HHsearch alignment for GI: 254780617 and conserved domain: cd01121

>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=97.36  E-value=0.006  Score=40.48  Aligned_cols=168  Identities=19%  Similarity=0.236  Sum_probs=96.9

Q ss_pred             HHHHCCHHHHHCCC--CCCCCCEEEEECCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCHHHHHHHHHHHC
Q ss_conf             14441602331011--1156833655247788611589999999886302466787606999951677678999998511
Q gi|254780617|r  144 EPLSTGIKAIDSLI--PIGRGQRELIIGDRKTGKTSIILDTFLNQKSSHDKGSEKDKVYCIYVAIGQKRSSVARFVKALE  221 (509)
Q Consensus       144 ~~l~TGI~~ID~l~--pigrGQR~~I~g~~g~GKt~l~~~~I~nq~~~~~~~~~~~~v~~V~~~IGer~~ev~~~~~~l~  221 (509)
T Consensus        62 ~R~~Tgi~ElDRVLGGGiVpGSvvLlgGePGIGKSTLLLQia~~la~~~--------~~vLYvSGEES~~QIk~RA~RL-  132 (372)
T cd01121          62 ERIPTGIEELDRVLGGGLVPGSVILIGGDPGIGKSTLLLQVAARLAKRG--------GKVLYVSGEESPEQIKLRADRL-  132 (372)
T ss_pred             CCCCCCCHHHHHHHCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHCC--------CCEEEEECHHHHHHHHHHHHHH-
T ss_conf             5444783666540057730671799825998868899999999998639--------9389982456789999899985-


Q ss_pred             CCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHCCCCCEEEEEECHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHH
Q ss_conf             46742115899728878889999988766666675420468847996164789999987545303787543337520012
Q gi|254780617|r  222 DRGALSYSIVVVASASDPAPMQLLAPFAGCAMGEYFRDNGYHALIAYDDLQKHAVAYRQLSLLLRRPPGREAYPGDVFYL  301 (509)
Q Consensus       222 ~~~~~~~tvvv~a~a~~~~~~r~~ap~~a~aiAEyfr~~G~~VLi~~Ddltr~A~a~reisl~~~~pp~~~gyp~~vf~~  301 (509)
T Consensus       133 --g~~~~~l~l~set~le~Il~------------~i-~~~kP~~lIIDSIQT~------------~~~~~~s~pGsvsQV  185 (372)
T cd01121         133 --GISTENLYLLAETNLEDILA------------SI-EELKPDLVIIDSIQTV------------YSSELTSAPGSVSQV  185 (372)
T ss_pred             --CCCCCCCEEEECCCHHHHHH------------HH-HHHCCCEEEEECHHHC------------CCCCCCCCCCCHHHH
T ss_conf             --87887727884356999999------------99-9719988999562202------------037767799878999


Q ss_pred             H--HHHHHHHHHCCCCCCCCCEEEEEE-EECCCCCCCCCHHHHHHHHHCCEEEEECC
Q ss_conf             4--678888750454458873567531-00367664431146688540616996150
Q gi|254780617|r  302 H--SRLLERAAKMSDALGAGSLTALPV-IETQVNDVSAYIPTNVISITDGQIFLETE  355 (509)
Q Consensus       302 ~--s~l~ERa~~~~~~~g~GSiT~~~~-v~~~~~D~~~~i~~~~~si~DG~i~l~~~  355 (509)
T Consensus       186 Reca~~L~~~AK~------~~i~~~lVGHVTK~G~iAGPkvL--EHmVDtVl~fEgd  234 (372)
T cd01121         186 RECTAELMRFAKE------RNIPIFIVGHVTKEGSIAGPKVL--EHMVDTVLYFEGD  234 (372)
T ss_pred             HHHHHHHHHHHHH------CCCEEEEEEEECCCCCCCCCHHH--EEEEEEEEEECCC
T ss_conf             9999999999986------19739999876268863774031--0021368875157