HHsearch alignment for GI: 254780289 and conserved domain: PRK05901
>PRK05901 RNA polymerase sigma factor; Provisional.
Probab=100.00 E-value=0 Score=878.34 Aligned_cols=384 Identities=47% Similarity=0.755 Sum_probs=343.8
Q ss_pred CCHHCCHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCEEECCCCCCCCCCCCCCCCCCHHHHH
Q ss_conf 43020289999999978784886789997526843599888999999998479778327841000012364321101112
Q gi|254780289|r 22 LVFDFSDDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASN 101 (682)
Q Consensus 22 ~~~d~~~~~ik~LI~~gke~GylTydeIn~~LP~d~~~~e~ie~i~~~L~~~GI~Vve~~~~~~~~~~~~~~~~~~~~~~ 101 (682)
T Consensus 14 ~~~~~~~~~lk~Li~~gKe~G~lTy~EIn~~Lp~~~~~~e~id~i~~~l~d~gi~v~~~~~~~~~~~~~~~~~---~~~~ 90 (398)
T PRK05901 14 AAKKKKQKKAKELKALAKEDGDITYEEIDEDLDLDFDEDEDIDDVIIFLDDLDEDVENEADVDEDKEDDEDDE---IAEK 90 (398)
T ss_pred HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCEECCCCCCCCCCCCCCCCC---CCCC
T ss_conf 4057899999999998862798369999975898679989999999999977973046763111233343332---1210
Q ss_pred HHHHHHHHHCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCHHH
Q ss_conf 23344442003457777289999998569768897889999999998899999998728238999999998731171036
Q gi|254780289|r 102 SSVFLQKRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLL 181 (682)
Q Consensus 102 e~~~~~~~~~~e~~rtdDPVRMYLREMG~V~LLTREgEIeIAKRIE~G~~~i~~al~~~P~ti~~il~~~e~i~~ge~~L 181 (682)
T Consensus 91 ~~~~~~~~~~~~~~~tdd~v~~yl~~~g~~~ll~~~~e~~~a~~~~~~~~~------------~---------------- 142 (398)
T PRK05901 91 SEKDRQARKDAELTATADPVKAYLKQIGKVKLLNAEEEVELAKRIEAGLYA------------E---------------- 142 (398)
T ss_pred HHHHHHHCCCCCCCCCCCCHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHH------------H----------------
T ss_conf 234444113333688897199999862755488879999999999840456------------7----------------
Q ss_pred HHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCHHHHHHHHHH
Q ss_conf 78764210135433333334333332110001110001000000001221000011111013566665303443100022
Q gi|254780289|r 182 REIIDLEACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDED 261 (682)
Q Consensus 182 rdIIDld~t~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~e~~~e~~~~~~~~~~~~~~~~~~e~e~~~~~~e~e 261 (682)
T Consensus 143 -~------------------------------------------------------------------------------ 143 (398)
T PRK05901 143 -E------------------------------------------------------------------------------ 143 (398)
T ss_pred -H------------------------------------------------------------------------------
T ss_conf -6------------------------------------------------------------------------------
Q ss_pred HHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 23345555644421023479876689999999999999875210120007999999999999998621005778878999
Q gi|254780289|r 262 EDDSAHTLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQ 341 (682)
Q Consensus 262 ~de~~~sla~~e~eLk~~v~e~l~~i~~~~~kl~k~~~~~~~~~~~~~~~kk~~kl~~eL~e~~~~lkl~~k~iE~L~~~ 341 (682)
T Consensus 144 ----------------------------------------------------------~~--------------~----- 146 (398)
T PRK05901 144 ----------------------------------------------------------LL--------------E----- 146 (398)
T ss_pred ----------------------------------------------------------HH--------------H-----
T ss_conf ----------------------------------------------------------67--------------6-----
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999999999999999712535777763167768989999986135510676554345677653223333222221
Q gi|254780289|r 342 LYDISKRIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETG 421 (682)
Q Consensus 342 l~~~~k~Ir~~Er~L~rl~~k~~i~R~~Fi~~f~gnEt~~~wl~~~~~~~~~~~~~~l~~~~~eI~~~q~kL~~ie~~~g 421 (682)
T Consensus 147 ------------~-------------~-----------~~~~-------------------------------------- 152 (398)
T PRK05901 147 ------------K-------------R-----------DLRW-------------------------------------- 152 (398)
T ss_pred ------------H-------------H-----------HHHH--------------------------------------
T ss_conf ------------7-------------7-----------7777--------------------------------------
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHH
Q ss_conf 12688999999876533211246899987555789998875223567778875443679999887438545731201028
Q gi|254780289|r 422 ISISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAM 501 (682)
Q Consensus 422 l~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~ 501 (682)
T Consensus 153 ---------------~~~~~~~Ar~~Li~aNLRLVvsIAkkY~~~Gl~l~DLIQEGniGLirAvekFDp~rG~rFSTYA~ 217 (398)
T PRK05901 153 ---------------IARDGKRAKNHLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYAT 217 (398)
T ss_pred ---------------HHHCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHH
T ss_conf ---------------53053999999999706999999976468998988999986899999999719777995421149
Q ss_pred HHHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCC
Q ss_conf 98999999999722870461420588989999999998776088999789998709998999999986089875536358
Q gi|254780289|r 502 WWVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIG 581 (682)
Q Consensus 502 ~~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~ 581 (682)
T Consensus 218 wWIRqaI~rai~~~~r~IRiP~h~~e~~~k~~r~~~~l~~~~gr~Pt~eEiA~~lg~~~~~v~~~~~~~~~~~SLd~~vg 297 (398)
T PRK05901 218 WWIRQAITRAMADQARTIRIPVHMVETINKLGRIERELLQELGREPTPEELAEEMDFTPEKVREIQKYAREPISLDKTIG 297 (398)
T ss_pred HHHHHHHHHHHHHCCCEEECCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCC
T ss_conf 99999999999966873523323999999999999999998489999999998819999999999997289855678778
Q ss_pred CCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf 89986047562389889989999999999999999732998899999998187986746889998996678999999999
Q gi|254780289|r 582 DEDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEA 661 (682)
Q Consensus 582 ~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~ 661 (682)
T Consensus 298 ~d~~~~l~d~i~D~~~~~p~~~~~~~~l~~~l~~~L~~L~~REr~Ii~~RyGL~~~~~~TL~eIg~~lgvSrERVRQIE~ 377 (398)
T PRK05901 298 DEGDSQFGDFIEDSEAVSPVDAVSFTLLQDQLQEVLETLSEREAGVIRMRFGLTDGQPKTLDEIGQVYGVTRERIRQIES 377 (398)
T ss_pred CCCCCCHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf 99865186641699999999999999999999999838999999999997589998960399999897969999999999
Q ss_pred HHHHHHCCHHHHHHHHHHHC
Q ss_conf 99998329677787566517
Q gi|254780289|r 662 KAIRKLKHPSRSKKLRSFLD 681 (682)
Q Consensus 662 ~a~~~l~~~~~~~~l~~~~~ 681 (682)
T Consensus 378 kAL~KLR~~~~~~~l~~~l~ 397 (398)
T PRK05901 378 KTMRKLRHPSRSQVLRDFLD 397 (398)
T ss_pred HHHHHHCCCHHHHHHHHHHC
T ss_conf 99999678378879999857