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177  structures 131  species 4  interactions 296  sequences 6  architectures

Family: Toxin_TOLIP (PF00087)

Summary: Snake toxin and toxin-like protein

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Snake venom". More...

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

This is the Wikipedia entry entitled "Three-finger toxin". More...

Three-finger toxin Edit Wikipedia article

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

Snake toxin and toxin-like protein Provide feedback

This family predominantly includes venomous neurotoxins and cytotoxins from snakes, but also structurally similar (non-snake) toxin-like proteins (TOLIPs) such as Lymphocyte antigen 6D and Ly6/PLAUR domain-containing protein. Snake toxins are short proteins with a compact, disulphide-rich structure. TOLIPs have similar structural features (abundance of spaced cysteine residues, a high frequency of charge residues, a signal peptide for secretion and a compact structure) but, are not associated with a venom gland or poisonous function. They are endogenous animal proteins that are not restricted to poisonous animals [1].

Literature references

  1. Tirosh Y, Ofer D, Eliyahu T, Linial M;, Toxins (Basel). 2013;5:1314-1331.: Short toxin-like proteins attack the defense line of innate immunity. PUBMED:23881252 EPMC:23881252

  2. Dufton MJ; , J Mol Evol 1984;20:128-134.: Classification of elapid snake neurotoxins and cytotoxins according to chain length: evolutionary implications. PUBMED:6433031 EPMC:6433031

  3. Jonassen I, Collins JF, Higgins DG; , Protein Sci 1995;4:1587-1595.: Finding flexible patterns in unaligned protein sequences. PUBMED:8520485 EPMC:8520485


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR035076

This domain is predominantly found in venomous neurotoxins and cytotoxins from snakes, but also structurally similar (non-snake) toxin-like proteins (TOLIPs) such as Lymphocyte antigen 6D and Ly6/PLAUR domain-containing protein. Snake toxins are short proteins with a compact, disulphide-rich structure. TOLIPs have similar structural features (abundance of spaced cysteine residues, a high frequency of charge residues, a signal peptide for secretion and a compact structure) but, are not associated with a venom gland or poisonous function. They are endogenous animal proteins that are not restricted to poisonous animals [PUBMED:23881252].

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 uPAR_Ly6_toxin (CL0117), which has the following description:

This superfamily contains snake toxins as well as extracellular cysteine rich domains.

The clan contains the following 7 members:

Activin_recp BAMBI ecTbetaR2 PLA2_inh Toxin_TOLIP UPAR_LY6 UPAR_LY6_2

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, the UniProtKB sequence database, 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.

  Seed
(11)
Full
(296)
Representative proteomes UniProt
(1254)
NCBI
(2271)
Meta
(0)
RP15
(60)
RP35
(113)
RP55
(249)
RP75
(302)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(11)
Full
(296)
Representative proteomes UniProt
(1254)
NCBI
(2271)
Meta
(0)
RP15
(60)
RP35
(113)
RP55
(249)
RP75
(302)
Alignment:
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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
(11)
Full
(296)
Representative proteomes UniProt
(1254)
NCBI
(2271)
Meta
(0)
RP15
(60)
RP35
(113)
RP55
(249)
RP75
(302)
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.

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: Overington
Previous IDs: toxin; toxin_1; Toxin_1; Toxin_1_; Toxin_1;
Type: Domain
Sequence Ontology: SO:0000417
Author: Eddy SR
Number in seed: 11
Number in full: 296
Average length of the domain: 72.60 aa
Average identity of full alignment: 31 %
Average coverage of the sequence by the domain: 57.47 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.1 21.1
Trusted cut-off 21.1 21.1
Noise cut-off 21.0 21.0
Model length: 67
Family (HMM) version: 21
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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Interactions

There are 4 interactions for this family. More...

Neur_chan_LBD Toxin_TOLIP Neur_chan_LBD COesterase

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 Toxin_TOLIP domain has been found. There are 177 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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