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