Conserved Protein Domain Family
RNA_pol_rpoA1

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TIGR02390: RNA_pol_rpoA1 
DNA-directed RNA polymerase subunit A'
This family consists of the archaeal A' subunit of the DNA-directed RNA polymerase. The example from Methanocaldococcus jannaschii contains an intein.
Statistics
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PSSM-Id: 274106
Aligned: 8 rows
Threshold Bit Score: 1483.04
Created: 8-Oct-2014
Updated: 25-Oct-2021
Structure
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Aligned Rows:
Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
BAB65243       7 EKIIKGIKFGILSPDEIRKMSVTAIITSEVYDEDGTPIEGGVMDPRLGVIEPGQKCPTCGNTLNGCPGHFGHIELVRPVI 86  Sulfolobus toko...
CAF30919       7 PKEIGDITFGLLSPEQIRTMSVAKIVTADTYDDDGYPIDGGLMDTRLGVIDPGLVCKSCSGRVGTCPGHFGHIELSKPVV 86  Methanococcus m...
AAM04682       8 PKRIASIKFGLMSPKEIRKMSATPIITADTYDDDGFPIDMGLMDTKLGVIDPGLRCKTCSGRAGECPGHFGHIELVAPVV 87  Methanosarcina ...
Q03585         5 SKRISSIKFALLSPDEIRKLSQVKVITADTYDDDGYPIEHGLMDLHMGVIEPGLRCATCGGKVDECPGHFGHIELAMPVV 84  Thermoplasma ac...
WP_010876677   5 LKKISQINFGLMSPEDIRKMSVTQIVTPDTYDEDGYPIENGLMDPRLGVIDPSLRCRTCGAKGGECPGHFGSINLARPVI 84  Methanothermoba...
WP_011007407  12 KKVIKSIKFGVLSPEMIRKYSVMEVTTSEVYDEGGLPVRGGIADRRLGVAEPGSRCETCGQTHDVCPGHFGHIELVKPVI 91  Pyrobaculum aer...
WP_010866638  11 TNLLDKILFGVLSPHEIRQLAKVTVVRGDLYEADGTPVSGGLRDPHFGAIEPGERCPVCGNSREECPGHFGKIELARPVL 90  Aeropyrum pernix
WP_011153484   3 IKKLGLIDLRPLDPEVIRKLSVVEVKIPEPYDRDGLPIENGPMDPRMGVIDPGLRCKTCGGKYGECLGHFGRIELARPVY 82  Nanoarchaeum eq...
BAB65243      87 HVGFVKHVYDILRATCRHCGRLKIKEEDLQRYSRIYHAIKDRWPSAa------RRLVEYIKKNAMKNMECPHCGEKQFKI 160 Sulfolobus toko...
CAF30919      87 HIGFAKDIYKILKAVCPHCGKVTITEIKRDEYLEKMAKLEEDGGDP-------WTLCDDLLKEAAKGSVCPSCGEVKADV 159 Methanococcus m...
AAM04682      88 HVGFNKVIRKLLRATCRKCSRLLLEPAQKQQFLDQLLAVEEIGHMP-------DDLINEVYKEASKVKTCPYCNEEQLEI 160 Methanosarcina ...
Q03585        85 HVGFVKEIKMFLDATCRSCGRIKLTDDEIRTYLPEIQKMDFETGDPed----iEILTKKYVDLASQRMVCPHCGAQQSKI 160 Thermoplasma ac...
WP_010876677  85 HVGFADTIHKILRSTCRKCGRVLLTETEIEEYRQRILDAMEKEESL-------TPIIKEIYAEA-RRDKCPHCEEEQEEI 156 Methanothermoba...
WP_011007407  92 HVGFARIIYDVLRATCPNCGRIMLRDEEIERYRERLNKLKARWRLLa------LNLHEKIRKKATERMTCPHCGYKRNKV 165 Pyrobaculum aer...
WP_010866638  91 IPHYTDYVYKILQATCRVCGRITLPEEKIKYYRLIFRRLRGKWPQLa------KTFATMVVKEAAQATQCPHCGKPQYKV 164 Aeropyrum pernix
WP_011153484  83 HVKFLNEIKRLLQYTCPKCGRAIIPQKLKEQFLKKINEYINEGKYDelsnfiqSTVIPKINEYRKKHKKCPYCNAELKEI 162 Nanoarchaeum eq...
BAB65243     161 KLEKPYNFYEERKEG-V----IRLTPSDIRERLERIPDSDYELLGYDPKYSRPEWMILTVLPVPPITIRPSITIESGIRA 235 Sulfolobus toko...
CAF30919     160 KYDKPTAYHQLDGKA-Q----KQLTSSEVREILEKIPAEDCKLLGINAKVARPEFMVLTVLPVPPVTVRPSITLESGERS 234 Methanococcus m...
AAM04682     161 KFEKPSEYLENG---------EKLTPTEIRDRFENVPDEDIRVIGMDPKNARPEWMILTVLPVPPVTVRPSITLESGQRS 231 Methanosarcina ...
Q03585       161 ILDKPTTFREEGTN-------VKITPKEIRERLERIPDDDLIFFGFNPKTARPEWMVLTVLPVPPINVRPSITLETGERS 233 Thermoplasma ac...
WP_010876677 157 KLDKPVSIVE----G-D----YKLTPSEVRERLERISDDDALILGVNPEVARPEWMVLTVLPVPPVTVRPSITLETGERS 227 Methanothermoba...
WP_011007407 166 RFERPYYFYEETKSGaL----VKLDPEVLRERLSKVPSEDLELLGINPSVARPEWAILKVLPVPPPHVRPSIQLETGIRS 241 Pyrobaculum aer...
WP_010866638 165 VYIRPFHFYEKKPEG-D----VKLTPSEIRERLEKTGSE-IEILGVHPERSRPEWMVATVLIVPPLAVRPSITLETGLRS 238 Aeropyrum pernix
WP_011153484 163 KFEKPWYFYIKEKIG-DkeewVKLTPLDVRQWLEKIPDEDAKLFGIIN--GRPEWLVLTVILVPPVTARPSIILETGERS 239 Nanoarchaeum eq...
BAB65243     236 EDDLTHKLVDIIRINERLKESIDAGAPQLIIEDLWDLLQYHVSTYFDNEIPGIPPAKHRSGRPLRTLAQRLKGKEGRFRG 315 Sulfolobus toko...
CAF30919     235 EDDLTHKLVDIIRINQRLEENINGGAPNLIIEDLWDLLQYHINTYFDNEAPGIPPARHRSGRPLRTLAQRLKGKEGRFRH 314 Methanococcus m...
AAM04682     232 EDDLTHKLVDIIRINQRFQENREAGAPQLIIEDLWELLQYHVTTFFDNSVSGIPPARHRSGRPLKTLSQRLKGKEGRFRG 311 Methanosarcina ...
Q03585       234 EDDLTHKLVDIIRISQRLRESRDNGSPQLIIEDLWDLLQFHVTTYFDNQTPGIPPARHRSGRALKTLVQRLKGKEGRFRS 313 Thermoplasma ac...
WP_010876677 228 EDDLTHKLVDILRINQRLKENMEAGAPQLIVEDLWELLQYHVTTYFDNEASGVPPARHRSGRPLKTLAQRLKGKEGRFRS 307 Methanothermoba...
WP_011007407 242 EDDLTHKLVDIIRMNEKLKIAIETGAPTNVVDNLWELLQYHVATYFDNELPGIPVAKHRGGRPLKGIAQRLKGKEGRFRG 321 Pyrobaculum aer...
WP_010866638 239 EDDLTHALAEIVRQNEKLRNVIVTNAPETLIEENWMVLQEMVAAYIDNELPGARRLTHRRKRYLKTLAQRLKGKDGRIRG 318 Aeropyrum pernix
WP_011153484 240 EDDLTHKIADIVRINNRIEELLSYGAPEPILEENWEMLQYHVATYFDNELPNVPKARHRSGRPLKGLLQRIKGKEGRLRR 319 Nanoarchaeum eq...
BAB65243     316 NLSGKRVDFSARTVISPDPNISIDEVGVPVAIAKTLTVPERVTKMNIERMRQYVINGPEKWP-------GANYVIRP--- 385 Sulfolobus toko...
CAF30919     315 NLAGKRVNFSARTVISPDPRLSINEVGIPKLIAKELTVPEKVTPYNIEKVRALLRNGSDNHP-------GVNYVVKKvrt 387 Methanococcus m...
AAM04682     312 SLSGKRVNFSARTVISPDPNLSINEVGVPMPIARTLTIPAVVTPRNIEQLKVYVRNGEDIHP-------GANYVFRs--- 381 Methanosarcina ...
Q03585       314 NLSGKRVSFSSRTVISPEPYLSVNEVGVPERAARELTVPVIVNQFNIDEMRELIKRGRNPRDqfgryvtGVNYVIRp--- 390 Thermoplasma ac...
WP_010876677 308 NLSGKRVNFSARTVISPDPNISINEVGVPEIIAREVTVPVYVTEWNIDRMREYIENGPDVHP-------GANYVIRP--- 377 Methanothermoba...
WP_011007407 322 SLSGKRVNFSARTVISPDPHISINEVGVPYDIAKVLTVPERVTAWNVDVLREYVIRGPESWP-------GANYVVTP--- 391 Pyrobaculum aer...
WP_010866638 319 NLSGKRVNYSARTVISPDPYISINEVGVPEEIAKTLTIAMRVTPYNLEEARRYVLNGPDKWP-------GALFVYKAs-- 389 Aeropyrum pernix
WP_011153484 320 NLAGKRVNFSARGVISVDPRIDIDEVGVPEQVAKELTFPEIVTEWNLDWLKQKVLNGPESLD-------GANYVIDP--- 389 Nanoarchaeum eq...
BAB65243     386 -DGR----RIDLRYVKdRKELASSLTPGYIVERHLIDGDIVLFNRQPSLHRISMMGHKVKVLPGRTFRLNLLVCPPYNAD 460 Sulfolobus toko...
CAF30919     388 kDGKeeeyKIKITDAN-KDMWVENITDGMVIERHLSDGDIVLYNRQPSLHRMSIMAHKVKVLPYRTFRHNLCVCPPYNAD 466 Methanococcus m...
AAM04682     382 -DGR----RIKVTNMN-KDDLAEKLEFGWTVERQLKDGDTVLFNRQPSLHKMSIMAHSVKVLPNKTFRLNPAVCPPYNAD 455 Methanosarcina ...
Q03585       391 -DGR----RIKITDQN-AAENADRIDIGWTVERQLMEGDIVLFNRQPSLHRMSMMGHTVRILPGQTFRFNLAVCTPYNAD 464 Thermoplasma ac...
WP_010876677 378 -DGR----KIRIYNET-KEVVLENLKPGYIVERHLKDGDIVLFNRQPSLHRMSMMAHQVRVLPYKTFRLNLCVCPPYNAD 451 Methanothermoba...
WP_011007407 392 -EGR----RIDLRYVKdRKALAERLAPGWIVERHLIDGDIVLFNRQPSLHRVSMMGHLVKVLPGRTFRLHLAVCPPYNAD 466 Pyrobaculum aer...
WP_010866638 390 -ERK----KYDLRFFKdYEKLAESLEPGDVVERHLINGDIVLFNRQPSLHRMSIMGHIVRVMPGKTFRLNLLVCPPYNAD 464 Aeropyrum pernix
WP_011153484 390 -NGR----RFKIMEEN-KEELAERLEPGWVVERHIINGDYALFNRQPSLHKMSMMGHRSVILPGKTFRLNPATTTPYNAD 463 Nanoarchaeum eq...
BAB65243     461 FDGDEMNLHVPQSEEAIAEAKEIMLVHRNIITPRYGGPIMGGAQDYISGAYLLTvkTTLLTREEVTTILGVTDFMGEIGE 540 Sulfolobus toko...
CAF30919     467 FDGDEMNVHVPQSEEARAEAEKLMLVEKHIVSPRFGGPIIGAIHDFISGAYVLT--SSLFTKDEALTLLKSSGLNVELGE 544 Methanococcus m...
AAM04682     456 FDGDEMNMHALQTEESRAEAKILMQVQENILSPRFGGPIIGGIHDHISGLFLLTrfENHISSHEAYDILRKSRARNLPEP 535 Methanosarcina ...
Q03585       465 FDGDEMNLHVIQKEEARAEARIIMKVQEQIMSPRFGGPIIGGIHDHVTALFLLThnNPRYTHEEMVHIMAYLEPDLLPEA 544 Thermoplasma ac...
WP_010876677 452 FDGDEMNMHVFQTEESRAEAKTLMRVQEHILSPRFGGPIIGGIHDHISGAYLLTrkSAVFSEEKVFQILKKAGLPLPD-- 529 Methanothermoba...
WP_011007407 467 FDGDEMNLHVPQTEEARAEARALMLVEKHIITPRYGGAIIGARQDYIIGAYLLShkSTFLTKKEVAFLLGAGKSQEDPPE 546 Pyrobaculum aer...
WP_010866638 465 FDGDEMNLHVPRLEEAQAEAREIMLVEKHILTPRYGGPIIGGRQDYVSGAYLLTvkTRLFTKEEVERLLSVAGYKGDLPE 544 Aeropyrum pernix
WP_011153484 464 FDGDEMNYHLVQNYEGKTEIEFLANVREHIVTPRYGLAIIGATEDIITGLYLLSlkDKIPFKDAIQLIEYNCKYFGKDKI 543 Nanoarchaeum eq...
BAB65243     541 P-AILAPRE----YYTGKQIVSLFLPKDFNFHGQANISKgF-RACKNEVCPHDSYIVIKNGILLEGVLDKKAIGNQQPeS 614 Sulfolobus toko...
CAF30919     545 PdVIENNIE----YYSGKSLFSKTLPEGLSLQYRAKICK-KcDTCTKEECEHDAYVVIRNGKLLRGVIDKNGFGSEAG-I 618 Methanococcus m...
AAM04682     536 AgHDEDGKP----FWTGKQIFSQILPETLNMEFAAQVCS-HcDTCKKEECPNDAYVVIRNGELILGTIDEAAIGAFKG-K 609 Methanosarcina ...
Q03585       545 R--IENGEK----YYYGRDIFSTILPKGLNVRFRSKLCSgSsERCEFEDDPSDTYVEIVDGKMIHGTIDEAAVSPFSG-A 617 Thermoplasma ac...
WP_010876677 530 -----SRGR----DWTGKEIFSMVLPDDLNMVYRAEVCRk-cEECLEMECENDAYVVIENGQLISGVIDEKAYGAFAG-K 598 Methanothermoba...
WP_011007407 547 P-AILHPVE----LWTGKQIISHFLPKDLNWVQPTAFKSk---CQNAYTCPTDEWIIVINGNLVKGVLDKKSIGAEQVdS 618 Pyrobaculum aer...
WP_010866638 545 P-AILKPEP----LWTGKQLASIFLPEDLSFKGKSKTNAg-dLACSDELCLHDSYIVITNGKLLEGVLDKKAIGAEEP-N 617 Aeropyrum pernix
WP_011153484 544 LkLVEKAKKegrdYLTGKEVFSALLPDDLDFEIKTKNGE----------------FVIKNGILLKGVIDKEIVGVEKG-K 606 Nanoarchaeum eq...
BAB65243     615 -ILHWLVREYGTEYGRWVMDNVFKLFIRFIELRGFTMTLDDVTIPPQAFKEIDEQIEVAYKKVEELIKQYNEGTLELIPG 693 Sulfolobus toko...
CAF30919     619 -VLNTLVKDFGSEDARLFLDAATKMSIKAMVLKGFTTGIDDEDIPAEAIQEIQDLLNKAEQDVEDIVEKYENGTLESLPG 697 Methanococcus m...
AAM04682     610 -IQDRIIKEVGPEAGARFVDDMTKLAIRSIMRTGLSFGIADEDIPKEARIQINEVLGKAEDAVQNLIKSYQNKELEPLPG 688 Methanosarcina ...
Q03585       618 -IIDKIFRKFGSQEAARFIDRMTRLAVGFITYRGFSTGISDYDIPESAVARIEELVAQAEDRINKLIETFRRGELQPAPG 696 Thermoplasma ac...
WP_010876677 599 -ILDHIVKEYGTDAAREFLDSATKLAIAGIMHAGFTTSTNDEEIPEEARERIEAHLRNAEARVDQLIEAYENGELEPLPG 677 Methanothermoba...
WP_011007407 619 -LWHRIARDYSPEVARRWLDSSLRLFLRFLDLRGFTFGMDSIYIPPEAYREIDNIIKASLEKVDKLIDDFRSGHLEAMPG 697 Pyrobaculum aer...
WP_010866638 618 nLLHIIALEYGNSKARQLLDSFYRMFIRMLELRGLTISLHDIDLPDRAKQEIEELIREYKGRVYSIIEEYRKGTLEPIPG 697 Aeropyrum pernix
WP_011153484 607 -LIRELFERYGPEFTFKWLSDVTRLSVNYLTREQLTISFSDIDIPKEVKEQIRKIIEKAKKEVDNLIERYKKGEIKPLPG 685 Nanoarchaeum eq...
BAB65243     694 RTAEESLEDHILETLDQLRKVAGDIATKYLDP-FNNVYIMAVTGARGSELNITQMTAMLGQQSVRGERIKRGYMTRTLPH 772 Sulfolobus toko...
CAF30919     698 RGVEESREAYIMQILGKARDQAGNVAEKYLSK-ENHAALMARTGARGSLLNITMMAASVGQQSVRGGRVFRGYRERTLPH 776 Methanococcus m...
AAM04682     689 RTLDETIEMSIMQKLGKARDETGGIADSHMGL-ENSAVIMARSGARGSILNLTQMAACVGQQAVRGERIRRGYAGRTLPH 767 Methanosarcina ...
Q03585       697 RSVEDTLEMEILSEAGVVRDESGKIASSYLGL-KVPSVIMARSGARATMLNISEVAGIVGQQSVRGGRLNRGYYNRTLPH 775 Thermoplasma ac...
WP_010876677 678 RSLEETLEMKIMQVLGEARDKSGEIAESYFDMdENHAVIMALTGARGSMLNLTQITACVGQQSVRGGRISRGYDNRTLPH 757 Methanothermoba...
WP_011007407 698 FTVEETFENKVTEILSKVREDAAVVVEKYIDK-NSEGYLMAKTGARGSIVNIVQMVATLGQQTIRGERIRRGFRTRTLPH 776 Pyrobaculum aer...
WP_010866638 698 RSLEESLEIKIMEVLDELRKRVQEVASNNLDP-FNDVFVMARTGARGSDVNISQMAAMLGQQAVRGRRIRRGLRNRVLAH 776 Aeropyrum pernix
WP_011153484 686 RTIEETLEIEILKVLNKARDEVGEVIEKHVDP-TKGTMILAKSGARGKLLNLIQVVGLVGQQSISGRRMEEGYKDRVLPH 764 Nanoarchaeum eq...
BAB65243     773 FKPGDISPDARGFVHNSFTRGLTPIEMFFHAAGGREGLVDTAVKTSQSGYMQRRLINALSDLRVEYDGTVRSLYGEVIEL 852 Sulfolobus toko...
CAF30919     777 FGKGSLDAKSHGFVRSCYKKGLAPTEYFFHAMGGREGLVDQAVRTAQSGYMQRRLVNALQDIRAEYDGTVRDSRGLVVQF 856 Methanococcus m...
AAM04682     768 FQEGDLGSDAHGFVKASYKSGLNPTEYFFHAIGGREGLVDTAVRTSQSGYLQRRLVNALQDLEVQYDLTVRDTRGVLVQF 847 Methanosarcina ...
Q03585       776 FKRGDIGADARGFVRSSYMTGLSPTEYFFHSIGGREGLVDTAVRTSRSGYMQRRLINAFEDLKVDDSREVKDTVGSLIQI 855 Thermoplasma ac...
WP_010876677 758 FKKGELGAKSRGFVHSSYKEGLDPIEFFFHAMGGREGLVDTAIRTAQSGYMQRRLVNALQDLTVDENGRVVDNRGVIIQN 837 Methanothermoba...
WP_011007407 777 FPVGDIGAFSGGFVRNCFRCGLTPVEYFFHAAAGRDGLIDTAVRTAQSGYMQRRLINALQDVYVAYDGTVRFGGAMLLQY 856 Pyrobaculum aer...
WP_010866638 777 FKENDIEPEAWGFVRSSFRKGLRPTEVFFHAAAGREGLVDTAVKTSQSGYMQRRLINALQDIVVTYDGTVRDLYGNLIQL 856 Aeropyrum pernix
WP_011153484 765 FKKGDKSAKARGFVEHGFADGLDPIEFFFHAASGKDALMDTTLRTPKSGYLYRRLVSVLRDLYVENDRTVRDTFGNIYQF 844 Nanoarchaeum eq...
BAB65243     853 AYGEDEVHPMYSSHGKTVDVNRII 876 Sulfolobus tokodaii str. 7
CAF30919     857 EYGEDLVDPAKADHGKGVDLDKIF 880 Methanococcus maripaludis S2
AAM04682     848 KYGEDGINPTKSDFSKPETIHRIV 871 Methanosarcina acetivorans C2A
Q03585       856 RYGEDGIDPTRSARGKAVDMNYIL 879 Thermoplasma acidophilum DSM 1728
WP_010876677 838 RFGEDGVDPAKSDYGKIVDLDKLV 861 Methanothermobacter thermautotrophicus
WP_011007407 857 LYGEDGVDVSRSDHGKVVDIKSLK 880 Pyrobaculum aerophilum
WP_010866638 857 KYGEDGVDPMKTYHGKPVDVKRII 880 Aeropyrum pernix
WP_011153484 845 IWGEDGIAVQKSEGGK-LNVEKIF 867 Nanoarchaeum equitans
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