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0  structures 135  species 0  interactions 2651  sequences 22  architectures

Family: POX (PF07526)

Summary: Associated with HOX

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.

Associated with HOX Provide feedback

The function of this domain is unknown [1]. It is often found in plant proteins associated with PF00046.

Literature references

  1. Doerks T, Copley RR, Schultz J, Ponting CP, Bork P; , Genome Res 2002;12:47-56.: Systematic identification of novel protein domain families associated with nuclear functions. PUBMED:11779830 EPMC:11779830


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006563

This domain in found exclusively in plant proteins, associated with homeobox domain INTERPRO which may suggest these proteins are homeodomain transcription factors. Proteins containing this domain include BEL1-like homeodomain protein 1 (BLH1) from Arabidopsis thaliana. BLH1 interacts with KNAT2 and KNAT5 [ PUBMED:17873098 ] and affects plant development [ PUBMED:20371112 ].

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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB 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
(105)
Full
(2651)
Representative proteomes UniProt
(3887)
RP15
(238)
RP35
(1380)
RP55
(2179)
RP75
(2909)
Jalview View  View  View  View  View  View  View 
HTML View  View           
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
(105)
Full
(2651)
Representative proteomes UniProt
(3887)
RP15
(238)
RP35
(1380)
RP55
(2179)
RP75
(2909)
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
(105)
Full
(2651)
Representative proteomes UniProt
(3887)
RP15
(238)
RP35
(1380)
RP55
(2179)
RP75
(2909)
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.

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: [1]
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Studholme DJ
Number in seed: 105
Number in full: 2651
Average length of the domain: 127.40 aa
Average identity of full alignment: 37 %
Average coverage of the sequence by the domain: 22.51 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 21.6 21.6
Trusted cut-off 21.7 22.1
Noise cut-off 21.4 21.5
Model length: 136
Family (HMM) version: 13
Download: download the raw HMM for this family

Species distribution

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Colour assignments

Archea Archea Eukaryota Eukaryota
Bacteria Bacteria Other sequences Other sequences
Viruses Viruses Unclassified Unclassified
Viroids Viroids Unclassified sequence Unclassified sequence

Selections

Align selected sequences to HMM

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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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Tree controls

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The tree shows the occurrence of this domain across different species. More...

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Please note: for large trees this can take some time. While the tree is loading, you can safely switch away from this tab but if you browse away from the family page entirely, the tree will not be loaded.

AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A096PXB1 View 3D Structure Click here
A0A0P0VTG7 View 3D Structure Click here
A0A0P0XZ22 View 3D Structure Click here
A0A0P0XZL7 View 3D Structure Click here
A0A0R0K2Y7 View 3D Structure Click here
A0A0R0KMH2 View 3D Structure Click here
A0A0R0KZM6 View 3D Structure Click here
A0A1D6DYM0 View 3D Structure Click here
A0A1D6EHV7 View 3D Structure Click here
A0A1D6FP22 View 3D Structure Click here
A0A1D6GKJ4 View 3D Structure Click here
A0A1D6H6M1 View 3D Structure Click here
A0A1D6JPR8 View 3D Structure Click here
A0A1D6K7I1 View 3D Structure Click here
A0A1D6KYQ9 View 3D Structure Click here
A0A1D6L365 View 3D Structure Click here
A0A1D6N753 View 3D Structure Click here
B4FBI0 View 3D Structure Click here
B4FS21 View 3D Structure Click here
B6SZ15 View 3D Structure Click here
C4IYV8 View 3D Structure Click here
C4J9N0 View 3D Structure Click here
I1J907 View 3D Structure Click here
I1JA88 View 3D Structure Click here
I1JGH7 View 3D Structure Click here
I1JQ89 View 3D Structure Click here
I1K6F5 View 3D Structure Click here
I1K7P2 View 3D Structure Click here
I1K7P3 View 3D Structure Click here
I1KPE2 View 3D Structure Click here
I1L9K6 View 3D Structure Click here
I1LGE2 View 3D Structure Click here
I1LTZ9 View 3D Structure Click here
I1M493 View 3D Structure Click here
I1M880 View 3D Structure Click here
I1MXZ4 View 3D Structure Click here
I1N2N9 View 3D Structure Click here
I1NAU4 View 3D Structure Click here
K7K312 View 3D Structure Click here
K7KHH8 View 3D Structure Click here
K7KHT4 View 3D Structure Click here
K7KI69 View 3D Structure Click here
K7KSE7 View 3D Structure Click here
K7KT71 View 3D Structure Click here
K7LNB7 View 3D Structure Click here
K7LQD5 View 3D Structure Click here
K7LTM0 View 3D Structure Click here
K7LTX2 View 3D Structure Click here
K7LVK3 View 3D Structure Click here
K7M356 View 3D Structure Click here
K7MHC0 View 3D Structure Click here
K7MNH9 View 3D Structure Click here
K7UPH8 View 3D Structure Click here
O65685 View 3D Structure Click here
P48731 View 3D Structure Click here
Q0DBI4 View 3D Structure Click here
Q0DF87 View 3D Structure Click here
Q10DD6 View 3D Structure Click here
Q10SF7 View 3D Structure Click here
Q1PFD1 View 3D Structure Click here
Q2QLM6 View 3D Structure Click here
Q2QXE1 View 3D Structure Click here
Q38897 View 3D Structure Click here
Q5KQP1 View 3D Structure Click here
Q60EM7 View 3D Structure Click here
Q6H6J2 View 3D Structure Click here
Q8LN25 View 3D Structure Click here
Q8S897 View 3D Structure Click here
Q941S9 View 3D Structure Click here
Q94KL5 View 3D Structure Click here
Q9AYD8 View 3D Structure Click here
Q9FWS9 View 3D Structure Click here
Q9FXG8 View 3D Structure Click here
Q9LZM8 View 3D Structure Click here
Q9SIW1 View 3D Structure Click here
Q9SJ56 View 3D Structure Click here
Q9SJJ3 View 3D Structure Click here
Q9SW80 View 3D Structure Click here

trRosetta Structure

The structural model below was generated by the Baker group with the trRosetta software using the Pfam UniProt multiple sequence alignment.

The InterPro website shows the contact map for the Pfam SEED alignment. Hovering or clicking on a contact position will highlight its connection to other residues in the alignment, as well as on the 3D structure.

Improved protein structure prediction using predicted inter-residue orientations. Jianyi Yang, Ivan Anishchenko, Hahnbeom Park, Zhenling Peng, Sergey Ovchinnikov, David Baker Proceedings of the National Academy of Sciences Jan 2020, 117 (3) 1496-1503; DOI: 10.1073/pnas.1914677117;