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