HHsearch alignment for GI: 254780289 and conserved domain: PRK12427
>PRK12427 flagellar biosynthesis sigma factor; Provisional.
Probab=100.00 E-value=1.4e-45 Score=378.77 Aligned_cols=221 Identities=19% Similarity=0.336 Sum_probs=193.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC---CCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHHH
Q ss_conf 987653321124689998755578999887522356---77788754436799998874385457312010289899999
Q gi|254780289|r 432 SMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRG---LQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMWWVKQAI 508 (682)
Q Consensus 432 r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~---~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~~i~~~i 508 (682)
T Consensus 2 ~~~~~~~~~~~~~k~~lV~~~L~LV~~ia~r~~~~~~~~vd~dDLiq~G~iGLi~Ai~rFD~~~g-~F~tYA~~rIrGaI 80 (229)
T PRK12427 2 REFEACLTLTAAEEGKYLNAYLPLVKRIVRQLSFQADSVIGKEDMQQIALMGLLEALRRYGHPDG-QFAAYAVHRIRGSI 80 (229)
T ss_pred CCCHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCC-CHHHHHHHHHHHHH
T ss_conf 65220356899999999999599999999999742877798888999999999999984499898-85999999999999
Q ss_pred HHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHH--HCCCCCCCCCCCCCCCC
Q ss_conf 9999722870461420588989999999998776088999789998709998999999986--08987553635889986
Q gi|254780289|r 509 TRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKI--TKEPISLETPIGDEDTS 586 (682)
Q Consensus 509 ~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~--~~~~~sl~~~~~~~~~~ 586 (682)
T Consensus 81 ~d~lR~~~~---~pR~~r~~~~ki~~a~~~l~~~lgr~Pt~~EiA~~l~is~~~v~~~~~~~~~~~~~sld~~~~~e~~~ 157 (229)
T PRK12427 81 LDQLREHDW---RPRRLRQKTHKTNEAIRQIAKRLGHEPNFEEISAELNLTADEYQEYLLLENAGAMESLDEILALEAHN 157 (229)
T ss_pred HHHHHHHCC---CCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCC
T ss_conf 999987213---75999999999999999999985889999999989199999999999987366875723344578876
Q ss_pred EEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf 04756238988998999999999999999973299889999999818798674688999899667899999999999998
Q gi|254780289|r 587 HLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAKAIRK 666 (682)
Q Consensus 587 ~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~a~~~ 666 (682)
T Consensus 158 ~---~~~~---~~~~---e~~~~~~~L~~al~~L~erEr~Vi~l~y----~e~ltlkEIa~~LgvS~~RVsQi~~kal~k 224 (229)
T PRK12427 158 D---ILQS---RDLE---ENIIIEDNLKQAISQLDEREQMILHLYY----QQELSMKEIAQVLDLTEARICQLNKKLVQK 224 (229)
T ss_pred C---CCCC---CCHH---HHHHHHHHHHHHHHHCCHHHHHHHHHHC----CCCCCHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_conf 5---4567---6646---7899999999999719999999999980----589989999999798899999999999999
Q ss_pred HCC
Q ss_conf 329
Q gi|254780289|r 667 LKH 669 (682)
Q Consensus 667 l~~ 669 (682)
T Consensus 225 LR~ 227 (229)
T PRK12427 225 IKS 227 (229)
T ss_pred HHH
T ss_conf 884