HHsearch alignment for GI: 254780237 and conserved domain: smart00662

>smart00662 RPOLD RNA polymerases D. DNA-directed RNA polymerase subunit D and bacterial alpha chain
Probab=100.00  E-value=0  Score=335.61  Aligned_cols=195  Identities=40%  Similarity=0.639  Sum_probs=179.3

Q ss_pred             EEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCCCEEEECCC-------
Q ss_conf             5899996169756678889999987416983068899988714431466462444999998401141777279-------
Q gi|254780237|r   27 RTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGD-------   99 (340)
Q Consensus        27 ~g~f~~~Ple~G~g~TlGNaLRRvLLssi~G~ait~vkI~gv~HEfs~i~GV~EDV~eIiLNLK~I~~k~~~~-------   99 (340)
T Consensus         1 ~~kF~l~~----~~~tiaNALRR~lLseip~~AI~~V~I~~------n~s~l~eevl~~rL~Lipi~~~~~~~~~~~~~~   70 (224)
T smart00662        1 RAKFVLEP----YGLTLANALRRVLLSSVPGMAVTEVEIEG------NTSGVQDEVLAHRLGLKPLASDPDGDEYQRDCE   70 (224)
T ss_pred             CCEEEEEC----CCCHHHHHHHHHHHHCCCCEEEEEEEEEE------CCCCCHHHHHHHHHCCCEEEEECCCCCCCCCCC
T ss_conf             96899968----87157999999998659540579999980------898864679999846830687424444443322


Q ss_pred             -------CCEEEEEEEECCEEEEEEEEECC--CCEEEECCCEEEEEECCCCEEEEEEEEECCCCCEECCCCCC---CCCC
Q ss_conf             -------82799999944716996335138--98599888808999778964999999746876320344446---5575
Q gi|254780237|r  100 -------SHKRVTIFKRGPGVVTAGDIQTV--NDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRT---ENDP  167 (340)
Q Consensus       100 -------~~~~~~l~~~Gp~~vtA~Di~~p--~~veivNpd~~IaTl~~~~~l~iel~ie~G~GY~~~e~~~~---~~~~  167 (340)
T Consensus        71 ~~~~~~~~~v~~~L~~~gp~~V~a~Dl~~~~~~~v~~vn~~i~I~~L~~gq~l~~~~~~~~G~G~~hak~~p~~~~~~~~  150 (224)
T smart00662       71 CEEGCEKCSVTLTLDVKGPGEVTAGDLKSDSDPDVEIVNPDIPIAKLREGQELELEARAEKGRGYVHAKWSPVSTVEYRY  150 (224)
T ss_pred             CCCCCCCCEEEEEEEEECCCEEEHHHCCCCCCCCCEECCCCEEEEEECCCCEEEEEEEEECCCCCCCCCCCCCCCCCCCC
T ss_conf             24578773699999985464468566104788971760899089996799759999999956721102106666433442


Q ss_pred             CCEECCCCCHHEEEEEEEEEEEECCCCCCC----------CCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             430212431111442235776411688776----------2189999993896177799999999999988876
Q gi|254780237|r  168 IGLITIDALYSPIKKVSYTVESAREGQVLD----------YDKLSMTIDTDGSITGEDSVALASRILQDQLGMF  231 (340)
Q Consensus       168 ig~i~iDa~FsPV~~Vny~Ve~~rvg~~t~----------~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~f  231 (340)
T Consensus       151 ~~~i~id~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~f~IeT~Gsi~p~~al~~A~~iL~~kl~~f  224 (224)
T smart00662      151 IPRIPVDASFSPVDRVAYQVECPRVVQRTDCCRECDEGEEYDKLIFDVETNGSLKPEEAVLEAAKILKEKLEAF  224 (224)
T ss_pred             CCEEEECCCCCHHHEEEEEEECCCCCCCCCCCCCCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHCC
T ss_conf             20354025227012353244267553424443000135888779999995787499999999999999997539