HHsearch alignment for GI: 254780810 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=94.16  E-value=0.066  Score=31.66  Aligned_cols=60  Identities=23%  Similarity=0.262  Sum_probs=41.7

Q ss_pred             HHHHHHHHHH--HHHCCCCEEEECCCCCCHHHHHHHHHHHHHHCCCCCEEEEEECCCCHHHHHHH
Q ss_conf             3688899886--55102312220487787899999999998611886469999508787899999
Q gi|254780810|r  160 ISSRVIDLIA--PIGKGQRSLIVAPPRTGKTILLQNIAHSIKKNHPECYLIVLLIDERPEEVTDM  222 (423)
Q Consensus       160 ~~~~~id~~~--pig~gqr~~i~~~~~~gkt~ll~~ia~~~~~~~~~v~~i~~ligEr~~ev~e~  222 (423)
T Consensus        87 s~~~ElDrVLGGGivpGsliLiGG~PG~GKSTLLLqV~~~LA~~~~--~~LYV-sGEES~~Q~kl  148 (481)
T TIGR00416        87 SGFGELDRVLGGGIVPGSLILIGGDPGIGKSTLLLQVACQLAKNSM--KVLYV-SGEESLQQIKL  148 (481)
T ss_pred             CCCCCCCEEECCCCCCCCEEEECCCCCCCHHHHHHHHHHHHHHCCC--CEEEE-EECCHHHHHHH
T ss_conf             0664100110672224416984688996356789999999840488--16899-72301677888