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0  structures 589  species 0  interactions 2920  sequences 71  architectures

Family: RAP (PF08373)

Summary: RAP domain

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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.

RAP domain Provide feedback

This domain is found in various eukaryotic species, where it is found in proteins that are important in various parasite-host cell interactions. It is thought to be an RNA-binding domain [1]. The domain is involved in plant defence in response to bacterial infection [2,3].

Literature references

  1. Lee I, Hong W; , Trends Biochem Sci 2004;29:567-570.: RAP--a putative RNA-binding domain. PUBMED:15501674 EPMC:15501674

  2. Katiyar-Agarwal S, Gao S, Vivian-Smith A, Jin H;, Genes Dev. 2007;21:3123-3134.: A novel class of bacteria-induced small RNAs in Arabidopsis. PUBMED:18003861 EPMC:18003861

  3. Katiyar-Agarwal S, Jin H;, Annu Rev Phytopathol. 2010;48:225-246.: Role of small RNAs in host-microbe interactions. PUBMED:20687832 EPMC:20687832

Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR013584

The ~60-residue RAP (an acronym for RNA-binding domain abundant in Apicomplexans) domain is found in various proteins in eukaryotes. It is particularly abundant in apicomplexans and might mediate a range of cellular functions through its potential interactions with RNA [ PUBMED:15501674 ].

The RAP domain consists of multiple blocks of charged and aromatics residues and is predicted to be composed of alpha helical and beta strand structures. Two predicted loop regions that are dominated by glycine and tryptophan residues are found before and after the central beta sheet [ PUBMED:15501674 ].

Some proteins known to contain a RAP domain are listed below:

  • Human hypothetical protein MGC5297,
  • Mammalian FAST kinase domain-containing proteins (FASTKDs),
  • Chlamydomonas reinhardtii chloroplastic trans-splicing factor Raa3.

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 PDDEXK (CL0236), which has the following description:

This clan includes a large number of nuclease families related to holliday junction resolvases [1,2].

The clan contains the following 149 members:

AHJR-like ArenaCapSnatch BamHI BpuJI_N BpuSI_N Bse634I BsuBI_PstI_RE Cas_APE2256 Cas_Cas02710 Cas_Cas4 Cas_Csm6 Cas_DxTHG Cas_NE0113 CdiA_C CdiA_C_tRNase CoiA Csa1 Dna2 DpnI DpnII DpnII-MboI DUF1780 DUF1829 DUF1887 DUF2034 DUF2161 DUF234 DUF2357 DUF2726 DUF2800 DUF2887 DUF3799 DUF4143 DUF4263 DUF4420 DUF559 DUF5614 DUF6035 DUF6293 DUF6671 EC042_2821 EcoRI EcoRII-C eIF-3_zeta Endonuc-BglII Endonuc-BsobI Endonuc-EcoRV Endonuc-HincII Endonuc-MspI Endonuc-PvuII Endonuc_BglI Endonuc_Holl ERCC4 Exo5 Flu_PA FokI_cleav_dom Herpes_UL24 Hjc HSDR_N HSDR_N_2 L_protein_N McrBC MepB-like MmcB-like Mrr_cat Mrr_cat_2 MTES_1575 MutH MvaI_BcnI NaeI NERD NgoMIV_restric NotI NOV_C NucS PDCD9 PDDEXK_1 PDDEXK_10 PDDEXK_11 PDDEXK_12 PDDEXK_2 PDDEXK_3 PDDEXK_4 PDDEXK_5 PDDEXK_7 PDDEXK_9 Pet127 Phage_endo_I PND R-HINP1I Rad10 RAI1 RAP RE_AlwI RE_ApaLI RE_Bpu10I RE_BsaWI RE_Bsp6I RE_CfrBI RE_Eco47II RE_EcoO109I RE_endonuc RE_HaeII RE_HindIII RE_HindVP RE_HpaII RE_LlaJI RE_LlaMI RE_MjaI RE_NgoBV RE_NgoPII RE_SacI RE_ScaI RE_SinI RE_TaqI RE_TdeIII RE_XamI RE_XcyI RecC_C RecU RestrictionMunI RestrictionSfiI RmuC RNA_pol_Rpb5_N Sen15 SfsA Spo0A_C TBPIP_N ThaI Tn7_TnsA-like_N Tox-REase-2 Tox-REase-3 Tox-REase-5 Tox-REase-7 Tox-REase-9 Transposase_31 tRNA_int_endo Tsp45I Uma2 UPF0102 Viral_alk_exo VirArc_Nuclease VRR_NUC Vsr XhoI XisH YaeQ YhcG_C YqaJ


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...

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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.

Representative proteomes UniProt
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PP/heatmap 1 View           

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

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Representative proteomes UniProt

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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
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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: Pfam-B_5583 (release 17.0)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Fenech M
Number in seed: 63
Number in full: 2920
Average length of the domain: 58.60 aa
Average identity of full alignment: 28 %
Average coverage of the sequence by the domain: 8.11 %

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 24.2 24.2
Trusted cut-off 24.2 24.2
Noise cut-off 24.1 24.1
Model length: 58
Family (HMM) version: 13
Download: download the raw HMM for this family

Species distribution

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Colour assignments

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


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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...

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


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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
A0A0R4IJX1 View 3D Structure Click here
A0A144A2U7 View 3D Structure Click here
A0A1D6MHH6 View 3D Structure Click here
A0A5K1K936 View 3D Structure Click here
B0S618 View 3D Structure Click here
C6KSP6 View 3D Structure Click here
D3ZFR0 View 3D Structure Click here
E7F3K7 View 3D Structure Click here
E7F8W7 View 3D Structure Click here
F1RE69 View 3D Structure Click here
I1KIG2 View 3D Structure Click here
K7KC75 View 3D Structure Click here
Q14296 View 3D Structure Click here
Q14CZ7 View 3D Structure Click here
Q28DE0 View 3D Structure Click here
Q3SZK4 View 3D Structure Click here
Q53R41 View 3D Structure Click here
Q58CX2 View 3D Structure Click here
Q5M7V7 View 3D Structure Click here
Q5M9G9 View 3D Structure Click here
Q5R776 View 3D Structure Click here
Q5RFI6 View 3D Structure Click here
Q68FN9 View 3D Structure Click here
Q6DI86 View 3D Structure Click here
Q6DJ55 View 3D Structure Click here
Q7L8L6 View 3D Structure Click here
Q7TMV3 View 3D Structure Click here
Q7YS91 View 3D Structure Click here
Q84MH1 View 3D Structure Click here
Q8BSN9 View 3D Structure Click here
Q8I289 View 3D Structure Click here
Q8I3K5 View 3D Structure Click here
Q8I3S7 View 3D Structure Click here
Q8I3U8 View 3D Structure Click here
Q8I5F2 View 3D Structure Click here
Q8IAY8 View 3D Structure Click here
Q8IC11 View 3D Structure Click here
Q8IIC7 View 3D Structure Click here
Q8IJA7 View 3D Structure Click here
Q8IJF8 View 3D Structure Click here

trRosetta Structure

The structural model below was generated by the Baker group with the trRosetta software using the Pfam UniProt multiple sequence alignment.

The InterPro website shows the contact map for the Pfam SEED alignment. Hovering or clicking on a contact position will highlight its connection to other residues in the alignment, as well as on the 3D structure.

Improved protein structure prediction using predicted inter-residue orientations. Jianyi Yang, Ivan Anishchenko, Hahnbeom Park, Zhenling Peng, Sergey Ovchinnikov, David Baker Proceedings of the National Academy of Sciences Jan 2020, 117 (3) 1496-1503; DOI: 10.1073/pnas.1914677117;