HHsearch alignment for GI: 254780619 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=92.50  E-value=0.048  Score=34.74  Aligned_cols=171  Identities=19%  Similarity=0.286  Sum_probs=94.4

Q ss_pred             CEEEEECCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHCCCCCEEEEEECCCCCHHHHHHHHHH-HCCC
Q ss_conf             619984475315799999999998514684799715210013445554303897689962355723566789999-7199
Q gi|254780619|r  219 AVSLISGVTGSGKTEVYLEIVAAVLHLGKQVLILLPEISLTSAILERFQKRFGVKPAEWHSSLSTSMREKIWRQV-ARGA  297 (731)
Q Consensus       219 ~~~LL~GvTGSGKTEVYl~li~~~L~~GkqvLiLvPEI~Lt~Q~~~rl~~rF~~~v~v~HS~ls~~eR~~~w~~i-~~G~  297 (731)
T Consensus       104 sliLiGG~PG~GKSTLLLqV~~~LA~~~~~~LYVsGEES~-~Q~klR-A~RLGit-----~~~~~sqaqdGinnlahdG~  176 (481)
T TIGR00416       104 SLILIGGDPGIGKSTLLLQVACQLAKNSMKVLYVSGEESL-QQIKLR-ATRLGIT-----DLVEPSQAQDGINNLAHDGN  176 (481)
T ss_pred             CEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEEECCHH-HHHHHH-HHHCCCC-----CCCCHHHHHHHHHHHHCCCC
T ss_conf             1698468899635678999999984048816899723016-778888-7545532-----47870234432454302675


Q ss_pred             CEEEEECCHH-HH--HHHCCCEEEEEEECCCCCCHHC--CCCC--CCHHHHHHHH---HHHCCCCEECCCC--------C
Q ss_conf             7399940012-11--0010001367740553210000--2443--2248999997---5110321000024--------5
Q gi|254780619|r  298 ISVIVGVRSA-LF--LPFKKLGLIVIDEEHDISYKQE--EGIL--YNARDMSIVR---GKIESFPVVLVSA--------T  359 (731)
Q Consensus       298 ~~IVIGtRSA-if--~P~~nLglIIvDEEHd~sykq~--~~pr--y~aRdvA~~R---a~~~~~~lilgSA--------T  359 (731)
T Consensus       177 L~~L~Et~~e~I~~~~e~~~P~~~ViDSIQ-~ly~~di~SaPGSVsQVRE~t~~Lmr~AKt~~iaifiVGHVTKeGsiAG  255 (481)
T TIGR00416       177 LYVLSETNLEQICAEIEELNPQVVVIDSIQ-TLYLPDISSAPGSVSQVRECTAELMRLAKTRGIAIFIVGHVTKEGSIAG  255 (481)
T ss_pred             CCCCCCCCHHHHHHHHHHHCCCEEEEECCC-CCCCHHHCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCC
T ss_conf             321575798999999985299489991421-0000000258884238889999998765216865799700435675434


Q ss_pred             CCH-HH-----HHHH-H-HHHHHHHC-CCCCCCCCCCCCCEECCCCCCC
Q ss_conf             432-46-----7753-2-12344412-4322367654332110222233
Q gi|254780619|r  360 PSI-ES-----RVNG-I-SRRYHSVH-LSTRYRNSALPHLQVIDMRGQT  399 (731)
Q Consensus       360 PSl-es-----~~~~-~-~g~~~~~~-l~~R~~~~~~P~i~ivDm~~~~  399 (731)
T Consensus       256 PkvLEH~vD~vLyfeGd~~~~~R~LRS~KNRFGat~--E~G~FeM~e~G  302 (481)
T TIGR00416       256 PKVLEHMVDTVLYFEGDRDSRFRILRSVKNRFGATN--EIGIFEMTEQG  302 (481)
T ss_pred             CHHHHHHHHHHEECCCCCCCCCCHHHCCCCCCCCCC--CCCCCCCCHHH
T ss_conf             046663433110115887534440100015678734--21010000233