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