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43  structures 1490  species 0  interactions 18464  sequences 139  architectures

Family: FF (PF01846)

Summary: FF 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.

FF domain Provide feedback

This domain has been predicted to be involved in protein-protein interaction [1]. This domain was recently shown to bind the hyperphosphorylated C-terminal repeat domain of RNA polymerase II, confirming its role in protein-protein interactions [2].

Literature references

  1. Bedford MT, Leder P; , Trends Biochem Sci 1999;24:264-265.: The FF domain: a novel motif that often accompanies WW domains. PUBMED:10390614 EPMC:10390614

  2. Carty SM, Goldstrohm AC, Sune C, Garcia-Blanco MA, Greenleaf AL; , Proc Natl Acad Sci U S A 2000;97:9015-9020.: Protein-interaction modules that organize nuclear function: FF domains of CA150 bind the phosphoCTD of RNA polymerase II. PUBMED:10908677 EPMC:10908677


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR002713

The FF domain may be involved in protein-protein interaction [ PUBMED:10390614 ]. It often occurs as multiple copies and often accompanies WW domains INTERPRO . PRP40 from yeast encodes a novel, essential splicing component that associates with the yeast U1 small nuclear ribonucleoprotein particle [ PUBMED:8622699 ].

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 FF (CL0584), which has the following description:

This superfamily contains FF domains.

The clan contains the following 2 members:

FF RhoGAP-FF1

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
(114)
Full
(18464)
Representative proteomes UniProt
(26951)
RP15
(2782)
RP35
(6675)
RP55
(13310)
RP75
(18887)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

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

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

Format an alignment

  Seed
(114)
Full
(18464)
Representative proteomes UniProt
(26951)
RP15
(2782)
RP35
(6675)
RP55
(13310)
RP75
(18887)
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
(114)
Full
(18464)
Representative proteomes UniProt
(26951)
RP15
(2782)
RP35
(6675)
RP55
(13310)
RP75
(18887)
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: [1]
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Bedford MT, Bateman A
Number in seed: 114
Number in full: 18464
Average length of the domain: 52.4 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 18.5 %

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 22.0 22.0
Trusted cut-off 22.0 22.0
Noise cut-off 21.9 21.9
Model length: 51
Family (HMM) version: 22
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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The tree shows the occurrence of this domain across different species. More...

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Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

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 FF domain has been found. There are 43 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
A0A044QNB0 View 3D Structure Click here
A0A044V4F6 View 3D Structure Click here
A0A077Z3U9 View 3D Structure Click here
A0A077ZD87 View 3D Structure Click here
A0A077ZQU4 View 3D Structure Click here
A0A0B4KFB8 View 3D Structure Click here
A0A0D2GVQ5 View 3D Structure Click here
A0A0D2H186 View 3D Structure Click here
A0A0G2K7N9 View 3D Structure Click here
A0A0K0EHI1 View 3D Structure Click here
A0A0K0EI80 View 3D Structure Click here
A0A0P0V3J7 View 3D Structure Click here
A0A0R0HSA7 View 3D Structure Click here
A0A158Q3R6 View 3D Structure Click here
A0A158Q4E6 View 3D Structure Click here
A0A175VZY8 View 3D Structure Click here
A0A175WG35 View 3D Structure Click here
A0A1C1CV09 View 3D Structure Click here
A0A1C1CYP8 View 3D Structure Click here
A0A1D6GP79 View 3D Structure Click here
A0A1D6NNG0 View 3D Structure Click here
A0A1D6NNQ8 View 3D Structure Click here
A0A1P6BRW8 View 3D Structure Click here
A0A2R8QK73 View 3D Structure Click here
A0A3P7FJE7 View 3D Structure Click here
A0A3P7FJM1 View 3D Structure Click here
A0A5K1K8A8 View 3D Structure Click here
A0A5K4F278 View 3D Structure Click here
A0A5S6PVQ3 View 3D Structure Click here
A5PF53 View 3D Structure Click here
B6EUA9 View 3D Structure Click here
C0NJB4 View 3D Structure Click here
C0NRU3 View 3D Structure Click here
C1GWH1 View 3D Structure Click here
C1HBJ9 View 3D Structure Click here
D3ZJ92 View 3D Structure Click here
D3ZTL0 View 3D Structure Click here
D4AE82 View 3D Structure Click here
E7F3A6 View 3D Structure Click here
E7F8G5 View 3D Structure Click here