HHsearch alignment for GI: 254780332 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=99.85  E-value=3.4e-19  Score=165.62  Aligned_cols=207  Identities=28%  Similarity=0.418  Sum_probs=156.2

Q ss_pred             CCCCCCCHHHHHHH-HHHCCCCEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCEEEEEECCCCHHHHH
Q ss_conf             64432101377655-64167726776213100276999999999985101112333332124797589995852179998
Q gi|254780332|r  200 AGVSTGIQTLDKQM-GGLQRSDLIIIAGRPGMGKTSLATNIAYNVADAYKAELQTDGSYKTINGGIVGFYSLEMSSEQLA  278 (504)
Q Consensus       200 ~Gi~TG~~~LD~~~-gGl~~G~l~Viaarpg~GKTalalniA~~~A~~~~~~~~~~~~~~~~~g~~Vl~fSlEMs~~el~  278 (504)
T Consensus        62 ~R~~Tgi~ElDRVLGGGiVpGSvvLlgGePGIGKSTLLLQia~~la~---------------~~~~vLYvSGEES~~QIk  126 (372)
T cd01121          62 ERIPTGIEELDRVLGGGLVPGSVILIGGDPGIGKSTLLLQVAARLAK---------------RGGKVLYVSGEESPEQIK  126 (372)
T ss_pred             CCCCCCCHHHHHHHCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHH---------------CCCCEEEEECHHHHHHHH
T ss_conf             54447836665400577306717998259988688999999999986---------------399389982456789999


Q ss_pred             HHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHCCEEEECCCCCCHHHHHHHHHHHCCCCCCCEEEECCHHHCCCC
Q ss_conf             78999987410110001213768899899999998627807825899889999998864022444746776713532566
Q gi|254780332|r  279 TRIISEQTEVPSSKIRRGELTRPDYEKIVACSQVMQKLPLYIDQTGGISMSQLATRARRLKRQRGLDLLIVDYIQLMTTS  358 (504)
Q Consensus       279 ~R~is~~s~I~~~~i~~g~l~~~e~~~i~~a~~~l~~~~l~I~d~~~~ti~~I~~~~r~~~~~~gi~~vvIDYLqli~~~  358 (504)
T Consensus       127 ~RA~----------------------RLg-----~~~~~l~l~se--t~le~Il~~i~~----~kP~~lIIDSIQT~~~~  173 (372)
T cd01121         127 LRAD----------------------RLG-----ISTENLYLLAE--TNLEDILASIEE----LKPDLVIIDSIQTVYSS  173 (372)
T ss_pred             HHHH----------------------HHC-----CCCCCCEEEEC--CCHHHHHHHHHH----HCCCEEEEECHHHCCCC
T ss_conf             8999----------------------858-----78877278843--569999999997----19988999562202037


Q ss_pred             CC-CCCHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHCCEEEEEECHHHCCCCCC
Q ss_conf             44-32113788999999999999882791999771382201689999840101432422331387889725566164423
Q gi|254780332|r  359 KK-IEENRVLEITGITMALKALAKELNIPIIALSQLSRQVENRDNKRPQLSDLRESGSIEQDADVVLFVIRDEYYIRNKE  437 (504)
Q Consensus       359 ~~-~~~~r~~~i~~is~~lK~lA~e~~ipvi~lsQLnR~~e~r~~krP~lsDLr~Sg~IEqdAD~v~~l~R~~~y~~~~~  437 (504)
T Consensus       174 ~~~s~pGsvsQVReca~~L~~~AK~~~i~~~lVGHVTK~G-----------~iAGPkvLEHmVDtVl~fEgd~-------  235 (372)
T cd01121         174 ELTSAPGSVSQVRECTAELMRFAKERNIPIFIVGHVTKEG-----------SIAGPKVLEHMVDTVLYFEGDR-------  235 (372)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHCCCEEEEEEEECCCC-----------CCCCCHHHEEEEEEEEEECCCC-------
T ss_conf             7677998789999999999999986197399998762688-----------6377403100213688751577-------


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCEEEEEEEECCCCCCEEEEEEEECCCCCEEECCC
Q ss_conf             3332221110000001123388389999740899725999997468540200774
Q gi|254780332|r  438 PTNKDDILAYTKWQEDLKRVKGIADIIIAKQRHGPTGTVTLAFQAEFTRFSALSD  492 (504)
Q Consensus       438 ~~~~~~~~~~~~~~~~~~~~~~~~elivaKnR~G~~g~~~~~f~~~~~~f~~~~~  492 (504)
T Consensus       236 -------------------~~~~R~LR~~KNRFG~t~EiGv-FeM~~~GL~~V~n  270 (372)
T cd01121         236 -------------------HSEYRILRSVKNRFGSTNELGV-FEMRENGLREVSN  270 (372)
T ss_pred             -------------------CCCEEEEEEECCCCCCCCEEEE-EEECCCCCEECCC
T ss_conf             -------------------6550356741156777540588-8731687056368