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18  structures 167  species 0  interactions 2336  sequences 42  architectures

Family: RALF (PF05498)

Summary: Rapid ALkalinization Factor (RALF)

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.

Rapid ALkalinization Factor (RALF) Provide feedback

Family members found in Arabidopsis include RALF23. It has been shown to reduce plant growth upon overexpression while mature plants were dwarfed and bushy. It has also been suggested that RALF23 of Arabidopsis, counteracts brassinosteroid (BR) growth-promoting effects which may be relieved by the down-regulation of RALF23 [1]

Literature references

  1. Srivastava R, Liu JX, Guo H, Yin Y, Howell SH;, Plant J. 2009;59:930-939.: Regulation and processing of a plant peptide hormone, AtRALF23, in Arabidopsis. PUBMED:19473327 EPMC:19473327


This tab holds annotation information from the InterPro database.

InterPro entry IPR008801

The plant RAPID ALKALINIZATION FACTOR (RALF) family consists of extracellular peptides that serve as extracellular signals. RALF1, a 5kDa ubiquitous polypeptide in plants, arrests root growth and development [ PUBMED:11675511 , PUBMED:29282286 ]. RALF4/19 peptides interact with LRX proteins to control pollen tube growth [ PUBMED:29242232 ].

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
(52)
Full
(2336)
Representative proteomes UniProt
(3557)
RP15
(222)
RP35
(1150)
RP55
(1825)
RP75
(2586)
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
(52)
Full
(2336)
Representative proteomes UniProt
(3557)
RP15
(222)
RP35
(1150)
RP55
(1825)
RP75
(2586)
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
(52)
Full
(2336)
Representative proteomes UniProt
(3557)
RP15
(222)
RP35
(1150)
RP55
(1825)
RP75
(2586)
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_4453 (release 8.0)
Previous IDs: none
Type: Family
Sequence Ontology: SO:0100021
Author: Finn RD , El-Gebali S
Number in seed: 52
Number in full: 2336
Average length of the domain: 61.30 aa
Average identity of full alignment: 39 %
Average coverage of the sequence by the domain: 49.60 %

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 21.3 21.3
Trusted cut-off 21.3 21.3
Noise cut-off 21.2 21.2
Model length: 65
Family (HMM) version: 13
Download: download the raw HMM for this family

Species distribution

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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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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 RALF domain has been found. There are 18 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
A0A0P0UYH2 View 3D Structure Click here
A0A0P0WJ24 View 3D Structure Click here
A0A0R0EP30 View 3D Structure Click here
A0A0R0IK43 View 3D Structure Click here
A0A1D6G4W6 View 3D Structure Click here
A0A1D6HWB9 View 3D Structure Click here
A0A1D6IN51 View 3D Structure Click here
A0A1D6LQI6 View 3D Structure Click here
A0A1D6ML12 View 3D Structure Click here
A0A1D6MXM3 View 3D Structure Click here
A7REE5 View 3D Structure Click here
A7REH2 View 3D Structure Click here
A8MQ92 View 3D Structure Click here
A8MQI8 View 3D Structure Click here
A8MQL7 View 3D Structure Click here
A8MQM2 View 3D Structure Click here
A8MQM7 View 3D Structure Click here
A8MQP2 View 3D Structure Click here
A8MR00 View 3D Structure Click here
A8MRD4 View 3D Structure Click here
A8MRF9 View 3D Structure Click here
A8MRK3 View 3D Structure Click here
A8MRM1 View 3D Structure Click here
B4FV46 View 3D Structure Click here
B6SJC1 View 3D Structure Click here
B6SMV8 View 3D Structure Click here
B6T8G2 View 3D Structure Click here
B6TDV1 View 3D Structure Click here
B6TEE3 View 3D Structure Click here
B6TGH9 View 3D Structure Click here
B6TUL0 View 3D Structure Click here
B6U664 View 3D Structure Click here
B6UE55 View 3D Structure Click here
B9FWB7 View 3D Structure Click here
C6T1A5 View 3D Structure Click here
C6T1Z2 View 3D Structure Click here
C6TB17 View 3D Structure Click here
F4ISE1 View 3D Structure Click here
F4ISE2 View 3D Structure Click here
I1J975 View 3D Structure Click here
I1JQK7 View 3D Structure Click here
I1JRA8 View 3D Structure Click here
I1K3S3 View 3D Structure Click here
I1KLL4 View 3D Structure Click here
I1KMZ0 View 3D Structure Click here
I1LBA3 View 3D Structure Click here
I1LHE0 View 3D Structure Click here
I1LN31 View 3D Structure Click here
I1LUI3 View 3D Structure Click here
I1M096 View 3D Structure Click here
I1MEK2 View 3D Structure Click here
K7L601 View 3D Structure Click here
K7L606 View 3D Structure Click here
K7M2N5 View 3D Structure Click here
K7MG37 View 3D Structure Click here
K7MJM9 View 3D Structure Click here
K7MZX4 View 3D Structure Click here
K7N1X6 View 3D Structure Click here
K7TUG2 View 3D Structure Click here
K7VAJ2 View 3D Structure Click here
K7W1S0 View 3D Structure Click here
O23262 View 3D Structure Click here
O23263 View 3D Structure Click here
O49320 View 3D Structure Click here
O64466 View 3D Structure Click here
O65919 View 3D Structure Click here
Q0V822 View 3D Structure Click here
Q10LK5 View 3D Structure Click here
Q1ECR9 View 3D Structure Click here
Q2HIM9 View 3D Structure Click here
Q2QP48 View 3D Structure Click here
Q2QP50 View 3D Structure Click here
Q2R4Y5 View 3D Structure Click here
Q3ECL0 View 3D Structure Click here
Q6ESP9 View 3D Structure Click here
Q6NME6 View 3D Structure Click here
Q7G716 View 3D Structure Click here
Q8L9P8 View 3D Structure Click here
Q8LGX9 View 3D Structure Click here
Q8LGY5 View 3D Structure Click here
Q942U5 View 3D Structure Click here
Q94DK4 View 3D Structure Click here
Q94DK6 View 3D Structure Click here
Q9AWJ6 View 3D Structure Click here
Q9FHA6 View 3D Structure Click here
Q9FZA0 View 3D Structure Click here
Q9LDU1 View 3D Structure Click here
Q9LH43 View 3D Structure Click here
Q9LK37 View 3D Structure Click here
Q9LSG0 View 3D Structure Click here
Q9LUS7 View 3D Structure Click here
Q9MA62 View 3D Structure Click here
Q9SDJ5 View 3D Structure Click here
Q9SIU6 View 3D Structure Click here
Q9SRY3 View 3D Structure Click here