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3  structures 139  species 0  interactions 2306  sequences 47  architectures

Family: Frigida (PF07899)

Summary: Frigida-like protein

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.

Frigida-like protein Provide feedback

This family is composed of plant proteins that are similar to FRIGIDA protein expressed by Arabidopsis thaliana (Q9FDW0). This protein is probably nuclear and is required for the regulation of flowering time in the late-flowering phenotype. It is known to increase RNA levels of flowering locus C. Allelic variation at the FRIGIDA locus is a major determinant of natural variation in flowering time [1].

Literature references

  1. Johanson U, West J, Lister C, Michaels S, Amasino R, Dean C; , Science 2000;290:344-347.: Molecular analysis of FRIGIDA, a major determinant of natural variation in Arabidopsis flowering time. PUBMED:11030654 EPMC:11030654


This tab holds annotation information from the InterPro database.

InterPro entry IPR012474

This family is composed of plant proteins that are similar to FRIGIDA protein expressed by Arabidopsis thaliana (Mouse-ear cress) ( SWISSPROT ). This protein is probably nuclear and is required for the regulation of flowering time in the late-flowering phenotype. It is known to increase RNA levels of flowering locus C. Allelic variation at the FRIGIDA locus is a major determinant of natural variation in flowering time [ PUBMED:11030654 ].

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
(49)
Full
(2306)
Representative proteomes UniProt
(3955)
RP15
(194)
RP35
(1266)
RP55
(1919)
RP75
(2582)
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
(49)
Full
(2306)
Representative proteomes UniProt
(3955)
RP15
(194)
RP35
(1266)
RP55
(1919)
RP75
(2582)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(49)
Full
(2306)
Representative proteomes UniProt
(3955)
RP15
(194)
RP35
(1266)
RP55
(1919)
RP75
(2582)
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_4728 (release 14.0)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Fenech M
Number in seed: 49
Number in full: 2306
Average length of the domain: 229.60 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 46.20 %

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 25.7 25.7
Trusted cut-off 25.7 26.6
Noise cut-off 25.6 25.6
Model length: 289
Family (HMM) version: 13
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 Frigida domain has been found. There are 3 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
A0A0P0W0I1 View 3D Structure Click here
A0A0R0F8D9 View 3D Structure Click here
A0A1D6F071 View 3D Structure Click here
A0A1D6F978 View 3D Structure Click here
A0A1D6FBQ4 View 3D Structure Click here
A0A1D6GM03 View 3D Structure Click here
A0A1D6HT97 View 3D Structure Click here
A0A1D6I0R6 View 3D Structure Click here
A0A1D6I0R8 View 3D Structure Click here
A0A1D6KWH2 View 3D Structure Click here
A0A1D6KWH6 View 3D Structure Click here
A0A1D6LBZ6 View 3D Structure Click here
A0A1D6P0Y3 View 3D Structure Click here
B4FTE5 View 3D Structure Click here
B4FTE5 View 3D Structure Click here
B4FTU1 View 3D Structure Click here
B7ZYB8 View 3D Structure Click here
C0P6D0 View 3D Structure Click here
I1JJG6 View 3D Structure Click here
I1JMD4 View 3D Structure Click here
I1K2A0 View 3D Structure Click here
I1K5U3 View 3D Structure Click here
I1KQ25 View 3D Structure Click here
I1LE46 View 3D Structure Click here
I1NGF2 View 3D Structure Click here
K7K6L2 View 3D Structure Click here
K7KE22 View 3D Structure Click here
K7KLA6 View 3D Structure Click here
K7KVE1 View 3D Structure Click here
K7LAA1 View 3D Structure Click here
K7LP44 View 3D Structure Click here
K7LP44 View 3D Structure Click here
K7LSG1 View 3D Structure Click here
K7LSG1 View 3D Structure Click here
K7MFT7 View 3D Structure Click here
K7MM08 View 3D Structure Click here
O04650 View 3D Structure Click here
O04650 View 3D Structure Click here
Q0J383 View 3D Structure Click here
Q10HH4 View 3D Structure Click here
Q10QK0 View 3D Structure Click here
Q5VR39 View 3D Structure Click here
Q5VR39 View 3D Structure Click here
Q5W6K5 View 3D Structure Click here
Q5XV31 View 3D Structure Click here
Q5XV31 View 3D Structure Click here
Q67Z93 View 3D Structure Click here
Q67ZB3 View 3D Structure Click here
Q6F379 View 3D Structure Click here
Q6K487 View 3D Structure Click here
Q6ZA60 View 3D Structure Click here
Q7XIP0 View 3D Structure Click here
Q851Y5 View 3D Structure Click here
Q940H8 View 3D Structure Click here
Q9C6S2 View 3D Structure Click here
Q9FFF1 View 3D Structure Click here
Q9LUV4 View 3D Structure Click here