HHsearch alignment for GI: 254780709 and conserved domain: cd01394

>cd01394 radB RadB. The archaeal protein radB shares similarity radA, the archaeal functional homologue to the bacterial RecA. The precise function of radB is unclear.
Probab=97.85  E-value=0.00042  Score=49.10  Aligned_cols=93  Identities=23%  Similarity=0.312  Sum_probs=55.4

Q ss_pred             CCEEECCCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHH-HHHHHHCCCC-CCCCCCCCCHHHHHHHHHH
Q ss_conf             4123113544444247899999998522674267743451245688999-9975303532-1223586612454228999
Q gi|254780709|r  111 PHVILVVGVNGVGKTTVIGKLSKKMSDAGLKVMLAAGDTFRSAAIDQLK-IWADRTSADF-VCSEIGSDAAALAYEAFKQ  188 (321)
Q Consensus       111 p~vil~vG~nG~GKTTT~aKLA~~~~~~g~kV~lva~DtfR~aA~eQL~-~~a~~~~v~~-~~~~~~~dp~~v~~~a~~~  188 (321)
T Consensus        19 G~it~i~G~pG~GKStl~lq~a~~~~~~g~~v~YidtE~~~~er~~qi~~~~~~~~~~~i~v~~~~~~~~~~~~i~~~~~   98 (218)
T cd01394          19 GTVTQVYGPPGTGKTNIAIQLAVETAGQGKKVAYIDTEGLSSERFRQIAGDRPERAASSIIVFEPMDFNEQGRAIQETET   98 (218)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCEEECCCCHHHHHHHHHHHHH
T ss_conf             87999989999849999999999986369869999665567699999987536665305146267876889999999997


Q ss_pred             HHHHCCCEEEEECCC
Q ss_conf             965148759986543
Q gi|254780709|r  189 AQAKKVDVLIIDTAG  203 (321)
Q Consensus       189 a~~~~~DvvliDTAG  203 (321)
T Consensus        99 ~~~~~~~lvViDSi~  113 (218)
T cd01394          99 FADEKVDLVVVDSAT  113 (218)
T ss_pred             HHHCCCCEEEEECCH
T ss_conf             641477299991404