HHsearch alignment for GI: 254780684 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=97.66  E-value=0.00095  Score=46.32  Aligned_cols=177  Identities=19%  Similarity=0.195  Sum_probs=88.4

Q ss_pred             HHHHHHHHHHHHH--HCCCCEEEEECCCCCCHHHHHHHHHHHCC--CCCEEEEECCCC--CHHHHHHHHHHHCCCCCCEE
Q ss_conf             1112458752002--23585037526678899999999874078--983899312465--22388999986427755328
Q gi|254780684|r  145 FKTGIRVIDIFTP--LCHGQRIGVFAGSGIGKSTLLSMFARSDC--FDKVIISLVGER--GREVREFIEDYLGDNLKKSV  218 (438)
Q Consensus       145 L~TGIr~ID~l~p--ig~GQR~gIfg~~GvGKt~Ll~~i~~~~~--~dv~V~alIGeR--~rev~efi~~~~~~~l~~tv  218 (438)
T Consensus         1 IsTG~~~lD~vLgGGi~~G~it~i~G~pG~GKStl~lq~a~~~~~~g~~v~Yi-dtE~~~~er~~qi~~~~~-~~~~~~i   78 (218)
T cd01394           1 LPTGCKGLDELLGGGVERGTVTQVYGPPGTGKTNIAIQLAVETAGQGKKVAYI-DTEGLSSERFRQIAGDRP-ERAASSI   78 (218)
T ss_pred             CCCCCHHHHHHHCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEE-ECCCCCCHHHHHHHHHHH-HHHHCCC
T ss_conf             99880789998569987887999989999849999999999986369869999-665567699999987536-6653051


Q ss_pred             EEEECCCCCHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHCCHHHHHHH
Q ss_conf             98415778803444444567778888642679889997098999999876654047784323663245542004444431
Q gi|254780684|r  219 VVVATSDESPILRKMAPLTAVTIAEYFSSKGDNVLLILDSITRFAHSIREIATNSGELPVARGYPTSVFSELPRLLERIG  298 (438)
Q Consensus       219 vv~~t~d~~~~~r~~a~~~a~~iAEyfr~~G~~Vll~~Ds~tr~a~A~reis~~~ge~P~~~gyp~~~~~~~~~l~ERag  298 (438)
T Consensus        79 ~v~~~~~~~~------~~~~i~~~~~~~~~~-~~lvViDSi~tl~~~e--~~~----~~~~~~~~r~l~~~~~~L~~~Ak  145 (218)
T cd01394          79 IVFEPMDFNE------QGRAIQETETFADEK-VDLVVVDSATALYRLE--LGD----DDTTIKNYRELAKQLTFLLWLAR  145 (218)
T ss_pred             EEECCCCHHH------HHHHHHHHHHHHHCC-CCEEEEECCHHHHHHH--CCC----CCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             4626787688------999999999764147-7299991404554554--068----96479999999999999999987


Q ss_pred             CCCCCCCCEEEEEE--EEECCC-CCCCHHH-HHHHHHCCCEEEEEHH
Q ss_conf             13678852355433--342167-6420278-9998612608987042
Q gi|254780684|r  299 PSEKEKGNITAVIS--VLVDGD-NHNDPIA-DSVRSILDGHIVLNRS  341 (438)
Q Consensus       299 ~~~~~~GSiT~~~~--v~~~~d-d~~~pi~-~~~~~i~DG~i~L~r~  341 (438)
T Consensus       146 -----~~~~~vil~nqVt~~~~~~~~~p~GG~~LeH~vd~vl~~e~~  187 (218)
T cd01394         146 -----KHDVAVVITNQVYSDVGSGSVRPLGGHTLEHWSKVILRLEKL  187 (218)
T ss_pred             -----HCCCEEEEEEEEEEECCCCCCCCCCCHHHHHHCCEEEEEECC
T ss_conf             -----669889999215884577756556720414110289999848