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0  structures 225  species 0  interactions 292  sequences 14  architectures

Family: Tropomyosin_1 (PF12718)

Summary: Tropomyosin like

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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.

Tropomyosin like Provide feedback

This family is a set of eukaryotic tropomyosins. Within the yeast Tmp1 and Tmp2, biochemical and sequence analyses indicate that Tpm2p spans four actin monomers along a filament, whereas Tpmlp spans five. Despite its shorter length, Tpm2p can compete with Tpm1p for binding to F-actin. Over-expression of Tpm2p in vivo alters the axial budding of haploids to a bipolar pattern, and this can be partially suppressed by co-over-expression of Tpm1p. This suggests distinct functions for the two tropomyosins, and indicates that the ratio between them is important for correct morphogenesis [1]. The family also contains higher eukaryote Tmp3 members.

Literature references

  1. Drees B, Brown C, Barrell BG, Bretscher A;, J Cell Biol. 1995;128:383-392.: Tropomyosin is essential in yeast, yet the TPM1 and TPM2 products perform distinct functions. PUBMED:7844152 EPMC:7844152

  2. Leung PS, Chen YC, Gershwin ME, Wong SH, Kwan HS, Chu KH;, J Allergy Clin Immunol. 1998;102:847-852.: Identification and molecular characterization of Charybdis feriatus tropomyosin, the major crab allergen. PUBMED:9819304 EPMC:9819304

  3. Saarne T, Kaiser L, Rasool O, Huecas S, van Hage-Hamsten M, Gafvelin G;, Int Arch Allergy Immunol. 2003;130:258-265.: Cloning and characterisation of two IgE-binding proteins, homologous to tropomyosin and alpha-tubulin, from the mite Lepidoglyphus destructor. PUBMED:12740526 EPMC:12740526


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000533

Tropomyosins [PUBMED:3606587], are a family of closely related proteins present in muscle and non-muscle cells. In striated muscle, tropomyosin mediate the interactions between the troponin complex and actin so as to regulate muscle contraction [PUBMED:12690456]. The role of tropomyosin in smooth muscle and non-muscle tissues is not clear. Tropomyosin is an alpha-helical protein that forms a coiled-coil structure of 2 parallel helices containing 2 sets of 7 alternating actin binding sites [PUBMED:6993480]. There are multiple cell-specific isoforms, created by differential splicing of the messenger RNA from one gene, but the proportions of the isoforms vary between different cell types. Muscle isoforms of tropomyosin are characterised by having 284 amino acid residues and a highly conserved N-terminal region, whereas non-muscle forms are generally smaller and are heterogeneous in their N-terminal region.

This entry represents tropomyosin (Tmp) 1, 2 and 3. Within the yeast Tmp1 and Tmp2, biochemical and sequence analyses indicate that Tpm2 spans four actin monomers along a filament, whereas Tpm1 spans five. Despite its shorter length, Tpm2 can compete with Tpm1 for binding to F-actin. Over-expression of Tpm2 in vivo alters the axial budding of haploids to a bipolar pattern, and this can be partially suppressed by co-over-expression of Tpm1. This suggests distinct functions for the two tropomyosins, and indicates that the ratio between them is important for correct morphogenesis [PUBMED:7844152].

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 Tropomyosin-lke (CL0452), which contains the following 2 members:

Tropomyosin Tropomyosin_1

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, 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
(41)
Full
(292)
Representative proteomes NCBI
(1155)
Meta
(1)
RP15
(56)
RP35
(93)
RP55
(142)
RP75
(176)
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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
(41)
Full
(292)
Representative proteomes NCBI
(1155)
Meta
(1)
RP15
(56)
RP35
(93)
RP55
(142)
RP75
(176)
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
(41)
Full
(292)
Representative proteomes NCBI
(1155)
Meta
(1)
RP15
(56)
RP35
(93)
RP55
(142)
RP75
(176)
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.

Pfam alignments:

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: manual
Previous IDs: none
Type: Family
Author: Coggill P
Number in seed: 41
Number in full: 292
Average length of the domain: 117.90 aa
Average identity of full alignment: 33 %
Average coverage of the sequence by the domain: 58.23 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 30.0 30.0
Trusted cut-off 30.0 30.0
Noise cut-off 29.9 29.9
Model length: 143
Family (HMM) version: 2
Download: download the raw HMM for this family

Species distribution

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