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