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0  structures 76  species 0  interactions 133  sequences 4  architectures

Family: Maelstrom (PF13017)

Summary: piRNA pathway germ-plasm component

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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.

piRNA pathway germ-plasm component Provide feedback

Maelstrom is a germ-plasm component protein, that is shown to be functionally involved in the piRNA pathway. It is conserved throughout Eukaryota, though it appears to have been lost from all examined teleost fish species. The domain architecture shows that it is coupled with several DNA- and RNA- related domains such as HMG box, SR-25-like and HDAC_interact domains. Sequence analysis and fold recognition have found a distant similarity between Maelstrom domain and the DnaQ 3'-5' exonuclease family with the RNase H fold (Exonuc_X-T, PF00929); notably, that the Maelstrom domains from basal eukaryotes contain the conserved 3'-5' exonuclease active site residues (Asp-Glu-Asp-His-Asp, DEDHD). However, the animal and some amoeba maelstrom contain another set of conserved residues (Glu-His-His-Cys-His-Cys, EHHCHC). This evolutionary link together with structural examinations leads to the hypothesis that Maelstrom domains may have a potential nuclease-transposase activity or RNA-binding ability that may be implicated in piRNA biogenesis. A protein function evolution mode, namely "active site switch", has been proposed [1] in which the amoeba Maelstrom domains are the possible evolutionary intermediates due to their harbouring of the specific characteristics of both 3'-5' exonuclease and Maelstrom domains.

Literature references

  1. Zhang D, Xiong H, Shan J, Xia X, Trudeau VL;, Biol Direct. 2008;3:48.: Functional insight into Maelstrom in the germline piRNA pathway: a unique domain homologous to the DnaQ-H 3'-5' exonuclease, its lineage-specific expansion/loss and evolutionarily active site switch. PUBMED:19032786 EPMC:19032786


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR024970

Maelstrom is a germ-plasm component protein that is involved in the piRNA pathway, though its precise function is not known. This protein contains a novel domain, known as the Maelstrom domain, which adopts the RNaseH fold. It has been suggested that Maelstrom domains have nuclease-transposase activity or RNA-binding ability that could be involved in piRNA biogenesis [PUBMED:19032786].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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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.

  Seed
(27)
Full
(133)
Representative proteomes NCBI
(141)
Meta
(6)
RP15
(26)
RP35
(30)
RP55
(64)
RP75
(89)
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Format an alignment

  Seed
(27)
Full
(133)
Representative proteomes NCBI
(141)
Meta
(6)
RP15
(26)
RP35
(30)
RP55
(64)
RP75
(89)
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
(27)
Full
(133)
Representative proteomes NCBI
(141)
Meta
(6)
RP15
(26)
RP35
(30)
RP55
(64)
RP75
(89)
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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

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: Zhang D
Previous IDs: none
Type: Family
Author: Zhang D, Coggill P
Number in seed: 27
Number in full: 133
Average length of the domain: 189.70 aa
Average identity of full alignment: 29 %
Average coverage of the sequence by the domain: 46.12 %

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 18.9 18.9
Trusted cut-off 18.9 21.2
Noise cut-off 18.7 18.8
Model length: 214
Family (HMM) version: 1
Download: download the raw HMM for this family

Species distribution

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