HHsearch alignment for GI: 254780237 and conserved domain: cd07030

>cd07030 RNAP_D D subunit of Archaeal RNA polymerase. The D subunit of archaeal RNA polymerase (RNAP) is involved in the assembly of RNAP subunits. RNAP is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. A single distinct RNAP complex is found in archaea, which may be responsible for the synthesis of all RNAs. The archaeal RNAP harbors homologues of all eukaryotic RNAP II subunits with two exceptions (RPB8 and RPB9). The 12 archaeal subunits are designated by letters and can be divided into three functional groups that are engaged in: (I) catalysis (A'/A", B'/B" or B); (II) assembly (L, N, D and P); and (III) auxiliary functions (F, E, H and K). The D subunit is equivalent to the RPB3 subunit of eukaryotic RNAP II. It contains two subdomains: one subdomain is similar the eukaryotic Rpb11/AC19/archaeal L subunit w
Probab=99.89  E-value=6.7e-22  Score=162.06  Aligned_cols=206  Identities=20%  Similarity=0.282  Sum_probs=153.7

Q ss_pred             CCCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEEEE---------CCCCCCCCCCCCCHHHHHHHHHHHCCC
Q ss_conf             78881589999616975667888999998741698306889998---------871443146646244499999840114
Q gi|254780237|r   22 QEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQI---------DGVLHEISSIKGVHEDLTDIILNIKGI   92 (340)
Q Consensus        22 ~~~~~~g~f~~~Ple~G~g~TlGNaLRRvLLssi~G~ait~vkI---------~gv~HEfs~i~GV~EDV~eIiLNLK~I   92 (340)
T Consensus         7 ~~~~~~~~F~l~----~~~~s~aNalRRillsevPt~Aid~V~i~~NtS~l~DE~laHRLglIPi~~~~~~~~--~~~~~   80 (259)
T cd07030           7 ELDDDRARFVLE----GVPPAFANAIRRAIISEVPTLAIDDVNIYENTSVLFDEMLAHRLGLIPLRTDLDLYK--YRSEC   80 (259)
T ss_pred             ECCCCEEEEEEE----CCCHHHHHHHHHHHHHCCCEEEEEEEEEEECCCCCCCHHHHHHHCCCCCCCCHHHHH--CCCCC
T ss_conf             768987999997----898999999999998739844778999997885254278887632654323644420--34432


Q ss_pred             EEEE--CCCCCEEEEEEEECCEEEEEEEEEC-CCCEEEECCCEEEEEECCCCEEEEEEEEECCCCC--------------
Q ss_conf             1777--2798279999994471699633513-8985998888089997789649999997468763--------------
Q gi|254780237|r   93 NLKM--SGDSHKRVTIFKRGPGVVTAGDIQT-VNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGY--------------  155 (340)
Q Consensus        93 ~~k~--~~~~~~~~~l~~~Gp~~vtA~Di~~-p~~veivNpd~~IaTl~~~~~l~iel~ie~G~GY--------------  155 (340)
T Consensus        81 ~~~~~~~~~~~v~~~l~~~~~~~v~s~dl~~~d~~v~p~~~dI~I~kL~~GQ~l~l~~~a~~G~Gk~HaKw~pv~~~~y~  160 (259)
T cd07030          81 SCGGAGCPLCTVTLTLSVEGPGTVYSGDLKSSDPDVKPVYDNIPIVKLGKGQKLVLEAYARLGRGKEHAKWQPTTACGYK  160 (259)
T ss_pred             CCCCCCCCCCEEEEEEEEECCCEEECCCCCCCCCCCEECCCCEEEEEECCCCEEEEEEEEECCCCCCCCCCCCCEEEEEE
T ss_conf             23568998738999999864956880214337998256689827999579998999999951533205402651489984


Q ss_pred             -EECCC---------CCCCCCCCCEECCCCCHHEEEEEEE---------EEEEECCCCCCCCCEEEEEEEECCCCCHHHH
Q ss_conf             -20344---------4465575430212431111442235---------7764116887762189999993896177799
Q gi|254780237|r  156 -VPAKH---------HRTENDPIGLITIDALYSPIKKVSY---------TVESAREGQVLDYDKLSMTIDTDGSITGEDS  216 (340)
Q Consensus       156 -~~~e~---------~~~~~~~ig~i~iDa~FsPV~~Vny---------~Ve~~rvg~~t~~dkL~lEI~TnGsi~P~eA  216 (340)
T Consensus       161 ~~p~i~~~~~~~~~~~~~~~~p~~v~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~I~~~~~~d~F~F~VES~G~l~p~~i  240 (259)
T cd07030         161 YYPVIEIDEDCDGCGKCVEECPRGVLELEEGKVVVEDLEDCSLCKLCERACDAGAIRVGWDEDRFIFEVESDGSLPPKEI  240 (259)
T ss_pred             CCCCEEEECCCHHHHHHHHHCCCCCCCCCCCCCEECCCCCCCHHHHHHHHCCCCCEEEEEECCEEEEEEEECCCCCHHHH
T ss_conf             04416861531577887765754421234575301354212077899864246834898508979999990387299999


Q ss_pred             HHHHHHHHHHHHHHHHC
Q ss_conf             99999999998887622
Q gi|254780237|r  217 VALASRILQDQLGMFIN  233 (340)
Q Consensus       217 l~~Aa~iL~~~l~~f~~  233 (340)
T Consensus       241 v~~A~~iL~~kl~~l~~  257 (259)
T cd07030         241 LLEALRILKEKADELIE  257 (259)
T ss_pred             HHHHHHHHHHHHHHHHH
T ss_conf             99999999999999996