HHsearch alignment for GI: 254780334 and conserved domain: TIGR00416
>TIGR00416 sms DNA repair protein RadA; InterPro: IPR004504 RadA/Sms is a highly conserved eubacterial protein that shares sequence similarity with both RecA strand transferase and lon protease. The RadA/Sms family are probable ATP-dependent proteases involved in both DNA repair and degradation of proteins, peptides, glycopeptides. They are classified in as non-peptidase homologues and unassigned peptidases in MEROPS peptidase family S16 (lon protease family, clan SJ). RadA/Sms is involved in recombination and recombinational repair, most likely involving the stabilisation or processing of branched DNA molecules or blocked replication forks because of its genetic redundancy with RecG and RuvABC .; GO: 0003684 damaged DNA binding, 0005524 ATP binding, 0006281 DNA repair.
Probab=100.00 E-value=0 Score=1235.91 Aligned_cols=450 Identities=48% Similarity=0.815 Sum_probs=426.3
Q ss_pred CCCC-CCEEEECCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCC----------CCCCCC--CCCCCCCCEECCCCCCC
Q ss_conf 9876-5278987675636300771788898670798852477655----------544444--55566564031333455
Q gi|254780334|r 1 MVKI-RSQYFCQSCGEIHSRWIGKCDSCNAWNTIIEDSSRKESDQ----------RFSKTI--KQGHSISLFMLSEESIE 67 (479)
Q Consensus 1 m~k~-k~~y~C~~Cg~~~~kW~G~Cp~C~~Wnt~~e~~~~~~~~~----------~~~~~~--~~~~~~~~~~l~~~~~~ 67 (479)
T Consensus 1 mAK~Pk~~FvC~~CG~~~p~W~G~C~~C~aw~t~~E~~~~~vssGtn~~s~~a~~~~~~~~~~g~~~~~K~~~~s~I~~~ 80 (481)
T TIGR00416 1 MAKAPKSKFVCQSCGAESPKWLGKCPACHAWNTLTEERLKKVSSGTNARSLKAQKNRRASLKAGVPQAQKAQTISAIELE 80 (481)
T ss_pred CCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCHHHHHHHHHCCCCCCCCCCCCHHHHHHHC
T ss_conf 98888774202235774504647388866531377787765302310001011245553115886521024123433420
Q ss_pred CCCCCCCCCHHHHHHHCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHCC---CCC
Q ss_conf 66632378124888865985787089995498751889999999998503981999986463047888875201---577
Q gi|254780334|r 68 EESRIQTHIDELDRVTGGGFVRGSVILVGGDPGIGKSTLLMQTAASLAYKKHRITYVSGEEAIGQIRLRAQRLN---TIN 144 (479)
Q Consensus 68 ~~~Ri~TGi~eLDrvLGGGl~~Gs~~Li~G~PGvGKSTL~Lqia~~~a~~g~~vlYvS~EEs~~Qi~~Ra~Rl~---~~~ 144 (479)
T Consensus 81 e~~rf~s~~~ElDrVLGGGivpGsliLiGG~PG~GKSTLLLqV~~~LA~~~~~~LYVsGEES~~Q~klRA~RLGit~~~~ 160 (481)
T TIGR00416 81 EEPRFSSGFGELDRVLGGGIVPGSLILIGGDPGIGKSTLLLQVACQLAKNSMKVLYVSGEESLQQIKLRATRLGITDLVE 160 (481)
T ss_pred CCCEEECCCCCCCEEECCCCCCCCEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHCCCCCCCC
T ss_conf 67605306641001106722244169846889963567899999998404881689972301677888875455324787
Q ss_pred C--------------CHHEECCCCHHHHHHHHHHCCCCCEEEECHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCC
Q ss_conf 5--------------10000347889999999731698289972168766542044556367999999999997530797
Q gi|254780334|r 145 S--------------SVYIAIETNVEDIIATLITNEKPDLVIIDSIQTLWSQTAESSPGTVIQVRTSVQAMIQYAKKNGV 210 (479)
Q Consensus 145 ~--------------~i~~~~e~~l~~il~~~i~~~~~~~vVIDSIQtl~~~~~~s~~GsvsQvre~~~~L~~~AK~~~i 210 (479)
T Consensus 161 ~sqaqdGinnlahdG~L~~L~Et~~e~I~~~-~e~~~P~~~ViDSIQ~ly~~di~SaPGSVsQVRE~t~~Lmr~AKt~~i 239 (481)
T TIGR00416 161 PSQAQDGINNLAHDGNLYVLSETNLEQICAE-IEELNPQVVVIDSIQTLYLPDISSAPGSVSQVRECTAELMRLAKTRGI 239 (481)
T ss_pred HHHHHHHHHHHHCCCCCCCCCCCCHHHHHHH-HHHHCCCEEEEECCCCCCCHHHCCCCCCHHHHHHHHHHHHHHHHHCCC
T ss_conf 0234432454302675321575798999999-985299489991421000000025888423888999999876521686
Q ss_pred EEEEEEEECCCCCCCCHHHHHHHHHEEEEEECCCCCCCCCCEEEEEEEECCCCCCCEEEEEECCCCCEEECCHHHHHHCC
Q ss_conf 89998630366543311457877530278515556665442156763202567651279985156631101404555114
Q gi|254780334|r 211 AMVLVGHVTKEGQIAGPRVIEHMVDAVLYFEGGTRNTQYDYRILRSVKNRFGPTDEIGVFEMSDKGLQEVSDPSKIFLSD 290 (479)
Q Consensus 211 ~vilighvTK~G~iAGp~~LeH~VD~vl~~ege~~~~~~~~R~Lr~~KNRfG~t~e~gvf~m~~~Gl~~v~~ps~~fl~~ 290 (479)
T Consensus 240 aifiVGHVTKeGsiAGPkvLEH~vD~vLyfeG---d~~~~~R~LRS~KNRFGat~E~G~FeM~e~GL~ev~nPS~iFL~~ 316 (481)
T TIGR00416 240 AIFIVGHVTKEGSIAGPKVLEHMVDTVLYFEG---DRDSRFRILRSVKNRFGATNEIGIFEMTEQGLREVLNPSAIFLSR 316 (481)
T ss_pred CEEEEEEECCCCCCCCCHHHHHHHHHHEECCC---CCCCCCCHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCC
T ss_conf 57997004356754340466634331101158---875344401000156787342101000023356453145664157
Q ss_pred CCCCCCCEEEEEEECCCCCCEEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHHHCCCCCCCCHHHEECCCCCCCCC
Q ss_conf 76676734899730489741155331011577877247760468666555589887511110246222100145611154
Q gi|254780334|r 291 RDSTSPGTAVFAGIEGTRALLVEIQSLVVPTSLGMPRRTVVGWDSSRLAMILAVLEARCNIKFGNHDVHLNIAGGYRISE 370 (479)
Q Consensus 291 ~~~~~~Gs~v~~~~eG~r~~lvEvQALv~~~~~~~p~R~~~G~d~~rl~~llAvl~k~~~~~~~~~Di~~nv~gG~~i~~ 370 (479)
T Consensus 317 ~~e~~~GSsitv~~EGtRPLlvEiQALVs~~s~anPrR~A~G~d~NRL~~LlAvLek~~Gl~l~~~Dvf~~V~GGvkv~E 396 (481)
T TIGR00416 317 REEVMSGSSITVALEGTRPLLVEIQALVSPTSFANPRRVATGLDQNRLALLLAVLEKRLGLPLADQDVFLNVAGGVKVSE 396 (481)
T ss_pred CCCCCCCCCEEEEECCCHHHHHHHHHHCCCCCCCCCCCEECCHHHHHHHHHHHHHHHHCCCCHHHCCEEEEEECCEEECC
T ss_conf 64566673012342373488888875226143688631004422568999999987640661111734798623505410
Q ss_pred CCCCHHHHHHHHHHHCCCCCCCCEEEEEEEECCCEEEEECCHHHHHHHHHHCCCCEEEECHHHHHH-CCCCCEEEEEECC
Q ss_conf 325879999999972488688785999874247316340788999999997699899977576532-2858808998383
Q gi|254780334|r 371 PAADVAVAAALISSILSIPLPSDFVYFGEVSLSGSVRAVGHMQQRLKEAEKIGFLSGVFPESAKGE-CKIGMLDRQYIKN 449 (479)
Q Consensus 371 pa~DLaia~ailSs~~~~~~~~~~~~~GEl~L~GeIR~V~~i~~ri~eA~~~G~~~~iiP~~n~~e-~~~~~i~i~~v~~ 449 (479)
T Consensus 397 pa~DLA~~~a~~SSFrdr~~~~~~~~lGEVGL~G~ir~vp~~~~R~kEaak~GFkraIvP~~~~~~W~~~~gi~~~~v~~ 476 (481)
T TIGR00416 397 PAVDLALLIALVSSFRDRPLDPDLVILGEVGLAGEIRPVPSLEERLKEAAKLGFKRAIVPKANLPKWTAPEGIKVIGVKK 476 (481)
T ss_pred HHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCCEEEECCCHHHHHHHHHHCCCCEEECCCCCCCCCCCCCCCEEEEHHH
T ss_conf 57889999999987517887856388876437770400776316799998468634421478888752445624760344
Q ss_pred HHHHH
Q ss_conf 99999
Q gi|254780334|r 450 LSDLV 454 (479)
Q Consensus 450 l~e~i 454 (479)
T Consensus 477 v~~al 481 (481)
T TIGR00416 477 VADAL 481 (481)
T ss_pred HHHHC
T ss_conf 65409