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0  structures 39  species 0  interactions 482  sequences 12  architectures

Family: tify (PF06200)

Summary: tify domain

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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


External database links

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:

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics 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
(48)
Full
(482)
Representative proteomes NCBI
(488)
Meta
(0)
RP15
(42)
RP35
(154)
RP55
(208)
RP75
(250)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(48)
Full
(482)
Representative proteomes NCBI
(488)
Meta
(0)
RP15
(42)
RP35
(154)
RP55
(208)
RP75
(250)
Alignment:
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Sequence:
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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
(48)
Full
(482)
Representative proteomes NCBI
(488)
Meta
(0)
RP15
(42)
RP35
(154)
RP55
(208)
RP75
(250)
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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

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
Author: Bateman A
Number in seed: 48
Number in full: 482
Average length of the domain: 35.50 aa
Average identity of full alignment: 41 %
Average coverage of the sequence by the domain: 13.34 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.9 20.9
Trusted cut-off 22.9 21.5
Noise cut-off 20.0 20.3
Model length: 36
Family (HMM) version: 9
Download: download the raw HMM for this family

Species distribution

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