!!

Powering down the Pfam website
On October 5th, we began redirecting traffic from Pfam (pfam.xfam.org) to InterPro (www.ebi.ac.uk/interpro). The Pfam website will remain 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.
78  structures 1567  species 0  interactions 54694  sequences 977  architectures

Family: RhoGAP (PF00620)

Summary: RhoGAP 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 "RhoGAP domain". More...

RhoGAP domain Edit Wikipedia article

RhoGAP domain
Identifiers
SymbolRhoGAP
PfamPF00620
InterProIPR000198
SMARTRhoGAP
SCOP21rgb / SCOPe / SUPFAM
OPM protein1xa6

RhoGAP domain is an evolutionary conserved protein domain of GTPase activating proteins towards Rho/Rac/Cdc42-like small GTPases.

Human proteins containing this domain

ABR; ARHGAP1; ARHGAP10; ARHGAP11A; ARHGAP11B; ARHGAP12; ARHGAP15; ARHGAP17; ARHGAP18; ARHGAP19; ARHGAP20; ARHGAP21; ARHGAP22; ARHGAP23; ARHGAP24; ARHGAP25; ARHGAP26; ARHGAP27; ARHGAP28; ARHGAP29; ARHGAP30; ARHGAP4; ARHGAP5; ARHGAP6; ARHGAP8; ARHGAP9; BCR; BPGAP1; C1; C5orf5; CDGAP; CENTD1; CENTD2; CENTD3; CHN1; CHN2; DEPDC1; DEPDC1A; DEPDC1B; DLC1; FAM13A1; FKSG42; GMIP; GRLF1; HMHA1; INPP5B; KIAA1688; LOC553158; MYO9A; MYO9B; OCRL; OPHN1; PIK3R1; PIK3R2; PRR5; RACGAP1; RACGAP1P; RALBP1; RICH2; RICS; SH3BP1; SLIT1; SNX26; SRGAP1; SRGAP2; SRGAP3; STARD13; STARD8; SYDE1; SYDE2; TAGAP;

References

  • [1]. Crystal structure of the breakpoint cluster region-homology domain from phosphoinositide 3-kinase p85 alpha subunit. Musacchio A, Cantley LC, Harrison SC; Proc Natl Acad Sci U S A 1996;93:14373-14378. PMID 8962058
  • [2]. The structure of the GTPase-activating domain from p50rhoGAP. Barrett T, Xiao B, Dodson EJ, Dodson G, Ludbrook SB, Nurmahomed K, Gamblin SJ, Musacchio A, Smerdon SJ, Eccleston JF; Nature 1997;385:458-461. PMID 9009196
  • [3]. Crystal structure of a small G protein in complex with the GTPase-activating protein rhoGAP. Rittinger K, Walker PA, Eccleston JF, Nurmahomed K, Owen D, Laue E, Gamblin SJ, Smerdon SJ; Nature 1997;388:693-697. PMID 9262406
  • [4]. Proteins regulating Ras and its relatives. Boguski MS, McCormick F; Nature 1993;366:643-654. PMID 8259209

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.

RhoGAP domain Provide feedback

GTPase activator proteins towards Rho/Rac/Cdc42-like small GTPases.

Literature references

  1. Musacchio A, Cantley LC, Harrison SC; , Proc Natl Acad Sci U S A 1996;93:14373-14378.: Crystal structure of the breakpoint cluster region-homology domain from phosphoinositide 3-kinase p85 alpha subunit. PUBMED:8962058 EPMC:8962058

  2. Barrett T, Xiao B, Dodson EJ, Dodson G, Ludbrook SB, Nurmahomed K, Gamblin SJ, Musacchio A, Smerdon SJ, Eccleston JF; , Nature 1997;385:458-461.: The structure of the GTPase-activating domain from p50rhoGAP. PUBMED:9009196 EPMC:9009196

  3. Rittinger K, Walker PA, Eccleston JF, Nurmahomed K, Owen D, Laue E, Gamblin SJ, Smerdon SJ; , Nature 1997;388:693-697.: Crystal structure of a small G protein in complex with the GTPase-activating protein rhoGAP. PUBMED:9262406 EPMC:9262406

  4. Boguski MS, McCormick F; , Nature 1993;366:643-654.: Proteins regulating Ras and its relatives. PUBMED:8259209 EPMC:8259209


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000198

Members of the Rho family of small G proteins transduce signals from plasma-membrane receptors and control cell adhesion, motility and shape by actin cytoskeleton formation. Like all other GTPases, Rho proteins act as molecular switches, with an active GTP-bound form and an inactive GDP-bound form. The active conformation is promoted by guanine-nucleotide exchange factors, and the inactive state by GTPase-activating proteins (GAPs) which stimulate the intrinsic GTPase activity of small G proteins. This entry is a Rho/Rac/Cdc42-like GAP domain, that is found in a wide variety of large, multi-functional proteins [ PUBMED:9009196 ]. A number of structure are known for this family [ PUBMED:9009196 , PUBMED:8962058 , PUBMED:9262406 ]. The domain is composed of seven alpha helices. This domain is also known as the breakpoint cluster region-homology (BH) domain.

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 GAP (CL0409), which has the following description:

Superfamily contains BCR-homology GTPase activation domain (BH-domain) and p120GAP domain-like, including the GAP related domain of neurofibromin, families.

The clan contains the following 3 members:

Msb1-Mug8_dom RasGAP RhoGAP

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
(83)
Full
(54694)
Representative proteomes UniProt
(87465)
RP15
(7503)
RP35
(18331)
RP55
(40878)
RP75
(55679)
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
(83)
Full
(54694)
Representative proteomes UniProt
(87465)
RP15
(7503)
RP35
(18331)
RP55
(40878)
RP75
(55679)
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
(83)
Full
(54694)
Representative proteomes UniProt
(87465)
RP15
(7503)
RP35
(18331)
RP55
(40878)
RP75
(55679)
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: SMART
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Ponting CP , Schultz J, Bork P
Number in seed: 83
Number in full: 54694
Average length of the domain: 143.2 aa
Average identity of full alignment: 27 %
Average coverage of the sequence by the domain: 15.7 %

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 24.5 24.5
Trusted cut-off 24.5 24.5
Noise cut-off 24.4 24.4
Model length: 149
Family (HMM) version: 30
Download: download the raw HMM for this family

Species distribution

Sunburst controls

Hide

Weight segments by...


Change the size of the sunburst

Small
Large

Colour assignments

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

Selections

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

Hide

The 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 RhoGAP domain has been found. There are 78 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
A0A044QMA4 View 3D Structure Click here
A0A044RAG8 View 3D Structure Click here
A0A044S023 View 3D Structure Click here
A0A044S2P2 View 3D Structure Click here
A0A044TB68 View 3D Structure Click here
A0A044TCJ7 View 3D Structure Click here
A0A044TLD8 View 3D Structure Click here
A0A044TS35 View 3D Structure Click here
A0A044U7G7 View 3D Structure Click here
A0A044UC42 View 3D Structure Click here
A0A044UCF6 View 3D Structure Click here
A0A044UTH6 View 3D Structure Click here
A0A044UZ35 View 3D Structure Click here
A0A044V178 View 3D Structure Click here
A0A044V6C3 View 3D Structure Click here
A0A044V9B4 View 3D Structure Click here
A0A044VA74 View 3D Structure Click here
A0A077YUU6 View 3D Structure Click here
A0A077YWS1 View 3D Structure Click here
A0A077YXC5 View 3D Structure Click here
A0A077YZ05 View 3D Structure Click here
A0A077Z0J9 View 3D Structure Click here
A0A077Z228 View 3D Structure Click here
A0A077Z2D7 View 3D Structure Click here
A0A077Z3C5 View 3D Structure Click here
A0A077Z4G0 View 3D Structure Click here
A0A077Z506 View 3D Structure Click here
A0A077Z6W7 View 3D Structure Click here
A0A077Z762 View 3D Structure Click here
A0A077Z9Q5 View 3D Structure Click here
A0A077ZAR4 View 3D Structure Click here
A0A077ZCZ5 View 3D Structure Click here
A0A077ZF56 View 3D Structure Click here
A0A077ZHC4 View 3D Structure Click here
A0A077ZJP8 View 3D Structure Click here
A0A077ZNL6 View 3D Structure Click here
A0A096MJZ4 View 3D Structure Click here
A0A0A0MPV6 View 3D Structure Click here
A0A0A2V423 View 3D Structure Click here
A0A0D2E1C7 View 3D Structure Click here