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16  structures 357  species 1  interaction 782  sequences 14  architectures

Family: NDT80_PhoG (PF05224)

Summary: NDT80 / PhoG like DNA-binding family

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NDT80 / PhoG like DNA-binding family Provide feedback

This family includes the DNA-binding region of NDT80 [1] as well as PhoG and its homologues. The family contains Q05534 or VIB-1. VIB-1 is thought to be a regulator of conidiation in Neurospora crassa and shares a region of similarity to PHOG, a possible phosphate nonrepressible acid phosphatase in Aspergillus nidulans. It has been found that vib-1 is not the structural gene for nonrepressible acid phosphatase, but rather may regulate nonrepressible acid phosphatase activity [2].

Literature references

  1. Montano SP, Pierce M, Cote ML, Vershon AK, Georgiadis MM; , Acta Crystallogr D Biol Crystallogr 2002;58:2127-2130.: Crystallographic studies of a novel DNA-binding domain from the yeast transcriptional activator Ndt80. PUBMED:12454476 EPMC:12454476

  2. Xiang Q, Glass NL; , Genetics 2002;162:89-101.: Identification of vib-1, a locus involved in vegetative incompatibility mediated by het-c in Neurospora crassa. PUBMED:12242225 EPMC:12242225

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR024061

The NDT80 DNA-binding domain is found in the following proteins, which might all be involved in sensing nutritional status [PUBMED:16464624]:

  • Yeast meiosis-specific transcription factor NDT80, the key transcription factor that ultimately allows the continuation of meiosis after the successful completion of recombination.
  • Emericella nidulans phoG (xprG), a transcriptional activator involved in the response to nutrient limitation.
  • Emericella nidulans putative uncharacterised protein AN6015.2.
  • Neurospora crassa transcription factor vib-1, involved in the control of heterokaryon incompatibility.
  • Neurospora crassa related to acid phosphatase NCU04729.
  • Neurospora crassa related to meiosis-specific protein NDT80 NCU09915.
The proteolytically resistant core NDT80 DNA-binding domain reveals a central beta-sandwich characteristic of an s-type Ig fold. The beta-sandwich contains a three-stranded sheet composed of strands a, b and e, packed against a four-stranded sheet composed of strands c', c, f and g. Each sheet of the beta-sandwich contains an additional beta-strand, as well as a variety of peripheral secondary structure elements. The NDT80 DNA-binding domain contains an N-terminal extension, which consists of a beta-hairpin and a loop [PUBMED:12411490].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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 P53-like (CL0073), which has the following description:

This clan contains a variety of DNA-binding domains that contain an immunoglobulin-like fold. It includes the DNA-binding domains of NF-kappaB, NFAT, p53, STAT-1, the T-domain and the Runt domain [1].

The clan contains the following 7 members:

CEP1-DNA_bind NDT80_PhoG P53 RHD_DNA_bind Runt STAT_bind T-box


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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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...


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: Wood V
Previous IDs: none
Type: Family
Author: Wood V, Bateman A, Glass NL, Moxon SJ
Number in seed: 16
Number in full: 782
Average length of the domain: 169.50 aa
Average identity of full alignment: 30 %
Average coverage of the sequence by the domain: 25.44 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 80369284 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 19.4 19.4
Trusted cut-off 19.6 19.8
Noise cut-off 18.2 19.3
Model length: 186
Family (HMM) version: 8
Download: download the raw HMM for this family

Species distribution

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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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There is 1 interaction for this family. More...



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 NDT80_PhoG domain has been found. There are 16 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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