Summary: TATA element modulatory factor 1 DNA binding
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TATA element modulatory factor 1 DNA binding Provide feedback
This is the middle region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes that contains at its N-terminal section a number of leucine zippers that could potentially form coiled coil structures.[1]. The whole proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal [3] and plant [4] cells.
Literature references
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Schwartz Y, Ben-Dor I, Navon A, Motro B, Nir U;, FEBS Lett. 1998;434:339-345.: Tyrosine phosphorylation of the TATA element modulatory factor by the FER nuclear tyrosine kinases. PUBMED:9742951 EPMC:9742951
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Garcia JA, Ou SH, Wu F, Lusis AJ, Sparkes RS, Gaynor RB;, Proc Natl Acad Sci U S A. 1992;89:9372-9376.: Cloning and chromosomal mapping of a human immunodeficiency virus 1 "TATA" element modulatory factor. PUBMED:1409643 EPMC:1409643
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Fridmann-Sirkis Y, Siniossoglou S, Pelham HR;, BMC Cell Biol. 2004;5:18.: TMF is a golgin that binds Rab6 and influences Golgi morphology. PUBMED:15128430 EPMC:15128430
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Latijnhouwers M, Gillespie T, Boevink P, Kriechbaumer V, Hawes C, Carvalho CM;, J Exp Bot. 2007;58:4373-4386.: Localization and domain characterization of Arabidopsis golgin candidates. PUBMED:18182439 EPMC:18182439
Internal database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR022092
This is the middle region of a family of TATA element modulatory factor 1 (TMF1) proteins conserved in eukaryotes that contains at its N-terminal section a number of leucine zippers that could potentially form coiled coil structures. The whole proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity by competing with the binding of TATA binding protein. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal [PUBMED:15128430] and plant [PUBMED:18182439] cells.
Domain organisation
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Alignments
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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 (47) |
Full (1048) |
Representative proteomes | UniProt (1744) |
NCBI (3363) |
Meta (0) |
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RP15 (123) |
RP35 (408) |
RP55 (709) |
RP75 (1050) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
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Seed (47) |
Full (1048) |
Representative proteomes | UniProt (1744) |
NCBI (3363) |
Meta (0) |
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RP15 (123) |
RP35 (408) |
RP55 (709) |
RP75 (1050) |
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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: | manual |
Previous IDs: | none |
Type: | Coiled-coil |
Sequence Ontology: | SO:0001080 |
Author: |
Wood V |
Number in seed: | 47 |
Number in full: | 1048 |
Average length of the domain: | 73.70 aa |
Average identity of full alignment: | 37 % |
Average coverage of the sequence by the domain: | 7.93 % |
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: | 74 | ||||||||||||
Family (HMM) version: | 9 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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