pred             CCCEEEEECCC---CCCCCCEEEEEEECCCEEEEEEEEECCCEEEEEECCCCCCCEEECHHH--EEEEEEEEE
Q ss_conf             78689993689---740588899997179689999999779879999685898875854786--599977998
Q gi|254780444|r  153 KGDILILNSAI---QVNCGDRLLIKPRTGDIVAKVLISRRGRSIDLMSLNCCYPVDTVEMSD--IEWIARILW  220 (223)
Q Consensus       153 ~Gd~vlVd~~~---~~~~g~~v~~~~~~~~~~iKrl~~~~~~~~~l~s~Np~y~~~~i~~~~--i~iigrVvw  220 (223)
T Consensus       149 ~gd~~~~~~~~g~~~~~~g~~~~~~~~~~~~~~~~~~~-~g~~~~l~~~~~~~~~~~~~~~~~~~~~~g~~~g  220 (227)
T TIGR00498       149 DGDLLLVRSQKGEEDAENGEIVAARIKDGEVTVKRFYK-EGTKVELKPENPEFDPIVLNAEDQNVEILGKVVG  220 (227)
T ss_pred             CCCEEEEECCCCCCCCCCCCEEEEEECCCCHHHHHHHC-CCCEEEEEECCCCCCCCEECCCCCCEEEHHHEEE
T ss_conf             44344764045510003673688862365011232320-5876898655755575010132223000110000