HHsearch alignment for GI: 254780289 and conserved domain: PRK12537
>PRK12537 RNA polymerase sigma factor; Provisional.
Probab=98.81 E-value=5.9e-07 Score=73.87 Aligned_cols=176 Identities=12% Similarity=0.185 Sum_probs=119.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEHHHHH
Q ss_conf 26889999998765332112468999875557899988752235677788754436799998874385457312010289
Q gi|254780289|r 423 SISEFRHIVSMVRKGECEASIAKKEMVEANLRLVISVAKKYTNRGLQFLDLIQEGNIGLMKAAEKFDWCLGYKFSTYAMW 502 (682)
Q Consensus 423 ~i~ElK~i~r~I~~ge~e~~~AK~~l~~anlr~v~~~~~~~~~~~~~~~~~~~~~~~~l~~a~~~~~~~~g~~f~tya~~ 502 (682)
T Consensus 6 ~p~d~e~ll~~~~~GD~---~Af~~Ly~~y~~~l~~~~~~~~~d~~~AeDivQe~Fl~~~~~~~~~~~~~~~-~~---~- 77 (184)
T PRK12537 6 APFDYEACLQACARGER---RALQRLYQQESARLLGVARRIVRDRALAEDIVHDAFIKIWTKAASFDAARGS-AR---G- 77 (184)
T ss_pred CCCCHHHHHHHHHHCCH---HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCCCCCCCC-HH---H-
T ss_conf 99999999999995889---9999999999999999999992999999999999999999860416844263-99---9-
Q ss_pred HHHHHHHHHHHHCCCEEECCCHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf 89999999997228704614205889899999999987760889997899987099989999999860898755363588
Q gi|254780289|r 503 WVKQAITRSIADQSCTIRIPVHMRDKIHKVVRTARRMSNKIKREPTPEEIAKKLAMPVEGVRKVLKITKEPISLETPIGD 582 (682)
Q Consensus 503 ~i~~~i~~~~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~sl~~~~~~ 582 (682)
T Consensus 78 WL~~Iarn~~----------------~~~lR~~~r~-------~~~~~~~~------------------~~~~~~----- 111 (184)
T PRK12537 78 WIYSVTRHLA----------------LNTLRDTRRE-------VVLDDDAS------------------EQATAQ----- 111 (184)
T ss_pred HHHHHHHHHH----------------HHHHHHHCCC-------CCCCCHHH------------------HHCCCC-----
T ss_conf 9999999999----------------9999985065-------66651002------------------101346-----
Q ss_pred CCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCHHHHHHHHHH
Q ss_conf 99860475623898899899999999999999997329988999999981879867468899989966789999999999
Q gi|254780289|r 583 EDTSHLGDFIEDKNAVSPLDSAIQANLRETTTRVLASLTPREERVLRMRFGIGMNTDHTLEEVGKQFCVTRERIRQIEAK 662 (682)
Q Consensus 583 ~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~l~~l~~re~~v~~~r~g~~~~~~~tl~e~~~~~~~~~er~rqi~~~ 662 (682)
T Consensus 112 ----------~~~~~~~---~~~~~~~~~~l~~~l~~L~~~~r~~i~l~~----~eg~s~~EIA~~l~is~~TVk~rl~r 174 (184)
T PRK12537 112 ----------GWQEIID---DFDLWVNSGKIHRCLEQLEPARRNCILHAY----VDGCSHAEIAQRLGAPLGTVKAWIKR 174 (184)
T ss_pred ----------CCCCCCC---HHHHHHHHHHHHHHHHHCCHHHHHHHHHHH----HCCCCHHHHHHHHCCCHHHHHHHHHH
T ss_conf ----------7777556---798999999999999809998999999988----43999999999989299999999999
Q ss_pred HHHHHCC
Q ss_conf 9998329
Q gi|254780289|r 663 AIRKLKH 669 (682)
Q Consensus 663 a~~~l~~ 669 (682)
T Consensus 175 A~~~LR~ 181 (184)
T PRK12537 175 SLKALRE 181 (184)
T ss_pred HHHHHHH
T ss_conf 9999998