Summary: Laminin G domain
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Laminin G domain Provide feedback
This family includes the Thrombospondin N-terminal-like domain, a Laminin G subfamily.
Internal database links
SCOOP: | DUF1080 Laminin_G_1 Laminin_G_3 Pentaxin Sialidase |
Similarity to PfamA using HHSearch: | Laminin_G_1 Laminin_G_3 |
External database links
SMART: | TSPN |
This tab holds annotation information from the InterPro database.
InterPro entry IPR001791
Laminins are large heterotrimeric glycoproteins involved in basement membrane function [PUBMED:15037599]. The Laminin G or LNS domain (for Laminin-alpha, Neurexin and Sex hormone-binding globulin) is an around 180 amino acid long domain found in a large and diverse set of extracellular proteins [PUBMED:1975589, PUBMED:9480764]. The laminin globular (G) domain can be found in one to several copies in various laminin family members, including a large number of extracellular proteins. The C terminus of the laminin alpha chain contains a tandem repeat of five laminin G domains, which are critical for heparin-binding and cell attachment activity [PUBMED:10747011]. Laminin alpha4 is distributed in a variety of tissues including peripheral nerves, dorsal root ganglion, skeletal muscle and capillaries; in the neuromuscular junction, it is required for synaptic specialisation [PUBMED:15823034]. The structure of the laminin-G domain has been predicted to resemble that of pentraxin [PUBMED:9480764].
Laminin G domains can vary in their function, and a variety of binding functions have been ascribed to different LamG modules. For example, the laminin alpha1 and alpha2 chains each have five C-teminal laminin G domains, where only domains LG4 and LG5 contain binding sites for heparin, sulphatides and the cell surface receptor dystroglycan [PUBMED:10747011]. Laminin G-containing proteins appear to have a wide variety of roles in cell adhesion, signalling, migration, assembly and differentiation. Proteins with laminin-G domains include:
- Laminin.
- Merosin.
- Agrin.
- Neurexins.
- Vitamin K dependent protein S.
- Sex steroid binding protein SBP/SHBG.
- Drosophila proteins Slit, Crumbs, Fat.
- several proteoglycan precursors.
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 Concanavalin (CL0004), which has the following description:
This superfamily includes a diverse range of carbohydrate binding domains and glycosyl hydrolase enzymes that share a common structure.
The clan contains the following 49 members:
Alginate_lyase2 ArabFuran-catal Arabino_trans_N Bac_rhamnosid Bact_lectin bCoV_S1_N Calreticulin Cleaved_Adhesin DUF1080 DUF1349 DUF1583 DUF1961 DUF2401 DUF3472 DUF4975 Exotox-A_bind Gal-bind_lectin GalBD_like GH131_N GH43_C2 Glyco_hydro_11 Glyco_hydro_12 Glyco_hydro_16 Glyco_hydro_32C Glyco_hydro_7 HA1 Laminin_G_1 Laminin_G_2 Laminin_G_3 Lectin_leg-like Lectin_legB MAM Methyltransf_FA Neuralized Pentaxin Peptidase_A4 Polysacc_lyase PRY Reoviridae_Vp9 Sial-lect-inser Sialidase SKN1 SPRY TgMIC1 Toxin_R_bind_N TSP_C VP4_haemagglut XET_C YrpDAlignments
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...
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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 (156) |
Full (32866) |
Representative proteomes | UniProt (53100) |
NCBI (151607) |
Meta (288) |
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RP15 (3699) |
RP35 (8711) |
RP55 (20601) |
RP75 (33613) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
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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 (156) |
Full (32866) |
Representative proteomes | UniProt (53100) |
NCBI (151607) |
Meta (288) |
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---|---|---|---|---|---|---|---|---|---|
RP15 (3699) |
RP35 (8711) |
RP55 (20601) |
RP75 (33613) |
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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: | Pfam-B_4211 (release 12.0) |
Previous IDs: | TSPN; TSP_N; |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Finn RD |
Number in seed: | 156 |
Number in full: | 32866 |
Average length of the domain: | 129.80 aa |
Average identity of full alignment: | 21 % |
Average coverage of the sequence by the domain: | 17.05 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 126 | ||||||||||||
Family (HMM) version: | 25 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Interactions
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 Laminin_G_2 domain has been found. There are 109 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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