Summary: Transforming growth factor beta like domain
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This is the Wikipedia entry entitled "Transforming growth factor beta superfamily". More...
Transforming growth factor beta superfamily Edit Wikipedia article
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Transforming growth factor beta like domain Provide feedback
No Pfam abstract.
Literature references
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Daopin S, Piez KA, Ogawa Y, Davies DR; , Science 1992;257:369-373.: Crystal structure of transforming growth factor-beta 2: an unusual fold for the superfamily. PUBMED:1631557 EPMC:1631557
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Griffith DL, Keck PC, Sampath TK, Rueger DC, Carlson WD; , Proc Natl Acad Sci U S A 1996;93:878-883.: Three-dimensional structure of recombinant human osteogenic protein 1: structural paradigm for the transforming growth factor beta superfamily. PUBMED:8570652 EPMC:8570652
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Eigenbrot C, Gerber N; , Nat Struct Biol 1997;4:435-438.: X-ray structure of glial cell-derived neurotrophic factor at 1.9 A resolution and implications for receptor binding. PUBMED:9187648 EPMC:9187648
External database links
HOMSTRAD: | tgfb |
PROSITE: | PDOC00223 |
SCOP: | 1tfg |
This tab holds annotation information from the InterPro database.
InterPro entry IPR001839
Transforming growth factor-beta (TGF-beta) is a multifunctional peptide that controls proliferation, differentiation and other functions in many cell types. TGF-beta-1 is a peptide of 112 amino acid residues derived by proteolytic cleavage from the C-terminal of a precursor protein [PUBMED:8679613].
A number of proteins are known to be related to TGF-beta-1 [PUBMED:1575734, PUBMED:8199356]. Proteins from the TGF-beta family are only active as homo- or heterodimer; the two chains being linked by a single disulphide bond. From X-ray studies of TGF-beta-2 [PUBMED:1631557], it is known that all the other cysteines are involved in intrachain disulphide bonds. There are four disulphide bonds in the TGF-beta's and in inhibin beta chains, while the other members of this family lack the first bond.
The regulatory cytokine TGFbeta exerts tumour-suppressive effects, but also modulates cell invasion and immune regulation [PUBMED:18662538]. Misregulation of the TGF-beta signalling pathway can result in tumour development.
Gene Ontology
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
Molecular function | growth factor activity (GO:0008083) |
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 Cystine-knot (CL0079), which has the following description:
The cytokine families in this clan have the cystine-knot fold. In this 6 cysteines form three disulphide bridges that are interlinked.
The clan contains the following 14 members:
Coagulin Cys_knot Cys_Knot_tox D_CNTX DAN Hormone_6 IL17 m_DGTX_Dc1a_b_c NGF Noggin PDGF Sclerostin Spaetzle TGF_betaAlignments
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 (291) |
Full (7872) |
Representative proteomes | UniProt (14873) |
NCBI (20867) |
Meta (0) |
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RP15 (863) |
RP35 (2216) |
RP55 (5309) |
RP75 (8094) |
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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 (291) |
Full (7872) |
Representative proteomes | UniProt (14873) |
NCBI (20867) |
Meta (0) |
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RP15 (863) |
RP35 (2216) |
RP55 (5309) |
RP75 (8094) |
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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: | Prosite |
Previous IDs: | TGF-beta; |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Sonnhammer ELL |
Number in seed: | 291 |
Number in full: | 7872 |
Average length of the domain: | 98.80 aa |
Average identity of full alignment: | 35 % |
Average coverage of the sequence by the domain: | 25.74 % |
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: | 102 | ||||||||||||
Family (HMM) version: | 21 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Colour assignments
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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 11 interactions for this family. More...
TGFb_propeptide TGFb_propeptide Activin_recp TGF_beta Kazal_1 Activin_recp ecTbetaR2 Kazal_2 GDNF GDNF NogginStructures
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 TGF_beta domain has been found. There are 222 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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