HHsearch alignment for GI: 254780611 and conserved domain: PRK12544

>PRK12544 RNA polymerase sigma factor; Provisional.
Probab=99.59  E-value=2.3e-13  Score=108.81  Aligned_cols=184  Identities=13%  Similarity=0.148  Sum_probs=120.4

Q ss_pred             CHHHHHH-----HHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCC
Q ss_conf             5999999-----99943077875655557999988899999988899898621853456899975778999999853202
Q gi|254780611|r   46 DLSAAHR-----LVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS  120 (302)
Q Consensus        46 d~~Ar~~-----Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~  120 (302)
T Consensus        12 ~~~~~~~~~~~~l~e~y~~~L~r~A~r~l~d~~~AEDlvQEtFlka~~~l~~F~g~--s~f~tWL~~Ia~N~~iD~lRk~   89 (207)
T PRK12544         12 SSDAVNVLQDPVFLEDLRAQMLKFAKLQLRDNHLAEDAVQEALFSAYQNADSFAGR--AAFKTWVFAILKNKIIDLLRQK   89 (207)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCC--CCHHHHHHHHHHHHHHHHHHHH
T ss_conf             28887611589999999999999999994999999999999999999817743888--8609899999999999999985


Q ss_pred             CCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCH
Q ss_conf             46001102300358999999997887866244788824677888618983211000000122343355202323453200
Q gi|254780611|r  121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQW  200 (302)
Q Consensus       121 ~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~  200 (302)
T Consensus        90 ~r~~~~~~--------------------~---~-~~~~~-----------------------~~~~~~~~d---~~g~~~  119 (207)
T PRK12544         90 KRHVSASQ--------------------L---E-DGDEG-----------------------EALIEALFD---ESGHWQ  119 (207)
T ss_pred             CCCCCCCC--------------------C---C-CCCCH-----------------------HHHHHHHHC---CCCCCC
T ss_conf             16565210--------------------1---3-45410-----------------------134666511---123433


Q ss_pred             HCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf             00012356870565566666667779999996219999999999982788888989999997789999999999999999
Q gi|254780611|r  201 QDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKV  280 (302)
Q Consensus       201 ~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kL  280 (302)
T Consensus       120 ~~e~p~~~~~p----ee~l~~~e~~~~l~~aL~~Lp~~~R~vl~Lr~~eg--lS~~EIAe~Lgis~~tVks~L~RAR~~L  193 (207)
T PRK12544        120 KDERPQKWDQP----EEGVEQEQFWRIFDACLDALPAKYARVFMMREFIE--LETPEICHNEDLTVSNLNVMLYRSRLRL  193 (207)
T ss_pred             CCCCCCCCCCH----HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf             33465333898----99999999999999999839999999999999819--9999999997979999999999999999


Q ss_pred             HHHHHHH
Q ss_conf             9999974
Q gi|254780611|r  281 QESIQKQ  287 (302)
Q Consensus       281 R~~l~~~  287 (302)
T Consensus       194 r~~Le~~  200 (207)
T PRK12544        194 RECLENH  200 (207)
T ss_pred             HHHHHHH
T ss_conf             9999984