HHsearch alignment for GI: 254780237 and conserved domain: cd06928

>cd06928 RNAP_alpha_NTD N-terminal domain of the Alpha subunit of Bacterial RNA polymerase. The bacterial alpha subunit of RNA polymerase (RNAP) consists of two independently folded domains: an amino-terminal domain (alphaNTD) and a carboxy-terminal domain (alphaCTD). AlphaCTD is not required for RNAP assembly but interacts with transcription activators. AlphaNTD is essential in vivo and in vitro for RNAP assembly and basal transcription. It is similar to the eukaryotic RPB3/AC40/archaeal D subunit, and contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit which is involved in dimerization; and the other is an inserted beta sheet subdomain. The alphaNTDs of plant plastid RNAP (PEP) are also included in this subfamily. PEP is largely responsible for the transcription of photosynthetic genes and is closely related to the multi-subunit bacterial RNAP, which is a large multi-subunit complex responsible for the synthesis of all bacterial RNAs. The bac
Probab=100.00  E-value=0  Score=570.42  Aligned_cols=212  Identities=50%  Similarity=0.813  Sum_probs=206.7

Q ss_pred             CCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCCCEEEECC-
Q ss_conf             3678881589999616975667888999998741698306889998871443146646244499999840114177727-
Q gi|254780237|r   20 LGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSG-   98 (340)
Q Consensus        20 ~~~~~~~~g~f~~~Ple~G~g~TlGNaLRRvLLssi~G~ait~vkI~gv~HEfs~i~GV~EDV~eIiLNLK~I~~k~~~-   98 (340)
T Consensus         3 ~~~~~~~yg~f~i~Pl~~G~g~TlGnaLRR~LLs~i~G~ait~vkI~gv~hEfs~i~GV~Edv~~IlLNLK~i~~~~~~~   82 (215)
T cd06928           3 VENKRENYGRFVIEPLERGQGTTLGNALRRVLLSSLPGAAITAVKIEGVLHEFSTIPGVREDVLEILLNLKEIVFKSDSE   82 (215)
T ss_pred             CCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHEEEEECCC
T ss_conf             01388857799996588972614678999988756984289999999942102348882340899997565049995279


Q ss_pred             CCCEEEEEEEECCEEEEEEEEECCCCEEEECCCEEEEEECCCCEEEEEEEEECCCCCEECCCCCCCCCCCCEECCCCCHH
Q ss_conf             98279999994471699633513898599888808999778964999999746876320344446557543021243111
Q gi|254780237|r   99 DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITIDALYS  178 (340)
Q Consensus        99 ~~~~~~~l~~~Gp~~vtA~Di~~p~~veivNpd~~IaTl~~~~~l~iel~ie~G~GY~~~e~~~~~~~~ig~i~iDa~Fs  178 (340)
T Consensus        83 ~~~~~~~l~~~Gp~~vtA~Di~~p~~ieivNpdq~IaTl~~~~~l~~el~i~~G~GY~~~~~~~~~~~~~g~i~iDa~Fs  162 (215)
T cd06928          83 DEPQVLRLKVKGPGVVTAADIELPSGVEIVNPDQYIATLTEDASLEMELRIEKGRGYVPAEENKSEEKPIGFIPIDAIFS  162 (215)
T ss_pred             CCCEEEEEEEECCEEEEEEHCCCCCCEEEECCCEEEEEECCCCEEEEEEEEECCEEEEEHHHCCCCCCCCCEEECCCCCC
T ss_conf             98489999970680599203058886699689979999778965999999989642467444466667675087687554


Q ss_pred             EEEEEEEEEEEECCCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             14422357764116887762189999993896177799999999999988876
Q gi|254780237|r  179 PIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMF  231 (340)
Q Consensus       179 PV~~Vny~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eAl~~Aa~iL~~~l~~f  231 (340)
T Consensus       163 PV~~Vny~Ve~~~~~~~~~~e~L~lEI~TnGsi~P~~Al~~Aa~iL~~~~~~f  215 (215)
T cd06928         163 PVRKVNYSVESTRVGQRTDYEKLILEIWTNGSISPEEALAQAAKILINHFSPF  215 (215)
T ss_pred             CEEEEEEEEEEEECCCCCCCEEEEEEEEECCCCCHHHHHHHHHHHHHHHHHCC
T ss_conf             64799999999405889874699999998998999999999999999986269