SII-SWORD/CoKE huggingface dataset:
FXYD domain-containing ion transport regulator 7 (FXYD7)
Type: Family

This entry represents FXYD domain-containing ion transport regulator 7 (FXYD7) and similar proteins from vertebrates. FXYD7 has a potential splice variant with an additional 3 residues. In rats, expression of FXYD7 was restricted to the brain, with highest levels in the cerebrum, followed by brainstem, and hippocampus, and relatively weak expression in the hypothalamus. Immunofluorescence microscopy demonstrated colocalization with synaptophysin and modest colocalization with glial fibrillary acidic protein, indicating predominant expression in neurons and lower expression in astroglial cells .
SAGA-associated factor 29, second Tudor domain (Tudor_SGF29_rpt2)
Type: Domain

This entry represents the second Tudor domain of SGF29 and similar eukaryotic proteins.

SAGA-associated factor 29 (SGF29) is a chromatin reader and a component of the transcription regulatory histone acetylation (HAT) complexes SAGA and SLIK . In the SAGA complex, SGF29 binds histone H3 that has been methylated at Lys-4 (H3K4me), and preferably binds the trimethylated form (H3K4me3) . SGF29 also acts as a boundary, preventing the spread of heterochromatin into neighbouring genes . SGF29 contains two Tudor domains.
SAGA-associated factor 29, first Tudor domain (Tudor_SGF29_rpt1)
Type: Domain

This entry represents the first Tudor domain of SGF29 and similar eukaryotic proteins.

SAGA-associated factor 29 (SGF29) is a chromatin reader and a component of the transcription regulatory histone acetylation (HAT) complexes SAGA and SLIK . In the SAGA complex, SGF29 binds histone H3 that has been methylated at Lys-4 (H3K4me), and preferably binds the trimethylated form (H3K4me3) . SGF29 also acts as a boundary, preventing the spread of heterochromatin into neighbouring genes . SGF29 contains two Tudor domains.
Aprataxin, forkhead associated domain (FHA_APTX)
Type: Domain

This entry represents the forkhead associated (FHA) domain found at the N-terminal end of Aprataxin. The FHA domain is a small phosphopeptide recognition module.

Aprataxin (

/

) is a DNA-binding protein involved in single-strand DNA break repair, double-strand DNA break repair, and base excision repair . It catalyses the release of adenylate groups covalently linked to 5'-phosphate termini, resulting in the production of 5'-phosphate termini that can be efficiently rejoined. It can also hydrolyse adenosine 5'-monophosphoramidate (AMP-NH(2)) and diadenosine tetraphosphate (AppppA), but with lower catalytic activity. Likewise, it catalyses the release of 3'-linked guanosine (DNAppG) and inosine (DNAppI) from DNA but has higher specific activity with 5'-linked adenosine (AppDNA) . Mutations in the gene APTX have been associated with ataxia-ocular apraxia and with coenzyme 10 deficiency .
Nesprin-1-like, first calponin homology domain (CH_SYNE1_rpt1)
Type: Domain

This entry represents the first calponin homology (CH) domain of SYNE-1 and similar proteins predominantly found in vertebrates and arthropods. CH domains are actin filament (F-actin) binding motifs.

Nesprin-1, also called Synaptic nuclear envelope protein 1 (SYNE-1), is a multi-isomeric modular protein which forms a linking network between organelles and the actin cytoskeleton to maintain subcellular spatial organization. SYNE-1 also acts as a component of the LINC (LInker of Nucleoskeleton and Cytoskeleton) complex, which is involved in the connection between the nuclear lamina and the cytoskeleton. This protein is involved in the pathogenesis of Emery Dreifuss muscular dystrophy and lead to a type of autosomal recessive cerebellar ataxia. SYNE-1 contains two copies of the CH domain . The homologue from Drosophila melanogaster, named Muscle-specific protein 300 kDa, is also included in this group. It collaborates with Klar to promote even spacing of the myonuclei at the periphery of striated muscle fibres and is essential for anchoring nuclei, mitochondria and endoplasmic reticulum (ER) structures to the Z-disks .
Nesprin-1-like, second calponin homology domain (CH_SYNE1_rpt2)
Type: Domain

This entry represents the second calponin homology (CH) domain of SYNE-1 and similar proteins predominantly found in vertebrates and arthropodes. CH domains are actin filament (F-actin) binding motifs.

Nesprin-1, also called Synaptic nuclear envelope protein 1 (SYNE-1), is a multi-isomeric modular protein which forms a linking network between organelles and the actin cytoskeleton to maintain subcellular spatial organization. SYNE-1 also acts as a component of the LINC (LInker of Nucleoskeleton and Cytoskeleton) complex, which is involved in the connection between the nuclear lamina and the cytoskeleton. This protein is involved in the pathogenesis of Emery Dreifuss muscular dystrophy and lead to a type of autosomal recessive cerebellar ataxia. SYNE-1 contains two copies of the CH domain . The homologue from Drosophila melanogaster, named Muscle-specific protein 300 kDa, is also included in this group. It collaborates with Klar to promote even spacing of the myonuclei at the periphery of striated muscle fibres and is essential for anchoring nuclei, mitochondria and endoplasmic reticulum (ER) structures to the Z-disks .
DENN domain-containing protein 5B, second RUN domain (RUN2_DENND5B)
Type: Domain

This entry represents the second RUN domain of DENND5B and similar proteins from vertebrates.

This entry includes DENN domain-containing protein 5B (DENND5B, also called Rab6-interacting protein 1 (Rab6IP1)-like protein) which functions in membrane trafficking at a crossroads between the Golgi and the endosomal system . It is composed of an N-terminal DENN domain (

) followed by two RUN domains flanking a PLAT domain (

) .
DENN domain-containing protein 5B, first RUN domain (RUN1_DENND5B)
Type: Domain

This entry represents the first RUN domain of DENND5B and similar proteins from vertebrates.

This entry includes DENN domain-containing protein 5B (DENND5B, also called Rab6-interacting protein 1 (Rab6IP1)-like protein) which functions in membrane trafficking at a crossroads between the Golgi and the endosomal system . It is composed of an N-terminal DENN domain (

) followed by two RUN domains flanking a PLAT domain (

) .
DENN domain-containing protein 5A, first RUN domain (RUN1_DENND5A)
Type: Domain

This entry represents the first RUN domain of DENND5A and similar proteins from vertebrates. This domain is required for Rab6-dependent recruitment of DENND5A on Golgi membranes .

DENND5A, also called Rab6-interacting protein 1 (Rab6IP1), is present predominantly in developing neuronal tissue, and functions in membrane trafficking at a crossroads between the Golgi and the endosomal system. It is a guanine nucleotide exchange factor (GEFs) that binds Rab6 and Rab11A in their GTP-bound conformation . It is composed of an N-terminal DENN domain (

) followed by two RUN domains flanking a PLAT domain (

) .
DENN domain-containing protein 5A, second RUN domain (RUN2_DENND5A)
Type: Domain

This entry represents the second RUN domain of DENND5A and similar proteins from vertebrates.

DENND5A, also called Rab6-interacting protein 1 (Rab6IP1), is present predominantly in developing neuronal tissue, and functions in membrane trafficking at a crossroads between the Golgi and the endosomal system. It is a guanine nucleotide exchange factor (GEFs) that binds Rab6 and Rab11A in their GTP-bound conformation . It is composed of an N-terminal DENN domain (

) followed by two RUN domains flanking a PLAT domain (

) .
UvrC/Cho-like, GIY-YIG domain (GIY-YIG_UvrC_Cho)
Type: Domain

This entry represents the catalytic GIY-YIG domain localised at the N-terminal of nucleotide excision repair endonucleases UvrC, Cho (UvrC homologue) and similar proteins predominantly found in prokaryotes. This domain is also known as Uri domain and it is responsible for the 3' incision reaction.

UvrC is essential for nucleotide excision repair (NER). Besides UvrC, protein Cho serves as a second endonuclease in E. coli NER. Cho contains GIY-YIG motif followed by a Cys-rich region and shares sequence homology with the N-terminal half of UvrC. It is capable of incising the DNA at the 3' side of a lesion in the presence of the UvrA and UvrB proteins during NER. The C-terminal half of Cho is a unique uncharacterised domain, which is distinct from that of UvrC. Moreover, unlike UvrC, Cho does not require the UvrC-binding domain of UvrB for the 3' incision reaction, which might cause the shift in incision position and the difference in incision efficiencies between Cho and UvrC on different damaged substrates. Due to this, the range of NER in E. coli can be broadened by combining action of Cho and UvrC .
Ion-transport regulator, FXYD motif (FXYD_motif)
Type: Conserved_site

This entry represents the FXYD motif of a family of vertebrate small membrane proteins that are involved in the control of ion transport including Phospholemman (FXYD1) and FXYD domain-containing ion transport regulators FXYD2-8 . This motif contains 35 invariant and conserved amino acid residues . Except for FXYD5, all these proteins are very small and their size range from 58 residues for FXYD2 to 95 for FXYD6. FXYD5 is longer (178 residues) due to a N-terminal extension. They all contain a single transmembrane domain. With the exception of FXYD2, they all seem to have a N-terminal signal peptide.
Survival motor neuron protein, Tudor domain, eumetazoa (Tudor_SMN_eumet)
Type: Domain

This entry represents the central, highly conserved Tudor domain of SMN and similar animal proteins. This domain is required for U snRNP assembly and Sm protein binding and has been shown to bind arginine-glycine-rich motifs in an methylarginine-dependent manner .

Survival motor neuron protein (SMN) is part of a multimeric SMN complex that includes spliceosomal Sm core proteins and plays a catalyst role in the assembly of small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome. Mutations in human SMN lead to motor neuron degeneration and spinal muscular atrophy .
Dickkopf-related protein 4, second cysteine-rich domain (Dkk4_Cys2)
Type: Domain

This entry represents the second cysteine-rich (Cys-2) domain of Dkk4 and similar proteins from chordates. This domain is closely similar to those in the colipase family; it has been suggested that the Cys-2 domain of Dkks may enable interaction with lipids in order to regulate Wnt function .

Dickkopf 4 (Dkk4) is a secreted protein which directly binds to LRP5/6 (low-density lipoprotein receptor related protein 5 and 6), and is an inhibitor of Wnt/beta-catenin signalling. Dkk4, which is upregulated by the activated Wnt pathway, contributes to tumour malignancy in variable tumours, promoting tumour cell invasion and progression. Aberrant accumulation of Dkk4 has been shown to promote tumour progression by forming the immune suppressive microenvironment in gastrointestinal stromal tumour, and thus Dkk4 may be used as a tumour biomarker for prognosis prediction and recurrence monitoring. Dkk4 belongs to the Dickkopf (Dkk) family that comprises a discrete class of secreted Wnt inhibitors that are expressed in a variety of tissues and organs, and are required for many developmental processes, including segmentation, endoderm development, limb polarity, neural crest differentiation, kidney morphogenesis, sex determination and brain development. Dkks 1-4 each possesses an N-terminal signal peptide and contains two conserved cysteine-rich domains (Cys-1 and Cys-2) separated by a linker region. Each domain possesses 10 conserved cysteine residues. .
Dickkopf-related protein 3, second cysteine-rich domain (Dkk3_Cys2)
Type: Domain

This entry represents the second cysteine-rich (Cys-2) domain of Dkk3 and similar proteins from vertebrates. This domain is closely similar to those in the colipase family; it has been suggested that the Cys-2 domain of Dkks may enable interaction with lipids in order to regulate Wnt function .

Dickkopf 3 (Dkk3) is a secreted protein which, in contrast to Dkk1, Dkk2, and Dkk4, does not interact with LRP5/6 (low-density lipoprotein receptor related protein 5 and 6), and thus is a divergent family member that is not considered a true Wnt signalling antagonist. The role of Dkk proteins in cancer is considered mainly tumour suppressive since they are usually down-regulated in cancer cells. Dkk3 links heat shock factor 1 (HSF1) and YAP/TAZ signalling to control aggressive behaviours in cancer-associated fibroblasts; it does so via canonical Wnt signalling. Dkks 1-4 each possesses an N-terminal signal peptide and contains two conserved cysteine-rich domains (Cys-1 and Cys-2) separated by a linker region. Each domain possesses 10 conserved cysteine residues .
Dickkopf-related protein 3, N-terminal domain (Dkk3_N)
Type: Domain

This entry represents the N-terminal domain of Dkk3, which includes the Cys-1 domain and a region to its N-terminal that shows similarity to Dickkopf-like protein 1 (Dkkl1).

Dickkopf 3 (Dkk3) is a secreted protein which, in contrast to Dkk1, Dkk2, and Dkk4, does not interact with LRP5/6 (low-density lipoprotein receptor related protein 5 and 6), and thus is a divergent family member that is not considered a true Wnt signalling antagonist. The role of Dkk proteins in cancer is considered mainly tumour suppressive since they are usually down-regulated in cancer cells. Dkk3 links heat shock factor 1 (HSF1) and YAP/TAZ signalling to control aggressive behaviours in cancer-associated fibroblasts; it does so via canonical Wnt signalling. Dkks 1-4 each possesses an N-terminal signal peptide and contains two conserved cysteine-rich domains (Cys-1 and Cys-2) separated by a linker region. Each domain possesses 10 conserved cysteine residues .
Dickkopf-related protein 2, second cysteine-rich domain (Dkk2_Cys2)
Type: Domain

This entry represents the second cysteine-rich (Cys-2) domain of Dkk2 and similar proteins from vertebrates. This domain is closely similar to those in the colipase family; it has been suggested that the Cys-2 domain of Dkks may enable interaction with lipids in order to regulate Wnt function .

Dickkopf 2 (Dkk2) is a secreted protein which directly binds to LRP5/6 (low-density lipoprotein receptor related protein 5 and 6), and is an inhibitor of Wnt/beta-catenin signalling. Dkk2 expression is modulated by expression of micro RNA-221 (miRNA-221) in esophageal cancer, and inactivation of Dkk2 may increase Wnt activity with accelerating tumour progression. Dkk2 belongs to the Dickkopf (Dkk) family that comprises a discrete class of secreted Wnt inhibitors. The Wnt gene family is a large class of secreted proteins that are expressed in a variety of tissues and organs, and are required for many developmental processes, including segmentation, endoderm development, limb polarity, neural crest differentiation, kidney morphogenesis, sex determination and brain development. Dkks 1-4 each possesses an N-terminal signal peptide and contains two conserved cysteine-rich domains (Cys-1 and Cys-2) separated by a linker region. Each domain possesses 10 conserved cysteine residues .
Dickkopf-related protein 2, first cysteine-rich domain (Dkk2_Cys1)
Type: Domain

This entry represents the first cysteine-rich (Cys-1) domain of Dkk2 and similar proteins from vertebrates.

Dickkopf 2 (Dkk2) is a secreted protein which directly binds to LRP5/6 (low-density lipoprotein receptor related protein 5 and 6), and is an inhibitor of Wnt/beta-catenin signalling. Dkk2 expression is modulated by expression of micro RNA-221 (miRNA-221) in esophageal cancer, and inactivation of Dkk2 may increase Wnt activity with accelerating tumour progression. Dkk2 belongs to the Dickkopf (Dkk) family that comprises a discrete class of secreted Wnt inhibitors. The Wnt gene family is a large class of secreted proteins that are expressed in a variety of tissues and organs, and are required for many developmental processes, including segmentation, endoderm development, limb polarity, neural crest differentiation, kidney morphogenesis, sex determination and brain development. Dkks 1-4 each possesses an N-terminal signal peptide and contains two conserved cysteine-rich domains (Cys-1 and Cys-2) separated by a linker region. Each domain possesses 10 conserved cysteine residues .
Dickkopf-related protein 1, second cysteine-rich domain (Dkk1_Cys2)
Type: Domain

This entry represents the second cysteine-rich (Cys-2) domain of Dkk1 and similar proteins from vertebrates. This domain is closely similar to those in the colipase family; it has been suggested that the Cys-2 domain of Dkks may enable interaction with lipids in order to regulate Wnt function .

Dickkopf-1 (Dkk1) is a secreted protein which directly binds to LRP5/6 (low-density lipoprotein receptor related protein 5 and 6), and is an inhibitor of Wnt/beta-catenin signalling. Elevated expression of Dkk-1 may serve as a negative regulator for modulating the wnt/beta-catenin signal pathway. Dkk1 is expressed in various human cancers. It has been studied extensively in mouse models of multiple myeloma that results in osteolytic bone lesions. Studies show that Dkk1 levels in bone marrow plasma and serum inhibit the differentiation of osteoblast precursors. Dkk1 belongs to the Dickkopf (Dkk) family that comprises a discrete class of secreted Wnt inhibitors. The Wnt gene family is a large class of secreted proteins that are expressed in a variety of tissues and organs, and are required for many developmental processes, including segmentation, endoderm development, limb polarity, neural crest differentiation, kidney morphogenesis, sex determination and brain development. Dkks 1-4 each possesses an N-terminal signal peptide and contains two conserved cysteine-rich domains (Cys-1 and Cys-2) separated by a linker region. Each domain possesses 10 conserved cysteine residues .
Dickkopf-related protein 1, N-terminal domain (Dkk1_N)
Type: Domain

This entry represents the N-terminal domain of Dkk1, which includes the Cys-1 domain and a region to its N terminus that shows similarity to Dickkopf-like protein 1 (Dkkl1).

Dickkopf-1 (Dkk1) is a secreted protein which directly binds to LRP5/6 (low-density lipoprotein receptor related protein 5 and 6), and is an inhibitor of Wnt/beta-catenin signalling. Elevated expression of Dkk-1 may serve as a negative regulator for modulating the wnt/beta-catenin signal pathway. Dkk1 is expressed in various human cancers. It has been studied extensively in mouse models of multiple myeloma that results in osteolytic bone lesions. Studies show that Dkk1 levels in bone marrow plasma and serum inhibit the differentiation of osteoblast precursors. Dkk1 belongs to the Dickkopf (Dkk) family that comprises a discrete class of secreted Wnt inhibitors. The Wnt gene family is a large class of secreted proteins that are expressed in a variety of tissues and organs, and are required for many developmental processes, including segmentation, endoderm development, limb polarity, neural crest differentiation, kidney morphogenesis, sex determination and brain development. Dkks 1-4 each possesses an N-terminal signal peptide and contains two conserved cysteine-rich domains (Cys-1 and Cys-2) separated by a linker region. Each domain possesses 10 conserved cysteine residues .
RNA-dependent RNA polymerase, matonavirus (Matonaviridae_RdRp)
Type: Domain

This entry represents the catalytic core domain of the RNA-directed RNA polymerase p90 of RNA viruses belonging to the family Matonaviridae, which is cleaved from the C-terminal region of Non-structural polyprotein p200. Members of the family Matonaviridae have a (+)ssRNA genome enclosed by an icosahedral capsid . Matonaviridae has a single genus, Rubivirus, which contains three species: Rubivirus rubella (commonly called rubella virus), Rubivirus ruteetense (commonly called ruhugu virus), and Rubivirus strelense (commonly called rustrela virus). Rubella virus (RuV) is the etiologic agent of the disease rubella (also called German measles). RuV is transmitted only between humans via the respiratory route, and is the main cause of congenital rubella syndrome (severe congenital birth defects, miscarriage, and stillbirth) when infection occurs during the first trimester of pregnancy . In vitro studies with cell lines showed that RuV has an apoptotic effect on certain cell types; there is evidence for a p53-dependent mechanism. The catalytic RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in the fidelity of processes such as correct incorporation and reorganization of nucleotides .
RNA-dependent RNA polymerase, hepevirus (Hepeviridae_RdRp)
Type: Domain

This entry represents the catalytic core domain or RNA-directed RNA polymerase (RdRp) domain of Non-structural polyprotein pORF1 of RNA viruses belonging to the family Hepeviridae. The family Hepeviridae includes enterically transmitted small non-enveloped (+)ssRNA viruses . It includes the genera Piscihepevirus, whose members infect fish, and Orthohepevirus, whose members infect mammals and birds. Members of latter include hepatitis E virus , which is responsible for self-limiting acute hepatitis in humans and several mammalian species; the infection may become chronic in immunocompromised individuals. Avian hepatitis E virus causes hepatitis-splenomegaly syndrome in chickens. Hepeviridae genomes (approximately 7.2 kb) have 5' methyl G caps and 3' poly (A) tails, and contain three ORFS. They have two mRNAs, a genome length and a subgenomic mRNA: the genome-length mRNA is translated to produce proteins required for RNA replication while the subgenomic mRNA is used to produce the capsid protein. Some of the capsid protein is glycosylated, which is an unusual finding for an unenveloped virus .

This domain displays a right hand with three functional subdomains, called fingers, palm, and thumb and contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains . All these motifs have been implicated in the fidelity on processes of correct incorporation and reorganization of nucleotides.
RNA-dependent RNA polymerase, closterovirus (Closteroviridae_RdRp)
Type: Domain

This entry represents the catalytic domain RdRp of the RNA-directed RNA polymerase (RdRp) of RNA viruses belonging to the family Closteroviridae, order Martellivirales, which is cleaved from Replicase polyprotein 1ab . Viruses in the family Closteroviridae have a mono-, bi- or tripartite (+)ssRNA genome of 13-19 kb, and non-enveloped, filamentous particles 650-2200 nm long and 12 nm in diameter . They infect plants, mainly dicots, many of which are fruit crops . Members of the family are classified into four genera: Ampelovirus, Closterovirus, Crinivirus and Velarivirus. Their genetic diversity is primarily influenced by strong negative selection and recombination. Closteroviridae viruses are mostly phloem-restricted and induce specific cytoplasmic aggregates of virus particles intermingled with membranous vesicles derived from the endoplasmic reticulum and possibly mitochondria. Their transmission is by aphids, whiteflies, pseudococcid mealybugs or soft scale insects in a semi-persistent manner. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. It contains conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in the fidelity of processes such as correct incorporation and reorganization of nucleotides .