# STOCKHOLM 1.0 #=GF ID RNA_pol_Rpb1_2 #=GF AC PF00623.21 #=GF DE RNA polymerase Rpb1, domain 2 #=GF AU Finn RD;0000-0001-8626-2148 #=GF SE Manual #=GF GA 24.70 24.70; #=GF TC 24.80 24.70; #=GF NC 24.60 24.60; #=GF BM hmmbuild HMM.ann SEED.ann #=GF SM hmmsearch -Z 47079205 -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 DR SO; 0000417; polypeptide_domain; #=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 19 #=GS Q8I410_PLAF7/732-907 AC Q8I410.1 #=GS RPA1_DROME/416-591 AC P91875.2 #=GS RPA1_HUMAN/434-614 AC O95602.2 #=GS RPA1_YEAST/473-653 AC P10964.2 #=GS RPA1_YEAST/473-653 DR PDB; 5N5Z A; 473-653; #=GS RPA1_YEAST/473-653 DR PDB; 6H67 A; 473-653; #=GS RPA1_YEAST/473-653 DR PDB; 5M5Y A; 473-653; #=GS RPA1_YEAST/473-653 DR PDB; 6HKO A; 473-653; #=GS RPA1_YEAST/473-653 DR PDB; 4C3H A; 473-653; #=GS RPA1_YEAST/473-653 DR PDB; 5LMX A; 474-653; #=GS RPA1_YEAST/473-653 DR PDB; 5M5W A; 473-653; #=GS RPA1_YEAST/473-653 DR PDB; 6HLR A; 473-653; #=GS RPA1_YEAST/473-653 DR PDB; 5M5X A; 473-653; #=GS RPA1_YEAST/473-653 DR PDB; 4C2M A; 473-653; #=GS RPA1_YEAST/473-653 DR PDB; 5M64 A; 473-653; #=GS RPA1_YEAST/473-653 DR PDB; 4C3I A; 473-653; #=GS RPA1_YEAST/473-653 DR PDB; 6HLQ A; 473-653; #=GS RPA1_YEAST/473-653 DR PDB; 6H68 A; 473-653; #=GS RPA1_YEAST/473-653 DR PDB; 5M3M A; 473-653; #=GS RPA1_YEAST/473-653 DR PDB; 5OA1 A; 473-653; #=GS RPA1_YEAST/473-653 DR PDB; 5N60 A; 473-653; #=GS RPA1_YEAST/473-653 DR PDB; 5M3F A; 473-653; #=GS RPA1_YEAST/473-653 DR PDB; 5W66 A; 473-653; #=GS RPA1_YEAST/473-653 DR PDB; 4C2M P; 473-653; #=GS RPA1_YEAST/473-653 DR PDB; 5N61 A; 473-653; #=GS RPA1_YEAST/473-653 DR PDB; 4C3J A; 473-653; #=GS RPA1_YEAST/473-653 DR PDB; 6HLS A; 473-653; #=GS RPA1_YEAST/473-653 DR PDB; 5W5Y A; 473-653; #=GS RPA1_YEAST/473-653 DR PDB; 5W65 A; 473-653; #=GS RPA1_YEAST/473-653 DR PDB; 5W64 A; 473-653; #=GS RPA1_YEAST/473-653 DR PDB; 5N5Y A; 473-653; #=GS RPA1_YEAST/473-653 DR PDB; 5G5L A; 473-653; #=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_YEAST/370-537 DR PDB; 6EU2 A; 370-537; #=GS RPC1_YEAST/370-537 DR PDB; 6CND A; 370-537; #=GS RPC1_YEAST/370-537 DR PDB; 6EU3 A; 370-537; #=GS RPC1_YEAST/370-537 DR PDB; 5FJ8 A; 370-537; #=GS RPC1_YEAST/370-537 DR PDB; 6EU0 A; 370-537; #=GS RPC1_YEAST/370-537 DR PDB; 6F41 A; 370-537; #=GS RPC1_YEAST/370-537 DR PDB; 6CNF A; 370-537; #=GS RPC1_YEAST/370-537 DR PDB; 6F42 A; 370-537; #=GS RPC1_YEAST/370-537 DR PDB; 5FJA A; 370-537; #=GS RPC1_YEAST/370-537 DR PDB; 6CNC A; 370-537; #=GS RPC1_YEAST/370-537 DR PDB; 6CNB A; 370-537; #=GS RPC1_YEAST/370-537 DR PDB; 6F40 A; 370-537; #=GS RPC1_YEAST/370-537 DR PDB; 5FJ9 A; 370-537; #=GS RPC1_YEAST/370-537 DR PDB; 6F44 A; 370-537; #=GS RPC1_YEAST/370-537 DR PDB; 6EU1 A; 370-537; #=GS RPC1_SCHPO/352-519 AC O94666.1 #=GS NRPC1_ARATH/359-524 AC F4JXF9.1 #=GS RPOC_UREPA/402-553 AC Q9PQV5.1 #=GS RPOC_MYCPN/405-555 AC P75271.1 #=GS RPB1_ASFB7/316-483 AC P42486.1 #=GS Q8QUT2_ISKNN/277-426 AC Q8QUT2.1 #=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; 5U0S a; 348-513; #=GS RPB1_SCHPO/348-513 DR PDB; 3H0G A; 348-513; #=GS B8N404_ASPFN/357-522 AC B8N404.1 #=GS RPB1_CAEEL/350-515 AC P16356.3 #=GS O77375_PLAF7/375-540 AC O77375.1 #=GS C4VAM1_NOSCE/313-476 AC C4VAM1.1 #=GS Q584K3_TRYB2/349-512 AC Q584K3.1 Q8I410_PLAF7/732-907 GKRVNNCARTVISPDTFIETNQIGMPIEFAKVLTIDEYITQNNFTYIKKLIENGPNIYPGALSY.RDSNGRVFKLSHKYEDRL.KVIEKIEKLNFQT.......ENSYILHRHARDGDVVIMNRQPTLHKFSIMAHYLKIFEK..EKVFRLNYVNCSSYNADFDGDEMNLHLLQTPLARAEATHLMN. RPA1_DROME/416-591 GKRVNYAARTVITPDPNINVDEIGIPDIFAKKLSYPVPVTEWNVTELRKMVMNGPDVHPGANYI.QDKNGFTTYIPADNASKRESLAKLLLS..NPK.......DGIKIVHRHVLNGDVLLLNRQPSLHKPSIMGHKARILHG..EKTFRLHYSNCKAYNADFDGDEMNAHYPQSEVARAEAYNLVNV RPA1_HUMAN/434-614 GKRVDYAARSVICPDMYINTNEIGIPMVFATKLTYPQPVTPWNVQELRQAVINGPNVHPGASMV.INEDGSRTALSAVDM.T...QREAVAKQLLTPATGAPKPQGTKIVCRHVKNGDILLLNRQPTLHRPSIQAHRARILPE..EKVLRLHYANCKAYNADFDGDEMNAHFPQSELGRAEAYVLACT RPA1_YEAST/473-653 GKRVNYAARSVISPDPNIETNEIGVPPVFAVKLTYPEPVTAYNIAELRQAVINGPDKWPGATQI.QNEDGSLVSLIGMSVEQRKALANQLLTPSSNVST....HTLNKKVYRHIKNRDVVLMNRQPTLHKASMMGHKVRVLPN..EKTLRLHYANTGAYNADFDGDEMNMHFPQNENARAEALNLANT #=GR RPA1_YEAST/473-653 SS SEEESSEEEEEEEE-SSS-TTEEEE-HHHHCCSEEEEE-STTTHHHHHHHHHHTTTSSS-EEEE.E-TTS-EEE-TT--HHHHHHHHTTTTS--SSGTC....TT---EEEEE--TTSEEEEEESSTTSGGGEEEEEEEE-TT..-SSEEE-GGGHHHHT--SSS-EEEEE--SSHHHHHHHHHTSBG Q18566_CAEEL/354-521 GKRVDFSGRTVISPDPNLRIDQVGVPIHVAMTLTFPEIVNASNIEKMRQLVINGSDVHPGANYLVEKKTGNKKLLKYGKRDE...LAKNLRMGD..............TIERHLDDNDVVLFNRQPSLHKISIMSHRAKVMPG...RTFRFNECACTPYNADFDGDEMNLHLPQTYEAKAEASELMNV RPC1_HUMAN/358-525 GKRVDFSGRTVISPDPNLRIDEVAVPVHVAKILTFPEKVNKANINFLRKLVQNGPEVHPGANFIQQRHTQMKRFLKYGNREK...MAQELKYGD..............IVERHLIDGDVVLFNRQPSLHKLSIMAHLARVKPH...RTFRFNECVCTPYNADFDGDEMNLHLPQTEEAKAEALVLMGT RPC1_YEAST/370-537 GKRVDFSGRTVISPDPNLSIDEVAVPDRVAKVLTYPEKVTRYNRHKLQELIVNGPNVHPGANYLLKRNEDARRNLRYGDRMK...LAKNLQIGD..............VVERHLEDGDVVLFNRQPSLHRLSILSHYAKIRPW...RTFRLNECVCTPYNADFDGDEMNLHVPQTEEARAEAINLMGV #=GR RPC1_YEAST/370-537 SS SEEESSEEEEEEEE-SSS-TTEEEEEHHHHTTSEEEEE-STTSHHHHHHHHHHTTTSSSSEEEEE-SSTSSEEESSSS-STT...HHCH--TTS..............EEEEE--TTEEEEEEESS--SGGGEEEEEEEEESS...SSEEE-CGGHTTTT--STT-EEEEE---SHHHHHHHHHHSBT RPC1_SCHPO/352-519 GKRVDFSGRTVISPDPNLRIDQVAVPYRIAKILTFPERVTTQNKKHLQDCIRNGPDVHPGANYVIDRESGFKRFLRFGNRNR...IADDLKIGD..............IVERHLHDNDVVLFNRQPSLHKLSIMAHLVKVRPW...RTLRFNECVCGPYNADFDGDEMNLHVPQTEEAKTEALELMGI NRPC1_ARATH/359-524 GKRVEFTGRTVISPDPNLKITEVGIPILMAQILTFPECVSRHNIEKLRQCVRNGPNKYPGARNV.RYPDGSSRTLVGDYRKR...IADELAIGC..............IVDRHLQEGDVVLFNRQPSLHRMSIMCHRARIMPW...RTLRFNESVCNPYNADFDGDEMNMHVPQTEEARTEAITLMG. RPOC_UREPA/402-553 GKRVDYSGRSVIVVGPELKMYEVGIPALMILKLFRPYIISELIRKRDELGNEIQPICA........NIKLAEQKILAQ........DNEIW.................PVVEKVIKQRPVILNRAPTLHRLGIQAFEPKMVDG...KAIRLHPLVTTAFNADFDGDQMAVHIPLSKEAVAEARSILLA RPOC_MYCPN/405-555 GKRVDYSGRSVIVVGPELKMYEVGIPALMILKLFKPFIIHGLINKFDS....NGNEIRPIAS....SIRQAEDMIKNQ........DDLIW.................GIVYDVIKDRPVLLNRAPTLHRLGIQAFEPRIVDG...KAIRLHPLVTTAFNADFDGDQMAVHVPLSENAVNEARAILL. RPB1_ASFB7/316-483 GSQVWSISRSTICGNSDLHLDEVGYPISFARTLQVAETVQHYNINRLMPYFLNGKRQYPGCSRVYKQITQSVHDIEGLKQ......DFRLEVGD..............ILYRDVVTGDVAFFNRQPSLERSSIGVHRIVVLENPKISTFQMNVSACAWYNADFDGDQMNLWVPWSVMSRVEAELLCSV Q8QUT2_ISKNN/277-426 GKRRNYTARSVVGPESTLALDQVGVPLQVADTLTIEEPVTKYNIEHVRQMRATGHLKA.....L.YDADGQERHVVRC..............GL..............TLHRSLRDGDVVVLNRQPTLHRNSMLGMRVKVLPG...NTIRVNLAVTHGFNMDFDGDEGNLYLPRSLLARAEVATLMS. 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 B8N404_ASPFN/357-522 GKRVDFSARTVITGDPNLSLDEVGVPKSIARTLTYPEVVTPYNIDKLQQLVSNGPNEHPGARYI.VRDNGERIDLRHAKR.A...GGQQLLYGW..............KVERHVMDGDVILFNRQPSLHKESMMGHRVRVMPY...STFRLNLSVTTPYNADFDGDEMNLHVPQSEESRAELLQLALV RPB1_CAEEL/350-515 GKRVDFSARTVITADPNLPIDTVGVPRTIAQNLTFPEIVTPFNVDKLQELVNRGDTQYPGAKYI.IRENGARVDLRYHPR.A...ADLHLQPGY..............RVERHMKDGDIIVFNRQPTLHKMSMMGHRVKILPW...STFRMNLSVTSPYNADFDGDEMNLHLPQSLETRAEIEEIAMV O77375_PLAF7/375-540 GKRVDFSARTVITGDPNLNIDYIGVPKSVAMTLTFCETVTPLNYDNLKKLVERGPYEWPGAKYI.IRDNGTKYDLRHVRR.N...SEKELEYGY..............KVERHMTDEDYILFNRQPSLHKMSIMGHKAKILPY...STFRLNLSVTSPYNADFDGDEMNLHLAQSHETRSEIKHLMIV C4VAM1_NOSCE/313-476 GKRVDFSARSVITPDANISLEEVGVPLEIAKIHTFPETITPYNIERLTRLVSNGPNEYPGANYV.IRSDGQRIDLNFN...R...GDIKLEEGY..............IVERHMQNGDVVLFNRQPSLHKMSMMGHFVRVMEG...KTFRLNLSCTSPYNADFDGDEMNLHMPQSYNTKAELEELCLV Q584K3_TRYB2/349-512 GKRVDFSARTVITGDPNIDVDEVGVPFSVAMTLTFPERVNTVNKKRLTEFAR..RTVYPSANYI.HHPNGTITKLALLRD.R...SKVTLNIGD..............VVERHVINGDVVLFNRQPTLHRMSMMGHRVRVLNY...NTFRLNLSCTTPYNADFDGDEMNLHVPQSLLTKAELIEMMMV #=GC SS_cons SEEESSEEEEEEEEESSS-TTEEEEEHHHHTCSEEEEE-STTTHHHHHHHHHHTTTSSSSEEEEEESTTSSEEETTTT-SCCHHHHHCCTTSTSSSGTC....TT...EEEEE--TTCEEEEEESSTTSGGGEEEEEEEEESS...SSEEEEGGGHCCCT--SSS-EEEEE--SSHHHHHHHHHCSBT #=GC seq_cons GKRVDaSuRTVIosDPNLplDEVGVPhphAppLTaPEhVTthNlccLpphltNGPshaPGAphl.hcpsGpcppLphtpp.p...hsppLthG...............hVcRHlpcGDVVLFNRQPoLH+hSIMuH+s+lhPh...+TFRLNhussosYNADFDGDEMNLHlPQScpuRAEAhpLhhs //