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0  structures 139  species 0  interactions 3878  sequences 59  architectures

Family: tify (PF06200)

Summary: tify domain

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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 Provide feedback

This short possible domain is found in a variety of plant transcription factors that contain GATA domains as well as other motifs. Although previously known as the Zim domain this is now called the tify domain after its most conserved amino acids. TIFY proteins can be further classified into two groups depending on the presence (group I) or absence (group II) of a C2C2-GATA domain. Functional annotation of these proteins is still poor, but several screens revealed a link between TIFY proteins of group II and jasmonic acid-related stress response.

Literature references

  1. Nishii A, Takemura M, Fujita H, Shikata M, Yokota A, Kohchi T; , Biosci Biotechnol Biochem 2000;64:1402-1409.: Characterization of a novel gene encoding a putative single zinc-finger protein, ZIM, expressed during the reproductive phase in Arabidopsis thaliana. PUBMED:10945256 EPMC:10945256

  2. Shikata M, Matsuda Y, Ando K, Nishii A, Takemura M, Yokota A, Kohchi T; , J Exp Bot. 2004;55:631-639.: Characterization of Arabidopsis ZIM, a member of a novel plant-specific GATA factor gene family. PUBMED:14966217 EPMC:14966217

  3. Vanholme B, Grunewald W, Bateman A, Kohchi T, Gheysen G; , Trends Plant Sci. 2007;12:239-244.: The tify family previously known as ZIM. PUBMED:17499004 EPMC:17499004


This tab holds annotation information from the InterPro database.

InterPro entry IPR010399

The tify domain is a 36-amino acid domain only found among Embryophyta (land plants). It has been named after the most conserved amino acid pattern (TIF[F/Y]XG) it contains, but was previously known as the Zim domain. As the use of uppercase characters (TIFY) might imply that the domain is fully conserved across proteins, a lowercase lettering has been chosen in an attempt to highlight the reality of its natural variability.

Based on the domain architecture, tify domain containing proteins can be classified into two groups. Group I is formed by proteins possessing a CCT (CONSTANS, CO-like, and TOC1) domain and a GATA-type zinc finger in addition to the tify domain. Group II contains proteins characterised by the tify domain but lacking a GATA-type zinc finger. Tify domain containing proteins might be involved in developmental processes and some of them have features that are characteristic for transcription factors: a nuclear localisation and the presence of a putative DNA-binding domain [ PUBMED:17499004 ]. Some proteins known to contain a tify domain include:

  • Arabidopsis thaliana GATA transcription factors (Zinc-finger protein expressed in Inflorescence Meristem, ZIM), a putative transcription factor involved in inflorescence and flower development [ PUBMED:10945256 , PUBMED:14966217 ].
  • A. thaliana ZIM-like proteins (ZML) [ PUBMED:14966217 ].
  • A. thaliana Protein TIFY 1-11 [ PUBMED:16916932 ].

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
(96)
Full
(3878)
Representative proteomes UniProt
(5962)
RP15
(328)
RP35
(2007)
RP55
(3251)
RP75
(4375)
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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
(96)
Full
(3878)
Representative proteomes UniProt
(5962)
RP15
(328)
RP35
(2007)
RP55
(3251)
RP75
(4375)
Alignment:
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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
(96)
Full
(3878)
Representative proteomes UniProt
(5962)
RP15
(328)
RP35
(2007)
RP55
(3251)
RP75
(4375)
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_3326 (release 9.0)
Previous IDs: Zim;
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 96
Number in full: 3878
Average length of the domain: 33.10 aa
Average identity of full alignment: 42 %
Average coverage of the sequence by the domain: 12.12 %

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 20.9 20.9
Trusted cut-off 20.9 20.9
Noise cut-off 20.8 20.7
Model length: 34
Family (HMM) version: 16
Download: download the raw HMM for this family

Species distribution

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Selections

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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
A0A060D1S0 View 3D Structure Click here
A0A060D890 View 3D Structure Click here
A0A096QX45 View 3D Structure Click here
A0A0P0XTR0 View 3D Structure Click here
A0A0R0ECK5 View 3D Structure Click here
A0A0R0FMW4 View 3D Structure Click here
A0A0R0I593 View 3D Structure Click here
A0A0R0ISW8 View 3D Structure Click here
A0A0R0IW01 View 3D Structure Click here
A0A1D6EED3 View 3D Structure Click here
A0A1D6EEQ0 View 3D Structure Click here
A0A1D6EPM4 View 3D Structure Click here
A0A1D6F1D1 View 3D Structure Click here
A0A1D6FJF9 View 3D Structure Click here
A0A1D6GI61 View 3D Structure Click here
A0A1D6GMR9 View 3D Structure Click here
A0A1D6GR78 View 3D Structure Click here
A0A1D6GUV7 View 3D Structure Click here
A0A1D6H6Q7 View 3D Structure Click here
A0A1D6HSJ3 View 3D Structure Click here
A0A1D6I409 View 3D Structure Click here
A0A1D6KMZ2 View 3D Structure Click here
A0A1D6L3P2 View 3D Structure Click here
A0A1D6L8G4 View 3D Structure Click here
A0A1D6LG84 View 3D Structure Click here
A0A1D6LNQ5 View 3D Structure Click here
A0A1D6LTR5 View 3D Structure Click here
A0A1D6MTS9 View 3D Structure Click here
A0A1D6NQW6 View 3D Structure Click here
A0A1D6Q1C6 View 3D Structure Click here
A0A1D6Q421 View 3D Structure Click here
A0A1D6Q8H0 View 3D Structure Click here
B4F860 View 3D Structure Click here
B4FQE1 View 3D Structure Click here
B4G0I3 View 3D Structure Click here
B6SNX5 View 3D Structure Click here
B6TTL0 View 3D Structure Click here
B6TXD0 View 3D Structure Click here
B6TYH5 View 3D Structure Click here
B6U6B4 View 3D Structure Click here
B6UG02 View 3D Structure Click here
C0HHL9 View 3D Structure Click here
C0P4B4 View 3D Structure Click here
C0PFI1 View 3D Structure Click here
C0PIV0 View 3D Structure Click here
C4IZT6 View 3D Structure Click here
C6SVN6 View 3D Structure Click here
C6T1G4 View 3D Structure Click here
C6TCZ5 View 3D Structure Click here
C6TNM1 View 3D Structure Click here
I1J9Q4 View 3D Structure Click here
I1JUH9 View 3D Structure Click here
I1JV86 View 3D Structure Click here
I1JV87 View 3D Structure Click here
I1K3F4 View 3D Structure Click here
I1K5P7 View 3D Structure Click here
I1K8Z7 View 3D Structure Click here
I1K9S5 View 3D Structure Click here
I1K9S6 View 3D Structure Click here
I1KL59 View 3D Structure Click here
I1KQ77 View 3D Structure Click here
I1KQX6 View 3D Structure Click here
I1L1S4 View 3D Structure Click here
I1L1X4 View 3D Structure Click here
I1L2W4 View 3D Structure Click here
I1L443 View 3D Structure Click here
I1LGV3 View 3D Structure Click here
I1LY77 View 3D Structure Click here
I1LYC4 View 3D Structure Click here
I1MB13 View 3D Structure Click here
I1MF23 View 3D Structure Click here
I1MHH9 View 3D Structure Click here
I1MHL9 View 3D Structure Click here
I1MS21 View 3D Structure Click here
I1MS89 View 3D Structure Click here
K7K9Y2 View 3D Structure Click here
K7KHK3 View 3D Structure Click here
K7KSH5 View 3D Structure Click here
K7MMX1 View 3D Structure Click here
K7VPS1 View 3D Structure Click here
O64687 View 3D Structure Click here
Q0DNU1 View 3D Structure Click here
Q10F25 View 3D Structure Click here
Q10QW3 View 3D Structure Click here
Q58G47 View 3D Structure Click here
Q5Z4U5 View 3D Structure Click here
Q69NY7 View 3D Structure Click here
Q69P94 View 3D Structure Click here
Q6ES51 View 3D Structure Click here
Q6Z2K1 View 3D Structure Click here
Q6Z433 View 3D Structure Click here
Q6ZJU3 View 3D Structure Click here
Q7XA73 View 3D Structure Click here
Q7XEZ1 View 3D Structure Click here
Q7XEZ4 View 3D Structure Click here
Q7XEZ4 View 3D Structure Click here
Q7XEZ6 View 3D Structure Click here
Q7XPM8 View 3D Structure Click here
Q7XV97 View 3D Structure Click here
Q84MB2 View 3D Structure Click here
Q84R94 View 3D Structure Click here
Q8GRS2 View 3D Structure Click here
Q8GSI0 View 3D Structure Click here
Q8GXL7 View 3D Structure Click here
Q8GY55 View 3D Structure Click here
Q8H1G0 View 3D Structure Click here
Q8H395 View 3D Structure Click here
Q8LBM2 View 3D Structure Click here
Q8S1Y4 View 3D Structure Click here
Q8W4J8 View 3D Structure Click here
Q93ZM9 View 3D Structure Click here
Q94LG1 View 3D Structure Click here
Q9C5K8 View 3D Structure Click here
Q9C9E3 View 3D Structure Click here
Q9LDU5 View 3D Structure Click here
Q9LMA8 View 3D Structure Click here
Q9LRH6 View 3D Structure Click here
Q9LVI4 View 3D Structure Click here
Q9M246 View 3D Structure Click here
Q9M246 View 3D Structure Click here
Q9S7M2 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;