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36  structures 353  species 3  interactions 7538  sequences 300  architectures

Family: RhoGAP (PF00620)

Summary: RhoGAP domain

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

RhoGAP domain Edit Wikipedia article

RhoGAP domain
PDB 1rgb EBI.jpg
Structure of Phospholipase A2.[1]
Identifiers
Symbol RhoGAP
Pfam PF00620
InterPro IPR000198
SMART RhoGAP
PROSITE PDOC50238
SCOP 1rgb
SUPERFAMILY 1rgb
OPM protein 1xa6
CDD cd00159

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

Human proteins containing this domain[edit]

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[disambiguation needed]; 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;

Notes[edit]

  1. ^ Georgieva DN, Rypniewski W, Gabdoulkhakov A, Genov N, Betzel C (July 2004). "Asp49 phospholipase A(2)-elaidoylamide complex: a new mode of inhibition". Biochem. Biophys. Res. Commun. 319 (4): 1314–21. doi:10.1016/j.bbrc.2004.05.106. PMID 15194511. 

References[edit]

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...

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Pfam Clan

This family is a member of clan GAP (CL0409), which contains the following 3 members:

DUF1708 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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, 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
(87)
Full
(7538)
Representative proteomes NCBI
(7012)
Meta
(27)
RP15
(1311)
RP35
(1920)
RP55
(3077)
RP75
(4418)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(87)
Full
(7538)
Representative proteomes NCBI
(7012)
Meta
(27)
RP15
(1311)
RP35
(1920)
RP55
(3077)
RP75
(4418)
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
(87)
Full
(7538)
Representative proteomes NCBI
(7012)
Meta
(27)
RP15
(1311)
RP35
(1920)
RP55
(3077)
RP75
(4418)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

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
Author: Ponting C, Schultz J, Bork P
Number in seed: 87
Number in full: 7538
Average length of the domain: 147.00 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 17.80 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -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: 152
Family (HMM) version: 22
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 3 interactions for this family. More...

C1_1 RhoGAP Ras

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 36 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 seqence.

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