HHsearch alignment for GI: 254780831 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=90.64  E-value=0.49  Score=26.91  Aligned_cols=84  Identities=19%  Similarity=0.364  Sum_probs=52.2

Q ss_pred             CCCHHHHHHHHHHHHHHHHCCCCCCCEEE----ECCCCCCCCCCC------------------------CCC--C-CC-C
Q ss_conf             87847899999999999860676342355----032223433322------------------------234--6-54-2
Q gi|254780831|r   49 HTIAHQLQSLRSNAQQIIQNIPTVKNAVV----TLTENKNPPQQR------------------------NNL--N-VK-K   96 (341)
Q Consensus        49 ~~~cp~~~~l~~~i~~~l~~i~gv~~v~V----~lt~~~~~~~~~------------------------~~~--~-~~-~   96 (341)
T Consensus        25 C~~C~aw~t~~E~~~~~vssGtn~~s~~a~~~~~~~~~~g~~~~~K~~~~s~I~~~e~~rf~s~~~ElDrVLGGGivpGs  104 (481)
T TIGR00416        25 CPACHAWNTLTEERLKKVSSGTNARSLKAQKNRRASLKAGVPQAQKAQTISAIELEEEPRFSSGFGELDRVLGGGIVPGS  104 (481)
T ss_pred             CCCCCCCCHHHHHHHHHHHCCCCCCCCHHHHHHHHHCCCCCCCCCCCCHHHHHHHCCCCEEECCCCCCCEEECCCCCCCC
T ss_conf             88866531377787765302310001011245553115886521024123433420676053066410011067222441


Q ss_pred             CEECCCCCCCCCHHHHHHHHHHHHCCCCCEEEEEECC
Q ss_conf             0102446665425789999898723577506988224
Q gi|254780831|r   97 FVAVASGKGGVGKSTTVVNIACALKNKGKNVAILDAD  133 (341)
Q Consensus        97 iiav~SgKGGVGKSt~s~nLa~ala~~G~~V~liDaD  133 (341)
T Consensus       105 liLiG-G~PG~GKSTLLLqV~~~LA~~~~~~LYVsGE  140 (481)
T TIGR00416       105 LILIG-GDPGIGKSTLLLQVACQLAKNSMKVLYVSGE  140 (481)
T ss_pred             EEEEC-CCCCCCHHHHHHHHHHHHHHCCCCEEEEEEC
T ss_conf             69846-8899635678999999984048816899723