3H0G,4V1M


Conserved Protein Domain Family
RNA_pol_Rpb1_1

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pfam04997: RNA_pol_Rpb1_1 
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RNA polymerase Rpb1, domain 1
RNA polymerases catalyze the DNA dependent polymerization of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). This domain, domain 1, represents the clamp domain, which a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand.
Statistics
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PSSM-Id: 398595
Aligned: 25 rows
Threshold Bit Score: 270.7
Threshold Setting Gi: 75462932
Created: 11-May-2020
Updated: 7-Aug-2020
Structure
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Program:
Drawing:
Aligned Rows:
PubMed ReferencesClick to see Conserved Features Help

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
3H0G_M   13 LRRVEEVQFGILSPEEIR-SMSVAKIEFPETMDESgqRPRVGGLLDPRLGTIDRQFKCQTCGETMA------------DC 79   Schizosaccharomyces...
Q98Q24   12 EEKILKVSLSLATKEDVL-EWSHGEVTKPETINYKsyKPERHGLFDELIFGPATDYKCPICGKKYKksnegltcnntpQC 90   Mycoplasma pulmonis...
Q9KW13   14 TEEFNGIKIGLASPDLIR-SWSFGEVKKPETINYRtfKPEREGLFCARIFGPVKDYEC-LCGKYKRlkhrg---viceKC 88   Shewanella violacea
O51349    4 IKDFERIKIKIASPDQIR-NWSYGEVKKSETINYRtlRPEKDGLFCERIFGTTKEWEC-YCGKFKSvrykg---iicdRC 78   Borreliella burgdor...
O83270    4 IRDFDSLQIKLASPDTIR-AWSYGEVKKPETINYRtlRPEREGLFCERIFGTTKEWEC-FCGKFKSiryrg---vicdRC 78   Treponema pallidum ...
O84316   15 EGLFDKLEIGIASDVTIRdKWSCGEIKKPETINYRtfKPEKGGLFCEKIFGPTKDWEC-YCGKYKKikhkg---ivcdRC 90   Chlamydia trachomat...
P47582   14 YKNIKAIKLSIASNDTIL-NWSEGEVTKAETINYKslKPEPGGLFDEAIFGPVKDYEC-ACGKFKKikyrg---vrcdRC 88   Mycoplasma genitali...
Q9PQV5    3 QKGIKSLTISIASPEQIL-NWSKGEITKPETINYKslKPEPNGLFDESIFGPSKDYEC-YCGKYRKvkhkg---kiceRC 77   Ureaplasma parvum s...
O77375   14 LKRVKRLELGVLDPEIIK-KISVCEIVNVDIYKDG--FPREGGLNDIRMGTIDYRTLCGTCNMNVK------------YC 78   Plasmodium falcipar...
Q9AXN0   14 VKKVKAVQFGVLSPDEIR-RMSVCEIKFETAFEMG--KPKTEGLMDPRLGAIGRDLPCKTCHCDEK------------NC 78   Glaucosphaera vacuo...
3H0G_M   80 PG-------------HFGHIELAKPVFHIGFLSK--------------------IKKILECVCWNCGKLKIDSS------ 120  Schizosaccharomyces...
Q98Q24   91 EIekpeilpkisrrsRMGHIALQTPVVHFWFFKIdnsiiskllvlrvgesneyvSKNDLENIIYYKSHIVLDNGglk--- 167  Mycoplasma pulmonis...
Q9KW13   89 GVevtqt---kvrreRMGHIDLASPVAHIWFLKSlpsrig---------lmldmTLRDIERVLYFESFVVIEPGmts--- 153  Shewanella violacea
O51349   79 NVevthf---kvrreRMGHIELAAPVAHIWYYKYipsrig---------llldiTASSLNSILYYEKYVVIEPGdtd--- 143  Borreliella burgdor...
O83270   79 GVevthf---kvrreRMGHIELATPVSHIWYYRCvpsrmg---------llldlQVIALRSVLYYEKYIVIEPGdtd--- 143  Treponema pallidum ...
O84316   91 GVevtls---kvrreRMAHIELAVPIVHIWFFKTtpsrig---------nvlgmTASDLERVIYYEEYVVIDPGntd--- 155  Chlamydia trachomat...
P47582   89 GVwvtes---ivrreRMGHIALVSPVAHIWMSKElpspski-------slvlniSYKEVEQVLYFVNYIVLDTGkikddk 158  Mycoplasma genitali...
Q9PQV5   78 HVeites---ivrreRMGHIELAAPVAHIWFTKElpspski-------sllldiTYKEVDQVVYFVNYIVLDEGnnvydg 147  Ureaplasma parvum s...
O77375   79 PG-------------HFGHIELAKPMYHYGFMNV--------------------VLNVLRCVCYHCGRLLCNVN------ 119  Plasmodium falcipar...
Q9AXN0   79 PG-------------HFGHIELVKPMFNIGFFGM--------------------TLRVLRCVCFFCSKLLIDPR------ 119  Glaucosphaera vacuo...
3H0G_M  121 ---------------NP----KFN----DTQryRDPK------------------------------------------- 134  Schizosaccharomyces...
Q98Q24  168 ------------slpKNkiinINNaaqiYKDalIELRelnlndadaleiidgtinhlndivgs---kvgndygvdfyeln 232  Mycoplasma pulmonis...
Q9KW13  154 -------------leRGqmltEES----YLDalEEYGdef---------------------------------------- 176  Shewanella violacea
O51349  144 -------------lkKMqllnEDE----YIEarERYGmsf---------------------------------------- 166  Borreliella burgdor...
O83270  144 -------------lkKNqlltETE----YNDaqERYGggf---------------------------------------- 166  Treponema pallidum ...
O84316  156 -------------lvKKqllnDAK----YREvvEKWGkdaf--------------------------------------- 179  Chlamydia trachomat...
P47582  159 impf-kfkevldltgKGslstRQK----MRRviGYIFrnlikskssedyrkgkifyeslkn--------sslpfslndaf 225  Mycoplasma genitali...
Q9PQV5  148 ksifnkkevldltspKNsirsRNK----LRRtlRNIQeriedelnherealiqdfdyrlavtydqmlkdsnipfsvkdvm 223  Ureaplasma parvum s...
O77375  120 ---------------SS----KVK----YIEkiKVNS------------------------------------------- 133  Plasmodium falcipar...
Q9AXN0  120 ---------------DPkadfEVK----KVLriKNRI------------------------------------------- 137  Glaucosphaera vacuo...
3H0G_M  135 ------------NRLNAVWNVCKTKMVcdtglsagsdnfdlsnp-----------------------------sanmghg 173  Schizosaccharomyces...
Q98Q24  233 evieeyssakiqTGSKAIEFLLENIDL----------------------------------------------------- 259  Mycoplasma pulmonis...
Q9KW13  177 ---------eakMGAEAVLELLRAIEL----------------------------------------------------- 194  Shewanella violacea
O51349  167 ---------nasMGAEAIKTLLENLDL----------------------------------------------------- 184  Borreliella burgdor...
O83270  167 ---------tagMGAEAIRTLLQNLDL----------------------------------------------------- 184  Treponema pallidum ...
O84316  180 ---------vakMGGEAVYDLLKSEDL----------------------------------------------------- 197  Chlamydia trachomat...
P47582  226 nyikkytgfrvgIGAEAILELLNKIDL----------------------------------------------------- 252  Mycoplasma genitali...
Q9PQV5  224 afiekhtgvrfgIGAEAIRELLEKLNL----------------------------------------------------- 250  Ureaplasma parvum s...
O77375  134 ------------LRLRKLAELCLGIRAcdhsveeeglnindnslnnfynndlsnlnmnqqmllnksnytnifemvskedv 201  Plasmodium falcipar...
Q9AXN0  138 ------------NRLKKVQNLCSKVKIckhcsn----------------------------------------------- 158  Glaucosphaera vacuo...
3H0G_M  174 gcgaaqptiRKDGLRLWGSWKRGKDesdlPEK-RLLSPLEVHTIFTHISsedlAHLGLNEQYARPDWMIITVLPVPPPSV 252  Schizosaccharomyces...
Q98Q24  260 ---------EEEQRKIKSKIKEINN----LEKtSSSRKQDLSKLYKRLQ----VVESFINSGQKPTSMLIYNLPVIPAEL 322  Mycoplasma pulmonis...
Q9KW13  195 ---------EKEIESLREELPSINS------------ETRRKKMTKRLK----LIEAFFHSGNKPEWMILKVLPVLPPDL 249  Shewanella violacea
O51349  185 ---------DELSSKLRIQMIDKDD-------------KTDKKLLRRLE----IIENFKISGNKPEWMIMEVLPVIPPEI 238  Borreliella burgdor...
O83270  185 ---------DALVAQLREKMMEKGA-------------KSDKRLLRRIE----IVENFRVSGNKPEWMILSVIPVIPPDL 238  Treponema pallidum ...
O84316  198 ---------ESLLGELKERLRKTKS------------QQARMKLAKRLK----IVEGFVSSSNRPEWMVLKNIPVVPPDL 252  Chlamydia trachomat...
P47582  253 ---------NLEFSRLNDALRKAKK--------DSVEDAKVKKILRQLE----TISWFRNSKLHPKNMILHTVPVIPPDI 311  Mycoplasma genitali...
Q9PQV5  251 ---------EEEHEKIKQAIQNSPN----------AYDQKTKRLLRRLE----CVRWIKDSGSKPEWMVMTRIPVTPSET 307  Ureaplasma parvum s...
O77375  202 dcgcvqpkySREGPNMYIQFLHSSEedidESK-RKLSAEEALEILKKIRkeemSILGFNSDRCVPASLILTCIPIPPPCA 280  Plasmodium falcipar...
Q9AXN0  159 ----eqpkfAKEGLQFRAEFKGSADdt-mEKK-QIVSAEKVLSIFKHISdddiEIMGLSPQHSRPEWFILTLFPVPPPHI 232  Glaucosphaera vacuo...
3H0G_M  253 RPSISVDGTSRGEDDLTHKLSDIIKANANVRRCEQEGA-PAHIVSEYEQLLQFHVATYMDNEIAGQPQALQKSGRPLKSI 331  Schizosaccharomyces...
Q98Q24  323 RPLVQLDGGRHSTSDINELYRRIIIRNNRLRKWIELNA-PTLITQNELRMIQEAVDALIDNSKKKPKPVTSKDNRNLKSI 401  Mycoplasma pulmonis...
Q9KW13  250 RPLVPLDGGRFATSDLNDLYRRVINRNNRLKRLLDLAA-PDIIVRNEKRMLQESVDALLDNGRRG-RAITGSNKRPLKSL 327  Shewanella violacea
O51349  239 RPMVQLDGGRFATSDLNDLYRRVINRNNRLRKLLLLNA-PEIIVRNEKRMLQESVDSLFDNSHKR-KVVKGSSSRPLKSL 316  Borreliella burgdor...
O83270  239 RPMVQLDGGRFATSDLNDLYRRVIHRNSRLIRLMELKA-PDIIIRNEKRMLQEAVDALFDNSKRK-PAIKGASNRPLKSI 316  Treponema pallidum ...
O84316  253 RPLVPLDGGRFATSDLNDLYRRVINRNNRLKAILRLKT-PEVIVRNEKRMLQEAVDALFDNGRHG-HPVMGAGNRPLKSL 330  Chlamydia trachomat...
P47582  312 RPIIQLDGAKFTTSDINNFYRRVIIRNDRLRRILEDGTvPSIVVNNEKRLLQESVDALFDNSSRH-KPSLSKDKRSLKSL 390  Mycoplasma genitali...
Q9PQV5  308 RPIISLDGGRFTTSDTNNFYRKIIIRNERLKQMQATDA-PEILLDNEKRLLQEAVDSLFDNNSRK-KPVVGKDKRPLKSL 385  Ureaplasma parvum s...
O77375  281 RPYVQYGN-QRSEDDLTLKLLDIVKTNIQLKRQTDRGA-KSHVLQDLCSLLQFHITTLFDNDIPGMPIATTRSKKPIKAI 358  Plasmodium falcipar...
Q9AXN0  233 RPSVMMDASMRGEDDLTYKLGDIVRNNNALREMERTGA-PAHRLNEQIHVLQAHIITIMNNDLPGMPRAHQKSGRPIKSI 311  Glaucosphaera vacuo...
3H0G_M  332 RARLKGKEGRLRGNL 346  Schizosaccharomyces pombe 972h-
Q98Q24  402 SDALTGKKGRFRQNL 416  Mycoplasma pulmonis UAB CTIP
Q9KW13  328 ADMIKGKQGRFRQNL 342  Shewanella violacea
O51349  317 SDALKGKQGRFRQNL 331  Borreliella burgdorferi B31
O83270  317 SDMLKGKQGRFRQNL 331  Treponema pallidum subsp. pallidum str. Nichols
O84316  331 SEMLKGKNGRFRQNL 345  Chlamydia trachomatis D/UW-3/CX
P47582  391 TDRLKGKQGLFRHNL 405  Mycoplasma genitalium G37
Q9PQV5  386 SNHLKGKQGLFRQNL 400  Ureaplasma parvum serovar 3 str. ATCC 700970
O77375  359 RTRLKGKEGRLRGNL 373  Plasmodium falciparum 3D7
Q9AXN0  312 SQRLKGKEGRVRGNL 326  Glaucosphaera vacuolata
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