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13  structures 161  species 0  interactions 1956  sequences 47  architectures

Family: Alfin (PF12165)

Summary: Alfin

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.

Alfin Provide feedback

The Alfin family includes PHD finger protein Alfin1 and Alfin1-like proteins. Alfin1 is a histone-binding component that specifically recognises H3 tails trimethylated on 'Lys-4' (H3K4me3), which marks transcription start sites of virtually all active genes [1, 2].

Literature references

  1. Winicov I I, Bastola DR;, Plant Physiol. 1999;120:473-480.: Transgenic overexpression of the transcription factor alfin1 enhances expression of the endogenous MsPRP2 gene in alfalfa and improves salinity tolerance of the plants. PUBMED:10364398 EPMC:10364398

  2. Winicov I;, Planta. 2000;210:416-422.: Alfin1 transcription factor overexpression enhances plant root growth under normal and saline conditions and improves salt tolerance in alfalfa. PUBMED:10750899 EPMC:10750899


This tab holds annotation information from the InterPro database.

InterPro entry IPR021998

The Alfin family includes PHD finger protein Alfin1 and Alfin1-like proteins. Alfin1 is a histone-binding component that specifically recognises H3 tails trimethylated on 'Lys-4' (H3K4me3), which marks transcription start sites of virtually all active genes [ PUBMED:10364398 , PUBMED:10750899 ].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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
(25)
Full
(1956)
Representative proteomes UniProt
(2820)
RP15
(179)
RP35
(977)
RP55
(1649)
RP75
(2137)
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
(25)
Full
(1956)
Representative proteomes UniProt
(2820)
RP15
(179)
RP35
(977)
RP55
(1649)
RP75
(2137)
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
(25)
Full
(1956)
Representative proteomes UniProt
(2820)
RP15
(179)
RP35
(977)
RP55
(1649)
RP75
(2137)
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_2040 (release 23.0)
Previous IDs: DUF3594;
Type: Family
Sequence Ontology: SO:0100021
Author: Assefa S , Coggill P , Bateman A
Number in seed: 25
Number in full: 1956
Average length of the domain: 116.00 aa
Average identity of full alignment: 66 %
Average coverage of the sequence by the domain: 48.01 %

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 21.0 21.0
Trusted cut-off 21.1 21.0
Noise cut-off 20.9 20.9
Model length: 127
Family (HMM) version: 10
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 Alfin domain has been found. There are 13 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
A0A0P0UZ01 View 3D Structure Click here
A0A0R0FQK5 View 3D Structure Click here
A0A0R0FQK5 View 3D Structure Click here
A0A0R0JZR3 View 3D Structure Click here
A0A0R0K9Y0 View 3D Structure Click here
A0A0R0KC88 View 3D Structure Click here
A0A0R0L1U1 View 3D Structure Click here
A0A1D6FJL6 View 3D Structure Click here
A0A1D6FQ18 View 3D Structure Click here
A0A1D6G7C6 View 3D Structure Click here
A0A1D6G7C6 View 3D Structure Click here
A0A1D6GEK2 View 3D Structure Click here
A0A1D6H0B5 View 3D Structure Click here
A0A1D6HAX1 View 3D Structure Click here
A0A1D6IJA0 View 3D Structure Click here
A0A1D6IJA0 View 3D Structure Click here
A0A1D6IX22 View 3D Structure Click here
A0A1D6J7E5 View 3D Structure Click here
A0A1D6JWT5 View 3D Structure Click here
A0A1D6LLI2 View 3D Structure Click here
A0A1D6LYQ7 View 3D Structure Click here
A0A1D6MY24 View 3D Structure Click here
A0A1D6NIB4 View 3D Structure Click here
A0A1D6PRK9 View 3D Structure Click here
A0A1D6Q3E8 View 3D Structure Click here
B4FCH3 View 3D Structure Click here
B4FK95 View 3D Structure Click here
B4FM57 View 3D Structure Click here
B6TK34 View 3D Structure Click here
C0PCY4 View 3D Structure Click here
C4J6F2 View 3D Structure Click here
C6T7X8 View 3D Structure Click here
I1JLE1 View 3D Structure Click here
I1KH84 View 3D Structure Click here
I1KKF5 View 3D Structure Click here
I1L1N8 View 3D Structure Click here
I1LY29 View 3D Structure Click here
I1M961 View 3D Structure Click here
I1MD29 View 3D Structure Click here
I1MQU2 View 3D Structure Click here
I1N2Y0 View 3D Structure Click here
K7K966 View 3D Structure Click here
K7L425 View 3D Structure Click here
K7LV30 View 3D Structure Click here
O81488 View 3D Structure Click here
Q06A73 View 3D Structure Click here
Q06A77 View 3D Structure Click here
Q06A78 View 3D Structure Click here
Q2R837 View 3D Structure Click here
Q5XEM9 View 3D Structure Click here
Q60DW3 View 3D Structure Click here
Q6YTY3 View 3D Structure Click here
Q6Z7F4 View 3D Structure Click here
Q75IR6 View 3D Structure Click here
Q7F2Z1 View 3D Structure Click here
Q7XUW3 View 3D Structure Click here
Q84TV4 View 3D Structure Click here
Q8H383 View 3D Structure Click here
Q8LA16 View 3D Structure Click here
Q8S8M9 View 3D Structure Click here
Q9FFF5 View 3D Structure Click here
Q9M2B4 View 3D Structure Click here
Q9SRM4 View 3D Structure Click here