Summary: FMRP KH0 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.
FMRP KH0 domain Provide feedback
This entry corresponds to the KH0 domain from the FMRP protein [1]. This is a divergent KH domain that was discovered through solving the structure of an N-terminal fragment of the FMRP protein [1]. KH0 does not have the canonical G-X-X-G motif between helices A and B [1]. It has been suggested that this domain may be involved in RNA binding [1].
Literature references
-
Myrick LK, Hashimoto H, Cheng X, Warren ST;, Hum Mol Genet. 2015;24:1733-1740.: Human FMRP contains an integral tandem Agenet (Tudor) and KH motif in the amino terminal domain. PUBMED:25416280 EPMC:25416280
This tab holds annotation information from the InterPro database.
InterPro entry IPR040472
This entry corresponds to the KH0 domain from the FMRP protein [PUBMED:25416280]. This is a divergent KH domain that was discovered through solving the structure of an N-terminal fragment of the FMRP protein [PUBMED:25416280]. KH0 does not have the canonical G-X-X-G motif between helices A and B [PUBMED:25416280]. It has been suggested that this domain may be involved in RNA binding [PUBMED:25416280].
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 SLSAlignments
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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics 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 (5) |
Full (1193) |
Representative proteomes | UniProt (2065) |
NCBI (3943) |
Meta (0) |
||||
---|---|---|---|---|---|---|---|---|---|
RP15 (125) |
RP35 (271) |
RP55 (707) |
RP75 (1242) |
||||||
Jalview | |||||||||
HTML | |||||||||
PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key:
available,
not generated,
— not available.
Format an alignment
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 (5) |
Full (1193) |
Representative proteomes | UniProt (2065) |
NCBI (3943) |
Meta (0) |
||||
---|---|---|---|---|---|---|---|---|---|
RP15 (125) |
RP35 (271) |
RP55 (707) |
RP75 (1242) |
||||||
Raw Stockholm | |||||||||
Gzipped |
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
Seed source: | ECOD:EUF04635 |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Bateman A |
Number in seed: | 5 |
Number in full: | 1193 |
Average length of the domain: | 84.30 aa |
Average identity of full alignment: | 58 % |
Average coverage of the sequence by the domain: | 14.31 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
|
||||||||||||
Model details: |
|
||||||||||||
Model length: | 85 | ||||||||||||
Family (HMM) version: | 2 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
Sunburst controls
HideWeight segments by...
Change the size of the sunburst
Colour assignments
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
![]() |
Selections
Align selected sequences to HMM
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...
Tree controls
HideThe tree shows the occurrence of this domain across different species. More...
Loading...
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 KH_9 domain has been found. There are 9 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...