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