HHsearch alignment for GI: 254780611 and conserved domain: PRK12546
>PRK12546 RNA polymerase sigma factor; Provisional.
Probab=99.43 E-value=1.5e-11 Score=96.66 Aligned_cols=161 Identities=13% Similarity=0.132 Sum_probs=109.4
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCH
Q ss_conf 85999999999430778756555579999888999999888998986218534568999757789999998532024600
Q gi|254780611|r 45 GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERGFRLATYSMWWIKAAMQEYILRSWSLV 124 (302)
Q Consensus 45 gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG~~FsTYA~~wIr~~I~~~i~~~~~~I 124 (302)
T Consensus 5 ~~~~~~~~l~e-H~p~L~~fa~r~~~~~~~AEDlvQEtflk~~~~l~~~~~~--~~~~tWL~~IarN~~~d~-------- 73 (188)
T PRK12546 5 KHRDPRDELVE-HLPALRAFAISLTRNVAAADDLVQDTVVKAWTNFDKFQEG--TNLRAWLFTILRNTFYSD-------- 73 (188)
T ss_pred CCHHHHHHHHH-HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHCCCC--CCHHHHHHHHHHHHHHHH--------
T ss_conf 30629999999-9999999999991999999999999999999978764765--313889999999999999--------
Q ss_pred HHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCHHCCC
Q ss_conf 11023003589999999978878662447888246778886189832110000001223433552023234532000001
Q gi|254780611|r 125 KIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNCRLAGDESLNALINSSDKNSSQWQDWL 204 (302)
Q Consensus 125 RiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~~~~~~~SLd~~i~~~d~~~~~~~d~l 204 (302)
T Consensus 74 --------------~Rk~~r~~--------~-----------------------------~~~~~~~---~-------~~ 92 (188)
T PRK12546 74 --------------RRKHKREV--------E-----------------------------DPEGVHA---A-------SL 92 (188)
T ss_pred --------------HHHHCCCC--------C-----------------------------CCCCCCC---C-------CC
T ss_conf --------------99744777--------7-----------------------------6421112---3-------34
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 23568705655666666677799999962199999999999827888889899999977899999999999999999999
Q gi|254780611|r 205 VYDHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQENPVTLENLSSEFEVSRERVRQIEARAFKKVQESI 284 (302)
Q Consensus 205 ~~~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~~~~Tl~EIa~~lgiS~eRVrQI~~~AL~kLR~~l 284 (302)
T Consensus 93 ~-~~~~~~~----~----~~~~~l~~aL~~LP~~~R~vl~L~~~eg--ls~~EIAe~Lgis~gTVKsRL~RAR~~Lr~~L 161 (188)
T PRK12546 93 A-VKPAHDG----R----LAMSDFRAAFAQLPDEQREALILVGASG--FSYEEAAEMCGVAVGTVKSRANRARARLAELL 161 (188)
T ss_pred C-CCCCCHH----H----HHHHHHHHHHHCCCHHHHHHHHHHHHCC--CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
T ss_conf 6-8987006----8----9999999999869999988958799829--89999999989399999999999999999987
Q ss_pred HHHH
Q ss_conf 9740
Q gi|254780611|r 285 QKQV 288 (302)
Q Consensus 285 ~~~~ 288 (302)
T Consensus 162 e~~~ 165 (188)
T PRK12546 162 QLEE 165 (188)
T ss_pred HCCC
T ss_conf 2721