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