HHsearch alignment for GI: 254780289 and conserved domain: PRK09210
>PRK09210 RNA polymerase sigma factor RpoD; Validated.
Probab=100.00 E-value=0 Score=823.65 Aligned_cols=357 Identities=53% Similarity=0.843 Sum_probs=328.4
Q ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf 89999999978784886789997526843599888999999998479778327841000012364321101112233444
Q gi|254780289|r 28 DDSWKKMIKLARQRGYVTIEELNAFLPPDEVSSEQMEDTVAMLSNMGINVVDGDDLEDEEGSEDSLDLASSASNSSVFLQ 107 (682)
Q Consensus 28 ~~~ik~LI~~gke~GylTydeIn~~LP~d~~~~e~ie~i~~~L~~~GI~Vve~~~~~~~~~~~~~~~~~~~~~~e~~~~~ 107 (682)
T Consensus 12 ~~~~~~l~~~~~~~g~~~~~ei~~~~~~~~~~~~~~~~~~~~l~~~~i~i~~~~~~~~~~~~~~~~~~~~------~~~~ 85 (368)
T PRK09210 12 EVVVKELIEKGKKRGTLTYDEIAEKLQPFELDSDQIDDLYERLEDAGISIVDENGNPSSKALQEEKKEEE------LEDE 85 (368)
T ss_pred HHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCEEECCCCCCCCCCCCCCCCCCC------HHHH
T ss_conf 9999999999987697559999987043489999999999999987898847877642100001111100------0000
Q ss_pred HHHCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCHHHHHHHHH
Q ss_conf 42003457777289999998569768897889999999998899999998728238999999998731171036787642
Q gi|254780289|r 108 KRKDSADRSTDDPVRMYLREMGSIELLSREGEIAIAKRIEAGRAMMMASLCESPLTFQALIIWRDELNDGTTLLREIIDL 187 (682)
Q Consensus 108 ~~~~~e~~rtdDPVRMYLREMG~V~LLTREgEIeIAKRIE~G~~~i~~al~~~P~ti~~il~~~e~i~~ge~~LrdIIDl 187 (682)
T Consensus 86 ~~~~~~~~~~~d~v~~YL~eI~~~pLLt~eEE~~La~r~~~GD------------------------------------- 128 (368)
T PRK09210 86 DLSVPPGVKINDPVRMYLKEIGRVPLLTAEEEIELAKRIEEGD------------------------------------- 128 (368)
T ss_pred CCCCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHCC-------------------------------------
T ss_conf 0132114655858999999956788999999999999988157-------------------------------------
Q ss_pred HHCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf 10135433333334333332110001110001000000001221000011111013566665303443100022233455
Q gi|254780289|r 188 EACIGPESKGGFFHGTEGHSYQKREDSSQEKERDDVQETEGDIESAAKVSKDDRSKVDSPPENAENDERNLDEDEDDSAH 267 (682)
Q Consensus 188 d~t~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~e~~~e~~~~~~~~~~~~~~~~~~e~e~~~~~~e~e~de~~~ 267 (682)
T Consensus 129 -------------------------------------------------------------------------------- 128 (368)
T PRK09210 129 -------------------------------------------------------------------------------- 128 (368)
T ss_pred --------------------------------------------------------------------------------
T ss_conf --------------------------------------------------------------------------------
Q ss_pred HHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 55644421023479876689999999999999875210120007999999999999998621005778878999999999
Q gi|254780289|r 268 TLSAMEDQLRPKVMCALDEIAEVYRELRSLQDNAVNGQKDEKSSVKCKVLKEKLVKLVGSLSLNQSRIDLLVEQLYDISK 347 (682)
Q Consensus 268 sla~~e~eLk~~v~e~l~~i~~~~~kl~k~~~~~~~~~~~~~~~kk~~kl~~eL~e~~~~lkl~~k~iE~L~~~l~~~~k 347 (682)
T Consensus 129 -------------------------------------------------------------------------------- 128 (368)
T PRK09210 129 -------------------------------------------------------------------------------- 128 (368)
T ss_pred --------------------------------------------------------------------------------
T ss_conf --------------------------------------------------------------------------------
Q ss_pred HHHHHHHHHHHHHHHHCCCHHHHHHHCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999999999712535777763167768989999986135510676554345677653223333222221126889
Q gi|254780289|r 348 RIMHNEGELLRLAQSYGIKRDVFLERHQGRELDPHWVSYAKDFPEGEWKNFVACEVDSILKIRNEIKSISVETGISISEF 427 (682)
Q Consensus 348 ~Ir~~Er~L~rl~~k~~i~R~~Fi~~f~gnEt~~~wl~~~~~~~~~~~~~~l~~~~~eI~~~q~kL~~ie~~~gl~i~El 427 (682)
T Consensus 129 -------------------------------------------------------------------------------- 128 (368)
T PRK09210 129 -------------------------------------------------------------------------------- 128 (368)
T ss_pred --------------------------------------------------------------------------------
T ss_conf --------------------------------------------------------------------------------
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHH
Q ss_conf 99999876533211246899987555789998875223567778875443679999887438545731201028989999
Q gi|254780289|r 428 RHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQA 507 (682)
Q Consensus 428 K~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~ 507 (682)
T Consensus 129 --------------~~Ar~~Li~aNLRLVVsIAkkY~~~Gl~l~DLIQEGNiGLmkAVeKFDp~rG~RFSTYA~WWIRqa 194 (368)
T PRK09210 129 --------------EEAKQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQA 194 (368)
T ss_pred --------------HHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHH
T ss_conf --------------999999999838999999986668998989999986799999999729877995334669999999
Q ss_pred HHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCE
Q ss_conf 99999722870461420588989999999998776088999789998709998999999986089875536358899860
Q gi|254780289|r 508 ITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGDEDTSH 587 (682)
Q Consensus 508 i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~~~~~~ 587 (682)
T Consensus 195 I~raI~~q~r~IRiPvh~~e~~~kl~r~~r~L~q~lGrePt~eEIA~~lgi~~e~V~~i~~~~~~~~SLd~pvg~e~~s~ 274 (368)
T PRK09210 195 ITRAIADQARTIRIPVHMVETINKLIRVQRQLLQELGRDPTPEEIAEEMDMPPEKVREILKIAQEPVSLETPIGEEDDSH 274 (368)
T ss_pred HHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCH
T ss_conf 99999982785135424999999999999999998389998899998949989999999985388856688678877552
Q ss_pred EEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf 47562389889989999999999999999732998899999998187986746889998996678999999999999983
Q gi|254780289|r 588 LGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRKL 667 (682)
Q Consensus 588 ~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~l 667 (682)
T Consensus 275 l~d~i~D~~~~~p~e~~~~~~l~~~l~~~L~~L~~REr~Il~~RfGL~~~~~~TLeEIg~~lgvSRERVRQIE~kAL~KL 354 (368)
T PRK09210 275 LGDFIEDQDATSPADHAAYELLKEQLEEVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKL 354 (368)
T ss_pred HHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf 87552489999989999999999999999817999999999997599968961499999896979899999999999997
Q ss_pred CCHHHHHHHHHHHC
Q ss_conf 29677787566517
Q gi|254780289|r 668 KHPSRSKKLRSFLD 681 (682)
Q Consensus 668 ~~~~~~~~l~~~~~ 681 (682)
T Consensus 355 R~~~~~~~l~~~l~ 368 (368)
T PRK09210 355 RHPSRSKQLKDFLE 368 (368)
T ss_pred CCCHHHHHHHHHHC
T ss_conf 67368789888739