HHsearch alignment for GI: 254780611 and conserved domain: PRK05657
>PRK05657 RNA polymerase sigma factor RpoS; Validated.
Probab=100.00 E-value=0 Score=529.99 Aligned_cols=265 Identities=30% Similarity=0.471 Sum_probs=235.2
Q ss_pred CCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 74059999998407999998999999999998285999999999430778756555579999888999999888998986
Q gi|254780611|r 12 GEIGLSRYIHEIRKIPMLEKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVK 91 (302)
Q Consensus 12 ~~~~~~~yl~~i~~~~~Lt~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~ 91 (302)
T Consensus 54 ~~d~~~~YL~eI~~~pLLt~eEE~~La~~~~-~GD~~Ar~~LI~sNLRLVvsIAkkY~~~Gl~l~DLIQEGniGLikAve 132 (328)
T PRK05657 54 VLDATQLYLNEIGYSPLLTAEEEVYFARRAL-RGDFAARQRMIESNLRLVVKIAKRYLNRGLALLDLIEEGNLGLIRAVE 132 (328)
T ss_pred CCCHHHHHHHHHCCCCCCCHHHHHHHHHHHH-CCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf 0556999999956789999999999999998-178999999999818999999985568998989999886899999999
Q ss_pred HCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCC
Q ss_conf 21853456899975778999999853202460011023003589999999978878662447888246778886189832
Q gi|254780611|r 92 KFDPERGFRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSES 171 (302)
Q Consensus 92 kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~ 171 (302)
T Consensus 133 KFDp~rG~RFSTYA~WWIRq~I~raI~~~~r~IRlP~~~~~-----~l~~i~ra~~~l~~~~gr~pt~eEIA~~lg~~~~ 207 (328)
T PRK05657 133 KFDPERGFRFSTYATWWIRQTIERAIMNQTRTIRLPVHVVK-----ELNVYLRAARELEHKLDHEPSAEEIAELLDKPVD 207 (328)
T ss_pred HCCCCCCCCEEEEEHHHHHHHHHHHHHHCCCCCCCCCHHHH-----HHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHH
T ss_conf 71976699842300999999999999965777775611999-----9999999999999984899989999999695999
Q ss_pred CCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCC--
Q ss_conf 110000001223433552023234532000001235687056556666666777999999621999999999998278--
Q gi|254780611|r 172 EVISMNCRLAGDESLNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQ-- 249 (302)
Q Consensus 172 ~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~-- 249 (302)
T Consensus 208 ~v~~~l~~~~~~~SLD~pv~~--d~~~tl~d~l~D~~~~~pd~~~---~~~~l~~~l~~~L~~L~~REr~II~~RfGL~~ 282 (328)
T PRK05657 208 DVSRMLALNERITSLDAPLGG--DPEKSLLDILADDQENGPEDTT---QDDDLKQSIVKWLFELNDKQREVIERRFGLNG 282 (328)
T ss_pred HHHHHHHHCCCCCCCCCCCCC--CCCCHHHHHHCCCCCCCHHHHH---HHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCC
T ss_conf 999999745876344453589--9851178886277899999999---99999999999980699999999999808899
Q ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 88889899999977899999999999999999999974
Q gi|254780611|r 250 ENPVTLENLSSEFEVSRERVRQIEARAFKKVQESIQKQ 287 (302)
Q Consensus 250 ~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l~~~ 287 (302)
T Consensus 283 ~e~~TL~EIg~~lgvSRERVRQIE~~AL~KLR~~l~~~ 320 (328)
T PRK05657 283 YEAATLEEVAREIGLTRERVRQIQVEALRRLREILQTQ 320 (328)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHC
T ss_conf 89605999998969799999999999999987999986