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33  structures 149  species 0  interactions 1482  sequences 28  architectures

Family: Transp_inhibit (PF18791)

Summary: Transport inhibitor response 1 protein domain

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

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.

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.

Transport inhibitor response 1 protein domain Provide feedback

The F-box protein Transport inhibitor response 1 (TIR1) is a receptor for auxin, triggering an auxin-enhanced and ubiquitin-mediated degradation of substrates [1]. The targets are recruited via interaction with the leucine-rich repeat region of the protein. This Pfam entry represents a specific unit of the LRR region, including an insertion of one short alpha-helix in the loop between the beta-strand and the following helix. It shares some sequence homology with a unit with similar structure of Coronatine-insensitive protein 1 [2].

Literature references

  1. Hayashi K, Tan X, Zheng N, Hatate T, Kimura Y, Kepinski S, Nozaki H;, Proc Natl Acad Sci U S A. 2008;105:5632-5637.: Small-molecule agonists and antagonists of F-box protein-substrate interactions in auxin perception and signaling. PUBMED:18391211 EPMC:18391211

  2. Sheard LB, Tan X, Mao H, Withers J, Ben-Nissan G, Hinds TR, Kobayashi Y, Hsu FF, Sharon M, Browse J, He SY, Rizo J, Howe GA, Zheng N;, Nature. 2010;468:400-405.: Jasmonate perception by inositol-phosphate-potentiated COI1-JAZ co-receptor. PUBMED:20927106 EPMC:20927106


This tab holds annotation information from the InterPro database.

InterPro entry IPR041101

The F-box protein transport inhibitor response 1 (TIR1) is a receptor for auxin, triggering an auxin-enhanced and ubiquitin-mediated degradation of substrates [ PUBMED:18391211 ]. The targets are recruited via interaction with the leucine-rich repeat region of the protein. This entry represents a specific unit of the LRR region, including an insertion of one short alpha-helix in the loop between the beta-strand and the following helix. It shares some sequence homology with a unit with similar structure of coronatine-insensitive protein 1 [ PUBMED:20927106 ].

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 LRR (CL0022), which has the following description:

Each Leucine Rich Repeat is composed of a beta-alpha unit. These units form elongated non-globular structures. Leucine Rich Repeats are often flanked by cysteine rich domains. This Pfam entry contains Leucine Rich Repeats not recognised by the Pfam:PF00560 model.

The clan contains the following 18 members:

DUF285 FBXL18_LRR FNIP LRR_1 LRR_10 LRR_11 LRR_12 LRR_2 LRR_3 LRR_4 LRR_5 LRR_6 LRR_8 LRR_9 LRR_RI_capping Recep_L_domain Transp_inhibit TTSSLRR

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...

View options

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
(71)
Full
(1482)
Representative proteomes UniProt
(2207)
RP15
(231)
RP35
(801)
RP55
(1312)
RP75
(1669)
Jalview View  View  View  View  View  View  View 
HTML View  View           
PP/heatmap 1 View           

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

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

Format an alignment

  Seed
(71)
Full
(1482)
Representative proteomes UniProt
(2207)
RP15
(231)
RP35
(801)
RP55
(1312)
RP75
(1669)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

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
(71)
Full
(1482)
Representative proteomes UniProt
(2207)
RP15
(231)
RP35
(801)
RP55
(1312)
RP75
(1669)
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: RepeatsDB
Previous IDs: none
Type: Repeat
Sequence Ontology: SO:0001068
Author: Paladin L , Piovesan D
Number in seed: 71
Number in full: 1482
Average length of the domain: 46.7 aa
Average identity of full alignment: 50 %
Average coverage of the sequence by the domain: 8.13 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 61295632 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 33.0 29.0
Trusted cut-off 33.8 30.0
Noise cut-off 32.8 28.9
Model length: 47
Family (HMM) version: 4
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

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 Transp_inhibit domain has been found. There are 33 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
A0A0P0Y299 View 3D Structure Click here
A0A0R0G9U2 View 3D Structure Click here
A0A0R0L1N9 View 3D Structure Click here
A0A1D6ECA1 View 3D Structure Click here
A0A1D6G883 View 3D Structure Click here
A0A1D6HKX9 View 3D Structure Click here
A0A1D6JR35 View 3D Structure Click here
A0A1D6M504 View 3D Structure Click here
A0A1D6PE20 View 3D Structure Click here
A2WX30 View 3D Structure Click here
A2XEV1 View 3D Structure Click here
B4FJG6 View 3D Structure Click here
B4FYV0 View 3D Structure Click here
B6TPN4 View 3D Structure Click here
C0PCZ0 View 3D Structure Click here
C4J3Z7 View 3D Structure Click here
I1JCY8 View 3D Structure Click here
I1JFG2 View 3D Structure Click here
I1JGX7 View 3D Structure Click here
I1JQG9 View 3D Structure Click here
I1JV53 View 3D Structure Click here
I1K9P6 View 3D Structure Click here
I1KLC7 View 3D Structure Click here
I1KQQ6 View 3D Structure Click here
I1MAY4 View 3D Structure Click here
I1MLC0 View 3D Structure Click here
I1MNN2 View 3D Structure Click here
I1MZ51 View 3D Structure Click here
I1N7Y8 View 3D Structure Click here
I1NB13 View 3D Structure Click here
K7LGY5 View 3D Structure Click here
K7U5R5 View 3D Structure Click here
K7UXQ0 View 3D Structure Click here
K7VGW5 View 3D Structure Click here
O04197 View 3D Structure Click here
Q0DKP3 View 3D Structure Click here
Q2R3K5 View 3D Structure Click here
Q45FY8 View 3D Structure Click here
Q570C0 View 3D Structure Click here
Q60EH4 View 3D Structure Click here