HHsearch alignment for GI: 254780611 and conserved domain: PRK12427

>PRK12427 flagellar biosynthesis sigma factor; Provisional.
Probab=100.00  E-value=0  Score=346.41  Aligned_cols=216  Identities=16%  Similarity=0.232  Sum_probs=176.3

Q ss_pred             HCCHHHHHHHHHHHHHHHHHHHHHHCCCC---CCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCC
Q ss_conf             28599999999943077875655557999---988899999988899898621853456899975778999999853202
Q gi|254780611|r   44 HGDLSAAHRLVTSHLRLVVKIAMGYRGYG---LPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRS  120 (302)
Q Consensus        44 ~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g---~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~  120 (302)
T Consensus         9 ~~~~~~k~~lV~~~L~LV~~ia~r~~~~~~~~vd~dDLiq~G~iGLi~Ai~rFD~~~g-~F~tYA~~rIrGaI~d~lR~~   87 (229)
T PRK12427          9 TLTAAEEGKYLNAYLPLVKRIVRQLSFQADSVIGKEDMQQIALMGLLEALRRYGHPDG-QFAAYAVHRIRGSILDQLREH   87 (229)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCC-CHHHHHHHHHHHHHHHHHHHH
T ss_conf             6899999999999599999999999742877798888999999999999984499898-859999999999999999872


Q ss_pred             CCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCC--CCCCCCHHHHCCCCCCCCC
Q ss_conf             46001102300358999999997887866244788824677888618983211000000--1223433552023234532
Q gi|254780611|r  121 WSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCR--LAGDESLNALINSSDKNSS  198 (302)
Q Consensus       121 ~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~--~~~~~SLd~~i~~~d~~~~  198 (302)
T Consensus        88 ~~~---p-----R~~r~~~~ki~~a~~~l~~~lgr~Pt~~EiA~~l~is~~~v~~~~~~~~~~~~~sld~~~~~e~~~~-  158 (229)
T PRK12427         88 DWR---P-----RRLRQKTHKTNEAIRQIAKRLGHEPNFEEISAELNLTADEYQEYLLLENAGAMESLDEILALEAHND-  158 (229)
T ss_pred             CCC---C-----HHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCC-
T ss_conf             137---5-----9999999999999999999858899999999891999999999999873668757233445788765-


Q ss_pred             CHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf             00000123568705655666666677799999962199999999999827888889899999977899999999999999
Q gi|254780611|r  199 QWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFK  278 (302)
Q Consensus       199 ~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~  278 (302)
T Consensus       159 ----~~-~-~~~~~e-------~~~~~~~L~~al~~L~erEr~Vi~l~y~e--~ltlkEIa~~LgvS~~RVsQi~~kal~  223 (229)
T PRK12427        159 ----IL-Q-SRDLEE-------NIIIEDNLKQAISQLDEREQMILHLYYQQ--ELSMKEIAQVLDLTEARICQLNKKLVQ  223 (229)
T ss_pred             ----CC-C-CCCHHH-------HHHHHHHHHHHHHHCCHHHHHHHHHHCCC--CCCHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf             ----45-6-766467-------89999999999971999999999998058--998999999979889999999999999


Q ss_pred             HHHHHH
Q ss_conf             999999
Q gi|254780611|r  279 KVQESI  284 (302)
Q Consensus       279 kLR~~l  284 (302)
T Consensus       224 kLR~~f  229 (229)
T PRK12427        224 KIKSFF  229 (229)
T ss_pred             HHHHHC
T ss_conf             988439