Powering down the Pfam website
On October 5th, we will start redirecting the traffic from Pfam (pfam.xfam.org) to InterPro (www.ebi.ac.uk/interpro). The Pfam website will be available at pfam-legacy.xfam.org until January 2023, when it will be decommissioned. You can read more about the sunset period in our blog post.

Please note: this site relies heavily on the use of javascript. Without a javascript-enabled browser, this site will not function correctly. Please enable javascript and reload the page, or switch to a different browser.
1242  structures 8892  species 0  interactions 19271  sequences 102  architectures

Family: KH_2 (PF07650)

Summary: KH domain

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "KH domain". More...

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

KH domain Provide feedback

No Pfam abstract.

Literature references

  1. Burd CG, Dreyfuss G; , Science 1994;265:615-621.: Conserved structures and diversity of functions of RNA-binding proteins. PUBMED:8036511 EPMC:8036511

  2. Musco G, Stier G, Joseph C, Castiglione Morelli MA, Nilges M, Gibson TJ, Pastore A; , Cell 1996;85:237-245.: Three-dimensional structure and stability of the KH domain: molecular insights into the fragile X syndrome. PUBMED:8612276 EPMC:8612276

Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR004044

The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins [ PUBMED:8036511 ]. It has been shown to bind RNA [ PUBMED:9302998 , PUBMED:10369774 ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently [ PUBMED:8036511 ].

According to structural analyses [ PUBMED:9302998 , PUBMED:10369774 , PUBMED:11160884 ], the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheets are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-2 KH domain include eukaryotic and prokaryotic S3 family of ribosomal proteins, and the prokaryotic GTP-binding protein era.

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...

Loading domain graphics...

Pfam Clan

This family is a member of clan KH (CL0007), which has the following description:

The KH domain is thought to be the second most prevalent RNA binding motif in proteins. The motif is characterised by a conserved GXXXGXXG in the middle of the domain. Structures of KH reveal that the KH domain is arranged as either a beta-alpha-alpha-beta-beta (mini-KH domain) or beta-alpha-alpha-beta-beta-alpha (maxi-KH domain). The secondary elements are separated by at least four loop segments. The second loop is located between beta-1 and al The KH domain can be found either as single or multiple copies. The KH domain usually binds RNA as a multimer.

The clan contains the following 14 members:

DUF2096 DUF370 KH_1 KH_10 KH_2 KH_4 KH_5 KH_6 KH_7 KH_8 KH_9 MOEP19 MRP-S24 SLS


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.

Representative proteomes UniProt
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

Representative proteomes UniProt

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.

Representative proteomes UniProt
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...


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: Context_Domains
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Finn RD
Number in seed: 127
Number in full: 19271
Average length of the domain: 76.4 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 27.42 %

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: 78
Family (HMM) version: 20
Download: download the raw HMM for this family

Species distribution

Sunburst controls


Weight segments by...

Change the size of the sunburst


Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence


Generate a FASTA-format file

Clear selection

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...

Loading sunburst data...

Tree controls


The tree shows the occurrence of this domain across different species. More...


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.


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 KH_2 domain has been found. There are 1242 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.

Loading structure mapping...

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
A0A044UZ83 View 3D Structure Click here
A0A077Z7F8 View 3D Structure Click here
A0A0D2DN25 View 3D Structure Click here
A0A0G2K689 View 3D Structure Click here
A0A0H3GRT7 View 3D Structure Click here
A0A0H3GU21 View 3D Structure Click here
A0A0J9XU21 View 3D Structure Click here
A0A0K0ECP0 View 3D Structure Click here
A0A0N4U9X8 View 3D Structure Click here
A0A0R0G342 View 3D Structure Click here
A0A0R0HSV1 View 3D Structure Click here
A0A0R0I0B9 View 3D Structure Click here
A0A0R0JAM9 View 3D Structure Click here
A0A1C1CBL8 View 3D Structure Click here
A0A1D6PVR8 View 3D Structure Click here
A0A1D8PSV5 View 3D Structure Click here
A0A3P7DZI7 View 3D Structure Click here
A0B9W4 View 3D Structure Click here
A0JZ78 View 3D Structure Click here
A0KF27 View 3D Structure Click here
A0L5X9 View 3D Structure Click here
A0LIJ6 View 3D Structure Click here
A0LRM6 View 3D Structure Click here
A0PXV2 View 3D Structure Click here
A0Q1Q0 View 3D Structure Click here
A0QSD7 View 3D Structure Click here
A0RVX9 View 3D Structure Click here
A0T0I5 View 3D Structure Click here
A0T0X9 View 3D Structure Click here
A1A075 View 3D Structure Click here
A1ALU7 View 3D Structure Click here
A1APR8 View 3D Structure Click here
A1AVK6 View 3D Structure Click here
A1B033 View 3D Structure Click here
A1BJ28 View 3D Structure Click here
A1KB21 View 3D Structure Click here
A1R8T9 View 3D Structure Click here
A1RXG6 View 3D Structure Click here
A1S224 View 3D Structure Click here
A1SHZ4 View 3D Structure Click here