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:

"
Cysteine Rich Protein
".

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.
« Back to all FunFams

FunFam 16: LIM domain only 3

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 16 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
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).
111 M9PHX4 (/IPI) M9PI02 (/IPI) O77284 (/IPI) P25791 (/IPI) P25791 (/IPI) P25791 (/IPI) P25791 (/IPI) P25791 (/IPI) P25791 (/IPI) P25791 (/IPI)
(101 more)
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.
22 P25791 (/IDA) P25791 (/IDA) P25791 (/IDA) P25791 (/IDA) P25791 (/IDA) P25791 (/IDA) P25791 (/IDA) P25791 (/IDA) P25791 (/IDA) P25791 (/IDA)
(12 more)
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.
22 P25791 (/IDA) P25791 (/IDA) P25791 (/IDA) P25791 (/IDA) P25791 (/IDA) P25791 (/IDA) P25791 (/IDA) P25791 (/IDA) P25791 (/IDA) P25791 (/IDA)
(12 more)
RNA polymerase II activating transcription factor binding GO:0001102
Interacting selectively and non-covalently with an RNA polymerase II transcription activating factor, a protein involved in positive regulation of transcription.
22 P25791 (/IPI) P25791 (/IPI) P25791 (/IPI) P25791 (/IPI) P25791 (/IPI) P25791 (/IPI) P25791 (/IPI) P25791 (/IPI) P25791 (/IPI) P25791 (/IPI)
(12 more)
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.
22 P25791 (/IDA) P25791 (/IDA) P25791 (/IDA) P25791 (/IDA) P25791 (/IDA) P25791 (/IDA) P25791 (/IDA) P25791 (/IDA) P25791 (/IDA) P25791 (/IDA)
(12 more)
BHLH transcription factor binding GO:0043425
Interacting selectively and non-covalently with any of the basic Helix-Loop-Helix (bHLH) superfamily of transcription factors, important regulatory components in transcriptional networks of many developmental pathways.
22 P25791 (/IPI) P25791 (/IPI) P25791 (/IPI) P25791 (/IPI) P25791 (/IPI) P25791 (/IPI) P25791 (/IPI) P25791 (/IPI) P25791 (/IPI) P25791 (/IPI)
(12 more)
Cofactor binding GO:0048037
Interacting selectively and non-covalently with a cofactor, a substance that is required for the activity of an enzyme or other protein. Cofactors may be inorganic, such as the metal atoms zinc, iron, and copper in certain forms, or organic, in which case they are referred to as coenzymes. Cofactors may either be bound tightly to active sites or bind loosely with the substrate.
22 P25791 (/IPI) P25791 (/IPI) P25791 (/IPI) P25791 (/IPI) P25791 (/IPI) P25791 (/IPI) P25791 (/IPI) P25791 (/IPI) P25791 (/IPI) P25791 (/IPI)
(12 more)
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.
22 P25791 (/IDA) P25791 (/IDA) P25791 (/IDA) P25791 (/IDA) P25791 (/IDA) P25791 (/IDA) P25791 (/IDA) P25791 (/IDA) P25791 (/IDA) P25791 (/IDA)
(12 more)
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.
3 P25801 (/ISO) P25801 (/ISO) P25801 (/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.
3 P25801 (/ISO) P25801 (/ISO) P25801 (/ISO)
RNA polymerase II activating transcription factor binding GO:0001102
Interacting selectively and non-covalently with an RNA polymerase II transcription activating factor, a protein involved in positive regulation of transcription.
3 P25801 (/ISO) P25801 (/ISO) P25801 (/ISO)
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.
3 P25801 (/ISO) P25801 (/ISO) P25801 (/ISO)
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.
3 P25801 (/IDA) P25801 (/IDA) P25801 (/IDA)
BHLH transcription factor binding GO:0043425
Interacting selectively and non-covalently with any of the basic Helix-Loop-Helix (bHLH) superfamily of transcription factors, important regulatory components in transcriptional networks of many developmental pathways.
3 P25801 (/ISO) P25801 (/ISO) P25801 (/ISO)
Cofactor binding GO:0048037
Interacting selectively and non-covalently with a cofactor, a substance that is required for the activity of an enzyme or other protein. Cofactors may be inorganic, such as the metal atoms zinc, iron, and copper in certain forms, or organic, in which case they are referred to as coenzymes. Cofactors may either be bound tightly to active sites or bind loosely with the substrate.
3 P25801 (/ISO) P25801 (/ISO) P25801 (/ISO)
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.
3 P25801 (/ISO) P25801 (/ISO) P25801 (/ISO)

There are 38 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 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.
79 A9ED84 (/IMP) A9ED84 (/IMP) A9ED84 (/IMP) A9ED84 (/IMP) A9ED84 (/IMP) A9ED84 (/IMP) A9ED84 (/IMP) A9ED84 (/IMP) A9ED84 (/IMP) A9ED84 (/IMP)
(69 more)
Regulation of hematopoietic stem cell differentiation GO:1902036
Any process that modulates the frequency, rate or extent of hematopoietic stem cell differentiation.
53 P25791 (/TAS) P25791 (/TAS) P25791 (/TAS) P25791 (/TAS) P25791 (/TAS) P25791 (/TAS) P25791 (/TAS) P25791 (/TAS) P25791 (/TAS) P25791 (/TAS)
(43 more)
Positive regulation of peroxisome proliferator activated receptor signaling pathway GO:0035360
Any process that activates or increases the frequency, rate or extent of the peroxisome proliferator activated receptor signaling pathway.
48 Q8TAP4 (/IDA) Q8TAP4 (/IDA) Q8TAP4 (/IDA) Q8TAP4 (/IDA) Q8TAP4 (/IDA) Q8TAP4 (/IDA) Q8TAP4 (/IDA) Q8TAP4 (/IDA) Q8TAP4 (/IDA) Q8TAP4 (/IDA)
(38 more)
Positive regulation of fat cell differentiation GO:0045600
Any process that activates or increases the frequency, rate or extent of adipocyte differentiation.
48 Q8TAP4 (/IMP) Q8TAP4 (/IMP) Q8TAP4 (/IMP) Q8TAP4 (/IMP) Q8TAP4 (/IMP) Q8TAP4 (/IMP) Q8TAP4 (/IMP) Q8TAP4 (/IMP) Q8TAP4 (/IMP) Q8TAP4 (/IMP)
(38 more)
Negative regulation of ERK1 and ERK2 cascade GO:0070373
Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
48 Q8TAP4 (/IDA) Q8TAP4 (/IDA) Q8TAP4 (/IDA) Q8TAP4 (/IDA) Q8TAP4 (/IDA) Q8TAP4 (/IDA) Q8TAP4 (/IDA) Q8TAP4 (/IDA) Q8TAP4 (/IDA) Q8TAP4 (/IDA)
(38 more)
Positive regulation of glucocorticoid receptor signaling pathway GO:2000324
Any process that activates or increases the frequency, rate or extent of glucocorticoid receptor signaling pathway.
48 Q8TAP4 (/IDA) Q8TAP4 (/IDA) Q8TAP4 (/IDA) Q8TAP4 (/IDA) Q8TAP4 (/IDA) Q8TAP4 (/IDA) Q8TAP4 (/IDA) Q8TAP4 (/IDA) Q8TAP4 (/IDA) Q8TAP4 (/IDA)
(38 more)
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).
22 P25791 (/TAS) P25791 (/TAS) P25791 (/TAS) P25791 (/TAS) P25791 (/TAS) P25791 (/TAS) P25791 (/TAS) P25791 (/TAS) P25791 (/TAS) P25791 (/TAS)
(12 more)
MRNA transcription by RNA polymerase II GO:0042789
The cellular synthesis of messenger RNA (mRNA) from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter.
22 P25791 (/IDA) P25791 (/IDA) P25791 (/IDA) P25791 (/IDA) P25791 (/IDA) P25791 (/IDA) P25791 (/IDA) P25791 (/IDA) P25791 (/IDA) P25791 (/IDA)
(12 more)
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.
22 P25791 (/IDA) P25791 (/IDA) P25791 (/IDA) P25791 (/IDA) P25791 (/IDA) P25791 (/IDA) P25791 (/IDA) P25791 (/IDA) P25791 (/IDA) P25791 (/IDA)
(12 more)
Cellular response to thyroid hormone stimulus GO:0097067
A change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a thyroid hormone stimulus.
22 P25791 (/IDA) P25791 (/IDA) P25791 (/IDA) P25791 (/IDA) P25791 (/IDA) P25791 (/IDA) P25791 (/IDA) P25791 (/IDA) P25791 (/IDA) P25791 (/IDA)
(12 more)
Imaginal disc-derived wing morphogenesis GO:0007476
The process in which the anatomical structures of the imaginal disc-derived wing are generated and organized. The wing is an appendage modified for flying.
5 M9PHX4 (/IGI) M9PI02 (/IGI) O77284 (/IGI) P91608 (/IGI) Q8IQX7 (/IGI)
Imaginal disc-derived wing morphogenesis GO:0007476
The process in which the anatomical structures of the imaginal disc-derived wing are generated and organized. The wing is an appendage modified for flying.
5 M9PHX4 (/IMP) M9PI02 (/IMP) O77284 (/IMP) P91608 (/IMP) Q8IQX7 (/IMP)
Reproductive process GO:0022414
A biological process that directly contributes to the process of producing new individuals by one or two organisms. The new individuals inherit some proportion of their genetic material from the parent or parents.
5 M9PHX4 (/IMP) M9PI02 (/IMP) O77284 (/IMP) P91608 (/IMP) Q8IQX7 (/IMP)
Chaeta development GO:0022416
The process whose specific outcome is the progression of a chaeta over time, from its formation to the mature structure. A chaeta is a sensory multicellular cuticular outgrowth of a specifically differentiated cell.
5 M9PHX4 (/IMP) M9PI02 (/IMP) O77284 (/IMP) P91608 (/IMP) Q8IQX7 (/IMP)
Leg disc development GO:0035218
Progression of the leg imaginal disc over time, from its initial formation through to its metamorphosis to form adult structures including the leg, coxa and ventral thoracic pleura.
5 M9PHX4 (/IMP) M9PI02 (/IMP) O77284 (/IMP) P91608 (/IMP) Q8IQX7 (/IMP)
Gastric emptying GO:0035483
The process in which the liquid and liquid-suspended solid contents of the stomach exit through the pylorus into the duodenum.
5 M9PHX4 (/IMP) M9PI02 (/IMP) O77284 (/IMP) P91608 (/IMP) Q8IQX7 (/IMP)
Imaginal disc-derived leg segmentation GO:0036011
Division of an imaginal disc-derived leg into a series of semi-repetitive parts or segments. The Drosophila leg, for example, has nine segments, each separated from the next by a flexible joint.
5 M9PHX4 (/IMP) M9PI02 (/IMP) O77284 (/IMP) P91608 (/IMP) Q8IQX7 (/IMP)
Response to cocaine GO:0042220
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 a cocaine stimulus. Cocaine is a crystalline alkaloid obtained from the leaves of the coca plant.
5 M9PHX4 (/IMP) M9PI02 (/IMP) O77284 (/IMP) P91608 (/IMP) Q8IQX7 (/IMP)
Locomotor rhythm GO:0045475
The rhythm of the locomotor activity of an organism during its 24 hour activity cycle.
5 M9PHX4 (/IMP) M9PI02 (/IMP) O77284 (/IMP) P91608 (/IMP) Q8IQX7 (/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.
5 M9PHX4 (/IMP) M9PI02 (/IMP) O77284 (/IMP) P91608 (/IMP) Q8IQX7 (/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.
5 P25801 (/IGI) P25801 (/IGI) P25801 (/IGI) Q924W9 (/IGI) Q924W9 (/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.
5 P25801 (/ISO) P25801 (/ISO) P25801 (/ISO) Q924W9 (/ISO) Q924W9 (/ISO)
Erythrocyte differentiation GO:0030218
The process in which a myeloid precursor cell acquires specializes features of an erythrocyte.
3 Q90XH3 (/IGI) Q90XH3 (/IGI) Q9PTJ3 (/IGI)
Embryonic hemopoiesis GO:0035162
The stages of blood cell formation that take place within the embryo.
3 P25801 (/IGI) P25801 (/IGI) P25801 (/IGI)
MRNA transcription by RNA polymerase II GO:0042789
The cellular synthesis of messenger RNA (mRNA) from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter.
3 P25801 (/ISO) P25801 (/ISO) P25801 (/ISO)
Negative regulation of erythrocyte differentiation GO:0045647
Any process that stops, prevents, or reduces the frequency, rate or extent of erythrocyte differentiation.
3 P25801 (/IMP) P25801 (/IMP) P25801 (/IMP)
Cellular response to thyroid hormone stimulus GO:0097067
A change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a thyroid hormone stimulus.
3 P25801 (/ISO) P25801 (/ISO) P25801 (/ISO)
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.
2 Q924W9 (/IGI) Q924W9 (/IGI)
Regulation of T cell homeostatic proliferation GO:0046013
Any process that modulates the frequency, rate or extent of resting T cell proliferation.
2 Q924W9 (/IDA) Q924W9 (/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.
1 A9ED79 (/IMP)
Blood vessel development GO:0001568
The process whose specific outcome is the progression of a blood vessel over time, from its formation to the mature structure. The blood vessel is the vasculature carrying blood.
1 Q9PTJ3 (/IMP)
Endothelial cell proliferation GO:0001935
The multiplication or reproduction of endothelial cells, resulting in the expansion of a cell population. Endothelial cells are thin flattened cells which line the inside surfaces of body cavities, blood vessels, and lymph vessels, making up the endothelium.
1 Q9PTJ3 (/IMP)
Hemopoiesis GO:0030097
The process whose specific outcome is the progression of the myeloid and lymphoid derived organ/tissue systems of the blood and other parts of the body over time, from formation to the mature structure. The site of hemopoiesis is variable during development, but occurs primarily in bone marrow or kidney in many adult vertebrates.
1 Q9PTJ3 (/IMP)
Erythrocyte differentiation GO:0030218
The process in which a myeloid precursor cell acquires specializes features of an erythrocyte.
1 Q5M8V8 (/ISS)
Fin regeneration GO:0031101
The regrowth of fin tissue following its loss or destruction.
1 Q9PTJ3 (/IMP)
Embryonic hemopoiesis GO:0035162
The stages of blood cell formation that take place within the embryo.
1 Q9PTJ3 (/IMP)
Erythrocyte development GO:0048821
The process whose specific outcome is the progression of an erythrocyte over time, from its formation to the mature structure.
1 Q9PTJ3 (/IMP)
Retinal blood vessel morphogenesis GO:0061304
The process whose specific outcome is the progression of a blood vessel of the retina over time, from its formation to the mature structure.
1 Q9PTJ3 (/IMP)

There are 9 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.
74 P25800 (/ISS) P25800 (/ISS) P25800 (/ISS) P25800 (/ISS) P25800 (/ISS) P25800 (/ISS) P25800 (/ISS) P25800 (/ISS) P25800 (/ISS) P25800 (/ISS)
(64 more)
Nucleoplasm GO:0005654
That part of the nuclear content other than the chromosomes or the nucleolus.
53 P25791 (/TAS) P25791 (/TAS) P25791 (/TAS) P25791 (/TAS) P25791 (/TAS) P25791 (/TAS) P25791 (/TAS) P25791 (/TAS) P25791 (/TAS) P25791 (/TAS)
(43 more)
Cytoplasm GO:0005737
All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
48 Q8TAP4 (/IDA) Q8TAP4 (/IDA) Q8TAP4 (/IDA) Q8TAP4 (/IDA) Q8TAP4 (/IDA) Q8TAP4 (/IDA) Q8TAP4 (/IDA) Q8TAP4 (/IDA) Q8TAP4 (/IDA) Q8TAP4 (/IDA)
(38 more)
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.
22 P25791 (/IDA) P25791 (/IDA) P25791 (/IDA) P25791 (/IDA) P25791 (/IDA) P25791 (/IDA) P25791 (/IDA) P25791 (/IDA) P25791 (/IDA) P25791 (/IDA)
(12 more)
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 P25801 (/IDA) P25801 (/IDA) P25801 (/IDA) Q924W9 (/IDA) Q924W9 (/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.
5 M9PHX4 (/NAS) M9PI02 (/NAS) O77284 (/NAS) P91608 (/NAS) Q8IQX7 (/NAS)
Protein-containing complex GO:0032991
A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together.
4 Q5M8V8 (/ISS) Q90XH3 (/ISS) Q90XH3 (/ISS) Q9PTJ3 (/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.
3 P25801 (/ISO) P25801 (/ISO) P25801 (/ISO)
Protein-containing complex GO:0032991
A stable assembly of two or more macromolecules, i.e. proteins, nucleic acids, carbohydrates or lipids, in which at least one component is a protein and the constituent parts function together.
3 P25801 (/IPI) P25801 (/IPI) P25801 (/IPI)
CATH-Gene3D is a Global Biodata Core Resource Learn more...