HHsearch alignment for GI: 254780611 and conserved domain: TIGR02997

>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family.
Probab=100.00  E-value=0  Score=603.79  Aligned_cols=257  Identities=28%  Similarity=0.522  Sum_probs=240.0

Q ss_pred             HHHHHHHHHHHCCCCCCHHHHHHHHHHHH----------------H----------------------------------
Q ss_conf             05999999840799999899999999999----------------8----------------------------------
Q gi|254780611|r   14 IGLSRYIHEIRKIPMLEKQEEYVLAKRYR----------------E----------------------------------   43 (302)
Q Consensus        14 ~~~~~yl~~i~~~~~Lt~eee~~l~~~~~----------------~----------------------------------   43 (302)
T Consensus         1 D~Vr~YL~eIGRvPLLt~eEEI~LArqVQry~~LLa~r~~~~~~~~~~~l~~~~~~l~~~~g~~ps~~ewA~~~~~~~~~   80 (336)
T TIGR02997         1 DLVRLYLQEIGRVPLLTPEEEIELARQVQRYEALLAVRDKADEKVQMMALEELREELEEQLGREPSKEEWAAALGLSEAE   80 (336)
T ss_pred             CCCHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHCCCCHHH
T ss_conf             92004445056678987688999989999999998875327889999999988999998508999878999871899889


Q ss_pred             -----H--------------------CCHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             -----2--------------------859999999994307787565555799998889999998889989862185345
Q gi|254780611|r   44 -----H--------------------GDLSAAHRLVTSHLRLVVKIAMGYRGYGLPISEVVSEGNIGLMQAVKKFDPERG   98 (302)
Q Consensus        44 -----~--------------------gd~~Ar~~Li~~nlrlV~~iA~~y~~~g~~~~DLiQeG~iGLi~Ai~kFDp~kG   98 (302)
T Consensus        81 l~~~l~G~~aWA~~a~l~leLk~~~r~G~RAK~kMi~ANLRLVVSvAKKYq~RglElLDLIQEG~lGL~RAVEKFDPtrG  160 (336)
T TIGR02997        81 LRQRLRGLQAWAEAAQLELELKLVLRQGQRAKEKMIKANLRLVVSVAKKYQNRGLELLDLIQEGTLGLERAVEKFDPTRG  160 (336)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCCCCCCC
T ss_conf             99998765788998422589999999789999999876022688999985136883356887634312211233577778


Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCCHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCC
Q ss_conf             68999757789999998532024600110230035899999999788786624478882467788861898321100000
Q gi|254780611|r   99 FRLATYSMWWIKAAMQEYILRSWSLVKIGTTANQKRLFFNLRRLKGHLQAITDNNLKPEQVVAIAKKLNVSESEVISMNC  178 (302)
Q Consensus        99 ~~FsTYA~~wIr~~I~~~i~~~~~~IRiP~~~~~r~l~~~~rk~~~~~~~~~~~~~~~~~~~eiA~~Lgis~~~v~~l~~  178 (302)
T Consensus       161 YKFSTYAYWWIRQ~ITRAIA~qSRTIRLPiH~~E-----KLnkiKK~qReL~q~lGR~Ps~~EiAe~lel~~~qvR~~l~  235 (336)
T TIGR02997       161 YKFSTYAYWWIRQGITRAIANQSRTIRLPIHITE-----KLNKIKKVQRELSQKLGRRPSEAEIAEALELEPEQVRELLQ  235 (336)
T ss_pred             CCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCHHH-----HHHHHHHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             8633012468756889998436883247410766-----66899899899999838897868999883889889999999


Q ss_pred             CCCCCCCHHHHC-CCCCCCCCCHHCCCCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCC--CCCC
Q ss_conf             012234335520-2323453200000123-56870565566666667779999996219999999999982788--8889
Q gi|254780611|r  179 RLAGDESLNALI-NSSDKNSSQWQDWLVY-DHDGQEQVLIEKEERKNRRNMLTRSMSVLNPRERRIFEARRLQE--NPVT  254 (302)
Q Consensus       179 ~~~~~~SLd~~i-~~~d~~~~~~~d~l~~-~~~~~~~~~~e~~e~~~~~~~L~~~l~~L~~rEr~II~~ry~~~--~~~T  254 (302)
T Consensus       236 ~~~~p~SLd~~VrG~--e~dt~LgdLl~d~~~~~P~~~~~----~~~l~~dL~~lL~~L~p~e~~VL~LRfGL~~~~~~T  309 (336)
T TIGR02997       236 RARQPVSLDTRVRGD--EEDTELGDLLEDEDGESPEEQVE----QESLRQDLESLLAELTPRERQVLRLRFGLDDGEPLT  309 (336)
T ss_pred             HHCCCCCCCCCCCCC--CCCCHHHHHCCCCCCCCCHHHHH----HHHHHHHHHHHHHHCCHHHHHHHHHHCCCCCCCCCC
T ss_conf             707874457732688--85422654326888998278999----999999999988637988999999857899897532


Q ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHH
Q ss_conf             899999977899999999999999999
Q gi|254780611|r  255 LENLSSEFEVSRERVRQIEARAFKKVQ  281 (302)
Q Consensus       255 l~EIa~~lgiS~eRVrQI~~~AL~kLR  281 (302)
T Consensus       310 L~eiG~~l~lSRERVRQiE~~AL~kLR  336 (336)
T TIGR02997       310 LAEIGERLNLSRERVRQIEAKALRKLR  336 (336)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHCC
T ss_conf             789998838836888899999975349