Summary: L-seryl-tRNA selenium transferase
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L-seryl-tRNA selenium transferase Provide feedback
No Pfam abstract.
Internal database links
SCOOP: | Aminotran_1_2 Aminotran_5 Beta_elim_lyase Cys_Met_Meta_PP DegT_DnrJ_EryC1 Met_gamma_lyase SHMT |
Similarity to PfamA using HHSearch: | Aminotran_5 DegT_DnrJ_EryC1 Cys_Met_Meta_PP Beta_elim_lyase |
This tab holds annotation information from the InterPro database.
InterPro entry IPR018319
In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3-prime or 5-prime non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation.
This family describes SelA and pyridoxal phosphate enzymes of unknown function. A close homologue of SelA is found in Helicobacter pylori, but all other required elements are missing and the protein is shorter at the N terminus than SelA from other species.
Domain organisation
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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Pfam Clan
This family is a member of clan PLP_aminotran (CL0061), which has the following description:
This superfamily contains a variety of PLP-dependent enzymes.
The clan contains the following 16 members:
Alliinase_C Aminotran_1_2 Aminotran_3 Aminotran_5 Asp_aminotransf Beta_elim_lyase ComK Cys_Met_Meta_PP DegT_DnrJ_EryC1 GDC-P Met_gamma_lyase OKR_DC_1 Pyridoxal_deC SelA SepSecS SHMTAlignments
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 (10) |
Full (2463) |
Representative proteomes | UniProt (19374) |
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RP15 (336) |
RP35 (1229) |
RP55 (2569) |
RP75 (4641) |
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Jalview | |||||||
HTML | |||||||
PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
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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 (10) |
Full (2463) |
Representative proteomes | UniProt (19374) |
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RP15 (336) |
RP35 (1229) |
RP55 (2569) |
RP75 (4641) |
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Raw Stockholm | |||||||
Gzipped |
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
Seed source: | TIGRFAMs |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
TIGRFAMs, Griffiths-Jones SR |
Number in seed: | 10 |
Number in full: | 2463 |
Average length of the domain: | 330.3 aa |
Average identity of full alignment: | 36 % |
Average coverage of the sequence by the domain: | 76.05 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 367 | ||||||||||||
Family (HMM) version: | 16 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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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 SelA domain has been found. There are 48 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.