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0  structures 133  species 0  interactions 293  sequences 2  architectures

Family: TF_Otx (PF03529)

Summary: Otx1 transcription factor

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Otx1 transcription factor Provide feedback

No Pfam abstract.

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR013851

Otx proteins constitute a class of vertebrate homeodomain-containing transcription factors that have been shown to be essential for anterior head formation, including brain morphogenesis. They are orthologous to the product of the Drosophila head gap gene, orthodenticle (Otd), and appear to play similar roles in both, since the developmental abnormalities caused by disruption of these transcription factors in one, can be recovered by substitution of the factor(s) from the other. Such studies have provided strong evidence that there exists a conserved genetic programme for insect and mammalian brain development, which presumably arose in a more primitive common ancestor [PUBMED:10199636, PUBMED:10440864].

Two vertebrate orthodenticle-related transcription factors have been indentified, Otx1 and Otx2, which have sizes of 355 and 289 residues respectively. They contain a bicoid-like homeodomain, which features a conserved lysine residue at position 9 of the DNA recognition helix, which is thought to confer high-affinity binding to TAATCC/T elements on DNA [PUBMED:10375352]. Otd-like transcription factors have also been found in zebrafish and certain lamprey species.

This entry represents a conserved region found in the C-terminal region of these proteins.

Gene Ontology

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

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.

  Seed
(22)
Full
(293)
Representative proteomes NCBI
(237)
Meta
(0)
RP15
(3)
RP35
(11)
RP55
(34)
RP75
(88)
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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
(22)
Full
(293)
Representative proteomes NCBI
(237)
Meta
(0)
RP15
(3)
RP35
(11)
RP55
(34)
RP75
(88)
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
(22)
Full
(293)
Representative proteomes NCBI
(237)
Meta
(0)
RP15
(3)
RP35
(11)
RP55
(34)
RP75
(88)
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: PRINTS
Previous IDs: none
Type: Family
Author: Griffiths-Jones SR
Number in seed: 22
Number in full: 293
Average length of the domain: 92.20 aa
Average identity of full alignment: 55 %
Average coverage of the sequence by the domain: 34.78 %

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 25.0 25.0
Trusted cut-off 27.1 27.1
Noise cut-off 22.3 21.6
Model length: 88
Family (HMM) version: 8
Download: download the raw HMM for this family

Species distribution

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