The name of this superfamily has been modified since the most recent official CATH+ release (v4_2_0). At the point of the last release, this superfamily was named:

"
Helix-loop-helix DNA-binding domain
".

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 5563: 48 related 1, isoform B

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 14 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 GO:0003677
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
6 Q4ZHW1 (/ISS) Q64305 (/ISS) Q6UDE8 (/ISS) Q7RTS3 (/ISS) Q7ZSX3 (/ISS) Q9QX98 (/ISS)
DNA binding GO:0003677
Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
2 Q64305 (/IDA) Q9QX98 (/IDA)
RNA polymerase II distal enhancer sequence-specific DNA binding GO:0000980
Interacting selectively and non-covalently with a RNA polymerase II (Pol II) distal enhancer. In mammalian cells, enhancers are distal sequences that increase the utilization of some promoters, and can function in either orientation and in any location (upstream or downstream) relative to the core promoter.
1 Q64305 (/IDA)
RNA polymerase II distal enhancer sequence-specific DNA binding GO:0000980
Interacting selectively and non-covalently with a RNA polymerase II (Pol II) distal enhancer. In mammalian cells, enhancers are distal sequences that increase the utilization of some promoters, and can function in either orientation and in any location (upstream or downstream) relative to the core promoter.
1 Q9QX98 (/ISO)
Transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding GO:0001077
Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.
1 Q9QX98 (/IDA)
Chromatin binding GO:0003682
Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
1 Q9QX98 (/IDA)
Transcription factor activity, sequence-specific DNA binding GO:0003700
Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
1 Q7ZSX3 (/IGI)
Transcription factor activity, sequence-specific DNA binding GO:0003700
Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
1 Q7ZSX3 (/IPI)
Transcription factor activity, sequence-specific DNA binding GO:0003700
Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
1 Q64305 (/TAS)
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).
1 Q9QX98 (/IPI)
Transcription factor binding GO:0008134
Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
1 Q20561 (/IPI)
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 Q9QX98 (/IDA)
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 Q7ZSX3 (/IPI)
E-box binding GO:0070888
Interacting selectively and non-covalently with an E-box, a DNA motif with the consensus sequence CANNTG that is found in the promoters of a wide array of genes expressed in neurons, muscle and other tissues.
1 Q9QX98 (/IDA)

There are 47 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
Regulation of transcription, DNA-templated GO:0006355
Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
11 A0A0B4KFD8 (/ISS) A0A0B4LH77 (/ISS) A0A0B4LH78 (/ISS) A0A0B4LIA7 (/ISS) Q4ZHW1 (/ISS) Q6UDE8 (/ISS) Q7RTS3 (/ISS) Q7ZSX3 (/ISS) Q9QX98 (/ISS) Q9VEY3 (/ISS)
(1 more)
Response to oxidative stress GO:0006979
Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
5 A0A0B4LH77 (/IMP) A0A0B4LH78 (/IMP) A0A0B4LIA7 (/IMP) Q20561 (/IMP) Q9VEY3 (/IMP)
Tissue development GO:0009888
The process whose specific outcome is the progression of a tissue over time, from its formation to the mature structure.
5 Q4ZHW1 (/ISS) Q64305 (/ISS) Q6UDE8 (/ISS) Q7ZSX3 (/ISS) Q9QX98 (/ISS)
Exocrine pancreas development GO:0031017
The process whose specific outcome is the progression of the exocrine pancreas over time, from its formation to the mature structure. The exocrine pancreas produces and store zymogens of digestive enzymes, such as chymotrypsinogen and trypsinogen in the acinar cells.
5 Q4ZHW1 (/ISS) Q6UDE8 (/ISS) Q7RTS3 (/ISS) Q7ZSX3 (/ISS) Q9QX98 (/ISS)
Generation of neurons GO:0048699
The process in which nerve cells are generated. This includes the production of neuroblasts and their differentiation into neurons.
5 A0A0B4LH77 (/IMP) A0A0B4LH78 (/IMP) A0A0B4LIA7 (/IMP) Q9QX98 (/IMP) Q9VEY3 (/IMP)
Embryo development GO:0009790
The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.
4 Q4ZHW1 (/ISS) Q64305 (/ISS) Q6UDE8 (/ISS) Q7ZSX3 (/ISS)
Positive regulation of gene expression GO:0010628
Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
4 A0A0B4LH77 (/IMP) A0A0B4LH78 (/IMP) A0A0B4LIA7 (/IMP) Q9VEY3 (/IMP)
Regulation of glucose metabolic process GO:0010906
Any process that modulates the rate, frequency or extent of glucose metabolism. Glucose metabolic processes are the chemical reactions and pathways involving glucose, the aldohexose gluco-hexose.
4 A0A0B4LH77 (/IMP) A0A0B4LH78 (/IMP) A0A0B4LIA7 (/IMP) Q9VEY3 (/IMP)
Hindbrain development GO:0030902
The process whose specific outcome is the progression of the hindbrain over time, from its formation to the mature structure. The hindbrain is the posterior of the three primary divisions of the developing chordate brain, or the corresponding part of the adult brain (in vertebrates, includes the cerebellum, pons, and medulla oblongata and controls the autonomic functions and equilibrium).
4 Q4ZHW1 (/ISS) Q64305 (/ISS) Q6UDE8 (/ISS) Q7ZSX3 (/ISS)
Locomotor rhythm GO:0045475
The rhythm of the locomotor activity of an organism during its 24 hour activity cycle.
4 A0A0B4LH77 (/IMP) A0A0B4LH78 (/IMP) A0A0B4LIA7 (/IMP) Q9VEY3 (/IMP)
Positive regulation of transcription, DNA-templated GO:0045893
Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
4 Q4ZHW1 (/ISS) Q64305 (/ISS) Q6UDE8 (/ISS) Q7ZSX3 (/ISS)
Retinoic acid receptor signaling pathway GO:0048384
The series of molecular signals generated as a consequence of a retinoic acid receptor binding to one of its physiological ligands.
4 Q4ZHW1 (/ISS) Q64305 (/ISS) Q6UDE8 (/ISS) Q7ZSX3 (/ISS)
Generation of neurons GO:0048699
The process in which nerve cells are generated. This includes the production of neuroblasts and their differentiation into neurons.
4 Q4ZHW1 (/ISS) Q64305 (/ISS) Q6UDE8 (/ISS) Q7ZSX3 (/ISS)
Negative regulation of oxidative stress-induced neuron death GO:1903204
Any process that stops, prevents or reduces the frequency, rate or extent of oxidative stress-induced neuron death.
4 A0A0B4LH77 (/IMP) A0A0B4LH78 (/IMP) A0A0B4LIA7 (/IMP) Q9VEY3 (/IMP)
Pancreas development GO:0031016
The process whose specific outcome is the progression of the pancreas over time, from its formation to the mature structure. The pancreas is an endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes.
3 Q7RTS3 (/IMP) Q7ZSX3 (/IMP) Q9QX98 (/IMP)
Regulation of transcription, DNA-templated GO:0006355
Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
2 Q64305 (/IDA) Q9QX98 (/IDA)
Retina layer formation GO:0010842
The process in which the vertebrate retina is organized into three laminae: the outer nuclear layer (ONL), which contains photoreceptor nuclei; the inner nuclear layer (INL), which contains amacrine, bipolar and horizontal cells; and the retinal ganglion cell (RGC) layer. Between the inner and outer nuclear layers, the outer plexiform layer (OPL) contains connections between the photoreceptors and bipolar and horizontal cells. The inner plexiform layer (IPL) is positioned between the INL and the ganglion cell layer and contains the dendrites of RGCs and processes of bipolar and amacrine cells. Spanning all layers of the retina are the radially oriented Mueller glia.
2 Q64305 (/ISS) Q7RTS3 (/ISS)
Cerebellum development GO:0021549
The process whose specific outcome is the progression of the cerebellum over time, from its formation to the mature structure. The cerebellum is the portion of the brain in the back of the head between the cerebrum and the pons. In mice, the cerebellum controls balance for walking and standing, modulates the force and range of movement and is involved in the learning of motor skills.
2 Q7RTS3 (/IMP) Q9QX98 (/IMP)
Cell differentiation GO:0030154
The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
2 Q7ZSX3 (/IMP) Q9QX98 (/IMP)
Amacrine cell differentiation GO:0035881
The process in which a relatively unspecialized cell acquires specialized features of an amacrine cell, an interneuron generated in the inner nuclear layer (INL) of the vertebrate retina. Amacrine cells integrate, modulate, and interpose a temporal domain in the visual message presented to the retinal ganglion cells, with which they synapse in the inner plexiform layer. Amacrine cells lack large axons.
2 Q7ZSX3 (/IMP) Q9QX98 (/IMP)
Amacrine cell differentiation GO:0035881
The process in which a relatively unspecialized cell acquires specialized features of an amacrine cell, an interneuron generated in the inner nuclear layer (INL) of the vertebrate retina. Amacrine cells integrate, modulate, and interpose a temporal domain in the visual message presented to the retinal ganglion cells, with which they synapse in the inner plexiform layer. Amacrine cells lack large axons.
2 Q64305 (/ISS) Q7RTS3 (/ISS)
Regulation of neural retina development GO:0061074
Any process that modulates the rate, frequency, or extent of neural retina development, the progression of the neural retina over time from its initial formation to the mature structure. The neural retina is the part of the retina that contains neurons and photoreceptor cells.
2 Q64305 (/ISS) Q7RTS3 (/ISS)
Regulation of transcription, DNA-templated GO:0006355
Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
1 Q9QX98 (/IMP)
Insulin receptor signaling pathway GO:0008286
The series of molecular signals generated as a consequence of the insulin receptor binding to insulin.
1 Q20561 (/IDA)
Embryo development GO:0009790
The process whose specific outcome is the progression of an embryo from its formation until the end of its embryonic life stage. The end of the embryonic stage is organism-specific. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant.
1 Q9QX98 (/IDA)
Animal organ morphogenesis GO:0009887
Morphogenesis of an animal organ. An organ is defined as a tissue or set of tissues that work together to perform a specific function or functions. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
1 Q7ZSX3 (/IMP)
Tissue development GO:0009888
The process whose specific outcome is the progression of a tissue over time, from its formation to the mature structure.
1 Q7RTS3 (/IDA)
Tissue development GO:0009888
The process whose specific outcome is the progression of a tissue over time, from its formation to the mature structure.
1 Q9QX98 (/ISO)
Retina layer formation GO:0010842
The process in which the vertebrate retina is organized into three laminae: the outer nuclear layer (ONL), which contains photoreceptor nuclei; the inner nuclear layer (INL), which contains amacrine, bipolar and horizontal cells; and the retinal ganglion cell (RGC) layer. Between the inner and outer nuclear layers, the outer plexiform layer (OPL) contains connections between the photoreceptors and bipolar and horizontal cells. The inner plexiform layer (IPL) is positioned between the INL and the ganglion cell layer and contains the dendrites of RGCs and processes of bipolar and amacrine cells. Spanning all layers of the retina are the radially oriented Mueller glia.
1 Q9QX98 (/IMP)
Cerebellum development GO:0021549
The process whose specific outcome is the progression of the cerebellum over time, from its formation to the mature structure. The cerebellum is the portion of the brain in the back of the head between the cerebrum and the pons. In mice, the cerebellum controls balance for walking and standing, modulates the force and range of movement and is involved in the learning of motor skills.
1 Q9QX98 (/ISO)
Cerebellum development GO:0021549
The process whose specific outcome is the progression of the cerebellum over time, from its formation to the mature structure. The cerebellum is the portion of the brain in the back of the head between the cerebrum and the pons. In mice, the cerebellum controls balance for walking and standing, modulates the force and range of movement and is involved in the learning of motor skills.
1 Q64305 (/ISS)
Hindbrain development GO:0030902
The process whose specific outcome is the progression of the hindbrain over time, from its formation to the mature structure. The hindbrain is the posterior of the three primary divisions of the developing chordate brain, or the corresponding part of the adult brain (in vertebrates, includes the cerebellum, pons, and medulla oblongata and controls the autonomic functions and equilibrium).
1 Q9QX98 (/IDA)
Pancreas development GO:0031016
The process whose specific outcome is the progression of the pancreas over time, from its formation to the mature structure. The pancreas is an endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes.
1 Q9QX98 (/ISO)
Exocrine pancreas development GO:0031017
The process whose specific outcome is the progression of the exocrine pancreas over time, from its formation to the mature structure. The exocrine pancreas produces and store zymogens of digestive enzymes, such as chymotrypsinogen and trypsinogen in the acinar cells.
1 Q64305 (/IDA)
Exocrine pancreas development GO:0031017
The process whose specific outcome is the progression of the exocrine pancreas over time, from its formation to the mature structure. The exocrine pancreas produces and store zymogens of digestive enzymes, such as chymotrypsinogen and trypsinogen in the acinar cells.
1 Q7ZSX3 (/IMP)
Endocrine pancreas development GO:0031018
The process whose specific outcome is the progression of the endocrine pancreas over time, from its formation to the mature structure. The endocrine pancreas is made up of islet cells that produce insulin, glucagon and somatostatin.
1 Q9QX98 (/TAS)
Dauer exit GO:0043054
Exit from the facultative diapause of the dauer (enduring) larval stage of nematode development.
1 Q20561 (/IMP)
Cell fate commitment GO:0045165
The commitment of cells to specific cell fates and their capacity to differentiate into particular kinds of cells. Positional information is established through protein signals that emanate from a localized source within a cell (the initial one-cell zygote) or within a developmental field.
1 Q9QX98 (/IMP)
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 Q9QX98 (/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.
1 Q7ZSX3 (/IGI)
Positive regulation of transcription from RNA polymerase II promoter GO:0045944
Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
1 Q9QX98 (/IDA)
Positive regulation of transcription from RNA polymerase II promoter GO:0045944
Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
1 Q9QX98 (/IMP)
Retinoic acid receptor signaling pathway GO:0048384
The series of molecular signals generated as a consequence of a retinoic acid receptor binding to one of its physiological ligands.
1 Q9QX98 (/IDA)
Neuron fate commitment GO:0048663
The process in which the developmental fate of a cell becomes restricted such that it will develop into a neuron.
1 Q9QX98 (/IDA)
Generation of neurons GO:0048699
The process in which nerve cells are generated. This includes the production of neuroblasts and their differentiation into neurons.
1 Q9QX98 (/IDA)
Retina morphogenesis in camera-type eye GO:0060042
The process in which the anatomical structure of the retina is generated and organized.
1 Q9QX98 (/IMP)
Regulation of neural retina development GO:0061074
Any process that modulates the rate, frequency, or extent of neural retina development, the progression of the neural retina over time from its initial formation to the mature structure. The neural retina is the part of the retina that contains neurons and photoreceptor cells.
1 Q9QX98 (/IMP)

There are 12 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
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.
5 Q4ZHW1 (/ISS) Q6UDE8 (/ISS) Q7RTS3 (/ISS) Q7ZSX3 (/ISS) Q9QX98 (/ISS)
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.
5 Q4ZHW1 (/ISS) Q6UDE8 (/ISS) Q7RTS3 (/ISS) Q7ZSX3 (/ISS) Q9QX98 (/ISS)
Cytoplasm GO:0005737
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
5 Q4ZHW1 (/ISS) Q6UDE8 (/ISS) Q7RTS3 (/ISS) Q7ZSX3 (/ISS) Q9QX98 (/ISS)
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 Q20561 (/TAS) Q64305 (/TAS)
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.
2 Q64305 (/IDA) Q9QX98 (/IDA)
Intracellular GO:0005622
The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
1 Q9QX98 (/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.
1 Q9QX98 (/IC)
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.
1 Q64305 (/IDA)
Nucleoplasm GO:0005654
That part of the nuclear content other than the chromosomes or the nucleolus.
1 Q9QX98 (/TAS)
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 Q9QX98 (/TAS)
Cytoplasm GO:0005737
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
1 Q64305 (/IDA)
Cytosol GO:0005829
The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
1 Q9QX98 (/TAS)
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