HHsearch alignment for GI: 254780334 and conserved domain: TIGR02239

>TIGR02239 recomb_RAD51 DNA repair protein RAD51; InterPro: IPR011941 Homologous recombination is an evolutionarily conserved mechanism for the repair of double-strand breaks in DNA and the generation of genetic diversity. The primary function of homologous recombination in mitotic cells is to repair double-strand breaks or single-strand gaps that form as a result of replication fork collapse, from processing of spontaneous damage, and from exposure to DNA-damaging agents. During meiosis, homologous recombination is essential to establish a physical connection between homologous chromosomes to ensure their correct disjunction at the first meiotic division. In addition, the high frequency of meiotic recombination contributes to diversity by creating new linkage arrangements between genes, or parts of genes . The central step of homologous recombination is synapsis, the process of bringing together the two homologous strands. Rad51, a eukaryotic homologue of the prokaryotic recombinase RecA, mediates this process in eukaryotes . Firstly a single-stranded DNA tail is coated by ATP-bound Rad51 to yield a nucleoprotein filament. This filament then searches for a homologous sequence within double-stranded DNA, and catalyses the exchange of strands between the single-stranded and double-stranded DNA substrates. The original broken end of the resulting branched DNA is now aligned with an appropriate matching sequence in an intact duplex, and is further processed by other enzymes . Rad51 contains an N-terminal alpha-helical DNA binding domain not found in RecA, and a RecA-like C-terminal ATPase domain , . The active form of this protein is a long helical filament where the catalytically active unit is a homodimer . ; GO: 0003684 damaged DNA binding, 0005524 ATP binding, 0008094 DNA-dependent ATPase activity, 0006281 DNA repair.
Probab=99.20  E-value=5e-11  Score=99.98  Aligned_cols=210  Identities=23%  Similarity=0.341  Sum_probs=147.2

Q ss_pred             CCCCCCCCCCCCHHHHHHHCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHH------CCCCCEEEEECCCCHHH--HHHH
Q ss_conf             455666323781248888659857870899954987518899999999985------03981999986463047--8888
Q gi|254780334|r   65 SIEEESRIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLA------YKKHRITYVSGEEAIGQ--IRLR  136 (479)
Q Consensus        65 ~~~~~~Ri~TGi~eLDrvLGGGl~~Gs~~Li~G~PGvGKSTL~Lqia~~~a------~~g~~vlYvS~EEs~~Q--i~~R  136 (479)
T Consensus        71 ~r~~~~~~~~Gs~~ld~~l~GG~e~Gsite~fGefr~Gk~q~Cht~~vtCql~~~~~G~~G~~lyid~e~tfr~~rl~~~  150 (317)
T TIGR02239        71 KRKEVIQLTTGSKELDKLLEGGIETGSITEIFGEFRTGKTQLCHTLAVTCQLPVDQGGGEGKALYIDTEGTFRPERLLAI  150 (317)
T ss_pred             HHHHHEECCCCHHHHHHHHCCCCCCCCHHHHHCCCCCCCHHHHHHEEEEEEECCCCCCCCCCEEEEECCCCCCHHHHHHH
T ss_conf             77654121035068999860875545032211000166202210011345301236787631688725653106899999


Q ss_pred             HHHCCCCCCCHH----EECCCCHHHH------HHHHHHCCCCCEEEECHHHHHHHHHHCCCCCCHH--H--HHHHHHHHH
Q ss_conf             752015775100----0034788999------9999731698289972168766542044556367--9--999999999
Q gi|254780334|r  137 AQRLNTINSSVY----IAIETNVEDI------IATLITNEKPDLVIIDSIQTLWSQTAESSPGTVI--Q--VRTSVQAMI  202 (479)
Q Consensus       137 a~Rl~~~~~~i~----~~~e~~l~~i------l~~~i~~~~~~~vVIDSIQtl~~~~~~s~~Gsvs--Q--vre~~~~L~  202 (479)
T Consensus       151 a~r~~l~~~~~l~nv~~ara~n~d~q~~ll~~a~~~~~~~~~~l~~vds~~alyr~d~~Gr-gel~~rq~~l~~flr~l~  229 (317)
T TIGR02239       151 AERYGLNGEDVLDNVAYARAYNTDHQLKLLLQAAALMAESRYALLIVDSATALYRTDYSGR-GELSARQMHLAKFLRSLQ  229 (317)
T ss_pred             HHHHCCCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHCCCEEEEHHHHHHHHHCCCCCC-HHHHHHHHHHHHHHHHHH
T ss_conf             9862688778888878876504168999999999988627721451133567763035550-458899999999999999


Q ss_pred             HHHHHCCCEEEEEEEECC--CCCC----C-------CHHHHHHHHHEEEEEECCCCCCCCCCEEEEEEEECCCCCCCEEE
Q ss_conf             975307978999863036--6543----3-------11457877530278515556665442156763202567651279
Q gi|254780334|r  203 QYAKKNGVAMVLVGHVTK--EGQI----A-------GPRVIEHMVDAVLYFEGGTRNTQYDYRILRSVKNRFGPTDEIGV  269 (479)
Q Consensus       203 ~~AK~~~i~vilighvTK--~G~i----A-------Gp~~LeH~VD~vl~~ege~~~~~~~~R~Lr~~KNRfG~t~e~gv  269 (479)
T Consensus       230 ~la~~f~vav~~tnqv~~~~dG~~~~~~~~~~~kPiGG~i~ah~s~trl~l~k----G~G~~r~~k~~~sP~l~~~~~-~  304 (317)
T TIGR02239       230 RLADEFGVAVVITNQVVAQVDGAASAMFAADAKKPIGGNIMAHASTTRLSLRK----GRGEQRICKIYDSPCLPESEA-V  304 (317)
T ss_pred             HHHHHCCEEEEEECHHHHCCCCCHHHHHCCCCCCCCCCCEEEECCCEEEEEEC----CCCCCEEEEEECCCCCCCHHH-H
T ss_conf             88863454689742001003540234431445688675123201000234441----777310232310677520134-4


Q ss_pred             EEECCCCCEEE
Q ss_conf             98515663110
Q gi|254780334|r  270 FEMSDKGLQEV  280 (479)
Q Consensus       270 f~m~~~Gl~~v  280 (479)
T Consensus       305 f~i~~~G~~d~  315 (317)
T TIGR02239       305 FAIAEDGIGDA  315 (317)
T ss_pred             HHHHHHCCCCC
T ss_conf             43344211223