1KHV,1RA6,1SH0,1GX6,1S4F,1KHW


Conserved Protein Domain Family
RNA_dep_RNAP

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cd01699: RNA_dep_RNAP 
Click on image for an interactive view with Cn3D
RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage. RdRp catalyzes synthesis of the RNA strand complementary to a given RNA template. RdRps of many viruses are products of processing of polyproteins. Some RdRps consist of one polypeptide chain, and others are complexes of several subunits. The domain organization and the 3D structure of the catalytic center of a wide range of RdRps, including those with a low overall sequence homology, are conserved. The catalytic center is formed by several motifs containing a number of conserved amino acid residues. This subfamily represents the RNA-dependent RNA polymerases from all positive-strand RNA eukaryotic viruses with no DNA stage.
Statistics
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PSSM-Id: 238843
Aligned: 71 rows
Threshold Bit Score: 129.711
Created: 12-Dec-2003
Updated: 25-Oct-2021
Structure
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Program:
Drawing:
Aligned Rows:
 
Conserved site includes 13 residues -Click on image for an interactive view with Cn3D
Feature 1:active site [active site]
Evidence:
  • Comment:Based primarily on the structure of the stalled complex of HIV-1 RT bound to NTP and DNA primer-template (1RTD).
  • Citation:PMID 9831551
  • Structure:1GX6_A; Hepatitis C virus RNA polymerase binds UTP and manganese; contacts at 3.5A.
    View structure with Cn3D

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                                                                                     
1KHV_A    147 LAKHLYKcwsvansgkalhhIYACGLKDELRPLDkv--keGKKRLLWGCDvgVAVCAAAVFHNICyklkm----varfgP 220  RHDV
1GX6_A    115 AVNHIHSvwkdlledtvtpiDTTIXAKNEVFCVQpekggrKPARLIVFPDlgVRVCEKXALYDVVstlpq----vvxgsS 190  Hepatitis C virus...
1685121   104 YHNARLSldeipl--drrdsHLRTFTKAEKFCVDlk--pdPAPRVIQPRSprYNLQVARYLKKTEhhiyrgldkiwggpC 179  SgCV
1039370   102 YQNAVDSlriggv--qrkdsYLSTFIKAEKIPIYrk--pdPAPRVIQPRNprYNVEVGRYLRPFEhhlyrgideimggpT 177  Cowpea mottle virus
1040741   342 YQQALEDischgl-nletdsKVKVFVKYEKTDHTsk--adPVPRVISPRDpkYNLALGRYLRPMEerifkalgklfghrT 418  Oat chlorotic stu...
133643    365 YQKAADSlekkpv--qwrdsKVQAFIKVEKLECDtk---dPVPRTIQPRSkrYNLAIGQYLRLNEkkmldsiddvfkekT 439  RCNMV
332142    392 YEGAVKSleglsv--qrrdaYLKTFVKAEKINTTkk--pdPAPRVIQPRNvrYNVEVGRYLRRFEhylyrgideiwngpT 467  MNSV
436018    126 YNAAVQSlkkkav--ersdaNVTAFLKMEKHLMSk----kIAPRLICPRNkrYNVELGRRLKFNEkkfmhaidstfdspT 199  Soybean dwarf virus
133638    562 YEKAVNSlyempv--syddaKLKTFVKAEKINLTkk--adPVPRVIQPRAprYNVELGRYLRPVEhpiyhaidkiwggpT 637  MCMV
264099    153 YANARDSilsnpl--spkdaRVKMFVKAEKINFTak--pdPAPRVIQPRDprSNIVLAKYIKPLEpmlykalgklykypA 228  PEMV-2
Feature 1                                    ######                                           
1KHV_A    221 IAVGVDMtsrdVDVIINNLTska--sdFLCLDYSKWDSTMSPCVVRLAIDILADCCeq------------tELTKSVVLt 286  RHDV
1GX6_A    191 YGFQYSPgq-rVEFLVNTWKskk-npxGFSYDTRCFDSTVTENDIRVEESIYQCCDlap---------earQAIKSLTEr 259  Hepatitis C virus...
1685121   180 VMKGYNVee-vASHIIGAWEqfq-kpvAIGFDMSRFDQHVSVPALQFEHSIYQAIFkgdrel---qqllswQLRNYGTGf 254  SgCV
1039370   178 VIKGYDVn--qIGNIMEKASgqfvrpvAVGFDMSRFDQHVSFDALQFEHGVYLQHFggdr--------flaKLLSWQLNn 247  Cowpea mottle virus
1040741   419 VMKGMDTdv-tARVIQEKWNmfn-kpvAIGLDASRFDQHVSLEALEFEHSVYLKCVrrmvdkrklgnilrhQLLNKCYGn 496  Oat chlorotic stu...
133643    440 VLSGLDNra-qGRAIAHKWRkyq-npiGIGLDASRFDQHCSVDALKFEQTFYKACFpgdqql---etllkwQLSNTGSAl 514  RCNMV
332142    468 IIKGYTVeq-iGKIARDAWDsfv-spvAIGFDMKRFDQHVSSDALKWEHSVYLDAFchdsyl---aellkwQLVNKGVGy 542  MNSV
436018    200 VLSGYDSfr-vGKIIANKWSkfk-rpvAIGVDASRFDQHVGVEALQWEHSIYNGAFkdp---------ilkELLHWQTEn 268  Soybean dwarf virus
133638    638 IMKGYSVeq-iGRHIENAFRsft-dpvAIGFDASRFDQHVSVEALRWEHSVYSRIYgype--------lltQLLRWQIHn 707  MCMV
264099    229 VAKGFNAve-tGEIIAGKWRcfk-dpvVVGLDASRFDQHVSVEALQFTHAVYRGFIksr---------efnNLLQMMYTn 297  PEMV-2
Feature 1                              ##                                          # ##       
1KHV_A    287 l--ksHPMTIld--amIVQTKRGLPSGMPFTSVINSICHWLLWSAAVYkscaeiglhcsnlyedAPFYTYGDDGVYAMtp 362  RHDV
1GX6_A    260 l--yiGGPLTnsk-gqNCGYRRCRASGVLTTSCGNTLTCYLKASAACRaak----------lqdCTXLVNGDDLVVICes 326  Hepatitis C virus...
1685121   255 -----AHDGLi-----RYKVDGCRMSGDMNTALGNCILACLITKHICRgl-------------dARLINNGDDCVLICet 311  SgCV
1039370   248 kgfanLPEGKv-----KYTRRGCRMSGDMNTAMGNCLLACAITWDLMKgi-------------kYRLLNNGDDCVVITes 309  Cowpea mottle virus
1040741   497 -----TPDGAv-----SYTIEGTRMSGDMNTSLGNCVLMCMMIHAYGLhks-----------vnIQLANNGDDCVVFLeq 555  Oat chlorotic stu...
133643    515 -----LPTGEl----vRYRTKGCRMSGDINTGLGNKILMCSMVHAFLKetg-----------vrASLANNGDDCVLFCek 574  RCNMV
332142    543 -----ASDGMi-----KYKVDGCRMSGDMNTAMGNCLIACAITHDFFRsrg-----------irARLMNNGDDCVVICek 601  MNSV
436018    269 -----RIMLFvedkilKFKVKGHRMSGDINTSSGNKLIMCGMMHYYFKtlg-----------vkAELCNNGDDCVIICer 332  Soybean dwarf virus
133638    708 rgtayASDGAf-----NYQVDGKRMSGDMNISLGNCILATAITHDFVTklg-----------ipARLINNGDDNVLICpa 771  MCMV
264099    298 rglgsAKDGFv-----RYKVKGRRMSGDMDTSLGNCVLMVLLTRNLCKvlg-----------ipHELFNNGDDCIVFFdr 361  PEMV-2
Feature 1                                                ##                               
1KHV_A    363 ----mmVSLLPAIIENLRdYGLSPTAAdktefidvcplnkISFLKRTFELTdi-----gWVSKLDKSSILRQLEWS 429  RHDV
1GX6_A    327 agtqedAASLRVFTEAXTrYSAPPGDPpqpey----dlelITSCSSNVSVAhdasgkrvYYLTRDPTTPLARAAWE 398  Hepatitis C virus (is...
1685121   312 r--dvgRVVDKLTTAWLH-FGFTCIAEepvy-----epekIRFCQMAPVYDge-----kWVMVRDPKVSLSKDAFS 374  SgCV
1039370   310 k---nvDFVCKQLERFRD-YGFTCIAEepvy-----elekLEFCNLHPLYDgs-----sWTVMRKPSVSLAKDTYC 371  Cowpea mottle virus
1040741   556 s---dlATFSEGLFEWFLeMGFNMAIEepsy-----elehIEFCQCRPVFDgv-----kYTMCRNPRTAIAKDSVY 618  Oat chlorotic stunt v...
133643    575 g---dyEQINRNLEQWFLcRGFEMTVEkpvd-----vlekVAFCRSQPVCIat-----qWAMVRQLGSLSRDCFST 637  RCNMV
332142    602 e--caaVVKADMVRHWRQ-FGFQCELEcdae-----ifeqIEFCQMRPVYDge-----kYVMVRNPLVSLSKDSYS 664  MNSV
436018    333 ----kdENKFQHMHSWFKdYGFDMQIEtpvy-----kigqIEFCQSKPVKIng-----yYRMVRKPESISKDAHSL 394  Soybean dwarf virus
133638    772 v--evgRVRQELYRHWLN-YGFEVISEepvy-----ileqVEFCQMRPVFDgt-----qYTMMRDPRTTMSKDAYA 834  MCMV
264099    362 c---hlEKFNNAVKTYFAdLGFKMKVEppvd-----vlekIEFCQTQPIYDge-----kWRTVRCISSIGKDCSSV 424  PEMV-2

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