HHsearch alignment for GI: 254781218 and conserved domain: PRK05657
>PRK05657 RNA polymerase sigma factor RpoS; Validated.
Probab=92.77 E-value=0.78 Score=24.97 Aligned_cols=125 Identities=13% Similarity=0.140 Sum_probs=66.3
Q ss_pred CCCCHHHHHHHHCCCHHHHHHHHCCC-CCCCHHHHHHHHHHHCCCHHHHHCCCCCCCCCCCCCC---HHHHHH--HHHHH
Q ss_conf 59988999998489999999887799-8889999999999828999996145322100002321---345546--77799
Q gi|254781218|r 43 NNKTQKEMAIGANQLESAVNLFENGM-CSTSIRYALYLRNEYEISFDWIYDGEVIDRRYEDVTN---KKRLDP--YAIGA 116 (205)
Q Consensus 43 ~gltQ~elA~~~gis~~~is~~E~G~-~~psi~~l~~la~~~~vs~d~Ll~ge~~~~~~~~~~~---~~~~d~--~~iG~ 116 (205)
T Consensus 191 r~pt~eEIA~~lg~~~~~v~~~l~~~~~~~SLD~pv--~~d~~~tl~d~l~D~~~~~pd~~~~~~~l~~~l~~~L~~L~~ 268 (328)
T PRK05657 191 HEPSAEEIAELLDKPVDDVSRMLALNERITSLDAPL--GGDPEKSLLDILADDQENGPEDTTQDDDLKQSIVKWLFELND 268 (328)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCC--CCCCCCHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCH
T ss_conf 999899999996959999999997458763444535--899851178886277899999999999999999999806999
Q ss_pred HHHHHHH-------HCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHH
Q ss_conf 9999999-------72983899999977999999997414889998999999998289999952
Q gi|254781218|r 117 RLKSIRK-------DKGMSQIEFGKLLGMPNSTLSNYEQGRTIPEIKPARKIKQVTKKHLDWIY 173 (205)
Q Consensus 117 rLk~lR~-------~~glsq~elA~~lgis~~tis~~E~g~~~Ps~~~l~kIa~~lgvs~d~L~ 173 (205)
T Consensus 269 REr~II~~RfGL~~~e~~TL~EIg~~lgvSRERVRQIE~~----AL~KLR~~l~~~~l~~~~~~ 328 (328)
T PRK05657 269 KQREVIERRFGLNGYEAATLEEVAREIGLTRERVRQIQVE----ALRRLREILQTQGLSKDALF 328 (328)
T ss_pred HHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHH----HHHHHHHHHHHCCCCHHHCC
T ss_conf 9999999980889989605999998969799999999999----99998799998699734249