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0  structures 1438  species 0  interactions 1810  sequences 48  architectures

Family: DBR1 (PF05011)

Summary: Lariat debranching enzyme, C-terminal domain

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

Lariat debranching enzyme, C-terminal domain Provide feedback

This presumed domain is found at the C-terminus of lariat debranching enzyme. This domain is always found in association with PF00149.

Literature references

  1. Chapman KB, Boeke JD; , Cell 1991;65:483-492.: Isolation and characterization of the gene encoding yeast debranching enzyme. PUBMED:1850323 EPMC:1850323

  2. Nam K, Lee G, Trambley J, Devine SE, Boeke JD; , Mol Cell Biol 1997;17:809-818.: Severe growth defect in a Schizosaccharomyces pombe mutant defective in intron lariat degradation. PUBMED:9001235 EPMC:9001235

  3. Ooi SL, Dann C 3rd, Nam K, Leahy DJ, Damha MJ, Boeke JD; , Methods Enzymol 2001;342:233-248.: RNA lariat debranching enzyme. PUBMED:11586896 EPMC:11586896


This tab holds annotation information from the InterPro database.

InterPro entry IPR007708

This presumed domain is found at the C terminus of lariat debranching enzyme. This domain is always found in association with a metallo-phosphoesterase domain INTERPRO . RNA lariat debranching enzyme is capable of digesting a variety of branched nucleic acid substrates and multicopy single-stranded DNAs. The enzyme degrades intron lariat structures during splicing.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(131)
Full
(1810)
Representative proteomes UniProt
(3025)
RP15
(375)
RP35
(853)
RP55
(1383)
RP75
(1842)
Jalview View  View  View  View  View  View  View 
HTML View  View           
PP/heatmap 1 View           

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(131)
Full
(1810)
Representative proteomes UniProt
(3025)
RP15
(375)
RP35
(853)
RP55
(1383)
RP75
(1842)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(131)
Full
(1810)
Representative proteomes UniProt
(3025)
RP15
(375)
RP35
(853)
RP55
(1383)
RP75
(1842)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Pfam-B_9676 (release 7.6)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Wood V , Bateman A
Number in seed: 131
Number in full: 1810
Average length of the domain: 133.2 aa
Average identity of full alignment: 32 %
Average coverage of the sequence by the domain: 25.29 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 26.0 26.0
Trusted cut-off 26.0 26.1
Noise cut-off 25.9 25.9
Model length: 137
Family (HMM) version: 16
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A044SIG7 View 3D Structure Click here
A0A077ZC20 View 3D Structure Click here
A0A0D2F649 View 3D Structure Click here
A0A0K0EE06 View 3D Structure Click here
A0A0K0J870 View 3D Structure Click here
A0A0N4UH33 View 3D Structure Click here
A0A175WF57 View 3D Structure Click here
A0A1C1C7X8 View 3D Structure Click here
A0A1D8PPT8 View 3D Structure Click here
A0A3P7E9D4 View 3D Structure Click here
A0A5K1K8J0 View 3D Structure Click here
A0A5S6PDZ8 View 3D Structure Click here
A4HXG1 View 3D Structure Click here
B2RYJ2 View 3D Structure Click here
B6U6X4 View 3D Structure Click here
C0NT47 View 3D Structure Click here
C1H331 View 3D Structure Click here
G4VB14 View 3D Structure Click here
I1JU50 View 3D Structure Click here
O13765 View 3D Structure Click here
P24309 View 3D Structure Click here
Q29FE1 View 3D Structure Click here
Q4D7X4 View 3D Structure Click here
Q54VL9 View 3D Structure Click here
Q57ZT2 View 3D Structure Click here
Q5ZLM2 View 3D Structure Click here
Q61D44 View 3D Structure Click here
Q6AU07 View 3D Structure Click here
Q6P886 View 3D Structure Click here
Q7T3E4 View 3D Structure Click here
Q923B1 View 3D Structure Click here
Q94K01 View 3D Structure Click here
Q966M6 View 3D Structure Click here
Q9UK59 View 3D Structure Click here
Q9VSD7 View 3D Structure Click here
U7PHA3 View 3D Structure Click here

trRosetta Structure

The structural model below was generated by the Baker group with the trRosetta software using the Pfam UniProt multiple sequence alignment.

The InterPro website shows the contact map for the Pfam SEED alignment. Hovering or clicking on a contact position will highlight its connection to other residues in the alignment, as well as on the 3D structure.

Improved protein structure prediction using predicted inter-residue orientations. Jianyi Yang, Ivan Anishchenko, Hahnbeom Park, Zhenling Peng, Sergey Ovchinnikov, David Baker Proceedings of the National Academy of Sciences Jan 2020, 117 (3) 1496-1503; DOI: 10.1073/pnas.1914677117;