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12  structures 141  species 0  interactions 5432  sequences 55  architectures

Family: Auxin_resp (PF06507)

Summary: Auxin response factor

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Auxin response factor Provide feedback

A conserved region of auxin-responsive transcription factors.

Literature references

  1. Sato Y, Nishimura A, Ito M, Ashikari M, Hirano HY, Matsuoka M; , Genes Genet Syst 2001;76:373-380.: Auxin response factor family in rice. PUBMED:11922106 EPMC:11922106


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR010525

This pattern represents a conserved region of auxin-responsive transcription factors.

The plant hormone auxin (indole-3-acetic acid) can regulate the gene expression of several families, including Aux/IAA, GH3 and SAUR families. Two related families of proteins, Aux/IAA proteins ( INTERPRO ) and the auxin response factors (ARF), are key regulators of auxin-modulated gene expression [ PUBMED:12036262 ]. There are multiple ARF proteins, some of which activate, while others repress transcription. ARF proteins bind to auxin-responsive cis-acting promoter elements (AuxREs) using an N-terminal DNA-binding domain. It is thought that Aux/IAA proteins activate transcription by modifying ARF activity through the C-terminal protein-protein interaction domains found in both Aux/IAA and ARF proteins.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB 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
(79)
Full
(5432)
Representative proteomes UniProt
(8000)
RP15
(442)
RP35
(2705)
RP55
(4427)
RP75
(5947)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(79)
Full
(5432)
Representative proteomes UniProt
(8000)
RP15
(442)
RP35
(2705)
RP55
(4427)
RP75
(5947)
Alignment:
Format:
Order:
Sequence:
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Download options

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
(79)
Full
(5432)
Representative proteomes UniProt
(8000)
RP15
(442)
RP35
(2705)
RP55
(4427)
RP75
(5947)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

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: Pfam-B_2015 (release 9.0)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Studholme DJ
Number in seed: 79
Number in full: 5432
Average length of the domain: 81.80 aa
Average identity of full alignment: 48 %
Average coverage of the sequence by the domain: 10.97 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 30.6 30.6
Trusted cut-off 30.6 30.6
Noise cut-off 30.5 30.5
Model length: 83
Family (HMM) version: 15
Download: download the raw HMM for this family

Species distribution

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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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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 Auxin_resp domain has been found. There are 12 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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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0P0XIX0 View 3D Structure Click here
A0A0R0G8P7 View 3D Structure Click here
A0A1D6DTV9 View 3D Structure Click here
A0A1D6DUQ4 View 3D Structure Click here
A0A1D6E5Y1 View 3D Structure Click here
A0A1D6E9Y6 View 3D Structure Click here
A0A1D6GBH2 View 3D Structure Click here
A0A1D6GSR8 View 3D Structure Click here
A0A1D6GTU9 View 3D Structure Click here
A0A1D6GVG1 View 3D Structure Click here
A0A1D6H0D1 View 3D Structure Click here
A0A1D6HAQ3 View 3D Structure Click here
A0A1D6JH51 View 3D Structure Click here
A0A1D6JHR5 View 3D Structure Click here
A0A1D6K5G7 View 3D Structure Click here
A0A1D6KEJ3 View 3D Structure Click here
A0A1D6KG94 View 3D Structure Click here
A0A1D6KJC5 View 3D Structure Click here
A0A1D6LPM9 View 3D Structure Click here
A0A1D6MCU5 View 3D Structure Click here
A0A1D6MEU8 View 3D Structure Click here
A0A1D6MTV6 View 3D Structure Click here
A0A1D6N2G9 View 3D Structure Click here
A0A1D6NBS6 View 3D Structure Click here
A0A1D6PTP1 View 3D Structure Click here
A0A1D6Q3A3 View 3D Structure Click here
A0A1D6QSK8 View 3D Structure Click here
A0A368UH06 View 3D Structure Click here
A0A368UH44 View 3D Structure Click here
A0A368UHB3 View 3D Structure Click here
A0A368UI53 View 3D Structure Click here
A3B9A0 View 3D Structure Click here
B6TEP4 View 3D Structure Click here
B8A0C3 View 3D Structure Click here
C0HDR1 View 3D Structure Click here
C0P7I4 View 3D Structure Click here
C0PGA8 View 3D Structure Click here
C0PGK8 View 3D Structure Click here
C0PH36 View 3D Structure Click here
C0PL36 View 3D Structure Click here
D9HNT5 View 3D Structure Click here
D9HNU2 View 3D Structure Click here
D9HNU4 View 3D Structure Click here
D9HNV4 View 3D Structure Click here
I1J4B0 View 3D Structure Click here
I1JHQ8 View 3D Structure Click here
I1JIZ7 View 3D Structure Click here
I1JM14 View 3D Structure Click here
I1JQG4 View 3D Structure Click here
I1JXQ2 View 3D Structure Click here
I1JZB4 View 3D Structure Click here
I1K651 View 3D Structure Click here
I1K6T1 View 3D Structure Click here
I1KBY0 View 3D Structure Click here
I1KJW6 View 3D Structure Click here
I1KK13 View 3D Structure Click here
I1KNS1 View 3D Structure Click here
I1KP28 View 3D Structure Click here
I1KRX2 View 3D Structure Click here
I1L1T2 View 3D Structure Click here
I1LL50 View 3D Structure Click here
I1LM27 View 3D Structure Click here
I1LQY7 View 3D Structure Click here
I1LR43 View 3D Structure Click here
I1LT90 View 3D Structure Click here
I1LTG4 View 3D Structure Click here
I1LTK0 View 3D Structure Click here
I1LW27 View 3D Structure Click here
I1LY86 View 3D Structure Click here
I1M054 View 3D Structure Click here
I1M1J4 View 3D Structure Click here
I1M1Y1 View 3D Structure Click here
I1M4J8 View 3D Structure Click here
I1MBP7 View 3D Structure Click here
I1MC56 View 3D Structure Click here
I1MJS6 View 3D Structure Click here
I1MS55 View 3D Structure Click here
I1MY19 View 3D Structure Click here
I1MZK6 View 3D Structure Click here
I1N2J8 View 3D Structure Click here
I1NHG1 View 3D Structure Click here
K7K310 View 3D Structure Click here
K7KH37 View 3D Structure Click here
K7KZU2 View 3D Structure Click here
K7L2T6 View 3D Structure Click here
K7L4N0 View 3D Structure Click here
K7LHL4 View 3D Structure Click here
K7LKL9 View 3D Structure Click here
K7LZP0 View 3D Structure Click here
K7MAG3 View 3D Structure Click here
K7MC63 View 3D Structure Click here
K7MET6 View 3D Structure Click here
K7MZ14 View 3D Structure Click here
K7MZF7 View 3D Structure Click here
K7TJD3 View 3D Structure Click here
K7UKA6 View 3D Structure Click here
K7UYC8 View 3D Structure Click here
O23661 View 3D Structure Click here
P92530 View 3D Structure Click here
P93022 View 3D Structure Click here
P93024 View 3D Structure Click here
Q0D9R7 View 3D Structure Click here
Q0DGS1 View 3D Structure Click here
Q0J951 View 3D Structure Click here
Q0JCZ4 View 3D Structure Click here
Q0JKI9 View 3D Structure Click here
Q2QM84 View 3D Structure Click here
Q2QQX6 View 3D Structure Click here
Q2R3F5 View 3D Structure Click here
Q5JK20 View 3D Structure Click here
Q5JMM1 View 3D Structure Click here
Q5NB85 View 3D Structure Click here
Q653H7 View 3D Structure Click here
Q653U3 View 3D Structure Click here
Q6H6V4 View 3D Structure Click here
Q6K223 View 3D Structure Click here
Q6YVY0 View 3D Structure Click here
Q6YZW0 View 3D Structure Click here
Q6Z2W3 View 3D Structure Click here
Q7XKK6 View 3D Structure Click here
Q7XSS9 View 3D Structure Click here
Q84WU6 View 3D Structure Click here
Q8L7G0 View 3D Structure Click here
Q8RYC8 View 3D Structure Click here
Q8S983 View 3D Structure Click here
Q8S985 View 3D Structure Click here
Q93YR9 View 3D Structure Click here
Q94JM3 View 3D Structure Click here
Q9AV47 View 3D Structure Click here
Q9C5W9 View 3D Structure Click here
Q9C7I9 View 3D Structure Click here
Q9C8N7 View 3D Structure Click here
Q9C8N9 View 3D Structure Click here
Q9FGV1 View 3D Structure Click here
Q9FX25 View 3D Structure Click here
Q9LQE3 View 3D Structure Click here
Q9LQE8 View 3D Structure Click here
Q9SKN5 View 3D Structure Click here
Q9XED8 View 3D Structure Click here
Q9XID4 View 3D Structure Click here
Q9ZPY6 View 3D Structure Click here
Q9ZTX8 View 3D Structure Click here
Q9ZTX9 View 3D Structure Click here