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3  structures 304  species 0  interactions 2667  sequences 46  architectures

Family: Neuralized (PF07177)

Summary: Neuralized

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The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

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.

Neuralized Provide feedback

This family contains a conserved region approximately 60 residues long within eukaryotic neuralized and neuralized-like proteins. Neuralized belongs to a group of ubiquitin ligases and is required in a subset of Notch pathway-mediated cell fate decisions during development of the Drosophila nervous system [1]. Some family members contain multiple copies of this region.

Literature references

  1. Justice NJ, Jan YN; , Curr Opin Neurobiol 2002;12:64-70.: Variations on the Notch pathway in neural development. PUBMED:11861166 EPMC:11861166

  2. He F, Saito K, Kobayashi N, Harada T, Watanabe S, Kigawa T, Guntert P, Ohara O, Tanaka A, Unzai S, Muto Y, Yokoyama S;, J Mol Biol. 2009;393:478-495.: Structural and functional characterization of the NHR1 domain of the Drosophila neuralized E3 ligase in the notch signaling pathway. PUBMED:19683535 EPMC:19683535


Internal database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006573

The neuralized homology repeat (NHR) domain is a module of ~160 amino acids, which has been identified as a tandem repeat in drosophila neuralized, a protein involved in development of the central and peripheral nervous system [PUBMED:9519875]. Several other fly, worm, and mammalian neuralized-like proteins were found to contain between one and six NHR domains associated with other modules, such as RING, SOCS, or SPRY [PUBMED:11779830, PUBMED:11731489]. It has been suggested that the NHR domain is required for the localization of neuralized to the plasma membrane [PUBMED:11696324]. As it has been proposed that NHR domains do partly resemble SPRY domains, it is possible that NHR possess microtubule-binding functions, similar to those proposed for SPRY domains [PUBMED:11731489].

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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, 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
(141)
Full
(2667)
Representative proteomes UniProt
(4146)
NCBI
(7943)
Meta
(1)
RP15
(639)
RP35
(1174)
RP55
(1924)
RP75
(2314)
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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.

Format an alignment

  Seed
(141)
Full
(2667)
Representative proteomes UniProt
(4146)
NCBI
(7943)
Meta
(1)
RP15
(639)
RP35
(1174)
RP55
(1924)
RP75
(2314)
Alignment:
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Sequence:
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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
(141)
Full
(2667)
Representative proteomes UniProt
(4146)
NCBI
(7943)
Meta
(1)
RP15
(639)
RP35
(1174)
RP55
(1924)
RP75
(2314)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

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: Pfam-B_16611 (release 10.0)
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Vella Briffa B
Number in seed: 141
Number in full: 2667
Average length of the domain: 156.50 aa
Average identity of full alignment: 28 %
Average coverage of the sequence by the domain: 54.02 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 23.3 23.3
Trusted cut-off 23.3 23.5
Noise cut-off 22.9 23.0
Model length: 150
Family (HMM) version: 12
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 Neuralized domain has been found. There are 3 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 sequence.

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