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12  structures 652  species 0  interactions 1739  sequences 25  architectures

Family: Smg8_Smg9 (PF10220)

Summary: Smg8_Smg9

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.

Smg8_Smg9 Provide feedback

Smg8 and Smg9 are two subunits of the Smg-1 complex. They suppress Smg-1 kinase activity in the isolated Smg-1 complex, and are involved in nonsense-mediated mRNA decay (NMD) in both mammals and nematodes [1].

Literature references

  1. Yamashita A, Izumi N, Kashima I, Ohnishi T, Saari B, Katsuhata Y, Muramatsu R, Morita T, Iwamatsu A, Hachiya T, Kurata R, Hirano H, Anderson P, Ohno S;, Genes Dev. 2009;23:1091-1105.: SMG-8 and SMG-9, two novel subunits of the SMG-1 complex, regulate remodeling of the mRNA surveillance complex during nonsense-mediated mRNA decay. PUBMED:19417104 EPMC:19417104


This tab holds annotation information from the InterPro database.

InterPro entry IPR019354

Smg8 and Smg9 are two subunits of the Smg-1 complex. They suppress Smg-1 kinase activity in the isolated Smg-1 complex, and are involved in nonsense-mediated mRNA decay (NMD) in both mammals and nematodes [ PUBMED:19417104 ]. NMD is a surveillance mechanism that detects and degrades mRNAs containing premature translation termination codons.

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
(22)
Full
(1739)
Representative proteomes UniProt
(2748)
RP15
(390)
RP35
(903)
RP55
(1491)
RP75
(1844)
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
(22)
Full
(1739)
Representative proteomes UniProt
(2748)
RP15
(390)
RP35
(903)
RP55
(1491)
RP75
(1844)
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
(22)
Full
(1739)
Representative proteomes UniProt
(2748)
RP15
(390)
RP35
(903)
RP55
(1491)
RP75
(1844)
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: KOGs (KOG3692)
Previous IDs: DUF2146;
Type: Family
Sequence Ontology: SO:0100021
Author: KOGs, Finn RD , Coggill P
Number in seed: 22
Number in full: 1739
Average length of the domain: 358.7 aa
Average identity of full alignment: 16 %
Average coverage of the sequence by the domain: 69.89 %

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 22.5 22.5
Trusted cut-off 22.5 22.5
Noise cut-off 22.4 22.4
Model length: 882
Family (HMM) version: 12
Download: download the raw HMM for this family

Species distribution

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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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Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Smg8_Smg9 domain has been found. There are 12 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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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
A0A044VHQ4 View 3D Structure Click here
A0A077Z2T0 View 3D Structure Click here
A0A1D6LL53 View 3D Structure Click here
A0A1D6QAI1 View 3D Structure Click here
A0A3P7T202 View 3D Structure Click here
A0A3Q0KPC8 View 3D Structure Click here
A1A4J7 View 3D Structure Click here
A8WP66 View 3D Structure Click here
B0W730 View 3D Structure Click here
B3MJV4 View 3D Structure Click here
B4GH42 View 3D Structure Click here
B4HWV2 View 3D Structure Click here
B4JE52 View 3D Structure Click here
B4KKN5 View 3D Structure Click here
B4LS82 View 3D Structure Click here
B4MV81 View 3D Structure Click here
B4Q9T2 View 3D Structure Click here
B5E0H4 View 3D Structure Click here
B5X165 View 3D Structure Click here
D3ZQ80 View 3D Structure Click here
E7F7F6 View 3D Structure Click here
E7FBA3 View 3D Structure Click here
J9FKW3 View 3D Structure Click here
K7LVL8 View 3D Structure Click here
K7LVL9 View 3D Structure Click here
K7M344 View 3D Structure Click here
O62301 View 3D Structure Click here
Q0VA04 View 3D Structure Click here
Q17G65 View 3D Structure Click here
Q2YDD2 View 3D Structure Click here
Q4D837 View 3D Structure Click here
Q4DPK8 View 3D Structure Click here
Q5PQS6 View 3D Structure Click here
Q6K9X0 View 3D Structure Click here
Q75JP6 View 3D Structure Click here
Q8ND04 View 3D Structure Click here
Q8VE18 View 3D Structure Click here
Q9DB90 View 3D Structure Click here
Q9H0W8 View 3D Structure Click here
Q9VKQ6 View 3D Structure Click here