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0  structures 923  species 0  interactions 1015  sequences 19  architectures

Family: Sde2_N_Ubi (PF13019)

Summary: Silencing defective 2 N-terminal ubiquitin domain

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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.

Silencing defective 2 N-terminal ubiquitin domain Provide feedback

Sde2 (silencing defective 2) is a ubiquitin‐fold‐containing splicing regulator that supports splicing of selected pre‐mRNAs in an intron‐specific manner in Schizosaccharomyces pombe. Both fission yeast and human Sde2 are translated as inactive precursor proteins harbouring the ubiquitin‐fold domain linked through an invariant GGKGG motif to a C‐terminal domain. The Sde2 protein has a ubiquitin‐fold at its N‐terminus, which must be cleaved by the ubiquitin‐specific proteases (USPs) Ubp5 and Ubp15. After cleavage, the C‐terminal domain of Sde2, which starts with a lysine, gets incorporated into the spliceosome [1]. This entry represents the ubiquitin fold N-terminal domain found in Sde2 proteins.

Literature references

  1. Thakran P, Pandit PA, Datta S, Kolathur KK, Pleiss JA, Mishra SK;, EMBO J. 2018;37:89-101.: Sde2 is an intron-specific pre-mRNA splicing regulator activated by ubiquitin-like processing. PUBMED:28947618 EPMC:28947618


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR024974

Sde2 has been identified in fission yeast as an important factor in telomere formation and maintenance. This domain is found in the N-terminal section of these nuclear proteins, and is essential for telomeric silencing and genomic stability.

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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...

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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
(16)
Full
(1015)
Representative proteomes UniProt
(1429)
NCBI
(1655)
Meta
(2)
RP15
(302)
RP35
(587)
RP55
(834)
RP75
(1014)
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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
(16)
Full
(1015)
Representative proteomes UniProt
(1429)
NCBI
(1655)
Meta
(2)
RP15
(302)
RP35
(587)
RP55
(834)
RP75
(1014)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(16)
Full
(1015)
Representative proteomes UniProt
(1429)
NCBI
(1655)
Meta
(2)
RP15
(302)
RP35
(587)
RP55
(834)
RP75
(1014)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   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_2457 (release 24.0)
Previous IDs: Ubiquitin-like; Telomere_Sde2;
Type: Domain
Sequence Ontology: SO:0000417
Author: Wood V , Coggill P , El-Gebali S
Number in seed: 16
Number in full: 1015
Average length of the domain: 145.50 aa
Average identity of full alignment: 31 %
Average coverage of the sequence by the domain: 41.66 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 26.4 16.0
Trusted cut-off 26.4 19.6
Noise cut-off 26.3 15.9
Model length: 164
Family (HMM) version: 6
Download: download the raw HMM for this family

Species distribution

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