The name of this superfamily has been modified since the most recent official CATH+ release (v4_3_0). At the point of the last release, this superfamily was named:

"
Homeodomain-like
".

Functional Families

Overview of the Structural Clusters (SC) and Functional Families within this CATH Superfamily. Clusters with a representative structure are represented by a filled circle.
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FunFam 93: ALX homeobox protein 1

Please note: GO annotations are assigned to the full protein sequence rather than individual protein domains. Since a given protein can contain multiple domains, it is possible that some of the annotations below come from additional domains that occur in the same protein, but have been classified elsewhere in CATH.

There are 19 GO terms relating to "molecular function"

The search results have been sorted with the annotations that are found most frequently at the top of the list. The results can be filtered by typing text into the search box at the top of the table.
GO Term Annotations Evidence
DNA-binding transcription factor activity, RNA polymerase II-specific GO:0000981
A protein or a member of a complex that interacts selectively and non-covalently with a specific DNA sequence (sometimes referred to as a motif) within the regulatory region of a RNA polymerase II-transcribed gene to modulate transcription. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units.
7 O95076 (/ISA) O95076 (/ISA) Q15699 (/ISA) Q15699 (/ISA) Q15699 (/ISA) Q15699 (/ISA) Q15699 (/ISA)
DNA-binding transcription factor activity, RNA polymerase II-specific GO:0000981
A protein or a member of a complex that interacts selectively and non-covalently with a specific DNA sequence (sometimes referred to as a motif) within the regulatory region of a RNA polymerase II-transcribed gene to modulate transcription. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units.
7 O95076 (/ISM) O95076 (/ISM) Q15699 (/ISM) Q15699 (/ISM) Q15699 (/ISM) Q15699 (/ISM) Q15699 (/ISM)
DNA-binding transcription factor activity, RNA polymerase II-specific GO:0000981
A protein or a member of a complex that interacts selectively and non-covalently with a specific DNA sequence (sometimes referred to as a motif) within the regulatory region of a RNA polymerase II-transcribed gene to modulate transcription. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units.
7 O95076 (/NAS) O95076 (/NAS) Q15699 (/NAS) Q15699 (/NAS) Q15699 (/NAS) Q15699 (/NAS) Q15699 (/NAS)
RNA polymerase II regulatory region sequence-specific DNA binding GO:0000977
Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II.
6 Q15699 (/IDA) Q15699 (/IDA) Q15699 (/IDA) Q15699 (/IDA) Q15699 (/IDA) Q6RW14 (/IDA)
Protein binding GO:0005515
Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
6 Q15699 (/IPI) Q15699 (/IPI) Q15699 (/IPI) Q15699 (/IPI) Q15699 (/IPI) Q8C8B0 (/IPI)
DNA-binding transcription activator activity, RNA polymerase II-specific GO:0001228
A protein or a member of a complex that interacts selectively and non-covalently with a specific DNA sequence (sometimes referred to as a motif) within the regulatory region of a RNA polymerase II-transcribed gene to activate or increase transcription. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units.
5 Q15699 (/IDA) Q15699 (/IDA) Q15699 (/IDA) Q15699 (/IDA) Q15699 (/IDA)
DNA-binding transcription factor activity GO:0003700
A protein or a member of a complex that interacts selectively and non-covalently with a specific DNA sequence (sometimes referred to as a motif) within the regulatory region of a gene to modulate transcription. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units, and include bacterial operons.
5 Q15699 (/TAS) Q15699 (/TAS) Q15699 (/TAS) Q15699 (/TAS) Q15699 (/TAS)
Transcription corepressor activity GO:0003714
A protein or a member of a complex that interacts specifically and non-covalently with a DNA-bound DNA-binding transcription factor to repress the transcription of specific genes. Corepressors often act by altering chromatin structure and modifications. For example, one class of transcription coregulators modifies chromatin structure through covalent modification of histones. A second ATP-dependent class modifies the conformation of chromatin. A third class occludes DNA-binding transcription factor protein-protein interaction domains. A fourth class of corepressors prevents interactions of DNA bound DNA-binding transcription factor with coactivators.
5 Q15699 (/TAS) Q15699 (/TAS) Q15699 (/TAS) Q15699 (/TAS) Q15699 (/TAS)
DNA-binding transcription factor activity GO:0003700
A protein or a member of a complex that interacts selectively and non-covalently with a specific DNA sequence (sometimes referred to as a motif) within the regulatory region of a gene to modulate transcription. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units, and include bacterial operons.
3 Q63087 (/IDA) Q63087 (/IDA) Q8C8B0 (/IDA)
DNA-binding transcription factor activity GO:0003700
A protein or a member of a complex that interacts selectively and non-covalently with a specific DNA sequence (sometimes referred to as a motif) within the regulatory region of a gene to modulate transcription. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units, and include bacterial operons.
3 O70137 (/ISO) O70137 (/ISO) Q8C8B0 (/ISO)
DNA binding GO:0003677
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
2 O70137 (/ISO) O70137 (/ISO)
DNA-binding transcription factor activity GO:0003700
A protein or a member of a complex that interacts selectively and non-covalently with a specific DNA sequence (sometimes referred to as a motif) within the regulatory region of a gene to modulate transcription. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units, and include bacterial operons.
2 Q63087 (/IMP) Q63087 (/IMP)
Protein homodimerization activity GO:0042803
Interacting selectively and non-covalently with an identical protein to form a homodimer.
2 Q63087 (/IDA) Q63087 (/IDA)
RNA polymerase II regulatory region sequence-specific DNA binding GO:0000977
Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II.
1 Q8C8B0 (/ISO)
DNA-binding transcription factor activity, RNA polymerase II-specific GO:0000981
A protein or a member of a complex that interacts selectively and non-covalently with a specific DNA sequence (sometimes referred to as a motif) within the regulatory region of a RNA polymerase II-transcribed gene to modulate transcription. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units.
1 Q6RW14 (/IDA)
DNA-binding transcription activator activity, RNA polymerase II-specific GO:0001228
A protein or a member of a complex that interacts selectively and non-covalently with a specific DNA sequence (sometimes referred to as a motif) within the regulatory region of a RNA polymerase II-transcribed gene to activate or increase transcription. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units.
1 Q8C8B0 (/ISO)
Protein homodimerization activity GO:0042803
Interacting selectively and non-covalently with an identical protein to form a homodimer.
1 Q8C8B0 (/ISO)
Sequence-specific DNA binding GO:0043565
Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
1 Q8C8B0 (/IDA)
Protein heterodimerization activity GO:0046982
Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
1 Q8C8B0 (/IPI)

There are 31 GO terms relating to "biological process"

The search results have been sorted with the annotations that are found most frequently at the top of the list. The results can be filtered by typing text into the search box at the top of the table.
GO Term Annotations Evidence
Positive regulation of transcription, DNA-templated GO:0045893
Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
7 Q15699 (/IDA) Q15699 (/IDA) Q15699 (/IDA) Q15699 (/IDA) Q15699 (/IDA) Q63087 (/IDA) Q63087 (/IDA)
Positive regulation of transcription, DNA-templated GO:0045893
Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
7 Q15699 (/IMP) Q15699 (/IMP) Q15699 (/IMP) Q15699 (/IMP) Q15699 (/IMP) Q63087 (/IMP) Q63087 (/IMP)
Positive regulation of transcription by RNA polymerase II GO:0045944
Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
6 Q15699 (/IDA) Q15699 (/IDA) Q15699 (/IDA) Q15699 (/IDA) Q15699 (/IDA) Q8C8B0 (/IDA)
Negative regulation of transcription by RNA polymerase II GO:0000122
Any process that stops, prevents, or reduces the frequency, rate or extent of transcription mediated by RNA polymerase II.
5 Q15699 (/IDA) Q15699 (/IDA) Q15699 (/IDA) Q15699 (/IDA) Q15699 (/IDA)
Cartilage condensation GO:0001502
The condensation of mesenchymal cells that have been committed to differentiate into chondrocytes.
5 Q15699 (/TAS) Q15699 (/TAS) Q15699 (/TAS) Q15699 (/TAS) Q15699 (/TAS)
Transcription by RNA polymerase II GO:0006366
The synthesis of RNA from a DNA template by RNA polymerase II (RNAP II), originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
5 Q15699 (/TAS) Q15699 (/TAS) Q15699 (/TAS) Q15699 (/TAS) Q15699 (/TAS)
Multicellular organism development GO:0007275
The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
5 Q15699 (/TAS) Q15699 (/TAS) Q15699 (/TAS) Q15699 (/TAS) Q15699 (/TAS)
Positive regulation of epithelial to mesenchymal transition GO:0010718
Any process that increases the rate, frequency, or extent of epithelial to mesenchymal transition. Epithelial to mesenchymal transition is where an epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell.
5 Q15699 (/IMP) Q15699 (/IMP) Q15699 (/IMP) Q15699 (/IMP) Q15699 (/IMP)
Positive regulation of epithelial to mesenchymal transition GO:0010718
Any process that increases the rate, frequency, or extent of epithelial to mesenchymal transition. Epithelial to mesenchymal transition is where an epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell.
5 Q1LVQ7 (/ISS) Q63087 (/ISS) Q63087 (/ISS) Q8C8B0 (/ISS) Q91574 (/ISS)
Positive regulation of transcription, DNA-templated GO:0045893
Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
5 Q1LVQ7 (/ISS) Q63087 (/ISS) Q63087 (/ISS) Q8C8B0 (/ISS) Q91574 (/ISS)
Embryonic skeletal system morphogenesis GO:0048704
The process in which the anatomical structures of the skeleton are generated and organized during the embryonic phase.
3 O70137 (/IGI) O70137 (/IGI) Q8C8B0 (/IGI)
Skeletal system development GO:0001501
The process whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton).
2 Q63087 (/TAS) Q63087 (/TAS)
Regulation of transcription, DNA-templated GO:0006355
Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
2 O70137 (/ISO) O70137 (/ISO)
Pattern specification process GO:0007389
Any developmental process that results in the creation of defined areas or spaces within an organism to which cells respond and eventually are instructed to differentiate.
2 O70137 (/IGI) O70137 (/IGI)
Embryonic forelimb morphogenesis GO:0035115
The process, occurring in the embryo, by which the anatomical structures of the forelimb are generated and organized. The forelimbs are the front limbs of an animal, e.g. the arms of a human.
2 O70137 (/IGI) O70137 (/IGI)
Embryonic hindlimb morphogenesis GO:0035116
The process, occurring in the embryo, by which the anatomical structures of the hindlimbs are generated and organized. The hindlimbs are the posterior limbs of an animal.
2 O70137 (/IGI) O70137 (/IGI)
Regulation of apoptotic process GO:0042981
Any process that modulates the occurrence or rate of cell death by apoptotic process.
2 O70137 (/IGI) O70137 (/IGI)
Negative regulation of transcription by RNA polymerase II GO:0000122
Any process that stops, prevents, or reduces the frequency, rate or extent of transcription mediated by RNA polymerase II.
1 Q8C8B0 (/ISO)
Neural crest cell migration GO:0001755
The characteristic movement of cells from the dorsal ridge of the neural tube to a variety of locations in a vertebrate embryo.
1 Q1LVQ7 (/IMP)
Neural tube closure GO:0001843
The last step in the formation of the neural tube, where the paired neural folds are brought together and fuse at the dorsal midline.
1 Q8C8B0 (/IMP)
Regulation of transcription by RNA polymerase II GO:0006357
Any process that modulates the frequency, rate or extent of transcription mediated by RNA polymerase II.
1 Q6RW14 (/IDA)
Anterior/posterior pattern specification GO:0009952
The regionalization process in which specific areas of cell differentiation are determined along the anterior-posterior axis. The anterior-posterior axis is defined by a line that runs from the head or mouth of an organism to the tail or opposite end of the organism.
1 Q8C8B0 (/IGI)
Positive regulation of epithelial to mesenchymal transition GO:0010718
Any process that increases the rate, frequency, or extent of epithelial to mesenchymal transition. Epithelial to mesenchymal transition is where an epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell.
1 Q8C8B0 (/ISO)
Mesenchymal cell development GO:0014031
The process aimed at the progression of a mesenchymal cell over time, from initial commitment of the cell to its specific fate, to the fully functional differentiated cell.
1 Q8C8B0 (/IMP)
Embryonic limb morphogenesis GO:0030326
The process, occurring in the embryo, by which the anatomical structures of the limb are generated and organized. A limb is an appendage of an animal used for locomotion or grasping.
1 Q8C8B0 (/IGI)
Negative regulation of transcription, DNA-templated GO:0045892
Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
1 Q8C8B0 (/ISO)
Positive regulation of transcription, DNA-templated GO:0045893
Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
1 Q8C8B0 (/ISO)
Positive regulation of transcription by RNA polymerase II GO:0045944
Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
1 Q8C8B0 (/IGI)
Positive regulation of transcription by RNA polymerase II GO:0045944
Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
1 Q8C8B0 (/ISO)
Embryonic cranial skeleton morphogenesis GO:0048701
The process in which the anatomical structures of the cranial skeleton are generated and organized during the embryonic phase.
1 Q1LVQ7 (/IMP)
Roof of mouth development GO:0060021
The biological process whose specific outcome is the progression of the roof of the mouth from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure. The roof of the mouth is the partition that separates the nasal and oral cavities.
1 Q8C8B0 (/IGI)

There are 10 GO terms relating to "cellular component"

The search results have been sorted with the annotations that are found most frequently at the top of the list. The results can be filtered by typing text into the search box at the top of the table.
GO Term Annotations Evidence
Nucleoplasm GO:0005654
That part of the nuclear content other than the chromosomes or the nucleolus.
10 Q15699 (/IDA) Q15699 (/IDA) Q15699 (/IDA) Q15699 (/IDA) Q15699 (/IDA) V9HWA7 (/IDA) V9HWA7 (/IDA) V9HWA7 (/IDA) V9HWA7 (/IDA) V9HWA7 (/IDA)
Golgi apparatus GO:0005794
A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
10 Q15699 (/IDA) Q15699 (/IDA) Q15699 (/IDA) Q15699 (/IDA) Q15699 (/IDA) V9HWA7 (/IDA) V9HWA7 (/IDA) V9HWA7 (/IDA) V9HWA7 (/IDA) V9HWA7 (/IDA)
Nuclear body GO:0016604
Extra-nucleolar nuclear domains usually visualized by confocal microscopy and fluorescent antibodies to specific proteins.
10 Q15699 (/IDA) Q15699 (/IDA) Q15699 (/IDA) Q15699 (/IDA) Q15699 (/IDA) V9HWA7 (/IDA) V9HWA7 (/IDA) V9HWA7 (/IDA) V9HWA7 (/IDA) V9HWA7 (/IDA)
Nucleus GO:0005634
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
8 Q15699 (/IDA) Q15699 (/IDA) Q15699 (/IDA) Q15699 (/IDA) Q15699 (/IDA) Q63087 (/IDA) Q63087 (/IDA) Q8C8B0 (/IDA)
Nucleus GO:0005634
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
3 O70137 (/ISO) O70137 (/ISO) Q8C8B0 (/ISO)
Nucleus GO:0005634
A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
2 Q1LVQ7 (/ISS) Q91574 (/ISS)
Nucleoplasm GO:0005654
That part of the nuclear content other than the chromosomes or the nucleolus.
1 Q8C8B0 (/ISO)
Transcription factor complex GO:0005667
A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.
1 Q8C8B0 (/IDA)
Golgi apparatus GO:0005794
A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
1 Q8C8B0 (/ISO)
Nuclear body GO:0016604
Extra-nucleolar nuclear domains usually visualized by confocal microscopy and fluorescent antibodies to specific proteins.
1 Q8C8B0 (/ISO)