HHsearch alignment for GI: 254780332 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=99.69 E-value=8.3e-16 Score=139.83 Aligned_cols=209 Identities=23% Similarity=0.368 Sum_probs=152.1
Q ss_pred CCCCCCHHHHHHH-HHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCEEEEEECCCCHHHHHH
Q ss_conf 4432101377655-641677267762131002769999999999851011123333321247975899958521799987
Q gi|254780332|r 201 GVSTGIQTLDKQM-GGLQRSDLIIIAGRPGMGKTSLATNIAYNVADAYKAELQTDGSYKTINGGIVGFYSLEMSSEQLAT 279 (504)
Q Consensus 201 Gi~TG~~~LD~~~-gGl~~G~l~Viaarpg~GKTalalniA~~~A~~~~~~~~~~~~~~~~~g~~Vl~fSlEMs~~el~~ 279 (504)
T Consensus 84 rf~s~~~ElDrVLGGGivpGsliLiGG~PG~GKSTLLLqV~~~LA~~---------------~~~~LYVsGEES~~Q~kl 148 (481)
T TIGR00416 84 RFSSGFGELDRVLGGGIVPGSLILIGGDPGIGKSTLLLQVACQLAKN---------------SMKVLYVSGEESLQQIKL 148 (481)
T ss_pred EEECCCCCCCEEECCCCCCCCEEEECCCCCCCHHHHHHHHHHHHHHC---------------CCCEEEEEECCHHHHHHH
T ss_conf 05306641001106722244169846889963567899999998404---------------881689972301677888
Q ss_pred HHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHH-HCCEEEECCCCCCHHHHHHHHHHHCCCCCCCEEEECCHHHCCCC
Q ss_conf 89999874101100012137688998999999986-27807825899889999998864022444746776713532566
Q gi|254780332|r 280 RIISEQTEVPSSKIRRGELTRPDYEKIVACSQVMQ-KLPLYIDQTGGISMSQLATRARRLKRQRGLDLLIVDYIQLMTTS 358 (504)
Q Consensus 280 R~is~~s~I~~~~i~~g~l~~~e~~~i~~a~~~l~-~~~l~I~d~~~~ti~~I~~~~r~~~~~~gi~~vvIDYLqli~~~ 358 (504)
T Consensus 149 RA~RL--Git-------~~~~~--sqaqdGinnlahdG~L~~--L~Et~~e~I~~~~e~~~----P~~~ViDSIQ~ly~~ 211 (481)
T TIGR00416 149 RATRL--GIT-------DLVEP--SQAQDGINNLAHDGNLYV--LSETNLEQICAEIEELN----PQVVVIDSIQTLYLP 211 (481)
T ss_pred HHHHC--CCC-------CCCCH--HHHHHHHHHHHCCCCCCC--CCCCCHHHHHHHHHHHC----CCEEEEECCCCCCCH
T ss_conf 87545--532-------47870--234432454302675321--57579899999998529----948999142100000
Q ss_pred C-CCCCHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHCCEEEEEECHHHCCCCCC
Q ss_conf 4-432113788999999999999882791999771382201689999840101432422331387889725566164423
Q gi|254780332|r 359 K-KIEENRVLEITGITMALKALAKELNIPIIALSQLSRQVENRDNKRPQLSDLRESGSIEQDADVVLFVIRDEYYIRNKE 437 (504)
Q Consensus 359 ~-~~~~~r~~~i~~is~~lK~lA~e~~ipvi~lsQLnR~~e~r~~krP~lsDLr~Sg~IEqdAD~v~~l~R~~~y~~~~~ 437 (504)
T Consensus 212 di~SaPGSVsQVRE~t~~Lmr~AKt~~iaifiVGHVTKeG------s-----iAGPkvLEH~vD~vLyfeGd------~- 273 (481)
T TIGR00416 212 DISSAPGSVSQVRECTAELMRLAKTRGIAIFIVGHVTKEG------S-----IAGPKVLEHMVDTVLYFEGD------R- 273 (481)
T ss_pred HHCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEEECCCC------C-----CCCCHHHHHHHHHHEECCCC------C-
T ss_conf 0025888423888999999876521686579970043567------5-----43404666343311011588------7-
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCEEEEEEEECCCCCCEEEEE
Q ss_conf 33322211100000011233883899997408997259999
Q gi|254780332|r 438 PTNKDDILAYTKWQEDLKRVKGIADIIIAKQRHGPTGTVTL 478 (504)
Q Consensus 438 ~~~~~~~~~~~~~~~~~~~~~~~~elivaKnR~G~~g~~~~ 478 (504)
T Consensus 274 -~-~~-----------------~R~LRS~KNRFGat~E~G~ 295 (481)
T TIGR00416 274 -D-SR-----------------FRILRSVKNRFGATNEIGI 295 (481)
T ss_pred -C-CC-----------------CCHHHCCCCCCCCCCCCCC
T ss_conf -5-34-----------------4401000156787342101