4XLN,3HKZ,5N5Z,6EU2,3H0G,4V1M


Conserved Protein Domain Family
RNA_pol_Rpb1_3

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pfam04983: RNA_pol_Rpb1_3 
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RNA polymerase Rpb1, domain 3
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 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking.
Statistics
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PSSM-Id: 398581
Aligned: 112 rows
Threshold Bit Score: 60.7162
Threshold Setting Gi: 75462964
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:
4XLN_J  768 NLLSPASGEPLAKPSRDIILGLYYITQVRkekk-----------------gagmAFATPEEALAAYERGEVALNAPIVVA 830  Thermus aquaticus
Q98Q24  563 NILGPKDGEPIINPSQDMILGIYYLTIEIagak-----------------geakVFQDVNSMLRAYEEGSVSLHARVAIP 625  Mycoplasma pulmonis...
P77917  478 HILAPKDGKPVVTPSQDMVIGNYWLTMERaesv-----------------gegmIFNDLDEVKLALQNGYVSIHTRIGVR 540  Pediococcus acidila...
P96177  412 HILAPKDGKPIVAPSQDMVIGNYYLTTEEagre-----------------gegmIFKDVNEVRTAYQNKYVHLHTRIGIQ 474  Weissella hellenica
P94892  479 HILAPKDGKPIVAPSQDMVIGNYYLTTEEagre-----------------gegmIFSSVDEARIAFASKVVHYHTRVGIQ 541  Leuconostoc mesente...
P95405  417 HILAPKDGKPIVAPSQDMTIGNYYLTTEEagik-----------------gegmIFSSADEVKMALQNHEVELHTRIGIA 479  Oenococcus oeni
P47582  561 HILGLKDGRPIVTPTQDMVLGNYYLTTERkgql-----------------gegiIFSTVYEARAAYESQKVHLHAIVGIS 623  Mycoplasma genitali...
Q9PQV5  556 HILGPKDGKPIITPTQDMILGIYYLTKEKfpqvieemmakdptqarvefinnfhIFSTQDEAIRAYKLKTIRINDVIGIT 635  Ureaplasma parvum s...
Q9J593  442 LLKHDVHGMPVYGSIQDEILAAYNLFREY-------------------------DLTQDEVLNILGKYGlef---ltdYE 493  Fowlpox virus strai...
Q9Q8N2  442 LLKHDIHGAPVYGSIQDEIVAAYSLFRME-------------------------DLTLDEVMNLLGKYGief-----daR 491  Myxoma virus
4XLN_J  831 gREtsvgrlkfvfanpdeallavahglldlqdvvtvrylGRRLETSPGRILFarivgEAVGDEkv--------------- 895  Thermus aquaticus
Q98Q24  626 fKKlqktf--------------------------nlkgdKGYIFSTVGKFIFn----QAFPENfpfifdssvssisdaqe 675  Mycoplasma pulmonis...
P77917  541 aSSmpekpf-------------------------tdqqrQQILITTAGKMLFn----DILPKDfvylnaptne--klvng 589  Pediococcus acidila...
P96177  475 tASlsaekp------------------------ftaeqrSRIMMTSVGKLFFn----DILPADfpylnepte---anlhe 523  Weissella hellenica
P94892  542 tSSfpsekp------------------------ftdeqrSKIMITSVGKLFFn----EILPSDfpyinepse---dnfkr 590  Leuconostoc mesente...
P95405  480 aSSfdkakp------------------------ftdhqrARIMVTTVGKVIFn----EILPDDfpyinepks---enfng 528  Oenococcus oeni
P47582  624 tKAfpnk----------------------------kfacQGTLITTVGKIIFn----DVLGNNvpyindgef----dena 667  Mycoplasma genitali...
Q9PQV5  636 tKAfnnkt----------------------------fskegILVTTVGKIIFn----QAFPVNfpyindvk-----nlyg 678  Ureaplasma parvum s...
Q9J593  494 rKD------------------------------------KYTGKDIFKFLINe---pEINYPG----------------- 517  Fowlpox virus strai...
Q9Q8N2  492 gKT------------------------------------KFSGKDIYTFLIGe----KVNYPG----------------- 514  Myxoma virus
4XLN_J  896 --aqELIQMDVPQe-------------kNSLKDLVYQAFLRLgmEKTARLLDALKYYGFTLSTTSGITIGIDDA 954  Thermus aquaticus
Q98Q24  676 ytkkYYIPYGLNIketiqntpindalskKDLSKIIRTIFDKYvpVLTKEDVASVINDVNHTNYKDT-STKFANL 748  Mycoplasma pulmonis UAB CTIP
P77917  590 tpdeYFLEAGEDiheqlnqrpllspfksGFLSDVIAEVYKQYkvTETSLLLDRMKDLGFYRSTLSGLTVGIADI 663  Pediococcus acidilactici
P96177  524 idnrFFLEPGEDikaryaetpilppfkkGYLSDIIAEVYKIYkvTETSLLLDRMKDLGYDESTKSGLTVGVADV 597  Weissella hellenica
P94892  591 vddsFFIDAGENihdyladtsivnpfkkGFLSDIIAEVYKRYkvTETSLLLDRMKDLGYDKSTESGLTVSMTDV 664  Leuconostoc mesenteroides...
P95405  529 idgrFFLDPGTDivgwfkneslngpfksGFLSDIIAQIYARYqvTRTSVLLDDMKDLGYNISTRSGLTVRMSDV 602  Oenococcus oeni
P47582  668 cpekFIVKQGEDVrqsilkhqiipafskKVISKLIDLLYLLLefKDLPKTLDNIKALGFKYSTFSSTTVSVFDI 741  Mycoplasma genitalium G37
Q9PQV5  679 enqfEIIGMHESildylkaynlkepltkKTLSTVIDYLYKVSeiEVVPQTMDKIKALGFKYSMISATSISAFDI 752  Ureaplasma parvum serovar...
Q9J593  518 -----IICNGEIIaenids----nfivsMKHMSISGLITDYKssVEGIKFINKASYVFKRYLKIYGFSITFRNL 582  Fowlpox virus strain NVSL
Q9Q8N2  515 -----ILKDGTVIapnvss----dfvvaMRHMSLAGLIADYTsnVEGVNFIIKSSYVFKRYLEIYGFGVTFKEL 579  Myxoma virus
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