Conserved Protein Domain Family
RT_Bac_retron_II
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cd03487: RT_Bac_retron_II 
RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The polymerase reaction of this enzyme leads to the production of a unique RNA-DNA complex called msDNA (multicopy single-stranded (ss)DNA) in which a small ssDNA branches out from a small ssRNA molecule via a 2'-5'phosphodiester linkage. Bacterial retron RTs produce cDNA corresponding to only a small portion of the retron genome.
Links
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Statistics
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PSSM-Id: 239569
Aligned: 61 rows
Threshold Bit Score: 135.008
Created: 3-May-2006
Updated: 2-Oct-2020
Structure
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Aligned Rows:
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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
Scroll to Sequence Alignment Display
Sequence Alignment
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Format: Row Display: Color Bits: Type Selection: 
Feature 1                                                                                       
CAA44468     46 KRHGGQRLVLA------PDYLLKTVQRNIlknvl----------sqfpLSPFATAYRPGCPIVSNAQPHCqq--pqILKL 107 Escherichia coli
NP_934564    36 KKPIEPHGISDvk---qGKLGTKSIFKLTpaksqylgrlnnkffchiqVNNSAVAYVEKKSYLDMFEPHRkn--tnFLRI 110 Vibrio vulnificu...
NP_249406    34 PVMVNGRLVYK------TDKDLRAYHRFLnkflf---------erlpvVDDVVFSYRKGVNAVDAVEKHAgs--kfYFQT 96  Pseudomonas aeru...
CAG22431     62 GKGGKPRKIQC------PCNGLEKIHSRIasll-----------crikTPDYLQSGKKGHSNVSNANVHLgs--scLLAT 122 Photobacterium p...
CAH07807     50 DGTIKKRTINS------TNKDLKVIQKRLynyll----------skttLPNYFFGGIPKKDNILNAKYHQgn--kyVFTT 111 Bacteroides frag...
YP_217686    56 FVNDAGRTIQE------PIAQLKAVHRKIgvll-----------srieLPPYLHSGRKKHSTLTNVESHKla--teLLKL 116 Salmonella enter...
ZP_01216116  27 KGNGKFRDIFV------GNEETKIFFKKVmnflekk------ysdilsKNQCSHGFRKKRSAISNAMCHMklergyILSI 94  Psychromonas sp....
ZP_00813439  38 KIGKKFAYSHQdnnkptHQKLSKIIFENFlsn--------------ipLNQSAIAYVKKKSYFDFIEPHRnn--yfFLRI 101 Shewanella putre...
ZP_01422151  57 VDKKTGREIQQ------PKPVLRSVHDRVgkll-----------srieTPDFLHSAIKGRSYISNATTHCpa--lpSVKV 117 Caulobacter sp. K31
YP_797537    45 GENGKLREIQE------PVYKLKSVHSKIqksl-----------asivAPEFLFSGVKGKSNISNASYHKdg--nyIVTA 105 Leptospira borgp...

Feature 1       ######                                                           ##             
CAA44468    108 DIENFFDSISWLQVWRVFrqaqlp----------rnvvtMLTWICCYnd-------------aLPQGAPTSPAISNLVMR 164 Escherichia coli
NP_934564   111 DIKSFFHSINREILAEALspyvtneiffesgkvkqslldALLNLVSLrvsteyndqslhnkdiLPIGFKSSPVISNIVFR 190 Vibrio vulnificu...
NP_249406    97 DLRDFFSSLTKSDVRRTLewakdvcvi----sdldvwveRILKLVTIgd-------------sLPMGFSTSPAISNACLY 159 Pseudomonas aeru...
CAG22431    123 DIKSFFPSTKRYMLFSFFfhsmec---------sadvadILSDLCTIng-------------hIPTGSQISMPLAFWANS 180 Photobacterium p...
CAH07807    112 DLKSFFPSINHKMVFYMFlklgct----------peiarTLTKLTTHny-------------qVPQGVPTSTLIANLVFK 168 Bacteroides frag...
YP_217686   117 DIHKFFPSTRAAKVYKAFvekfem---------spdvayIMTNLSTFag-------------kVPTGSPISMAMAFWANK 174 Salmonella enter...
ZP_01216116  95 DIKDFFSSIKKDMLRDIIs-------------------kKILDVCFIdd-------------vLPQGLSTSPVISNIVMC 142 Psychromonas sp....
ZP_00813439 102 DLKDFFHSISEDLLKRTLsdyfssesls--etikqsnidAIFTFLTVnlksdssnvkfldkkiLPIGFPLSPNLANIVFR 179 Shewanella putre...
ZP_01422151 118 DIKKFYPSTRAHAVYHFFldrmqc---------agdvagMLAAMLTVeg-------------hLATGSSASPILSFFAYE 175 Caulobacter sp. K31
YP_797537   106 DIQSFYINCNKEHIFRFFkytlrt---------sddiarILTELCCYkt-------------fLPTGSPVSQILAYHSYA 163 Leptospira borgp...

Feature 1                                # ##                                                   
CAA44468    165 RFDERIgew------cqARGITYTRYCDDMTFSGhfn-------------------arqVKNKVCGLla----elGLSLN 215 Escherichia coli
NP_934564   191 RFDIIIqel------caRSDIIYTRYADDMLFSSpehsky--------------lhtnkFLSEISYTls----lsGFKLN 246 Vibrio vulnificu...
NP_249406   160 SLDGILkth------clSNGVIYTRYADDLIFSSsnkq-----------------aldpLFGVVCRTlqse-fsgRMGIN 215 Pseudomonas aeru...
CAG22431    181 HMFDELyll------svKHAVKMTVYVDDLTFSGdavnk---------------lfmsvTQRIITKH--------NQVMH 231 Photobacterium p...
CAH07807    169 PVGDRIqal------akENNIKFSIFVDDITMSSsi----------------------dFHKKIPEIlsii-ttsGYKIS 219 Bacteroides frag...
YP_217686   175 DMFDELsnl------aaSNSLVFTAYVDDVAFSGskipk---------------gfaaqAKKCIRSH--------GLTSK 225 Salmonella enter...
ZP_01216116 143 NIDHVIekqlnslgiklDVNFCYSRYVDDLTISIysdnvddc----------flkiqkkVHEMIKNIli----fyGFYLN 208 Psychromonas sp....
ZP_00813439 180 KTDLLLekl------cdMHGVTYTRYADDMLFSSrgimeknllfrknnnykkpyihsdnFLSEIKYLvs----idGFFIN 249 Shewanella putre...
ZP_01422151 176 DMFGEIael------aeVRGCAMTCYVDDMVFTGkga-------------------tprLLFEIRNIa------kPYRLW 224 Caulobacter sp. K31
YP_797537   164 RIFNRIdaf------skANDITFSLYVDDITLSSek----------------------sIHRYILKTiskllksvNLSLK 215 Leptospira borgp...

Feature 1                      ##                              
CAA44468    216 KRKGCLiaackRQQVTGIVVnh---------kpQLAREARRALRQEV 253 Escherichia coli
NP_934564   247 QAKTIKdk--nMISVNGYVIesgeng--nsgsiRISEKKTKKIYKLI 289 Vibrio vulnificus YJ016
NP_249406   216 SQKTKYlrkggKIKLLGLNVlpn-------grvTVDMRHKKEIEVRL 255 Pseudomonas aeruginosa PAO1
CAG22431    232 PDKTKLyrgyeSKLITGVVVkgd--------nlLVRNEQHKMLFSDV 270 Photobacterium profundum SS9
CAH07807    220 HSKTFYkt--kNPIVTGVICqnnk-----lkipQSYNKRIKRIKADV 259 Bacteroides fragilis NCTC 9343
YP_217686   226 DKKERFypsseGKLLTGIVIqdgelkvrwahndSIGKEFATLAEAKD 272 Salmonella enterica subsp. enterica serovar Chole...
ZP_01216116 209 ESKTKYgnlndNFHVTGISLvn---------hgEPTRKTKRKLRAAL 246 Psychromonas sp. CNPT3
ZP_00813439 250 HNKTIKsv--nTLSLNGYTIsgtnfp-diegkiRLSNKKTKIIEKVI 293 Shewanella putrefaciens CN-32
ZP_01422151 225 THKAFAfgpgqPKVITGLAVtlg--------gpRLPNDRKAVIHESL 263 Caulobacter sp. K31
YP_797537   216 KEKTKFynknsYKIVTGCAIspdhi---llrpnKIMRKIDNKLCKHE 259 Leptospira borgpetersenii serovar Hardjo-bovis L550

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