RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The ...
60-282
1.18e-78
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.
Pssm-ID: 239569 [Multi-domain] Cd Length: 214 Bit Score: 247.10 E-value: 1.18e-78
retron St85 family RNA-directed DNA polymerase; All members of the seed alignment are reverse ...
27-315
6.92e-63
retron St85 family RNA-directed DNA polymerase; All members of the seed alignment are reverse transcriptases St85-like systems. However, members of this family may include reverse transcriptases from other types of retron system.
Pssm-ID: 468421 [Multi-domain] Cd Length: 290 Bit Score: 208.52 E-value: 6.92e-63
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
58-265
1.73e-17
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: 80.81 E-value: 1.73e-17
group II intron reverse transcriptase/maturase; Members of this protein family are ...
104-251
1.18e-09
group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]
Pssm-ID: 275209 [Multi-domain] Cd Length: 354 Bit Score: 60.16 E-value: 1.18e-09
RT_Bac_retron_II: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The ...
60-282
1.18e-78
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.
Pssm-ID: 239569 [Multi-domain] Cd Length: 214 Bit Score: 247.10 E-value: 1.18e-78
retron St85 family RNA-directed DNA polymerase; All members of the seed alignment are reverse ...
27-315
6.92e-63
retron St85 family RNA-directed DNA polymerase; All members of the seed alignment are reverse transcriptases St85-like systems. However, members of this family may include reverse transcriptases from other types of retron system.
Pssm-ID: 468421 [Multi-domain] Cd Length: 290 Bit Score: 208.52 E-value: 6.92e-63
Reverse transcriptase (RNA-dependent DNA polymerase); A reverse transcriptase gene is usually ...
58-265
1.73e-17
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: 80.81 E-value: 1.73e-17
RT_G2_intron: Reverse transcriptases (RTs) with group II intron origin. RT transcribes DNA ...
58-251
1.04e-09
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: 58.75 E-value: 1.04e-09
group II intron reverse transcriptase/maturase; Members of this protein family are ...
104-251
1.18e-09
group II intron reverse transcriptase/maturase; Members of this protein family are multifunctional proteins encoded in most examples of bacterial group II introns. These group II introns are mobile selfish genetic elements, often with multiple highly identical copies per genome. Member proteins have an N-terminal reverse transcriptase (RNA-directed DNA polymerase) domain (pfam00078) followed by an RNA-binding maturase domain (pfam08388). Some members of this family may have an additional C-terminal DNA endonuclease domain that this model does not cover. A region of the group II intron ribozyme structure should be detectable nearby on the genome by Rfam model RF00029. [Mobile and extrachromosomal element functions, Other]
Pssm-ID: 275209 [Multi-domain] Cd Length: 354 Bit Score: 60.16 E-value: 1.18e-09
RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is ...
173-265
2.56e-06
RT_like: Reverse transcriptase (RT, RNA-dependent DNA polymerase)_like family. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs.
Pssm-ID: 238185 [Multi-domain] Cd Length: 98 Bit Score: 46.19 E-value: 2.56e-06
RT_Bac_retron_I: Reverse transcriptases (RTs) in bacterial retrotransposons or retrons. The ...
130-249
6.48e-06
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: 46.55 E-value: 6.48e-06
RT_nLTR: Non-LTR (long terminal repeat) retrotransposon and non-LTR retrovirus reverse transcriptase (RT). This subfamily contains both non-LTR retrotransposons and non-LTR retrovirus RTs. RTs catalyze the conversion of single-stranded RNA into double-stranded DNA for integration into host chromosomes. RT is a multifunctional enzyme with RNA-directed DNA polymerase, DNA directed DNA polymerase and ribonuclease hybrid (RNase H) activities.
Pssm-ID: 238827 [Multi-domain] Cd Length: 220 Bit Score: 44.59 E-value: 5.69e-05
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.
of the residues that compose this conserved feature have been mapped to the query sequence.
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of your query sequence and the protein sequences used to curate the domain model,
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The thumbnail image, if present, provides an approximate view of the feature's location in 3 dimensions.
Click on the triangle for interactive 3D structure viewing options.
Functional characterization of the conserved domain architecture found on the query.
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This image shows a graphical summary of conserved domains identified on the query sequence.
The Show Concise/Full Display button at the top of the page can be used to select the desired level of detail: only top scoring hits
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Domains are color coded according to superfamilies
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Others (non-specific hits) and
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if a domain or superfamily has been annotated with functional sites (conserved features),
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click on the bars or triangles to view your query sequence embedded in a multiple sequence alignment of the proteins used to develop the corresponding domain model.
The table lists conserved domains identified on the query sequence. Click on the plus sign (+) on the left to display full descriptions, alignments, and scores.
Click on the domain model's accession number to view the multiple sequence alignment of the proteins used to develop the corresponding domain model.
To view your query sequence embedded in that multiple sequence alignment, click on the colored bars in the Graphical Summary portion of the search results page,
or click on the triangles, if present, that represent functional sites (conserved features)
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Concise Display shows only the best scoring domain model, in each hit category listed below except non-specific hits, for each region on the query sequence.
(labeled illustration) Standard Display shows only the best scoring domain model from each source, in each hit category listed below for each region on the query sequence.
(labeled illustration) Full Display shows all domain models, in each hit category below, that meet or exceed the RPS-BLAST threshold for statistical significance.
(labeled illustration) Four types of hits can be shown, as available,
for each region on the query sequence:
specific hits meet or exceed a domain-specific e-value threshold
(illustrated example)
and represent a very high confidence that the query sequence belongs to the same protein family as the sequences use to create the domain model
non-specific hits
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the domain superfamily to which the specific and non-specific hits belong
multi-domain models that were computationally detected and are likely to contain multiple single domains
Retrieve proteins that contain one or more of the domains present in the query sequence, using the Conserved Domain Architecture Retrieval Tool
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