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