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78  structures 130  species 3  interactions 588  sequences 31  architectures

Family: PI3K_rbd (PF00794)

Summary: PI3-kinase family, ras-binding domain

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

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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.

PI3-kinase family, ras-binding domain Provide feedback

Certain members of the PI3K family possess Ras-binding domains in their N-termini. These regions show some similarity (although not highly significant similarity) to Ras-binding PF00788 domains (unpublished observation).

Literature references

  1. Rodriguez-Viciana P, Warne PH, Vanhaesebroeck B, Waterfield MD, Downward J; , EMBO J 1996;15:2442-2451.: Activation of phosphoinositide 3-kinase by interaction with Ras and by point mutation. PUBMED:8665852 EPMC:8665852

  2. Kodaki T, Woscholski R, Hallberg B, Rodriguez-Viciana P, Downward J, Parker PJ; , Curr Biol 1994;4:798-806.: The activation of phosphatidylinositol 3-kinase by Ras. PUBMED:7820549 EPMC:7820549

  3. Rodriguez-Viciana P, Warne PH, Dhand R, Vanhaesebroeck B, Gout I, Fry MJ, Waterfield MD, Downward J; , Nature 1994;370:527-532.: Phosphatidylinositol-3-OH kinase as a direct target of Ras. PUBMED:8052307 EPMC:8052307


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000341

Phosphatidylinositol 3-kinases (PI3Ks) are lipid kinases that phosphorylate 4,5-bisphonate (PI(4,5) P2 or PIP2) at the 3-position of the inositol ring, and thus generate phosphatidylinositol 3,4,5-trisphosphate (PIP3), which, in turns, initiates a vast array of signaling events. PI3Ks can be grouped into three classes based on their domain organisation. Class I PI3Ks are heterodimers consisting of a p110 catalytic subunit and a regulatory subunit of either the p85 type (associated with the class IA p110 isoforms p110alpha, p110beta or p110delta) or the p101 type (associated with the class IB p110 isoform p110gamma). Common to all catalytic subunits are an N-terminal adaptor-binding domain (ABD) that binds to p85, a Ras- binding domain (RBD), a putative membrane-binding domain (C2), a helical domain of unknown function, and a kinase catalytic domain. Class II PI3Ks lack the ABD domain and are distinguished by a carboxy terminal C2 domain. Class III enzymes lack the ABD and RBD domains [PUBMED:17626883, PUBMED:18079394, PUBMED:20081827, PUBMED:10580505].

PI3K RBD is a small globular domain of about 100 residues in length with an alpha/beta-sandwich topology. The PI3K RBD domain consists of a five-stranded mixed beta-sheet flanked by two alpha-helices [PUBMED:17626883, PUBMED:18079394, PUBMED:20081827, PUBMED:10580505].

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 Ubiquitin (CL0072), which has the following description:

This family includes proteins that share the ubiquitin fold. It currently unites four SCOP superfamilies.

The clan contains the following 41 members:

APG12 Atg8 Blt1 Caps_synth_GfcC CIDE-N Cobl DUF1315 DUF2407 DUF4430 DWNN FERM_N Lambda_tail_I Multi_ubiq NQRA_SLBB PB1 PI3K_rbd Plug Prok_Ub RA Rad60-SLD Rad60-SLD_2 Ras_bdg_2 RBD SLBB Telomere_Sde2 TGS ThiS ThiS-like TmoB TUG-UBL1 Ub-Mut7C Ub-RnfH ubiquitin Ubiquitin_2 Ubiquitin_3 UBX Ufm1 UN_NPL4 Urm1 YchF-GTPase_C YukD

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...

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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
(12)
Full
(588)
Representative proteomes NCBI
(502)
Meta
(1)
RP15
(83)
RP35
(113)
RP55
(201)
RP75
(323)
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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
(12)
Full
(588)
Representative proteomes NCBI
(502)
Meta
(1)
RP15
(83)
RP35
(113)
RP55
(201)
RP75
(323)
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
(12)
Full
(588)
Representative proteomes NCBI
(502)
Meta
(1)
RP15
(83)
RP35
(113)
RP55
(201)
RP75
(323)
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: Alignment kindly provided by SMART
Previous IDs: none
Type: Family
Author: SMART
Number in seed: 12
Number in full: 588
Average length of the domain: 105.50 aa
Average identity of full alignment: 25 %
Average coverage of the sequence by the domain: 9.04 %

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 20.8 20.8
Trusted cut-off 20.8 21.1
Noise cut-off 20.7 20.7
Model length: 107
Family (HMM) version: 13
Download: download the raw HMM for this family

Species distribution

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Interactions

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

Ras PI3_PI4_kinase PI3Ka

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 PI3K_rbd 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 seqence.

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