HHsearch alignment for GI: 254780611 and conserved domain: PRK12517
>PRK12517 RNA polymerase sigma factor; Provisional.
Probab=99.50 E-value=3.2e-12 Score=101.22 Aligned_cols=163 Identities=15% Similarity=0.175 Sum_probs=115.1
Q ss_pred HCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf 28599999999943077875655557999988899999988899898621853456899975778999999853202460
Q gi|254780611|r 44 HGDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSL 123 (302)
Q Consensus 44 ~gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~ 123 (302)
T Consensus 19 ~~~~~AFe~L~~~y~~~ly~~a~~~~~d~~~AeDl~QEtFlk~~~~~~~~~~~~--~~~tWL~~-----I~---~~~--- 85 (188)
T PRK12517 19 LSKQRRYEALVKALHADIYRYAYWLCKDKHIAEDLVQETFLRAWRSLDSLKDEK--AAKAWLIT-----IL---RRE--- 85 (188)
T ss_pred HCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCC--CHHHHHHH-----HH---HHH---
T ss_conf 135999999999999999999999949999999999999999999887647963--18999999-----99---999---
Q ss_pred HHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCC
Q ss_conf 01102300358999999997887866244788824677888618983211000000122343355202323453200000
Q gi|254780611|r 124 VKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDW 203 (302)
Q Consensus 124 IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~ 203 (302)
T Consensus 86 --------------~~~r~~r~~-------~---~~------------------------~~~~~~~------------- 104 (188)
T PRK12517 86 --------------NARRFERKQ-------F---DL------------------------VDIEDDS------------- 104 (188)
T ss_pred --------------HHHHHHHCC-------C---CC------------------------CCCCCCC-------------
T ss_conf --------------889998615-------7---75------------------------6522000-------------
Q ss_pred CCCC-CCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q ss_conf 1235-687056556666666777999999621999999999998278888898999999778999999999999999999
Q gi|254780611|r 204 LVYD-HDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQE 282 (302)
Q Consensus 204 l~~~-~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~ 282 (302)
T Consensus 105 ~~~~~~~~~e~--------~~~~~~l~~~l~~Lp~~~R~vi~L~~~eg--~s~~EIA~~Lgis~~tVksrl~RAr~~Lr~ 174 (188)
T PRK12517 105 IEDDLSSSSEE--------EMEQYWLRRQIAKLDPEYREPLLLQVIGG--FSGEEIAEILDLNKNTVMTRLFRARNQLKE 174 (188)
T ss_pred CCCCCCCCCHH--------HHHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf 24666788168--------99999999999769999999999999839--999999999893999999999999999999
Q ss_pred HHHHHHCC
Q ss_conf 99974012
Q gi|254780611|r 283 SIQKQVEL 290 (302)
Q Consensus 283 ~l~~~~~~ 290 (302)
T Consensus 175 ~Le~~~e~ 182 (188)
T PRK12517 175 ALEKPDEV 182 (188)
T ss_pred HHCCHHHH
T ss_conf 97420275