Summary

Homeobox domain

No Pfam abstract.

Literature references

Gehring WJ; , Trends Biochem Sci 1992;17:277-280.: The homeobox in perspective. PUBMED:1357790

InterPro entry IPR001356

The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates PUBMED:2568852, PUBMED:1357790, PUBMED:. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies PUBMED:12445403. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA PUBMED:. The first helix helps to stabilise the structure.

The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.

Clan

This family is a member of clan HTH (CL0123), which contains the following 141 members:

Arg_repressor B-block_TFIIIC Bac_DnaA_C BetR BrkDBD CENP-B_N Coprinus_mating Cro Crp DDRGK Dimerisation DUF1133 DUF1153 DUF1323 DUF134 DUF1441 DUF1492 DUF1495 DUF1670 DUF1804 DUF1836 DUF2089 DUF2250 DUF2316 DUF293 DUF3116 DUF387 DUF739 DUF742 DUF977 E2F_TDP ELK Ets Exc F-112 FaeA Fe_dep_repr_C Fe_dep_repress FeoC Ftsk_gamma FUR GcrA GerE GntR Homeobox Homez HSF_DNA-bind HTH_1 HTH_10 HTH_11 HTH_12 HTH_13 HTH_14 HTH_15 HTH_3 HTH_5 HTH_6 HTH_7 HTH_8 HTH_9 HTH_AraC HTH_CodY HTH_DeoR HTH_IclR HTH_Mga HTH_psq HTH_WhiA HxlR IF2_N Ins_element1 KorB LacI LexA_DNA_bind MarR Med9 MerR MerR-DNA-bind Mga Mnd1 Mor MotA_activ Mu_DNA_bind Myb_DNA-bind_2 Myb_DNA-binding NUMOD1 PaaX PadR PAX PCI PCI_Csn8 Pencillinase_R Phage_AlpA Phage_antitermQ Phage_CI_repr Phage_CII Phage_rep_org_N Phage_terminase Pou Pox_D5 PuR_N Put_DNA-bind_N Rap1-DNA-bind Rep_3 RepA_C RepA_N RepC RepL RFX_DNA_binding Rio2_N RNA_pol_Rpc34 RP-C RPA RPA_C RQC Rrf2 RTP SAC3_GANP Sigma54_CBD Sigma54_DBD Sigma70_ECF Sigma70_r2 Sigma70_r3 Sigma70_r4 Sigma70_r4_2 SpoIIID Sulfolobus_pRN TBPIP Tc3_transposase Terminase_5 TetR_N TFIIE_alpha Trans_reg_C Transposase_14 Transposase_5 Transposase_8 Transposase_Tc5 TrfA TrmB Trp_repressor UPF0122 z-alpha

Gene Ontology

Cellular component	nucleus (GO:0005634)
Molecular function	sequence-specific DNA binding (GO:0043565)
Molecular function	transcription factor activity (GO:0003700)
Biological process	regulation of transcription, DNA-dependent (GO:0006355)

External database links

HOMSTRAD:	hom
PANDIT:	PF00046
PRINTS:	PR00024
PROSITE:	PDOC00027 PDOC00032 PDOC00033
SCOP:	1ahd
SYSTERS:	Homeobox

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

There are various ways to view or download the sequence alignments that we store. You can use a sequence viewer to look at either the seed or full alignment for the family, or you can look at a plain text version of the sequence in a variety of different formats. More...

View options

Alignment:	Seed (186) Full (13439) NCBI (20424) Metagenomics (26)
Viewer:

Formatting options

Alignment:	Seed (186) Full (13439)
Format:
Order:	Tree Alphabetical
Sequence:	Inserts lower case All upper case
Gaps:
Download/view:	Download View

Download options

Very large alignments can often cause problems for the formatting tool above. If you find that downloading or viewing a large alignment is problematic, you can also download a gzip-compressed, Stockholm-format file containing the seed or full alignment for this family.

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

The main seed and full alignments are generated using sequences from the UniProt sequence database. However, we also generate alignments using sequences from the NCBI sequence database and the "metaseq" metagenomics dataset.

You can view alignments from these two additional datasets using the form above, or you can download alignments of NCBI or metagenomics sequences, as gzip-compressed files.

Pfam alignments:	Seed (186) Full (13439) NCBI (20424) Metagenomics (26)
Full length sequences	Full-sequences (13439)

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 HMMER2.

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. 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 or full alignments.

Note: You can also download the data files for the seed, full, NCBI or metagenomics trees.

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

Seed source:

Unknown

Previous IDs:

homeobox;

Type:

Domain

Author:

Eddy SR

Number in seed:

186

Number in full:

13439

Average length of the domain:

53.70 aa

Average identity of full alignment:

34 %

Average coverage of the sequence by the domain:

16.86 %

HMM information

HMM build commands:

build method: hmmbuild -o /dev/null HMM SEED

search method: hmmsearch -Z 9421015 -E 1000 HMM pfamseq

Model details:

Parameter	Sequence	Domain
Gathering cut-off	20.7	20.7
Trusted cut-off	20.7	20.7
Noise cut-off	20.6	20.6

Model length:

57

Family (HMM) version:

22

Download:

download the raw HMM for this family

Species distribution

Tree controls

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

Species trees

We show the species tree in one of two ways. For smaller trees we try to show an interactive representation, which allows you to select specific nodes in the tree and view them as an alignment or as a set of Pfam domain graphics.

Unfortunately we have found that there are problems viewing the interactive tree when the it becomes larger than a certain limit. Furthermore, we have found that Internet Explorer can become unresponsive when viewing some trees, regardless of their size. We therefore show a text representation of the species tree when the size is above a certain limit or if you are using Internet Explorer to view the site.

If you are using IE you can still load the interactive tree by clicking the "Generate interactive tree" button, but please be aware of the potential problems that the interactive species tree can cause.

Interactive tree

For all of the domain matches in a full alignment, we count the number that are found on all sequences in the alignment. This total is shown in the purple box.

We also count the number of unique sequences on which each domain is found, which is shown in green. Note that a domain may appear multiple times on the same sequence, leading to the difference between these two numbers.

Finally, we group sequences from the same organism according to the NCBI code that is assigned by UniProt, allowing us to count the number of distinct sequences on which the domain is found. This value is shown in the pink boxes.

We use the NCBI species tree to group organisms according to their taxonomy and this forms the structure of the displayed tree. Note that in some cases the trees are too large (have too many nodes) to allow us to build an interactive tree, but in most cases you can still view the tree in a plain text, non-interactive representation. Those species which are represented in the seed alignment for this domain are highlighted.

You can use the tree controls to manipulate how the interactive tree is displayed:

show/hide the summary boxes
highlight species that are represented in the seed alignment
expand/collapse the tree or expand it to a given depth
select a sub-tree or a set of species within the tree and view them graphically or as an alignment
save a plain text representation of the tree

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Interactions

There are 2 interactions for this family. More...

Pou Homeobox

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 MSD 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 Homeobox domain has been found.

Loading structure mapping...

Family: Homeobox (PF00046)

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