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0  structures 162  species 0  interactions 4633  sequences 94  architectures

Family: TDBD (PF16135)

Summary: Tify domain binding 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.

Tify domain binding domain Provide feedback

This entry contains a C-terminal presumed zinc binding domain from the NINJA protein which interacts with the Tify domain of JAZ1 [1].

Literature references

  1. Pauwels L, Barbero GF, Geerinck J, Tilleman S, Grunewald W, Perez AC, Chico JM, Bossche RV, Sewell J, Gil E, Garcia-Casado G, Witters E, Inze D, Long JA, De Jaeger G, Solano R, Goossens A;, Nature. 2010;464:788-791.: NINJA connects the co-repressor TOPLESS to jasmonate signalling. PUBMED:20360743 EPMC:20360743

  2. Robert-Seilaniantz A, Grant M, Jones JD;, Annu Rev Phytopathol. 2011;49:317-343.: Hormone crosstalk in plant disease and defense: more than just jasmonate-salicylate antagonism. PUBMED:21663438 EPMC:21663438

  3. Kazan K, Manners JM;, Trends Plant Sci. 2012;17:22-31.: JAZ repressors and the orchestration of phytohormone crosstalk. PUBMED:22112386 EPMC:22112386

  4. De Geyter N, Gholami A, Goormachtig S, Goossens A;, Trends Plant Sci. 2012;17:349-359.: Transcriptional machineries in jasmonate-elicited plant secondary metabolism. PUBMED:22459758 EPMC:22459758


This tab holds annotation information from the InterPro database.

InterPro entry IPR032308

The Jas domain is a short region of sequence characterised by IxCxCx(12)HAG found in plant transcriptional repressors. This motif appears to bind to the Groucho/Tup1-type co-repressor TOPLESS (TPL) and TPL-related proteins (TPRs) [ PUBMED:20360743 ]. This binding is a crucial step in the jasmonate signalling pathway, involved in plant disease and defence [ PUBMED:21663438 ].

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...

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
(56)
Full
(4633)
Representative proteomes UniProt
(6718)
RP15
(378)
RP35
(2507)
RP55
(3959)
RP75
(5208)
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
(56)
Full
(4633)
Representative proteomes UniProt
(6718)
RP15
(378)
RP35
(2507)
RP55
(3959)
RP75
(5208)
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
(56)
Full
(4633)
Representative proteomes UniProt
(6718)
RP15
(378)
RP35
(2507)
RP55
(3959)
RP75
(5208)
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: PF07897
Previous IDs: Jas;
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A , Coggill P
Number in seed: 56
Number in full: 4633
Average length of the domain: 51.20 aa
Average identity of full alignment: 34 %
Average coverage of the sequence by the domain: 6.98 %

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 23.6 23.6
Trusted cut-off 23.6 23.6
Noise cut-off 23.5 23.5
Model length: 52
Family (HMM) version: 7
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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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
A0A0N7KJ32 View 3D Structure Click here
A0A0P0VW53 View 3D Structure Click here
A0A0P0VW53 View 3D Structure Click here
A0A0P0VW53 View 3D Structure Click here
A0A0P0W3M9 View 3D Structure Click here
A0A0R0FKZ1 View 3D Structure Click here
A0A0R0GL68 View 3D Structure Click here
A0A0R0GV05 View 3D Structure Click here
A0A0R0GV05 View 3D Structure Click here
A0A0R0H3K4 View 3D Structure Click here
A0A0R0KF87 View 3D Structure Click here
A0A0R0KJU4 View 3D Structure Click here
A0A0R0L087 View 3D Structure Click here
A0A1D6EAF6 View 3D Structure Click here
A0A1D6EV07 View 3D Structure Click here
A0A1D6GHI6 View 3D Structure Click here
A0A1D6GXJ5 View 3D Structure Click here
A0A1D6GXJ5 View 3D Structure Click here
A0A1D6HTA3 View 3D Structure Click here
A0A1D6IP68 View 3D Structure Click here
A0A1D6JQC2 View 3D Structure Click here
A0A1D6JYC7 View 3D Structure Click here
A0A1D6JYC7 View 3D Structure Click here
A0A1D6JZC0 View 3D Structure Click here
A0A1D6K5R7 View 3D Structure Click here
A0A1D6L433 View 3D Structure Click here
A0A1D6LJ27 View 3D Structure Click here
A0A1D6LJ27 View 3D Structure Click here
A0A1D6LYK2 View 3D Structure Click here
A0A1D6N0G8 View 3D Structure Click here
A0A1D6NXT5 View 3D Structure Click here
A0A1D6PR68 View 3D Structure Click here
A0A1I9LNF2 View 3D Structure Click here
A0A1I9LNX5 View 3D Structure Click here
A0A1I9LNX5 View 3D Structure Click here
A0A1P8B7I1 View 3D Structure Click here
A0A368UIK8 View 3D Structure Click here
A0A368UJT0 View 3D Structure Click here
A0A368UJT0 View 3D Structure Click here
B3H544 View 3D Structure Click here
B4FAF3 View 3D Structure Click here
B4FM28 View 3D Structure Click here
B6SLJ0 View 3D Structure Click here
B6SM63 View 3D Structure Click here
B6TNQ7 View 3D Structure Click here
B6UGG4 View 3D Structure Click here
F4IHN9 View 3D Structure Click here
F4IHN9 View 3D Structure Click here
F4IQY0 View 3D Structure Click here
F4IQY0 View 3D Structure Click here
F4IXE7 View 3D Structure Click here
F4JXC7 View 3D Structure Click here
F4K4G6 View 3D Structure Click here
I1J610 View 3D Structure Click here
I1J803 View 3D Structure Click here
I1JAT7 View 3D Structure Click here
I1JEF6 View 3D Structure Click here
I1JF96 View 3D Structure Click here
I1JM54 View 3D Structure Click here
I1KD19 View 3D Structure Click here
I1KWF4 View 3D Structure Click here
I1LFT6 View 3D Structure Click here
I1LK57 View 3D Structure Click here
I1LLM4 View 3D Structure Click here
I1LQT2 View 3D Structure Click here
I1M4F6 View 3D Structure Click here
I1M4F6 View 3D Structure Click here
I1MMB5 View 3D Structure Click here
I1N4K4 View 3D Structure Click here
I1N535 View 3D Structure Click here
K7K5J5 View 3D Structure Click here
K7KA70 View 3D Structure Click here
K7KME4 View 3D Structure Click here
K7KT35 View 3D Structure Click here
K7LHF0 View 3D Structure Click here
K7LHF0 View 3D Structure Click here
K7LHF4 View 3D Structure Click here
K7LHQ9 View 3D Structure Click here
K7LHQ9 View 3D Structure Click here
K7LQW1 View 3D Structure Click here
K7LVM3 View 3D Structure Click here
K7LVM3 View 3D Structure Click here
K7LWG2 View 3D Structure Click here
K7LZH4 View 3D Structure Click here
K7LZH4 View 3D Structure Click here
K7LZI0 View 3D Structure Click here
K7M817 View 3D Structure Click here
K7MN78 View 3D Structure Click here
K7TXX3 View 3D Structure Click here
Q10JI3 View 3D Structure Click here
Q10Q07 View 3D Structure Click here
Q5VMF2 View 3D Structure Click here
Q5VMF2 View 3D Structure Click here
Q6YVY6 View 3D Structure Click here
Q84NP5 View 3D Structure Click here
Q8RWG0 View 3D Structure Click here
Q8RWG0 View 3D Structure Click here
Q94F39 View 3D Structure Click here
Q9LMX5 View 3D Structure Click here
Q9LQ98 View 3D Structure Click here
Q9LUZ5 View 3D Structure Click here
Q9S7Z2 View 3D Structure Click here
Q9SV55 View 3D Structure Click here
Q9ZW00 View 3D Structure Click here

trRosetta Structure

The structural model below was generated by the Baker group with the trRosetta software using the Pfam UniProt multiple sequence alignment.

The InterPro website shows the contact map for the Pfam SEED alignment. Hovering or clicking on a contact position will highlight its connection to other residues in the alignment, as well as on the 3D structure.

Improved protein structure prediction using predicted inter-residue orientations. Jianyi Yang, Ivan Anishchenko, Hahnbeom Park, Zhenling Peng, Sergey Ovchinnikov, David Baker Proceedings of the National Academy of Sciences Jan 2020, 117 (3) 1496-1503; DOI: 10.1073/pnas.1914677117;