Summary: Transcription factor BRX N-terminal domain
The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.
Transcription factor BRX N-terminal domain Provide feedback
The BREVIS RADIX (BRX) domain was characterised as being a transcription factor in plants regulating the extent of cell proliferation and elongation in the growth zone of the root [1,2]. BRX is rate limiting for auxin-responsive gene-expression by mediating cross-talk with the brassino-steroid pathway. BRX has a ubiquitous, although quantitatively variable role in modulating the growth rate in both the root and the shoot . This family features a short region, also alpha-helical, N-terminal to the repeated alpha-helices of family BRX, PF08381 . BRX is expressed in the vasculature and is rate-limiting for transcriptional auxin action .
Mouchel CF, Briggs GC, Hardtke CS;, Genes Dev. 2004;18:700-714.: Natural genetic variation in Arabidopsis identifies BREVIS RADIX, a novel regulator of cell proliferation and elongation in the root. PUBMED:15031265 EPMC:15031265
Briggs GC, Mouchel CF, Hardtke CS;, Plant Physiol. 2006;140:1306-1316.: Characterization of the plant-specific BREVIS RADIX gene family reveals limited genetic redundancy despite high sequence conservation. PUBMED:16514016 EPMC:16514016
Scacchi E, Salinas P, Gujas B, Santuari L, Krogan N, Ragni L, Berleth T, Hardtke CS;, Proc Natl Acad Sci U S A. 2010;107:22734-22739.: Spatio-temporal sequence of cross-regulatory events in root meristem growth. PUBMED:21149702 EPMC:21149702
External database links
This tab holds annotation information from the InterPro database.
No InterPro data for this Pfam family.
- the number of sequences which exhibit this architecture
a textual description of the architecture, e.g. Gla, EGF x 2, Trypsin.
This example describes an architecture with one
Gladomain, followed by two consecutive
EGFdomains, and finally a single
- the UniProt description of the protein sequence
- the number of residues in the sequence
- the Pfam graphic itself.
Loading domain graphics...
We make a range of alignments for each Pfam-A family:
- the curated alignment from which the HMM for the family is built
- the alignment generated by searching the sequence database using the HMM
- Representative Proteomes (RPs) at 15%, 35%, 55% and 75% co-membership thresholds
- alignment generated by searching the NCBI sequence database using the family HMM
- alignment generated by searching the metagenomics sequence database using the family HMM
You can see the alignments as HTML or in three different sequence viewers:
- Pfam viewer
- an HTML-based viewer that uses DAS to retrieve alignment fragments on request
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
Format an alignment
If you find these logos useful in your own work, please consider citing the following article:
Note: You can also download the data file for the tree.
Curation and family details
|Number in seed:||53|
|Number in full:||188|
|Average length of the domain:||38.00 aa|
|Average identity of full alignment:||41 %|
|Average coverage of the sequence by the domain:||4.56 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||1|
|Download:||download the raw HMM for this family|
Weight segments by...
Change the size of the sunburst
selected sequences to HMM
a FASTA-format file
- 0 sequences
- 0 species
How the sunburst is generated
Colouring and labels
Anomalies in the taxonomy tree
Missing taxonomic levels
Unmapped species names
Too many species/sequences
The tree shows the occurrence of this domain across different species. More...
You can use the tree controls to manipulate how the interactive tree is displayed:
- show/hide the summary boxes
- highlight species that are represented in the seed alignment
- expand/collapse the tree or expand it to a given depth
- select a sub-tree or a set of species within the tree and view them graphically or as an alignment
- save a plain text representation of the tree