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0  structures 401  species 0  interactions 1033  sequences 39  architectures

Family: QLQ (PF08880)

Summary: QLQ

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

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.

QLQ Provide feedback

The QLQ domain is named after the conserved Gln, Leu, Gln motif. The QLQ domain is found at the N-terminus of SWI2/SNF2 protein, which has been shown to be involved in protein-protein interactions. This domain has thus been postulated to be involved in mediating protein interactions [1].

Literature references

  1. Kim JH, Choi D, Kende H; , Plant J. 2003;36:94-104.: The AtGRF family of putative transcription factors is involved in leaf and cotyledon growth in Arabidopsis. PUBMED:12974814 EPMC:12974814


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR014978

The QLQ domain is characterised by the conserved Gln-Leu-Gln residues. Another feature of this domain is the absolute conservation of bulky aromatic/hydrophobic and acidic amino acid residues such as Phe, Trp, Tyr, Leu, Glu, or their equivalents in terms of chemical and radial properties. The Pro residue is also absolutely conserved. These amino acid residues are critical for the function of the QLQ domain, probably for protein-protein interaction [PUBMED:12974814].

Some proteins known to conatin a QLQ domain are listed below:

  • Plant GROWTH-REGULATING FACTOR (GRF) proteins, putative transcription factors.
  • Eukaryotic SWI2/SNF2, transcriptional coactivators.
  • 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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    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...

    View options

    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
    (134)
    Full
    (1033)
    Representative proteomes NCBI
    (1419)
    Meta
    (0)
    RP15
    (92)
    RP35
    (331)
    RP55
    (497)
    RP75
    (580)
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    1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

    Format an alignment

      Seed
    (134)
    Full
    (1033)
    Representative proteomes NCBI
    (1419)
    Meta
    (0)
    RP15
    (92)
    RP35
    (331)
    RP55
    (497)
    RP75
    (580)
    Alignment:
    Format:
    Order:
    Sequence:
    Gaps:
    Download/view:

    Download options

    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
    (134)
    Full
    (1033)
    Representative proteomes NCBI
    (1419)
    Meta
    (0)
    RP15
    (92)
    RP35
    (331)
    RP55
    (497)
    RP75
    (580)
    Raw Stockholm Download   Download   Download   Download   Download   Download   Download    
    Gzipped 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.

    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: Manual
    Previous IDs: none
    Type: Domain
    Author: Riano D, Finn RD
    Number in seed: 134
    Number in full: 1033
    Average length of the domain: 34.70 aa
    Average identity of full alignment: 40 %
    Average coverage of the sequence by the domain: 3.54 %

    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 23.8 23.8
    Trusted cut-off 23.9 24.0
    Noise cut-off 23.6 23.7
    Model length: 35
    Family (HMM) version: 7
    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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