6CNB,4C2M,3H0G,1I6H


Conserved Protein Domain Family
RNA_pol_Rpb2_2

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pfam04561: RNA_pol_Rpb2_2 
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RNA polymerase Rpb2, domain 2
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). Rpb2 is the second largest subunit of the RNA polymerase. This domain forms one of the two distinctive lobes of the Rpb2 structure. This domain is also known as the lobe domain. DNA has been demonstrated to bind to the concave surface of the lobe domain, and plays a role in maintaining the transcription bubble. Many of the bacterial members contain large insertions within this domain, as region known as dispensable region 1 (DRI).
Statistics
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PSSM-Id: 398318
Aligned: 22 rows
Threshold Bit Score: 130.545
Threshold Setting Gi: 548822
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:
6CNB_B  201 SKNRIIVEADEKKGIVq-----------------ASVTSSTHERKSKTYVITKNGKIYLKHNsIAE-EIPIAIVLKACGI 262  Saccharomyces cerev...
Q10578  207 ATNTVYVFSMKDGKYAfktecrscl-enssrptsTMWVNMLARGGGGGKKTAMGQRIIGILPyIKQ-EIPIMIVFRALGF 284  Caenorhabditis elegans
P11513  166 ATNRVLVDYGKSGSNIth---------------vAKVTSSAAGYRVQVMIERLKDSTIQISFaTVPgRIPFAIIMRALGF 230  Sulfolobus acidocal...
Q10233  209 SKNRIIVEAEPKKGlw-----------------qASVTSSTHERKSKTYVITKNGKLYLKHN-SVAdDIPIVVVLKAMGL 270  Schizosaccharomyces...
P20028  185 RRNHPICVKRSSWKDrgqnfs-------dlgmlvQTVREDESSLSNVVHYLNNGTAKFMFSHvKRLsYVPVCLILKCLMD 257  fruit fly
4C2M_Q  210 RRNHPMAIIRPSFANrgasys-------hygiqiRSVRPDQTSQTNVLHYLNDGQVTFRFSWrKNEyLVPVVMILKALCH 282  baker's yeast
P38420  207 STNHVYVFKKRQPNKYayvgevrsmaenqnrppsTMFVRMLARASA---KGGSSGQYIRCTLpYIRtEIPIIIVFRALGF 283  thale cress
3H0G_N  204 AANIVQVFKKAAPSPIayvaei------rsalerGSRLISSMQIKLMARNTENSGQTIRATLpYIRsDIPIVIVFRALGV 277  Schizosaccharomyces...
1I6H_B  219 AGNIVQVFKKAAPSPIshvaei-------rsaleKGSRFISTLQVKLYGREGSSARTIKATLpYIKqDIPIVIIFRALGI 291  baker's yeast
O96236  218 ANNFIYVFKKKQPSKFgwvaeirsq-mersqatsGFSVKMKTRSGGSQYGSNKSGGQLVATLpYIRtEISVGILFRALGC 296  Plasmodium falcipar...
6CNB_B  263 LSdLEIMQLVCg-----NDSSYQDIFAVNLEESSKLDIYTQQQALEYIGakv--ktmRRQKLTILQEGIEAia------- 328  Saccharomyces cerev...
Q10578  285 VSdRDILGHIIy-----DFNDPEMMEMVKPSLDEAFVIQEQNVALNFIG--------ARGAKPGVTREQRIkyareilqk 351  Caenorhabditis elegans
P11513  231 VTdRDIVYAVS--------LDPQIQNELLPSLEQASSITSAEEALDFIGnrv---aiGQKRENRIQKAEQVid------k 293  Sulfolobus acidocal...
Q10233  271 QSdQEIFELVAg-----AEASYQDLFAPSIEECAKLNIYTAQQALEYIGarv--kvnRRAGANRLPPHEEAlev----la 339  Schizosaccharomyces...
P20028  258 YTdEEIYNRLVqg--yeSDQYYVSCVQAMLREVQNENVYTHAQCKSFIGnlf---raRFPEVPEWQPDDDVtdfi---lr 329  fruit fly
4C2M_Q  283 TSdREIFDGIIgndvkdSFLTDRLELLLRGFKKRYPHLQNRTQVLQYLGdkfrvvfqASPDQSDLEVGQevl------dr 356  baker's yeast
P38420  284 VAdKDILEHICy-----DFADTQMMELLRPSLEEAFVIQNQLVALDYIGkrg--atvGVTKEKRIKYARDIlq------k 350  thale cress
3H0G_N  278 VPdRDILEHICy-----DPNDFQMLEMMKPCIEEAFVIQDKDIALDYIGk--------RGSTTGVTREKRLryahdilqk 344  Schizosaccharomyces...
1I6H_B  292 IPdGEILEHICy-----DVNDWQMLEMLKPCVEDGFVIQDRETALDFIGrrg--talGIKKEKRIQYAKDIlq------- 357  baker's yeast
O96236  297 TSdRDILQRIVy-----DFNDKLMINALRETLEECIEYPTQDVCLDFIGkrg--ptvGASREKRILYAKELlr------k 363  Plasmodium falcipar...
6CNB_B  329 tTVIaHLTVEALDFRE---KALYIAMMTRRVVMAMYNPKMIDDRDYVGNKRLE 378  Saccharomyces cerevisiae S288C
Q10578  352 eLLP-HVGVSEHCETK---KAFFIGYMVHRLLLAALGRRELDDRDHIGNKRLD 400  Caenorhabditis elegans
P11513  294 yFLP-HLGTSPE---DrkkKGYYLASAVNKILELYLGRREPDDKDHYANKRVR 342  Sulfolobus acidocaldarius DSM 639
Q10233  340 aVVLaHINVFNLEFRP---KAVYIGIMARRVLMAMVDPLQVDDRDYVGNKRLE 389  Schizosaccharomyces pombe 972h-
P20028  330 eRVMiHLDTYED-------KFQLIVFMIQKLFQCAQGKYKVENVDSAMMQEVL 375  fruit fly
4C2M_Q  357 iVLV-HLGKDGSQD-----KFRMLLFMIRKLYSLVAGECSPDNPDATQHQEVL 403  baker's yeast
P38420  351 eMLP-HVGIGEHCETK---KAYYFGYIIHRLLLCALGRRPEDDRDHYGNKRLD 399  thale cress
3H0G_N  345 eLLP-HITTMEGFETR---KAFFLGYMIHRMLLCALERREPDDRDHFGKKRLD 393  Schizosaccharomyces pombe 972h-
1I6H_B  358 kEFLpHITQLEGFESR---KAFFLGYMINRLLLCALDRKDQDDRDHFGKKRLD 407  baker's yeast
O96236  364 eVLP-HMGTHPGVESK---KSYFIGYMINRLLLAELGRIKEDDRDHFGKKRLD 412  Plasmodium falciparum 3D7
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