Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
21  structures 273  species 1  interaction 418  sequences 11  architectures

Family: SepSecS (PF05889)

Summary: O-phosphoseryl-tRNA(Sec) selenium transferase, SepSecS

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.

O-phosphoseryl-tRNA(Sec) selenium transferase, SepSecS Provide feedback

Early annotation suggested this family, SepSecS, of several eukaryotic and archaeal proteins, was involved in antigen-antibodies responses in the liver and pancreas [1,2]. Structural studies show that the family is O-phosphoseryl-tRNA(Sec) selenium transferase, an enzyme involved in the synthesis of the amino acid selenocysteine (Sec). Sec is the only amino acid whose biosynthesis occurs on its cognate transfer RNA (tRNA). SepSecS catalyses the final step in the formation of the amino acid [3,4,5,6]. The early observation that autoantibodies isolated from patients with type I autoimmune hepatitis targeted a ribonucleoprotein complex containing tRNASec led to the identification and characterisation of the archaeal and the human SepSecS [2]. SepSecS forms its own branch in the family of fold-type I pyridoxal phosphate (PLP) enzymes that goes back to the last universal common ancestor which explains why the archaeal sequences Q8TXK0 and Q8TYR3 are annotated as being pyridoxal phosphate-dependent enzymes.

Literature references

  1. Wies I, Brunner S, Henninger J, Herkel J, Kanzler S, Meyer zum Buschenfelde KH, Lohse AW; , Lancet 2000;355:1510-1515.: Identification of target antigen for SLA/LP autoantibodies in autoimmune hepatitis. PUBMED:10801173 EPMC:10801173

  2. Kernebeck T, Lohse AW, Grotzinger J; , Hepatology 2001;34:230-233.: A bioinformatical approach suggests the function of the autoimmune hepatitis target antigen soluble liver antigen/liver pancreas. PUBMED:11481605 EPMC:11481605

  3. Xu XM, Carlson BA, Mix H, Zhang Y, Saira K, Glass RS, Berry MJ, Gladyshev VN, Hatfield DL;, PLoS Biol. 2007;5:e4.: Biosynthesis of selenocysteine on its tRNA in eukaryotes. PUBMED:17194211 EPMC:17194211

  4. Fukunaga R, Yokoyama S;, J Mol Biol. 2007;370:128-141.: Structural insights into the second step of RNA-dependent cysteine biosynthesis in archaea: crystal structure of Sep-tRNA:Cys-tRNA synthase from Archaeoglobus fulgidus. PUBMED:17512006 EPMC:17512006

  5. Ganichkin OM, Xu XM, Carlson BA, Mix H, Hatfield DL, Gladyshev VN, Wahl MC;, J Biol Chem. 2008;283:5849-5865.: Structure and catalytic mechanism of eukaryotic selenocysteine synthase. PUBMED:18093968 EPMC:18093968

  6. Araiso Y, Palioura S, Ishitani R, Sherrer RL, O'Donoghue P, Yuan J, Oshikane H, Domae N, Defranco J, Soll D, Nureki O;, Nucleic Acids Res. 2008;36:1187-1199.: Structural insights into RNA-dependent eukaryal and archaeal selenocysteine formation. PUBMED:18158303 EPMC:18158303

  7. Palioura S, Sherrer RL, Steitz TA, Soll D, Simonovic M;, Science. 2009;325:321-325.: The human SepSecS-tRNASec complex reveals the mechanism of selenocysteine formation. PUBMED:19608919 EPMC:19608919

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR008829

This family consists of several eukaryotic and archaeal proteins which are related to the Homo sapiens soluble liver antigen/liver pancreas antigen (SLA/LP autoantigen). Autoantibodies are a hallmark of autoimmune hepatitis, but most are not disease specific. Autoantibodies to soluble liver antigen (SLA) and to liver and pancreas antigen (LP) have been described as disease specific, occurring in about 30% of all patients with autoimmune hepatitis [PUBMED:10801173]. The function of SLA/LP is unknown, however, it has been suggested that the protein may function as a serine hydroxymethyltransferase and may be an important enzyme in the thus far poorly understood selenocysteine pathway [PUBMED:11481605]. The archaeal sequences SWISSPROT and SWISSPROT are annotated as being pyridoxal phosphate-dependent enzymes.

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...

Loading domain graphics...

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 15 members:

Alliinase_C Aminotran_1_2 Aminotran_3 Aminotran_5 Aminotran_MocR Beta_elim_lyase Cys_Met_Meta_PP DegT_DnrJ_EryC1 GDC-P Met_gamma_lyase OKR_DC_1 Pyridoxal_deC SelA SepSecS SHMT


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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics 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.

Representative proteomes NCBI
Jalview View  View  View  View  View  View  View  View 
HTML View  View  View  View  View  View     
PP/heatmap 1 View  View  View  View  View     
Pfam viewer View  View             

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

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

Format an alignment

Representative proteomes NCBI

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.

Representative proteomes NCBI
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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...


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_9614 (release 8.0)
Previous IDs: SLA_LP_auto_ag;
Type: Domain
Author: Moxon SJ
Number in seed: 5
Number in full: 418
Average length of the domain: 312.40 aa
Average identity of full alignment: 33 %
Average coverage of the sequence by the domain: 78.40 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.1 20.1
Trusted cut-off 20.1 20.1
Noise cut-off 20.0 20.0
Model length: 389
Family (HMM) version: 9
Download: download the raw HMM for this family

Species distribution

Sunburst controls


Weight segments by...

Change the size of the sunburst


Colour assignments

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


Align selected sequences to HMM

Generate a FASTA-format file

Clear selection

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...

Loading sunburst data...

Tree controls


The tree shows the occurrence of this domain across different species. More...


Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.


There is 1 interaction for this family. More...



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 SepSecS domain has been found. There are 21 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...