HHsearch alignment for GI: 254780611 and conserved domain: PRK09648

>PRK09648 RNA polymerase sigma factor SigD; Reviewed.
Probab=99.76  E-value=3.8e-16  Score=127.42  Aligned_cols=179  Identities=17%  Similarity=0.238  Sum_probs=127.0

Q ss_pred             CHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCC----CCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHH
Q ss_conf             989999999999982859999999994307787565555799----9988899999988899898621853456899975
Q gi|254780611|r   30 EKQEEYVLAKRYREHGDLSAAHRLVTSHLRLVVKIAMGYRGY----GLPISEVVSEGNIGLMQAVKKFDPERGFRLATYS  105 (302)
Q Consensus        30 t~eee~~l~~~~~~~gd~~Ar~~Li~~nlrlV~~iA~~y~~~----g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA  105 (302)
T Consensus         5 ~~~~l~~Li~~a~-~GD~~Af~~L~~~~~~~v~r~~~~~l~~~~~~~~dAeDl~Qe~fl~~~~~l~~f~~-~~~~f~~Wl   82 (187)
T PRK09648          5 AGEELDALVAEAV-AGDRRALREVLETIHPLVVRYCRARLGTVERSGLSADDVAQEVCLAVITALPRYRD-QGRPFLAFV   82 (187)
T ss_pred             CHHHHHHHHHHHH-HCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCCC-CCCCHHHHH
T ss_conf             2178999999998-45899999999999999999999997144587643999999999999983766266-778499999


Q ss_pred             HHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCC
Q ss_conf             77899999985320246001102300358999999997887866244788824677888618983211000000122343
Q gi|254780611|r  106 MWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDES  185 (302)
Q Consensus       106 ~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~S  185 (302)
T Consensus        83 ~~Ia~n~~~d~~----------------------R~~~r~--------~~~~~---------------------------  105 (187)
T PRK09648         83 YGIAAHKVADAH----------------------RAAGRD--------KAYPT---------------------------  105 (187)
T ss_pred             HHHHHHHHHHHH----------------------HHHHCC--------CCCCC---------------------------
T ss_conf             999999999999----------------------987467--------64321---------------------------


Q ss_pred             HHHHCCCCCCCCCCHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCC
Q ss_conf             35520232345320000012356870565566666667779999996219999999999982788888989999997789
Q gi|254780611|r  186 LNALINSSDKNSSQWQDWLVYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVS  265 (302)
Q Consensus       186 Ld~~i~~~d~~~~~~~d~l~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS  265 (302)
T Consensus       106 -~~-~~----------~-~~~~~~~pe~~~~~~----e~~~~l~~~l~~Lp~~~R~vl~L~~~~g--~s~~EIA~~lg~s  166 (187)
T PRK09648        106 -EE-VP----------E-RPSDEAGPEQRALEA----ESSARMRELLEILPEKQREILILRVVVG--LSAEETAEAVGST  166 (187)
T ss_pred             -CC-CC----------C-CCCCCCCHHHHHHHH----HHHHHHHHHHHHCCHHHHHHHHHHHHCC--CCHHHHHHHHCCC
T ss_conf             -12-33----------3-478778858999989----9999999999839999999999999849--9999999998939


Q ss_pred             HHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999999997
Q gi|254780611|r  266 RERVRQIEARAFKKVQESIQK  286 (302)
Q Consensus       266 ~eRVrQI~~~AL~kLR~~l~~  286 (302)
T Consensus       167 ~~tVk~~l~RA~~~Lr~~lE~  187 (187)
T PRK09648        167 PGAVRVAQHRALSRLRAEIEQ  187 (187)
T ss_pred             HHHHHHHHHHHHHHHHHHHCC
T ss_conf             999999999999999998659