Conserved Protein Domain Family
RT_LTR

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cd01647: RT_LTR 
RT_LTR: Reverse transcriptases (RTs) from retrotransposons and retroviruses which have long terminal repeats (LTRs) in their DNA copies but not in their RNA template. RT catalyzes DNA replication from an RNA template, and is responsible for the replication of retroelements. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs are present in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and Caulimoviruses.
Statistics
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PSSM-Id: 238825
Aligned: 84 rows
Threshold Bit Score: 94.5845
Threshold Setting Gi: 119196797
Created: 2-Aug-2004
Updated: 2-Oct-2020
Structure
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Aligned Rows:
 
putative activeputativeputative NTP
Feature 1:putative 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

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1                                                                                           
CAB78181        518 GFIRPSTSPwg--apVLFVKKKDg----------SFRLCID---------------YRELNRv-----------tVKNRY 559  thale cress
AAM08509       1345 SFIRRCRYAewvssiVPVIKKNG-----------KERVCID---------------FRDLNKa-----------tPKDEY 1387 Oryza sativ...
BAB08213       1871 GFIKEIQYPrwlaniVPVEKKNG-----------QVRVCVD---------------FRDLNRa-----------cPKDDF 1913 Oryza sativ...
AAX95475        615 KFIAASHYA------YQVLKMPGpkgtitiqgneKLAVQCD---------------KRSLDMvehtpntpataepPKKPF 673  Japanese rice
TIGR:At2g15410  809 GSIVEVRYPdwlrnpVVVKKKNG-----------KWRVCID---------------FTDLNKa-----------cPKDSF 851  thale cress
ABF96295        532 NVELTVGSPgdr-prPTFISKNLss-------efRTKLIEL---------------LKEYRDc-----------fAWEYY 577  Oryza sativ...
ABF96966        707 KFKAISHHN------YLKLKMPGp----------KGVIVVKglqpsaaskrdlaiiNRAVHNvete------pheRPKHT 764  Oryza sativ...
ABA93011        601 DDLEEIDIGpgdrpkPTFISKNLsa-------efRTKLIEL---------------LKEFRDc-----------fAWEYY 647  Japanese rice
ABE77575       1296 GFLVTSNYPqwlaniVPVPKKDG-----------KVRMCVD---------------YRDLNKa-----------sPKDDF 1338 barrel medic
AAM19047        847 DPLKEVDIGngtkprPTFVNKNMra-------dyKVKIIKL---------------LKEYVDc-----------fAWKYH 893  Oryza sativ...
Feature 1                                                       ######                              
CAB78181        560 PLPRIDElldqlr-----------------------gatcfsKIDLTSGYHQIPi------------------------a 592  thale cress
AAM08509       1388 PMPVADQlvdaas-----------------------gykilsFMDGNVGYNQIFm------------------------a 1420 Oryza sativ...
BAB08213       1914 PLPITEMvvd-----------------------------sttGYGALSGYNQIKm------------------------d 1940 Oryza sativ...
AAX95475        674 DMPGVPRevik---------------------------hkliVRPNAKPVKQKLrrfapd---------------rkqai 711  Japanese rice
TIGR:At2g15410  852 PLPHIDRlveata-----------------------gnellsFMDAFSGYNQILm------------------------h 884  thale cress
ABF96295        578 EMPGLSRsvve---------------------------hrlpIKPGIRPYQQPPr------------------------r 606  Oryza sativ...
ABF96966        765 PKPTPHGkva------------------------------kvQIDDFDPTKLVSlrsprlklrkmsadrqeaakaeihmn 814  Oryza sativ...
ABA93011        648 EMPGLSRsivehrlpikpgvrphqqpprrrkadmlepvkaeiKRLYDAGYNQIFm------------------------a 703  Japanese rice
ABE77575       1339 PLPHIDVlvdsta-----------------------kskvfsFMDGFFGYNQIKm------------------------a 1371 barrel medic
AAM19047        894 EMPGLSRelve---------------------------hrlpIKPGFRPYKQPPrhfnpll-------------ydrvke 933  Oryza sativ...
Feature 1                                                                           ##              
CAB78181        593 EADVRKTAFRTRYGHFef------------------------------------------vvMPFGLTNAPAVFMRLMNS 630  thale cress
AAM08509       1421 EEDIHKTAFRCPSAIGlfe----------------------------------------wvvMTFGLKSAGATYQRAMNY 1460 Oryza sativ...
BAB08213       1941 LLDAFDTAFRTPKGNFyy------------------------------------------tvMPFGLKNAGATYQRAMQF 1978 Oryza sativ...
AAX95475        712 REAIRKWRMCIDFTGLnkacpk----------------------------------dhfplpRIDQLVDSTAGFQGALND 757  Japanese rice
TIGR:At2g15410  885 QNDREKTVFITDQGTYcy------------------------------------------kvMPFGLKNAGATYPRLVNQ 922  thale cress
ABF96295        607 CKADMLEVVKAEVKHLyda----------------------------------------gfiHPCRYAEWVSNIVPVIKK 646  Oryza sativ...
ABF96966        815 PLNIPKTSFVTPFGTFcq------------------------------------------lrMPFGLRNAGATFARLVYK 852  Oryza sativ...
ABA93011        704 EEDIHKTAFRCPGAIGlfe----------------------------------------wvvMTFGLKSAGAMYQRAMNY 743  Japanese rice
ABE77575       1372 PEDREKTSFITPWGTFcy------------------------------------------kvMPFGLINAGATYQRGMTT 1409 barrel medic
AAM19047        934 EIDRLLKAGFIRPCRYaewvssivsvekkgsgkirvcidfrdlnkatpkdeypmpiadmminDASGHKNAGATYQRAMNL 1013 Oryza sativ...
Feature 1                       # ##                                                           ##   
CAB78181        631 VfqefldefVIIFIDDILVYskspeEQEVHLRRVMEKLRE--------------QKLFAKLSKCSFwq--reMGFLGHIV 694  thale cress
AAM08509       1461 IyhdliswlVEVYIDDVVVKskeieDHIADLRKVFERTRK--------------YGLKMNPTKCAFgv--saGQFLGFLV 1524 Oryza sativ...
BAB08213       1979 VlddlihhsVECYVDDMVVKtkdheHHQEDLRIVFERLRR--------------HQLKMNPLKCAFav--qsGVFLGFVI 2042 Oryza sativ...
AAX95475        758 Qlg----hnVEAYVDDIVVKkktsdSLIDDLRETFDNLRR--------------YRLMLNPKKCTFgv--psGKLLGSLV 817  Japanese rice
TIGR:At2g15410  923 MftdqldhsMEVYIDDMLVKslraeEHITHLRQCFQVLNR--------------YNMKLNPSKCTFgv--tsGEFLGYLV 986  thale cress
ABF96295        647 Ng------kVRVYIDDEVVIskeieDHIADLRKVFERTRK--------------YGLKMNPTKCAFgklepfTPLLRLKA 706  Oryza sativ...
ABF96966        853 VlgkqlgrnVKAYVDDIVVKihkafDHANNLQETFDSLRA--------------AGIKLNPEKCVFsv--raGKLLGFLV 916  Oryza sativ...
ABA93011        744 IyhdsigwlVEVYIDDVVVKskeigDHIANLRKFLRFLVHergievtqrsvnaiKKIQPPENKTKLqemigkINFVRRFI 823  Japanese rice
ABE77575       1410 LfhdmihkeIEVYVDDMIVKsiteeDHVKYLQKMFQRLRK--------------YKLRLNPNKCTFgv--rsGKLLGFIV 1473 barrel medic
AAM19047       1014 IfhdllgiiLEIYIDDIVVKsdgmeGHIADLRLAFERMRQ--------------YGLKMNPLKCAFgv--saGRFLGFMV 1077 Oryza sativ...

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