SII-SWORD/CoKE huggingface dataset:
Glycosyltransferase 13 (Glycosyltransferase_13)
Type: Family

The glycosyltransferase 13 family is responsible for the initiation of complex N-linked carbohydrate formation. Members of this family play a crucial role in the conversion of high-mannose N-glycans to hybrid and complex N-glycans. This enzymatic activity is essential for various biological processes, including proper protein folding and cellular signaling. In plants, such as Arabidopsis thaliana, the family member is also required for normal root growth and morphology, indicating a broader role in organismal development.
E2F-responsive SERTA domain-containing protein (E2F-SERTA_domain_protein)
Type: Family

This family of proteins includes coregulators that interact with E2F-responsive promoters, integrating signals from PHD- and bromodomain-containing transcription factors. They modulate the transcriptional activity of E2F1/TFDP1 complexes, influencing cell cycle progression and cellular proliferation. Members of this family can act as both coactivators and corepressors, affecting the expression of E2F-target genes. Additionally, some members are involved in the molecular regulation of hematopoietic stem cells and progenitor cell lineage commitment and differentiation. Certain proteins within this family also play a role in the regulation of fat storage by altering the expression of genes related to adipocyte lipolysis, thermogenesis, and oxidative metabolism.
GPI Anchor Biosynthesis Protein (GPI_Anchor_Biosynth)
Type: Family

This family of proteins is involved in the biosynthesis of glycosylphosphatidylinositol (GPI) anchors, which are glycolipid structures that anchor proteins to the cell membrane. Members of this family function as part of a complex that catalyzes the initial step of GPI biosynthesis, transferring N-acetylglucosamine from UDP-N-acetylglucosamine to phosphatidylinositol. This process is crucial for the proper localization and function of various cell surface proteins. In some organisms, these proteins also play a role in cell wall biosynthesis.
UPF0175 domain-containing protein (UPF0175_domain)
Type: Family

This family of proteins is characterized by a conserved domain of unknown function, denoted as UPF0175. The precise biological roles of these proteins remain to be elucidated. However, members of the UPF0175 family are found across a diverse range of organisms, suggesting a fundamental cellular role. The proteins may be involved in various cellular processes, but without specific experimental evidence, their exact functions are speculative. Further research, including experimental characterization, is required to determine the molecular functions and potential involvement in cellular pathways or structures.
Gamma-class Carbonic Anhydrase (Gamma-CA)
Type: Family

The gamma-class carbonic anhydrase family is involved in the reversible hydration of carbon dioxide, which is essential for photosynthetic carbon dioxide fixation in organisms that grow on acetate. Members of the family function as scaffold proteins for the assembly of beta-carboxysomes, structures that concentrate carbon dioxide for efficient fixation by RuBisCO. The family includes proteins that may support H(+)/CH(3)COO(-) symport mechanisms or convert CO(2) to HCO(3)(-), thus managing excess CO(2). Some members possess a carbonic anhydrase-like domain at the N-terminus and RuBisCO small subunit-like (SSUL) domains at the C-terminus, which bind and coalesce RuBisCO. The activity of these carbonic anhydrases is regulated by redox conditions and can be inhibited by certain agents. The family plays a crucial role in the formation and function of carboxysomes, impacting the photosynthetic efficiency and growth of the organisms.
Mitochondrial Rho GTPase/EF-hand domain-containing protein (Miro-EF-hand_domain)
Type: Family

This family of proteins includes mitochondrial Rho GTPases and EF-hand calcium-binding domain-containing proteins. The mitochondrial Rho GTPases are involved in the regulation of mitochondrial morphology, distribution, and development, playing crucial roles in cell division, gamete development, and pollen tube growth. They may also participate in calcium signaling during stress responses. The EF-hand calcium-binding domain-containing proteins are components of the EvC complex, which is essential for ciliary Hedgehog signaling and is necessary for the proper localization of the EVC2:EVC subcomplex at the base of primary cilia.
Nexin-Dynein Regulatory Complex Component (N-DRC_Component)
Type: Family

This family of proteins includes components of the nexin-dynein regulatory complex (N-DRC), which is crucial for ciliary and flagellar motility. They play a role in maintaining the alignment and integrity of the distal axoneme and regulate microtubule sliding in motile axonemes. Members of this family are characterized by belonging to the AAA ATPase family, with a specific subset forming the DRC11 subfamily, indicating a specialized function within the broader AAA ATPase family.
Sterile alpha motif domain-containing protein (SAM_domain-containing_protein)
Type: Family

This family of proteins includes members that are involved in important cellular signaling pathways. Specifically, one characterized member is essential for normal photoreceptor differentiation and is implicated in the epidermal growth factor receptor (EGFR) signaling cascade in the eye. It is believed to function in the activation of the Raf kinase, likely through cooperation with the connector enhancer of KSR (Cnk), which may involve the recruitment of an activating kinase. This suggests that other members of the family may also play roles in signal transduction processes, potentially through the mediation of protein-protein interactions facilitated by the sterile alpha motif (SAM) domain.
Golgi apparatus maintenance and PI4KB interaction protein (Golgi-PI4KB_interaction)
Type: Family

This family of proteins is involved in the structural maintenance of the Golgi apparatus by interacting with the protein giantin, which is crucial for protein transport between the endoplasmic reticulum and the Golgi. Members of this family are also implicated in hormone-induced steroid biosynthesis in Leydig cells. They play a role in recruiting and enhancing the activity of PI4KB at the Golgi membrane, thereby increasing the local concentration of its substrate. Additionally, some members are known to interact with viral proteins, suggesting a role in microbial infections by aiding in viral RNA replication.
Centrosome-associated contractile fiber protein (CACF_protein)
Type: Family

This family of proteins is involved in the structural integrity and dynamics of centrosome-associated contractile fibers. Members of this family interact with CETN2, a centrin protein, through specific binding regions that contain a conserved tryptophan residue at their C-terminal ends. This interaction is crucial for the proteins' function in the centrosome, suggesting a role in cell division and maintenance of the centrosome's architecture.
Glycerophosphoryl Diester Phosphodiesterase-Related (GDPD-Related)
Type: Family

This family of proteins is involved in the hydrolysis of lysoglycerophospholipids to generate lysophosphatidic acid (LPA) and corresponding amines. Members of this family exhibit lysophospholipase D activity, with a preference for substrates such as 1-O-alkyl-sn-glycero-3-phosphocholine, lysophosphatidylcholine, and N-acylethanolamine lysophospholipids. They play a role in the biosynthesis of bioactive N-acylethanolamines. These enzymes are regulated by divalent cations; magnesium and manganese can stimulate activity, while calcium can have an inhibitory effect, depending on the concentration. The presence of EDTA, a chelating agent, results in the loss of lysophospholipase D activity. These proteins do not possess glycerophosphodiester phosphodiesterase activity, as they are unable to hydrolyze glycerophosphoinositol or glycerophosphocholine.
GT106 glycosyltransferase (GT106_glycosyltransferase)
Type: Family

This family of proteins includes glycosyltransferases, specifically classified within the GT106 group. Members of this family are involved in the transfer of fucose residues to various substrates, a process that is critical for modifying the properties of proteins and other molecules. One characterized function within this family is the biosynthesis of pectic type-II arabinogalactans, which are complex polysaccharides that play a role in the structure and function of plant cell walls. The enzymatic activity of these proteins is essential for the proper modification of cell surface molecules and for the regulation of cell signaling pathways.
Peptidyl-prolyl cis-trans isomerase FKBP (PPIase_FKBP)
Type: Family

This family of proteins functions as peptidyl-prolyl cis-trans isomerases (PPIases) that catalyze the isomerization of proline imidic peptide bonds in oligopeptides, which is a rate-limiting step in protein folding. These enzymes are known to facilitate the proper folding of proteins during synthesis. Members of this family exhibit a specificity for substrates that have proline or hydroxyproline residues, such as certain types of collagen. They are also subject to inhibition by immunosuppressive drugs like tacrolimus, also known as FK506.
Krueppel-type C2H2 zinc-finger (Krueppel_C2H2_Zn-finger)
Type: Family

This family of proteins includes members that are likely to play a role in the regulation of gene expression. Each member contains C2H2-type zinc-finger motifs, which are commonly found in transcription factors. These motifs facilitate DNA binding, allowing the proteins to interact with specific gene promoter regions and influence the transcription of genes. The exact regulatory functions may vary among family members and could be context-dependent, involving complex interactions with other molecular components in the cell.
Mitochondrial Fe-S cluster assembly factor (Mt_Fe-S_assembly_factor)
Type: Family

This family of proteins functions as mitochondrial iron-sulfur (Fe-S) cluster assembly factors. They are involved in the insertion of [4Fe-4S] clusters into a subset of mitochondrial proteins, such as lipoyl synthase and succinate dehydrogenase. These proteins operate in the final step of the Fe-S protein assembly process, facilitating the incorporation of the iron-sulfur cluster into the target proteins. They are likely to act in conjunction with NFU1 and function downstream of other assembly factors like BOL1 and GRX5. The family's role is crucial for the proper functioning of mitochondrial proteins that require Fe-S clusters for their enzymatic activities.
Diphthamide biosynthesis and chaperone domain-containing protein (Diphthamide-biosynth_chaperone)
Type: Family

This family of proteins is involved in diverse cellular processes, including post-translational modification and molecular chaperoning. One member is essential for diphthamide biosynthesis, a unique modification of histidine in elongation factor 2, which is crucial for accurate protein synthesis. Another member functions as a molecular chaperone, contributing to the structural organization of cellular compartments and playing a role in plant development. These proteins may also have metal-binding capabilities, with a domain that can bind zinc or iron ions.
Inner Nuclear Membrane ESCRT-Associated Protein (INM_ESCRT-Associated)
Type: Family

This family of proteins is associated with the inner nuclear membrane and plays a crucial role in nuclear structure organization, maintenance of nuclear envelope integrity, and nuclear envelope reformation after mitosis. Members of this family function as transmembrane adapters for the ESCRT machinery, facilitating ESCRT-mediated nuclear envelope closure during anaphase. They are involved in the organization of heterochromatin at the nuclear envelope and help maintain its structure under mechanical stress. These proteins are essential for embryonic development, cardiac homeostasis, and proper heart function. They also participate in various signaling pathways, including MAPK and AKT, and are required for myoblast differentiation through ERK signaling regulation. Additionally, they have roles in chromosome segregation, anchoring chromosome arms at the nuclear periphery, and contributing to the closure of nuclear envelope holes post-mitosis.
Chordin-like dorsalizing regulators (Chordin-like_regulators)
Type: Family

This family of proteins includes dorsalizing factors that play a crucial role in early vertebrate embryogenesis. They are involved in the regulation of developmental processes by binding to and sequestering TGF-beta family bone morphogenetic proteins (BMPs), which are known as ventralizing factors. By forming latent complexes with BMPs, these proteins control the balance between dorsal and ventral cell fates during embryonic tissue development. Additionally, some members of this family have been implicated in the patterning of the dorsal-ventral axis and in the development of various structures, such as the neuroectoderm and the amnioserosa in invertebrates. They can exhibit both agonistic and antagonistic activities towards BMP signaling, which is essential for proper tissue and organ formation.
EngB GTPase (EngB_GTPase)
Type: Family

The EngB GTPase family is part of the TRAFAC class TrmE-Era-EngA-EngB-Septin-like GTPase superfamily. Members of the EngB GTPase family, such as GTP-binding protein 8, are involved in various cellular processes due to their ability to bind and hydrolyze GTP. One of the family members is known to be a component of MIOREX complexes, which are large expressome-like assemblies of ribosomes that play a role in all steps of post-transcriptional gene expression. This suggests that the EngB GTPase family may be involved in the regulation of gene expression at the post-transcriptional level, potentially through interaction with ribosomal components and influencing translation or other aspects of RNA metabolism.
HEPACAM domain-containing protein (HEPACAM_domain)
Type: Family

This family of proteins is involved in various cellular processes including cell-matrix adhesion, cell motility, and cell proliferation. Some members play a crucial role during prometaphase of cell division by ensuring centrosome maturation, which is vital for proper chromosome segregation. They facilitate the translocation of scaffold proteins to the centrosomes, aiding in the formation of microtubules. Other members are implicated in the regulation of cell-matrix interactions and may act to suppress cell growth by inhibiting proliferation. The cytoplasmic domain of some proteins within this family is particularly significant in controlling adhesion and motility.
GRB2-associated and regulator of MAPK (GAREM)
Type: Family

The GAREM family consists of adapter proteins that play a crucial role in the intracellular signaling pathways initiated by the activation of the epidermal growth factor receptor (EGFR) on the cell surface or by cytoplasmic protein tyrosine kinases. Members of this family are involved in promoting the activation of the MAPK/ERK signaling pathway, which is a key route in transmitting signals from the cell surface to the nucleus, leading to cell proliferation. The GAREM proteins may serve as a bridge between EGFR and the MAPK/ERK pathway, thereby influencing cellular responses such as growth and division.
Starch-active lytic polysaccharide monooxygenase (Starch-active_LPMO)
Type: Family

This family of proteins includes enzymes known as lytic polysaccharide monooxygenases (LPMOs) that are involved in the oxidative cleavage of polysaccharides. They are characterized by their ability to act on starch substrates by oxidizing the C1 position. These proteins typically contain a carbohydrate-binding module 20 (CBM20) domain, which is responsible for binding to starch, thereby facilitating the enzyme's activity on its substrate. The activity of these enzymes can be inhibited by compounds such as beta-cyclodextrin or amylose, which block access to the active site. While most members of this family are active on starch, there are variants within the family that are reported to be inactive on this substrate.
Genomic Stability and Neuronal Morphogenesis Regulator (GenomicStab_NeuMorph_Reg)
Type: Family

This family of proteins is involved in various cellular processes related to neurogenesis, neuronal morphology, and genomic stability. Members of this family contribute to the differentiation of oligodendrocytes and the morphogenesis of basket cells in the cortex during development. They play a role in the formation and maintenance of dendritic structures, including arborization and spine density, in cortical neurons. Additionally, these proteins are implicated in the negative regulation of neurite outgrowth. They are key participants in the homologous recombination repair pathway, essential for the resolution of DNA double-strand breaks and the recovery of stalled replication forks. Through interactions with proteins such as PARP1 and MRE11, they facilitate DNA end resection during replication fork recovery, thereby maintaining genomic integrity and preventing telomere dysfunction.
Collagen-modifying leprecan protein (Collagen_mod_leprecan)
Type: Family

This family of proteins is involved in the post-translational modification of collagen, specifically in the hydroxylation of prolyl and lysine residues within collagen alpha chains. These modifications are crucial for the proper assembly and cross-linking of collagen fibrils, which are essential for maintaining the structural integrity of various connective tissues. Members of this family are part of a complex that includes enzymes such as PLOD1, P3H3, and P3H4, and are necessary for normal bone density and skin stability.
Nuclear exosome targeting complex subunit (NEXT_complex_subunit)
Type: Family

This family of proteins includes RNA-binding subunits of the nuclear exosome targeting (NEXT) complex, which functions as an RNA exosome cofactor. They are involved in the surveillance and turnover of a subset of non-coding short-lived RNAs, including aberrant transcripts. These proteins bind preferentially to polyuridine sequences and are associated with newly synthesized RNAs such as pre-mRNAs, promoter upstream transcripts (PROMPTs), enhancer RNAs (eRNAs), and extended products from small nuclear RNAs (snRNAs). They play roles in biological processes like DNA damage response and stress response, with some members participating in the regulation of alternative splicing during neuron and germ cell differentiation. The RNA recognition motif (RRM) domain is key for RNA binding and interaction with non-coding RNAs.
Wnt/beta-catenin signaling inhibitor (Wnt_signaling_inhibitor)
Type: Family

This family of proteins may act as inhibitors of the Wnt/beta-catenin signaling pathway. They are thought to achieve this by indirectly interacting with the receptor LRP6, thereby blocking the internalization of Wnt3a-dependent LRP6. This interaction is crucial for the regulation of cell growth, proliferation, and differentiation processes that are governed by Wnt signaling. The proteins in this family are characterized by the presence of a leucine-rich repeat N-terminal (LRRNT) cap and at least one leucine-rich repeat (LRR) domain at the C-terminus, which are essential for their function in inhibiting the Wnt pathway.
Non-homologous end-joining factor (NHEJ_factor)
Type: Family

This family of proteins is involved in the DNA damage response, specifically in the repair of double-strand breaks (DSBs) through the non-homologous end joining (NHEJ) pathway. Members of this family play a crucial role in maintaining genomic stability by facilitating the ligation of DSBs, which can arise from various sources such as ionizing radiation, reactive oxygen species, or during V(D)J recombination. These proteins are characterized by their ability to form complexes with other NHEJ components, such as XRCC4, and to bridge broken DNA ends, effectively acting as a scaffold to hold the DNA fragments in proximity for repair. They are also known to interact with DNA polymerase lambda and the Ku heterodimer, which are essential for the processing of non-cohesive or mismatched DNA ends. The family is conserved across different species, indicating its fundamental role in cellular survival and the preservation of genetic information.
Glycosyl Hydrolase 45 Enzymes (GH45_Enzymes)
Type: Family

This family of proteins includes enzymes that catalyze the endohydrolysis of 1,4-beta-glucosidic linkages in various substrates such as cellulose, lichenin, and cereal beta-D-glucans. Members of this family are characterized by their ability to break down complex carbohydrates into simpler sugars, with a preference for barley beta-glucan and carboxymethylcellulose. The enzymatic activity results in the production of oligosaccharides of varying lengths, including cellobiose, cellotriose, and cellotetraose. These enzymes do not act on crystalline cellulose or shorter oligosaccharides like cellobiose or cellotriose. The activity of these enzymes is generally not affected by metal ions, with the exception of Mn(2+), which can reduce the activity. This family is part of the glycosyl hydrolase 45 group, which is implicated in the degradation of cell wall components in plants and microorganisms.
Calcyclin-binding ubiquitin ligase bridge (Calcyclin-binding_UBL-bridge)
Type: Family

This family of proteins is implicated in calcium-dependent processes that lead to the ubiquitination and proteasomal degradation of various target proteins. They are thought to act as molecular bridges within ubiquitin E3 complexes, facilitating the transfer of ubiquitin from E2 enzymes to substrates. A key role of these proteins includes the regulation of beta-catenin levels through its ubiquitin-mediated degradation pathway, which is crucial for cell signaling and homeostasis.
Sphingolipid C9-methyltransferase (Sphingo_C9-MT)
Type: Family

This family of proteins catalyzes the methylation of the sphingoid base component of glucosylceramides at the C9-position. The specific activity involves the use of 4,8-desaturated ceramides as substrates. These enzymes play a pivotal role in the growth, differentiation, and pathogenicity of fungi. The addition of a methyl group at the C9-position of glucosylceramides is a distinctive feature of fungal sphingolipids, setting them apart from those found in plants and animals. This modification is thought to be significant in host-pathogen interactions, potentially aiding in the recognition of fungal invasion by the host and the triggering of defense responses. However, the C9-methylation is not essential for certain interactions, such as the sensitivity to specific plant defensins.
Glucose repression regulatory protein (Glucose_repression_reg)
Type: Family

This family of proteins is involved in various cellular processes including RNA processing and the regulation of glucose repression. Members of this family have been shown to interact with protein phosphatases and kinases, suggesting a role in signal transduction pathways that influence cell growth and metabolism. Some proteins within this family appear to have regulatory functions, potentially through direct or indirect modulation of kinase activity. The family includes proteins that are still uncharacterized, indicating a potential diversity of functions yet to be discovered.
Serine-Rich Repeat Protein (SRRP) (SRRP)
Type: Family

The Serine-Rich Repeat Protein (SRRP) family is characterized by its involvement in host-pathogen interactions, particularly in bacterial species. Members of the SRRP family are known to possess serine-rich regions that contribute to their function in mediating adhesion to host cell glycoproteins, such as human platelets and plasma proteins like fetuin-A and fibronectin. These interactions are crucial for bacterial colonization, biofilm formation, and virulence. The serine-rich domains, often containing inexact repeats, are essential for hemagglutination and binding to sialoglycoconjugates. Additionally, some family members may have roles in cell wall biosynthesis, as seen with beta-mannosyltransferase activity. The SRRP family proteins typically have a basic region that may facilitate self-association or binding to host cell lysates, further implicating their role in virulence and pathogenicity.