Summary: Scd6-like Sm domain
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.
Scd6-like Sm domain Provide feedback
The Scd6-like Sm domain is found in Scd6p from S. cerevisiae, Rap55 from the newt Pleurodeles walt, and its orthologs from fungi, animals, plants and apicomplexans . The domain is also found in Dcp3p and the human EDC3/FLJ21128 protein where it is fused to the the Rossmanoid YjeF-N domain [1,2]. In addition both EDC3 and Scd6p are found fused to the FDF domain [1,2].
Anantharaman V, Aravind L;, BMC Genomics. 2004;5:45.: Novel conserved domains in proteins with predicted roles in eukaryotic cell-cycle regulation, decapping and RNA stability. PUBMED:15257761 EPMC:15257761
Tanaka KJ, Ogawa K, Takagi M, Imamoto N, Matsumoto K, Tsujimoto M;, J Biol Chem. 2006;281:40096-40106.: RAP55, a cytoplasmic mRNP component, represses translation in Xenopus oocytes. PUBMED:17074753 EPMC:17074753
Tritschler F, Eulalio A, Truffault V, Hartmann MD, Helms S, Schmidt S, Coles M, Izaurralde E, Weichenrieder O; , Mol Cell Biol. 2007;27:8600-8611.: A divergent Sm fold in EDC3 proteins mediates DCP1 binding and P-body targeting. PUBMED:17923697 EPMC:17923697
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR025609
The Lsm14 N-terminal domain is a type of LSM domain found in Lsm14 proteins (also known as Rap55) [PUBMED:17074753, PUBMED:18723115] and in the Saccharomyces cerevisiae homologue Scd6 [PUBMED:15225602]. The domain is also found in the human EDC3 protein (enhancer of mRNA-decapping protein 3) where it is fused to the the Rossmanoid YjeF-N domain [PUBMED:15257761]. In addition, both EDC3 and Scd6 are found fused to the FDF domain [PUBMED:15225602, PUBMED:15257761].
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
Loading domain graphics...
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
- Pfam viewer
- an HTML-based viewer that uses DAS to retrieve alignment fragments on request
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
If you find these logos useful in your own work, please consider citing the following article:
Note: You can also download the data file for the tree.
Curation and family details
|Seed source:||Anantharaman V|
|Number in seed:||156|
|Number in full:||564|
|Average length of the domain:||94.00 aa|
|Average identity of full alignment:||40 %|
|Average coverage of the sequence by the domain:||21.39 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||2|
|Download:||download the raw HMM for this family|
Weight segments by...
Change the size of the sunburst
selected sequences to HMM
a FASTA-format file
- 0 sequences
- 0 species
How the sunburst is generated
Colouring and labels
Anomalies in the taxonomy tree
Missing taxonomic levels
Unmapped species names
Too many species/sequences
The tree shows the occurrence of this domain across different species. More...
You can use the tree controls to manipulate how the interactive tree is displayed:
- show/hide the summary boxes
- highlight species that are represented in the seed alignment
- expand/collapse the tree or expand it to a given depth
- select a sub-tree or a set of species within the tree and view them graphically or as an alignment
- save a plain text representation of the tree
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 LSM14 domain has been found. There are 5 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 seqence.
Loading structure mapping...