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5  structures 76  species 0  interactions 227  sequences 30  architectures

Family: HeLo (PF14479)

Summary: Prion-inhibition and propagation

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Prion-inhibition and propagation Provide feedback

This N-terminal region, HeLo, has a prion-inhibitory effect in cis on its own prion-forming domain (PFD) and in trans on HET-s prion propagation [1]. The domain is found exclusively in the fungal kingdom. Its structure, as it occurs in the HET-s/HET-S proteins, consists of two bundles of alpha-helices that pack into a single globular domain [1]. The domain boundary determined from its structure and from protease-resistance experiments overlaps with the C-terminal prion-forming domain of HET-s (PF11558 [2]. The HeLo domains of HET-s and HET-S are very similar and their few differences (and not the prion-forming domains) determine the compatibility-phenotype of the fungi in which the proteins are expressed. The mechanism of the HeLo domain-function in heterokaryon-incompatibility is still under investigation, however the HeLo domain is found in similar protein architectures as other cell death and apoptosis-inducing domains. The only other HeLo protein to which a function has been associated is LopB from L. maculans [3]. Although its specific role in L. maculans is unknown, LopB- mutants have impaired ability to form lesions on oilseed rape. The HeLo domain is not related to the HET domain (PF06985) which is another domain involved in heterokaryon incompatibility.

Literature references

  1. Greenwald J, Buhtz C, Ritter C, Kwiatkowski W, Choe S, Maddelein ML, Ness F, Cescau S, Soragni A, Leitz D, Saupe SJ, Riek R;, Mol Cell. 2010;38:889-899.: The mechanism of prion inhibition by HET-S. PUBMED:20620958 EPMC:20620958

  2. Balguerie A, Dos Reis S, Ritter C, Chaignepain S, Coulary-Salin B, Forge V, Bathany K, Lascu I, Schmitter JM, Riek R, Saupe SJ;, EMBO J. 2003;22:2071-2081.: Domain organization and structure-function relationship of the HET-s prion protein of Podospora anserina. PUBMED:12727874 EPMC:12727874

  3. Fedorova ND, Badger JH, Robson GD, Wortman JR, Nierman WC;, BMC Genomics. 2005;6:177.: Comparative analysis of programmed cell death pathways in filamentous fungi. PUBMED:16336669 EPMC:16336669


External database links

This tab holds annotation information from the InterPro database.

No InterPro data for this Pfam family.

Domain organisation

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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.

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(65)
Full
(227)
Representative proteomes NCBI
(232)
Meta
(0)
RP15
(27)
RP35
(88)
RP55
(173)
RP75
(198)
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  Seed
(65)
Full
(227)
Representative proteomes NCBI
(232)
Meta
(0)
RP15
(27)
RP35
(88)
RP55
(173)
RP75
(198)
Alignment:
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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.

  Seed
(65)
Full
(227)
Representative proteomes NCBI
(232)
Meta
(0)
RP15
(27)
RP35
(88)
RP55
(173)
RP75
(198)
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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.

HMM logo

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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.

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Curation and family details

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Curation View help on the curation process

This family is new in this Pfam release.

Seed source: Pfam-B_407 (release 25.0)
Previous IDs: none
Type: Domain
Author: Greenwald J, Coggill P
Number in seed: 65
Number in full: 227
Average length of the domain: 189.70 aa
Average identity of full alignment: 16 %
Average coverage of the sequence by the domain: 32.69 %

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 23.2 23.0
Trusted cut-off 23.3 23.2
Noise cut-off 23.1 22.7
Model length: 212
Family (HMM) version: 1
Download: download the raw HMM for this family

Species distribution

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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 HeLo domain has been found. There are 5 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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