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0  structures 95  species 0  interactions 1230  sequences 7  architectures

Family: BEX (PF04538)

Summary: Brain expressed X-linked like family

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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.

Brain expressed X-linked like family Provide feedback

This is a family of transcription elongation factors which includes those referred to as Bex proteins as well as those named TCEAL7. Bex1 was shown to be a novel link between neurotrophin signalling, the cell cycle, and neuronal differentiation, suggesting it might function by coordinating internal cellular states with the ability of cells to respond to external signals [2]. TCEAL7 has been shown negatively to regulate the NF-kappaB pathway, hence being important in ovarian cancer as it one of the genes frequently downregulated in this cancer. A closely related protein, TFIIS/TCEA, found in PF07500 is involved in transcription elongation and transcript fidelity. TFIIS/TCEA promotes 3' endoribonuclease activity of RNA polymerase II (pol II) and allows pol II to bypass transcript pause or 'arrest' during elongation process. It is thus possible that BEX is also acting in this way [2].

Literature references

  1. Brown AL, Kay GF; , Hum Mol Genet 1999;8:611-619.: Bex1, a gene with increased expression in parthenogenetic embryos, is a member of a novel gene family on the mouse X chromosome. PUBMED:10072429 EPMC:10072429

  2. Vilar M, Murillo-Carretero M, Mira H, Magnusson K, Besset V, Ibanez CF;, EMBO J. 2006;25:1219-1230.: Bex1, a novel interactor of the p75 neurotrophin receptor, links neurotrophin signaling to the cell cycle. PUBMED:16498402 EPMC:16498402

  3. Rattan R, Narita K, Chien J, Maguire JL, Shridhar R, Giri S, Shridhar V;, Oncogene. 2009; [Epub ahead of print]: TCEAL7, a putative tumor suppressor gene, negatively regulates NF-kappaB pathway. PUBMED:19966855 EPMC:19966855


This tab holds annotation information from the InterPro database.

InterPro entry IPR021156

This is a family of transcription elongation factors which includes those referred to as Bex (brain-expressed X-linked) proteins as well as those named TCEAL (transcription elongation factor A protein-like). Bex proteins are expressed in a wide range of tissues and are known to play a role in neuronal development. They seem to have have distinct roles in cancers [ PUBMED:26408910 ]. Bex1 was shown to be a novel link between neurotrophin signalling, the cell cycle, and neuronal differentiation, suggesting it might function by coordinating internal cellular states with the ability of cells to respond to external signals [ PUBMED:16498402 ]. TCEAL7 has been shown negatively to regulate the NF-kappaB pathway, hence being important in ovarian cancer as it one of the genes frequently downregulated in this cancer [ PUBMED:19966855 , PUBMED:15870691 ]. Apart from TCEAL7, there are other five members of the TCEAL family, i.e. TCEAL1, TCEAL3, TCEAL4, TCEAL5 and TCEAL8. TCEAL1 was shown involved in the apoptosis of human cancer cells [ PUBMED:10051408 ].

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...

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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
(62)
Full
(1230)
Representative proteomes UniProt
(1560)
RP15
(38)
RP35
(206)
RP55
(697)
RP75
(1187)
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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
(62)
Full
(1230)
Representative proteomes UniProt
(1560)
RP15
(38)
RP35
(206)
RP55
(697)
RP75
(1187)
Alignment:
Format:
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Sequence:
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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
(62)
Full
(1230)
Representative proteomes UniProt
(1560)
RP15
(38)
RP35
(206)
RP55
(697)
RP75
(1187)
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: Pfam-B_3086 (release 7.5)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Finn RD
Number in seed: 62
Number in full: 1230
Average length of the domain: 115.40 aa
Average identity of full alignment: 30 %
Average coverage of the sequence by the domain: 74.24 %

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 26.1 26.1
Trusted cut-off 27.0 26.2
Noise cut-off 25.7 26.0
Model length: 118
Family (HMM) version: 15
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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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
A0A096MIT8 View 3D Structure Click here
A3KGA4 View 3D Structure Click here
B2RYT6 View 3D Structure Click here
D3ZT37 View 3D Structure Click here
M0RBL8 View 3D Structure Click here
M0RDJ7 View 3D Structure Click here
Q00994 View 3D Structure Click here
Q15170 View 3D Structure Click here
Q3MKP9 View 3D Structure Click here
Q3MKQ1 View 3D Structure Click here
Q3MKQ2 View 3D Structure Click here
Q3TZW7 View 3D Structure Click here
Q5H9J7 View 3D Structure Click here
Q5H9L2 View 3D Structure Click here
Q5PPP3 View 3D Structure Click here
Q6I7R5 View 3D Structure Click here
Q6IPX3 View 3D Structure Click here
Q6PDU5 View 3D Structure Click here
Q8CCT4 View 3D Structure Click here
Q8IYN2 View 3D Structure Click here
Q8R0A5 View 3D Structure Click here
Q921P9 View 3D Structure Click here
Q969E4 View 3D Structure Click here
Q96EI5 View 3D Structure Click here
Q9BRU2 View 3D Structure Click here
Q9BXY8 View 3D Structure Click here
Q9CWT2 View 3D Structure Click here
Q9CZY2 View 3D Structure Click here
Q9DB24 View 3D Structure Click here
Q9DD24 View 3D Structure Click here
Q9H3H9 View 3D Structure Click here
Q9HBH7 View 3D Structure Click here
Q9NWD9 View 3D Structure Click here
Q9R224 View 3D Structure Click here
Q9UHQ7 View 3D Structure Click here
Q9WTZ8 View 3D Structure Click here
Q9WTZ9 View 3D Structure Click here

trRosetta Structure

The structural model below was generated by the Baker group with the trRosetta software using the Pfam UniProt multiple sequence alignment.

The InterPro website shows the contact map for the Pfam SEED alignment. Hovering or clicking on a contact position will highlight its connection to other residues in the alignment, as well as on the 3D structure.

Improved protein structure prediction using predicted inter-residue orientations. Jianyi Yang, Ivan Anishchenko, Hahnbeom Park, Zhenling Peng, Sergey Ovchinnikov, David Baker Proceedings of the National Academy of Sciences Jan 2020, 117 (3) 1496-1503; DOI: 10.1073/pnas.1914677117;