HHsearch alignment for GI: 254780142 and conserved domain: TIGR02389

>TIGR02389 RNA_pol_rpoA2 DNA-directed RNA polymerase, subunit A''; InterPro: IPR012757 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of the archaeal A'' subunit of the DNA-directed RNA polymerase. The example from Methanococcus jannaschii contains an intein.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006350 transcription.
Probab=100.00  E-value=0  Score=568.27  Aligned_cols=339  Identities=27%  Similarity=0.364  Sum_probs=224.6

Q ss_pred             CCCEECHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEECCCCEEEEEEEEEEECC-CCCEEEEECCCCEEE
Q ss_conf             7852000101460211110078898776420245432221122024014876897211346517-887789742760466
Q gi|254780142|r  902 RGSLVNVGEAVGVIAAQSIGEPGTQLTMRTFHLGGAVTVMDRSFIESPCDGIVKIKNRNVCRNS-TNDLISMGRNTTLQI  980 (1398)
Q Consensus       902 ~~~lv~pGe~VG~iAAQSIGEP~TQmTLnTFHfAGVAS~~~~~~iknvTlGVPRlkEi~~~~n~-~~~~i~vs~~~~~~i  980 (1398)
T Consensus        38 ~~~li~P~EAvGiVAAQSiGEPGTQMTmRTFHYAGv~El-------nVTlGLPRLIEIVDArk~PSTP~MtI------YL  104 (397)
T TIGR02389        38 LRSLIDPGEAVGIVAAQSIGEPGTQMTMRTFHYAGVAEL-------NVTLGLPRLIEIVDARKTPSTPLMTI------YL  104 (397)
T ss_pred             HHHHCCCCCCCEEEEEEEECCCHHHHHHHHHHHHHHHHH-------HHHCCCCCCEEEECCCCCCCCCEEEE------EE
T ss_conf             764106688610388442188454787776657766788-------76447840145450666789863799------62


Q ss_pred             EECCCC----EEEEEECCCHHCCCCCCCCEEECCEEEEECCCCCCEEEECCCCEEEEEEECCCCEEHHHHHCCCCCEEEE
Q ss_conf             406776----0000001100001356785532250786213543113202463689753127832001230236860267
Q gi|254780142|r  981 LDMSGQ----EQYSHRIMYGAKLFVDDGGVIECGQRISEWDPHTFPIITEVSGTVGFEDLVDGISVIESIGESTGIAKRK 1056 (1398)
Q Consensus       981 ~d~~~~----~~~~~ki~~~~~~~v~~~~~v~~~~ii~~~Dp~~~~i~~e~~~~v~~~~~~~~~~~~~~~~~~t~~~~~~ 1056 (1398)
T Consensus       105 ~~ey~~dyaydrE~a~~va~kie~t~l~~v~~~i~~----D~~~~~v~i~Ld---------------~~~~~~r~~t~d~  165 (397)
T TIGR02389       105 EDEYEKDYAYDREKAEEVAKKIEATKLEDVAKDISI----DLADMTVIIELD---------------EEKLKERGITVDD  165 (397)
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHCCHHHHHCEEEE----EEECEEEEEEEC---------------HHHHHHCCCCHHH
T ss_conf             788632245667899999987520333252241248----875308999417---------------4886306986689


Q ss_pred             EEEHHHCCCCCCCCCCEEEE----CCCCCEEECCCCCCCEEECCCCCEEEECCCCCCCCCCEEEECHHHHCCCCCCCCCC
Q ss_conf             75101101221238534774----27782532247884202137784454136761354842221013202455433677
Q gi|254780142|r 1057 VIDWRFASRSQNLKPAIVVT----DENGVVLKSARGTDARWFLPVDALLSVSPGQKVSTGDVLARLPISSAKTKDITSGL 1132 (1398)
Q Consensus      1057 ~i~~~~~~~~~~~~~~~~i~----d~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~v~~~d~l~~~~~~~~k~~DIt~GL 1132 (1398)
T Consensus       166 v~~a-----~~~~~~~~~~~~~~~~~~~-v-------------seGGvkkvivy------~~i~---~~~~------~~~  211 (397)
T TIGR02389       166 VLKA-----IKKAKLGKVIEEVSEDVDN-V-------------SEGGVKKVIVY------STIT---IKAP------PKE  211 (397)
T ss_pred             HHHH-----HHHHHCCEEEEEECCCCCC-C-------------CCCCEEEEEEE------EEEE---ECCC------CCC
T ss_conf             9999-----9987464255664368676-5-------------34761489999------8897---1578------899


Q ss_pred             CHHH--HHHHHHCCCCCCEECCCCCEEEEE--EECCCCE--EEEEEECCCCCCEEEEEECCCCEEEEECCCEEECCCEEE
Q ss_conf             3288--988752511110111347867863--3127944--999983689840268981389658984198774086464
Q gi|254780142|r 1133 PRVA--ELFEARRPKNHAILAEISGTIRIK--RNYKNKS--RVVIEPFEDGVEPAEYFIPKNKHFYLQDGDHVEKGDYIL 1206 (1398)
Q Consensus      1133 PrV~--eLFEar~pk~~aiisei~Giv~i~--~~~~~k~--~~vi~~~~~g~~~~e~~ip~~~~l~v~dgd~V~~gd~lt 1206 (1398)
T Consensus       212 p~~~sneL~~l~~ki~~~~iKGikgIkrvvir~E~~k~dsyEy~i~--TeGSNL~~VL-------------~~eGVD~tR  276 (397)
T TIGR02389       212 PSLKSNELRKLKEKIKNLKIKGIKGIKRVVIRREEEKGDSYEYVIY--TEGSNLKEVL-------------KLEGVDKTR  276 (397)
T ss_pred             CCCCHHHHHHHHHHHCCEEEEEEECCEEEEEEEECCCCCEEEEEEE--ECCCCHHHHC-------------CCCCCCCCC
T ss_conf             8622267898887570415334504328999986688842799998--6063317650-------------889847742


Q ss_pred             CCCCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHCCE-ECHHHHHHHHHHHCCEEEEECCCCCCCCCCCCCCHHHHHHHHH
Q ss_conf             389999999875279999999999999999980970-0612560124762861489418864545664106999999999
Q gi|254780142|r 1207 DGNPVPQDILRIKGVEALASYLINEVQEVYRLEGVA-INHKHIEVVVRHMLQKVEITDPADTEYILGDNVDRIEVEELNR 1285 (1398)
Q Consensus      1207 ~Gsid~~eIl~vlGIEAAR~~Ii~EIq~V~~~~Gi~-IN~RHIeLIaD~MT~kg~I~~~Gdt~~i~g~~Inr~~~~~~Nr 1285 (1398)
T Consensus       277 T~TNdI~EI~~VLGIEAAR~AII~E~~~tL~EQGL~dVDiRHlmLvAD~MT~~G~V~~------IGRHGi----------  340 (397)
T TIGR02389       277 TTTNDIHEIEEVLGIEAARNAIIEEIKRTLEEQGLDDVDIRHLMLVADLMTWDGEVRQ------IGRHGI----------  340 (397)
T ss_pred             CEECCHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCCCEEEE------EEEEEC----------
T ss_conf             0015614455530668999999999999986428860248989888651078854841------012000----------


Q ss_pred             HHHHCCCCCCCEEEEEECHHHHHHCCCCHHHHCCCHHHHHHHHHHHHCCCEECCCCCCEEEECCCCCCCCCCHH
Q ss_conf             99972898752012100001453023107765040258999999745285523665322155073056553546
Q gi|254780142|r 1286 SLAQQGKKLVSFSPILQGITKASLQTKSFISAASFQETTKVLTEAAIAGKVDTLDGFKENVIVGRSIPAGTGAI 1359 (1398)
Q Consensus      1286 ~~~~~g~~pa~~~p~llGITKasl~t~S~Ls~ASFEeT~~vL~eAAi~ge~D~L~GvSENIIlGqliP~GTG~f 1359 (1398)
T Consensus       341 ----------------------~GeK~SVLARAAFEvTvKhLl~Aa~rGe~d~L~GV~ENIIvG~Pi~lGTG~V  392 (397)
T TIGR02389       341 ----------------------SGEKASVLARAAFEVTVKHLLDAAIRGEVDELKGVVENIIVGQPIRLGTGSV  392 (397)
T ss_pred             ----------------------CCCCCCHHHHCCCCCCHHHHHHHHHCCCHHHCCCEEEEEECCCCCCCCCCEE
T ss_conf             ----------------------3547853420012022346887520371214676799997077852154258