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Conserved domains on  [gi|835778743|ref|WP_047657908|]
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RNA-directed DNA polymerase [Escherichia coli]

Protein Classification

RNA-directed DNA polymerase( domain architecture ID 10108233)

RNA-directed DNA polymerase catalyzes DNA replication from an RNA template of bacterial retrotransposons or retrons

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RT_Bac_retron_I cd01646
RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The ...
 160-300 2.01e-28

RT_Bac_retron_I: 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.


:

Pssm-ID: 238824 [Multi-domain]  Cd Length: 158  Bit Score: 110.50  E-value: 2.01e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835778743 160 TDISNFYPSIYTHSFEWVFI-SKEEAKKKKSKNNPGGLIDSHIQMMMNNQTNGIPLGSTLMDTFAELILGQIDIELRKKt 238
Cdd:cd01646    1 LDISNFYDSIYTHSLPWALHgKIKAKQLLKLLRLLGNLLDLLLLSSQYGQTNGLPIGPLTSRFLANIYLNDVDHELKSK- 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 835778743 239 neLKIINYkvVRYRDDYRIFSNSKDDLDIISKCLVNVLGDFGLDLNSKKTELYEDIILHSLK 300
Cdd:cd01646   80 --LKGVDY--VRYVDDIRIFADSKEEAEEILEELKEFLAELGLSLNLSKTEILPLPEGTASK 137
 
Name Accession Description Interval E-value
RT_Bac_retron_I cd01646
RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The ...
 160-300 2.01e-28

RT_Bac_retron_I: 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.


Pssm-ID: 238824 [Multi-domain]  Cd Length: 158  Bit Score: 110.50  E-value: 2.01e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835778743 160 TDISNFYPSIYTHSFEWVFI-SKEEAKKKKSKNNPGGLIDSHIQMMMNNQTNGIPLGSTLMDTFAELILGQIDIELRKKt 238
Cdd:cd01646    1 LDISNFYDSIYTHSLPWALHgKIKAKQLLKLLRLLGNLLDLLLLSSQYGQTNGLPIGPLTSRFLANIYLNDVDHELKSK- 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 835778743 239 neLKIINYkvVRYRDDYRIFSNSKDDLDIISKCLVNVLGDFGLDLNSKKTELYEDIILHSLK 300
Cdd:cd01646   80 --LKGVDY--VRYVDDIRIFADSKEEAEEILEELKEFLAELGLSLNLSKTEILPLPEGTASK 137
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 208-291 6.13e-06

Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.


Pssm-ID: 395031 [Multi-domain]  Cd Length: 189  Bit Score: 46.91  E-value: 6.13e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835778743  208 QTNGIPLGSTLMDTFAELILGQIDIELRKKTNElkiinyKVVRYRDDYRIFSNSKDDLDIISKCLVNVLGDFGLDLNSKK 287
Cdd:pfam00078  99 EWKGLPQGLVLSPALFQLFMNELLRPLRKRAGL------TLVRYADDILIFSKSEEEHQEALEEVLEWLKESGLKINPEK 172


                  ....
gi 835778743  288 TELY 291
Cdd:pfam00078 173 TQFF 176
 
Name Accession Description Interval E-value
RT_Bac_retron_I cd01646
RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The ...
 160-300 2.01e-28

RT_Bac_retron_I: 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.


Pssm-ID: 238824 [Multi-domain]  Cd Length: 158  Bit Score: 110.50  E-value: 2.01e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835778743 160 TDISNFYPSIYTHSFEWVFI-SKEEAKKKKSKNNPGGLIDSHIQMMMNNQTNGIPLGSTLMDTFAELILGQIDIELRKKt 238
Cdd:cd01646    1 LDISNFYDSIYTHSLPWALHgKIKAKQLLKLLRLLGNLLDLLLLSSQYGQTNGLPIGPLTSRFLANIYLNDVDHELKSK- 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 835778743 239 neLKIINYkvVRYRDDYRIFSNSKDDLDIISKCLVNVLGDFGLDLNSKKTELYEDIILHSLK 300
Cdd:cd01646   80 --LKGVDY--VRYVDDIRIFADSKEEAEEILEELKEFLAELGLSLNLSKTEILPLPEGTASK 137
RVT_1 pfam00078
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
 208-291 6.13e-06

Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.


Pssm-ID: 395031 [Multi-domain]  Cd Length: 189  Bit Score: 46.91  E-value: 6.13e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835778743  208 QTNGIPLGSTLMDTFAELILGQIDIELRKKTNElkiinyKVVRYRDDYRIFSNSKDDLDIISKCLVNVLGDFGLDLNSKK 287
Cdd:pfam00078  99 EWKGLPQGLVLSPALFQLFMNELLRPLRKRAGL------TLVRYADDILIFSKSEEEHQEALEEVLEWLKESGLKINPEK 172


                  ....
gi 835778743  288 TELY 291
Cdd:pfam00078 173 TQFF 176
RT_G2_intron cd01651
RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA ...
 206-291 8.45e-03

RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA using RNA as template. Proteins in this subfamily are found in bacterial and mitochondrial group II introns. Their most probable ancestor was a retrotransposable element with both gag-like and pol-like genes. This subfamily of proteins appears to have captured the RT sequences from transposable elements, which lack long terminal repeats (LTRs).


Pssm-ID: 238828 [Multi-domain]  Cd Length: 226  Bit Score: 37.95  E-value: 8.45e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 835778743 206 NNQTNGIPLGSTLMDTFAELILGQIDIELRKKTNELKII------NYKVVRYRDDYRIFSNSKDDLDIISKCLVNVLGDF 279
Cdd:cd01651  121 VETEKGTPQGGVISPLLANIYLHELDKFVEEKLKEYYDTsdpkfrRLRYVRYADDFVIGVRGPKEAEEIKELIREFLEEL 200

                         90
                 ....*....|..
gi 835778743 280 GLDLNSKKTELY 291
Cdd:cd01651  201 GLELNPEKTRIT 212
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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