# STOCKHOLM 1.0 #=GF ID RNA_pol_Rpb1_2 #=GF AC PF00623.15 #=GF DE RNA polymerase Rpb1, domain 2 #=GF AU Finn RD #=GF SE Manual #=GF GA 23.40 23.40; #=GF TC 24.50 23.60; #=GF NC 22.90 23.20; #=GF BM hmmbuild HMM.ann SEED.ann #=GF SM hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq #=GF TP Domain #=GF RN [1] #=GF RM 8910400 #=GF RT Structural modules of the large subunits of RNA polymerase. #=GF RT Introducing archaebacterial and chloroplast split sites in the #=GF RT beta and beta' subunits of Escherichia coli RNA polymerase. #=GF RA Severinov K, Mustaev A, Kukarin A, Muzzin O, Bass I, Darst SA, #=GF RA Goldfarb A; #=GF RL J Biol Chem 1996;271:27969-27974. #=GF RN [2] #=GF RM 11313498 #=GF RT Structural basis of transcription: RNA polymerase II at 2.8 #=GF RT angstrom resolution. #=GF RA Cramer P, Bushnell DA, Kornberg RD; #=GF RL Science 2001;292:1863-1876. #=GF DR INTERPRO; IPR000722; #=GF DR SCOP; 1i50; fa; #=GF CC RNA polymerases catalyse the DNA dependent polymerisation of #=GF CC RNA. Prokaryotes contain a single RNA polymerase compared to #=GF CC three in eukaryotes (not including mitochondrial. and #=GF CC chloroplast polymerases). This domain, domain 2, contains the #=GF CC active site. The invariant motif -NADFDGD- binds the active site #=GF CC magnesium ion [1,2]. #=GF SQ 33 #=GS Q26008_PLAFA/731-907 AC Q26008.1 #=GS RPA1_YEAST/473-653 AC P10964.2 #=GS RPA1_HUMAN/434-614 AC O95602.2 #=GS RPA1_DROME/416-591 AC P91875.2 #=GS RPB1B_TRYBB/350-513 AC P17545.1 #=GS Q9AXN0_9RHOD/328-493 AC Q9AXN0.1 #=GS O77375_PLAF7/375-540 AC O77375.1 #=GS RPB1_CAEEL/350-515 AC P16356.3 #=GS Q9HGZ5_ASPOZ/357-522 AC Q9HGZ5.1 #=GS RPB1_SCHPO/348-513 AC P36594.1 #=GS RPB1_SCHPO/348-513 DR PDB; 3H0G M; 348-513; #=GS RPB1_SCHPO/348-513 DR PDB; 3H0G A; 348-513; #=GS O96446_9MICR/313-476 AC O96446.1 #=GS Q9AVW8_GUITH/327-492 AC Q9AVW8.1 #=GS Q9QTF4_RSIV/277-427 AC Q9QTF4.1 #=GS RPB1_ASFB7/316-483 AC P42486.1 #=GS Q98RN1_GUITH/314-480 AC Q98RN1.1 #=GS Q9AW39_GUITH/417-601 AC Q9AW39.1 #=GS Q9AIH0_CARRU/318-460 AC Q9AIH0.1 #=GS RPOC_MYCPU/418-560 AC Q98Q24.1 #=GS RPOC_MYCGE/407-558 AC P47582.1 #=GS RPOC_UREPA/402-553 AC Q9PQV5.1 #=GS RPOC_CHLTR/347-489 AC O84316.1 #=GS RPOC_THEMA/635-779 AC P36252.1 #=GS RPOC_THEAQ/620-765 AC Q9KWU6.2 #=GS RPOC_THEAQ/620-765 DR PDB; 1YNJ D; 620-765; #=GS RPOC_THEAQ/620-765 DR PDB; 1I6V D; 620-765; #=GS RPOC_THEAQ/620-765 DR PDB; 1YNN D; 620-765; #=GS RPOC_THEAQ/620-765 DR PDB; 2GHO D; 329-474; #=GS RPOC_THEAQ/620-765 DR PDB; 1HQM D; 620-765; #=GS RPOC_AQUAE/474-616 AC O67763.1 #=GS RPOC_XYLFA/344-486 AC Q9PA87.2 #=GS RPOC_TREPA/333-475 AC O83270.1 #=GS RPOC_BORBU/333-475 AC O51349.1 #=GS O21238_RECAM/354-506 AC O21238.1 #=GS Q9LVH0_ARATH/359-525 AC Q9LVH0.1 #=GS Q18566_CAEEL/354-521 AC Q18566.2 #=GS RPC1_HUMAN/358-525 AC O14802.2 #=GS RPC1_YEAST/370-537 AC P04051.1 #=GS RPC1_SCHPO/352-519 AC O94666.1 Q26008_PLAFA/731-907 GKRVNNCARTVISPDTFIETNQIGMPIEFAKVLTIDEYITQNNFTYIKKLIENGPNIYPGALSY.RDSNGRVFKLSHKYEDRL..KVIEKIEKLNFQT.......ENSYILHRHARDGDVVIMNRQPTLHKFSIMAHYLKIFEK..EKVFRLNYVNCSSYNADFDGDEMNLHLLQTPLARAEATHLMNC RPA1_YEAST/473-653 GKRVNYAARSVISPDPNIETNEIGVPPVFAVKLTYPEPVTAYNIAELRQAVINGPDKWPGATQI.QNEDGSLVSLIGMSVEQR.KALANQLLTPSSNVST....HTLNKKVYRHIKNRDVVLMNRQPTLHKASMMGHKVRVLPN..EKTLRLHYANTGAYNADFDGDEMNMHFPQNENARAEALNLANT RPA1_HUMAN/434-614 GKRVDYAARSVICPDMYINTNEIGIPMVFATKLTYPQPVTPWNVQELRQAVINGPNVHPGASMV.INEDGSRTALSAVDM.T....QREAVAKQLLTPATGAPKPQGTKIVCRHVKNGDILLLNRQPTLHRPSIQAHRARILPE..EKVLRLHYANCKAYNADFDGDEMNAHFPQSELGRAEAYVLACT RPA1_DROME/416-591 GKRVNYAARTVITPDPNINVDEIGIPDIFAKKLSYPVPVTEWNVTELRKMVMNGPDVHPGANYI.QDKNGFTTYIPADNASKR.ESLAKLLLS..NPK.......DGIKIVHRHVLNGDVLLLNRQPSLHKPSIMGHKARILHG..EKTFRLHYSNCKAYNADFDGDEMNAHYPQSEVARAEAYNLVNV RPB1B_TRYBB/350-513 GKRVDFSARTVITGDPNIDVDEVGVPFSVAMTLTFPERVNTINKKRLTEFARR..TVYPSANYI.HHPNGTITKLALLRD.R....SKVTLNIGD..............VVERHVINGDVVLFNRQPTLHRMSMMGHRVRVLNY...NTFRLNLSCTTPYNADFDGDEMNLHVPQSLLTKAELIEMMMV Q9AXN0_9RHOD/328-493 GKRVDFSGRTVISPDPNLRLDQVGVPQTIAMNLTYPEVVTPFNVEKMRRLVMNGPNEYPGAKYI.ERLDGSKVNLAFVKN.R....SDIHLNNGE..............KVIRHLLDGDYVIFNRQPSLHKMSIMGHRVKVMRY...SSFRLNLSCTSPYNADFDGDEMNLHVPQSPQARAEVMQLMMV O77375_PLAF7/375-540 GKRVDFSARTVITGDPNLNIDYIGVPKSVAMTLTFCETVTPLNYDNLKKLVERGPYEWPGAKYI.IRDNGTKYDLRHVRR.N....SEKELEYGY..............KVERHMTDEDYILFNRQPSLHKMSIMGHKAKILPY...STFRLNLSVTSPYNADFDGDEMNLHLAQSHETRSEIKHLMIV RPB1_CAEEL/350-515 GKRVDFSARTVITADPNLPIDTVGVPRTIAQNLTFPEIVTPFNVDKLQELVNRGDTQYPGAKYI.IRENGARVDLRYHPR.A....ADLHLQPGY..............RVERHMKDGDIIVFNRQPTLHKMSMMGHRVKILPW...STFRMNLSVTSPYNADFDGDEMNLHLPQSLETRAEIEEIAMV Q9HGZ5_ASPOZ/357-522 GKRVDFSARTVITGDPNLSLDEVGVPKSIARTLTYPEVVTPYNIDKLQQLVSNGPNEHPGARYI.VRDNGERIDLRHAKR.A....GGQQLLYGW..............KVERHVMDGDVILFNRQPSLHKESMMGHRVRVMPY...STFRLNLSVTTPYNADFDGDEMNLHVPQSEESRAELLQLALV RPB1_SCHPO/348-513 GKRVDFSARTVITGDPNLSLDELGVPRSIAKTLTYPETVTPYNIYQLQELVRNGPDEHPGAKYI.IRDTGERIDLRYHKR.A....GDIPLRYGW..............RVERHIRDGDVVIFNRQPSLHKMSMMGHRIRVMPY...STFRLNLSVTSPYNADFDGDEMNMHVPQSEETRAEIQEITMV #=GR RPB1_SCHPO/348-513 SS S---SSEEEEEEEEETTS-TTB-B--HHHHTS-----B--TTTHHHHHHHHHH-TTSSS-EEEE.E-TT--B--TTTT-S.-....------SS-..............EEEE---S--EEEEE-SS--SGGGEEEEE----SS...SSEEEEGGGSGGGT--SSS-EEEEE---STTHHHHHHHS--T O96446_9MICR/313-476 GKRVDFSARSVITPDPNISVEEVGVPSEIAKIHTFPEIITPFNIDRLTKLVSNGPNEYPGANYV.IRNDGQRIDLNFNR.......GDIKLEEGY..............VVERHMQDGDVVLFNRQPSLHKMSMMAHFVRVMEG...KTFRLNLSCVSPYNADFDGDEMNLHMPQSYNSKAELEELCLV Q9AVW8_GUITH/327-492 GKRVDFSARTVITPDPNIKLDELGVPLSIAMNLTFPEIVTSFNIEYMKFLLYNGPYKHPGAKYL.IRNDNNRIDLRYVKY.L....SNINLENGY..............CVERHLQNGDLVLFNRQPSLHKMSMMGHIVKVMKF...STFRLNLSATSPYNADFDGDEMNLHFPQNVESKSELKNLLMV Q9QTF4_RSIV/277-427 GKRRNYTARSVVGPESTLALDQVGVPPQVADTLTIEEPVTKYNIEHVRRMRATGHLKA......LYDVDGQVRHVVRC.................G............LTLHRSLRDGDVVVLNRQPTLHRNSMLGMRVKVLPG...NTIRVNLAVTHGFNMDFDGDEGNLYLPRSLSARAEVATLMSP RPB1_ASFB7/316-483 GSQVWSISRSTICGNSDLHLDEVGYPISFARTLQVAETVQHYNINRLMPYFLNGKRQYPGCSRVYKQITQSVHDIEGLKQ.......DFRLEVGD..............ILYRDVVTGDVAFFNRQPSLERSSIGVHRIVVLENPKISTFQMNVSACAWYNADFDGDQMNLWVPWSVMSRVEAELLCSV Q98RN1_GUITH/314-480 GKRVDFSARTVISPDPNLFLSQIGIPIIICKNLSFPEKLNFYNYERLKRCILRGNDRYPGVVSVITRD.NKKIFLNKSNKKN....MMFFSKIGN..............SIQRHLVKNDIILFNRQPSLHRLSIMAHRIRIFKE...KTFRLNHCVCKPYNADFDGDEMNLHVPQSETSRTEAITLLNS Q9AW39_GUITH/417-601 GKRVLNSARSVIAPDPFLKTFEVGVPKEFAKDLYVPESINLINILKVFLDFLKIKNFKKKKL.ILEILNGNKISISQQDFLFKLKKISISYKYFKLFSLFS.KNKYGFNKFLRNLKKNDISILNRQPSLHKTSIMAHKVRILKS..SKCLKLHYSNCNSYNADFDGDEMNLHIPQNYLSISESLYIAYV Q9AIH0_CARRU/318-460 GKRVDFSGRSVITVEPNLFLYECKIPIYIALELFKPILYYELKKKKIITTIS.FIDDY........YKKNKKQIIL..................................LLKNKVKSYFIMLNRAPTLHRMNFQSFKILLTED...KTIKIHPLVCLSYNADFDGDQMAIHLPLTNNAKVESNYLLLS RPOC_MYCPU/418-560 GKRVDYSGRSVIVVGPELKMNQVGIPREMAAKLFEPWIIKELID.........QEITL........SVKSARKLIDNL.........NPIIW.................PHVAKVIQGRPVLLNRAPTLHRLSIQAFEPVLIRG...KAIKLHPLVTTAFNADFDGDQMAVHVPISDEAVREAKELLFA RPOC_MYCGE/407-558 GKRVDYSGRSVIVVGPELKMYEVGIPALMILKLFKPFIIHGLINKFDENGNEIRPIAA........SIRQAEDMIKNQ.........DDLIW.................GIVYDVIKDRPVLLNRAPTLHRLGIQAFEPRIVDG...KAIRLHPLVTTAFNADFDGDQMAVHVPLSENAVNEARAVLLA RPOC_UREPA/402-553 GKRVDYSGRSVIVVGPELKMYEVGIPALMILKLFRPYIISELIRKRDELGNEIQPICA........NIKLAEQKILAQ.........DNEIW.................PVVEKVIKQRPVILNRAPTLHRLGIQAFEPKMVDG...KAIRLHPLVTTAFNADFDGDQMAVHIPLSKEAVAEARSILLA RPOC_CHLTR/347-489 GKRVDYSGRSVIIVGPELKFNQCGLPKEMALELFEPFIIKRLKDQGSVY.................TIRSAKKMIQRG.........APEVW.................DVLEEIIKGHPVLLNRAPTLHRLGIQAFEPVLIEG...KAIRVHPLVCAAFNADFDGDQMAVHVPLSIEAQLEAKVLMMA RPOC_THEMA/635-779 GKRVDYSGRAVIVVGPNLKIHQCGIPKKMAMELFKPFVLAKLLGEGSSSK................TMRKVKKAIIEK........EMPEAW.................EVLEEVIKGSVVLLNRAPTLHRMSIQAFEPKLVEG...NAIQLHPVVCPPFNADFDGDQMAVHVPLSAAAQAEARFLMLS RPOC_THEAQ/620-765 GKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPFLLKKMEEKAFAP.................NVKAARRMLERQRD......IKDEVW.................DALEEVIHGKVVLLNRAPTLHRLGIQAFQPVLVEG...QSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLS #=GR RPOC_THEAQ/620-765 SS --EESSEEEEEEEE-TSSSTTEE--BHHHHHHHHHHHHHHHHHHTSSSS.................SHHHHHHHHCSSS-......--HHHH.................HHHHHHHTT--EEEEESS--SGGGSEEEEE--BSS...SSEEE-TGGHHHHT--TSS-EEEEE---SHHHHHHHHHHCBC RPOC_AQUAE/474-616 GKRVDYSGRSVIVVGPELQMHQCGLPKIMALELFKPFVYRRLEEKGYAT.................SIKHAKRLVEQK.........TPEVW.................ECLEEVVKEHPVLLNRAPTLHRPSIQAFEPVLVEG...KAIQLHPLVCPPFNADFDGDQMAVHVPLGIEAQLESYILMLS RPOC_XYLFA/344-486 GKRVDYSARSVIIVGPNLRLHQCGLPKKMALELFKPFVFAKLQRRGLAT.................TIKAAKKLVERE.........EAEVW.................DILEEVISEHPVVLNRAPTLHRQGIQAFEPVLIEG...KAIQLHPLVCTAFNADFDGDQMAVHVPLSLEAQLEARALMMS RPOC_TREPA/333-475 GKRVDYSGRSVIVVGPELKLWQCGLPTKMALELFKPFIMKKLVEKEIVS.................NIKKAKMLVEQE.........SPKVF.................SVLDEVVKEHPVMLNRAPTLHRLGIQAFEPVLVEG...KAIRLHPLVCKPFNADFDGDQMAVHVPLTQAAQMECWTLMLS RPOC_BORBU/333-475 GKRVDYSGRSVIVVGPELKLHQCGLPAKMALELFKPFVIRRLIESEAVF.................NIKRAKNLIEQE.........VDEVW.................QILDLVIKEHPILLNRAPTLHRLGIQAFEPVLVEG...KAIKLHPLVCHAYNADFDGDQMAVHVPLTPAAQAESWALMLS O21238_RECAM/354-506 GKRINFSGRTVITSGPRLHLNQCGLPIELVLELFKPFIILKMRDLNICSQTS.LKNLK........TYDDFKQILFNKF.......TINLVF.................KLINSIISKHPVLLNRAPTLHRMNIQTFSPLLIYT...KAIQLHPLVCSSFNADFDGDTMAIYIPHTLRSQIESRVLMMS Q9LVH0_ARATH/359-525 GKRVEFTGRTVISPDPNLKITEVGIPILMAQILTFPECVSRHNIEKLRQCVRNGPNKYPGARNVRYPD.GSSRTLVGDYRKR....IADELAIGC..............IVDRHLQEGDVVLFNRQPSLHRMSIMCHRARIMPW...RTLRFNESVCNPYNADFDGDEMNMHVPQTEEARTEAITLMGV Q18566_CAEEL/354-521 GKRVDFSGRTVISPDPNLRIDQVGVPIHVAMTLTFPEIVNASNIEKMRQLVINGSDVHPGANYLVEKKTGNKKLLKYGKRDE....LAKNLRMGD..............TIERHLDDNDVVLFNRQPSLHKISIMSHRAKVMPG...RTFRFNECACTPYNADFDGDEMNLHLPQTYEAKAEASELMNV RPC1_HUMAN/358-525 GKRVDFSGRTVISPDPNLRIDEVAVPVHVAKILTFPEKVNKANINFLRKLVQNGPEVHPGANFIQQRHTQMKRFLKYGNREK....MAQELKYGD..............IVERHLIDGDVVLFNRQPSLHKLSIMAHLARVKPH...RTFRFNECVCTPYNADFDGDEMNLHLPQTEEAKAEALVLMGT RPC1_YEAST/370-537 GKRVDFSGRTVISPDPNLSIDEVAVPDRVAKVLTYPEKVTRYNRHKLQELIVNGPNVHPGANYLLKRNEDARRNLRYGDRMK....LAKNLQIGD..............VVERHLEDGDVVLFNRQPSLHRLSILSHYAKIRPW...RTFRLNECVCTPYNADFDGDEMNLHVPQTEEARAEAINLMGV RPC1_SCHPO/352-519 GKRVDFSGRTVISPDPNLRIDQVAVPYRIAKILTFPERVTTQNKKHLQDCIRNGPDVHPGANYVIDRESGFKRFLRFGNRNR....IADDLKIGD..............IVERHLHDNDVVLFNRQPSLHKLSIMAHLVKVRPW...RTLRFNECVCGPYNADFDGDEMNLHVPQTEEAKTEALELMGI #=GC SS_cons S-EESSEEEEEEEEETTSSTTEEB-BHHHHCCHHHHHCHHCCCHCCCCCHHHH.TTSSS.EEEE.ESCCHHCHHCCTTSS......--HHHHSS...............CCCCHHHTT-EEEEEESS--SGGGCEEEEE--BSS...SSEEEECGGCHHHT--TSS-EEEEE---SCCHHHHHHHCCBC #=GC seq_cons GKRVDaSuRoVIss-PsLclcplGlPhphAhpLphPphlsphNhcclpphh.pt.p.a.th..h..p.pus+phlptt.........s.plh.................tlhR+lhcuDlVLhNRQPoLH+hSIhuHcs+llpt...+ohRLp.sVCssYNADFDGDEMNlHlPpo.pA+uEuhpLhhs //