SII-SWORD/CoKE huggingface dataset:
F-box motif-containing protein (F-box_motif)
Type: Family

This family of proteins is characterized by the presence of an F-box motif, which is typically involved in protein-protein interactions. Members of this family are known to play crucial roles in the ubiquitin-proteasome pathway. They function as part of the SCF (SKP1-CUL1-F-box protein) complex, acting as substrate-recognition components for the E3 ubiquitin ligases. By recognizing specific target proteins for ubiquitination, they facilitate the regulated degradation of these proteins, thus controlling various cellular processes such as cell cycle progression, signal transduction, and transcription.
CRAL-TRIO domain-containing protein (CRAL-TRIO_domain)
Type: Family

This family of proteins includes members that contain the CRAL-TRIO domain, which is known for binding small lipophilic molecules, such as retinal, phosphatidylinositols, and tocopherols. These proteins are involved in diverse cellular processes including membrane trafficking, lipid metabolism, and signal transduction pathways. The CRAL-TRIO domain facilitates the transfer of these molecules between different cellular compartments, contributing to the regulation of their availability and function within the cell. The specific roles of individual family members can vary widely depending on the organism and the cellular context.
Chloroplast PPR-containing protein (Chloroplast_PPR)
Type: Family

This family of proteins includes regulators involved in the post-transcriptional modification of chloroplast transcripts, particularly those related to the large subunit of RuBisCO, a key enzyme in the photosynthetic carbon fixation process. Members of this family are thought to play a role in either the processing or the stabilization of these transcripts, potentially serving as a protective barrier against exonucleolytic degradation. They are characterized by the presence of pentatricopeptide repeat (PPR) motifs, which are known to mediate specific RNA interactions.
RNA M5U Methyltransferase (RNA_M5U_MTase)
Type: Family

This family of proteins includes RNA methyltransferases that are characterized by their similarity to the class I-like SAM-binding methyltransferase superfamily. Members of this family are involved in the methylation of the 5th carbon of uridine residues in RNA molecules, a modification that can affect the stability, structure, and function of various RNA species, including tRNA, rRNA, and mRNA. The enzymatic activity of these proteins typically involves the use of S-adenosylmethionine (SAM) as a methyl group donor to catalyze the transfer of a methyl group to the target uridine residue, thereby generating S-adenosylhomocysteine (SAH) as a byproduct.
Folate-binding receptor-like (Folate-binding_rcpt-like)
Type: Family

This family of proteins is involved in the binding and transport of folic acid, a vital nutrient. Members are implicated in the uptake and accumulation of folic acid within cells, particularly in response to salicylic acid-induced signals. They may play a role in the distribution of folates, facilitating their movement from production sites, such as leaves, to areas of storage and use, including fruits, seeds, and roots. The function suggests a significant role in the plant's folate homeostasis and overall nutritional status.
Mitochondrial ATP-independent inner membrane protease (Mitochondrial_IM_protease)
Type: Family

This family of proteins is involved in the processing of mitochondrial precursor proteins. Members of this family function as ATP-independent proteases located within the inner membrane of mitochondria. They are responsible for the cleavage of transit peptides from precursor proteins during their translocation into the mitochondrial inter-membrane space. This proteolytic activity is essential for the proper targeting and functioning of proteins within the mitochondrial matrix and inter-membrane space, thereby playing a crucial role in mitochondrial biogenesis and maintenance.
Vago-like (Vago-like)
Type: Family

This family includes a group of proteins from arthropods that contain the single domain Von Willebrand factor type C (

), including Protein Vago from Drosophila melanogaster, which is likely to play a significant role in the immune response against viral infections , and the toxin U-scoloptoxin(16)-Ssd1a from Scolopendra dehaani .
Balbiani Body Formation Protein (Balbiani_Body_Formation)
Type: Family

This family of proteins is involved in the early stages of oocyte development, specifically in the formation of the Balbiani body and germ plasm assembly. Members of this family exhibit prion-like characteristics that are essential for establishing oocyte polarity during oogenesis. They interact with tudor domain-containing proteins to enhance their mobility and aggregation properties, which are crucial for the formation of the Balbiani body. Additionally, these proteins play a role in the recruitment of germ plasm to embryonic cleavage furrows and are implicated in dorsoventral patterning. Their function is mediated through interactions with various RNA-binding proteins and is necessary for initiating a feedback loop amplification mechanism within the Balbiani body.
Flavoredoxin-like (Flavoredoxin-like)
Type: Family

This family of proteins is involved in redox reactions, where they participate in the transfer of electrons. Members of this family typically contain a flavin mononucleotide (FMN) or flavin adenine dinucleotide (FAD) as a cofactor, which is essential for their catalytic activity. These proteins play a role in various biological processes, including the response to oxidative stress, cellular respiration, and the detoxification of harmful compounds. They may interact with other proteins or molecular partners to facilitate electron transfer and are important for maintaining cellular redox homeostasis.
Mucosal Integrity Associated (Mucosal_Integrity_Assoc)
Type: Family

This family of proteins is involved in the protection and lubrication of mucosal surfaces. Members of this family are thought to contribute to the stabilization of the mucus layer, which serves as a barrier against environmental stress and pathogens. They may also play a role in cellular signaling processes that regulate the viscosity and production of mucus, thus aiding in the preservation of mucosal integrity and function.
Root Meristem Growth Factor (RGF)
Type: Family

This family of proteins is involved in the maintenance of the postembryonic root stem cell niche in plants. They play a crucial role in regulating the expression levels and spatial patterns of key transcription factors that are essential for root development. Members of this family are particularly important for the modulation of the transcription factor PLETHORA, which they influence mainly at the post-transcriptional level. Through this regulation, they contribute to promoting root elongation, ensuring proper root growth and development.
Peptidase C14A (Peptidase_C14A)
Type: Family

This family of proteins includes cysteine proteases that play a role in apoptosis and cellular homeostasis. Members are characterized by their ability to cleave themselves and other caspase proteins into active forms. They are involved in the programmed cell death of certain cells during embryogenesis and can be regulated by specific inhibitors. Additionally, these proteins may respond to environmental stressors, such as high levels of certain metal ions, by inducing neuronal degeneration.
Epigenetic regulator of gene expression (Epigenetic_reg_gene_expr)
Type: Family

This family of proteins is involved in the regulation of gene expression through epigenetic mechanisms. They play a role in preventing gene silencing by counteracting specific methylation of DNA and histones at certain genomic loci. These proteins are part of a complex that influences RNA processing, including alternative splicing, and the epigenetic status of genes with heterochromatin regions. They are implicated in the modulation of transposable element expression and contribute to disease resistance by controlling histone methylation at key immune receptor genes, thereby affecting the production of full-length transcripts and the occupancy of RNA polymerase II.
Tubulin polyglutamylase (Tubulin_polyglutamylase)
Type: Family

This family of proteins includes enzymes that modify tubulin by adding polyglutamate side chains, a process known as polyglutamylation. These modifications can regulate microtubule dynamics, which are crucial for various cellular processes including cell division and intracellular transport. Members of this family are thought to function in complexes with other proteins and may have roles in specific cellular contexts, such as in uterine muscle cells. While some members may not be essential for certain microtubule-related functions, they can influence the behavior of cells and organisms by affecting microtubule stability and interactions with microtubule-associated proteins.
Glycosyltransferase 64 (GT64)
Type: Family

Glycosyltransferase 64 (GT64) is involved in the biosynthesis of glycosylinositol phosphorylceramides (GIPCs) and is thought to be essential for cell-cell adhesion, organ integrity, and metabolite movement in plants . Members of the family, such as Glycosylinositol phosphorylceramide mannosyl transferase 1, function as mannosyl transferases (ManT) and are implicated in the prevention of abscisic acid-mediated developmental effects, including aspects like cell size, flowering time, and senescence . GT64 is also likely involved in the biosynthesis of beta-(1,4)-galactan, contributing to cell-wall synthesis and thus playing a critical role in plant development and structural stability .
Outer envelope protein 61 (OEP61)
Type: Family

Outer envelope protein 61 is involved in protein import into the endoplasmic reticulum and chloroplasts. It is thought to act as chaperone docking proteins during post-translational protein translocation into the ER. It also implicated in chaperone-mediated targeting of proteins to chloroplasts, interacting specifically with chloroplast precursors to facilitate their delivery to the chloroplast translocase. The TPR region within this protein is essential for interaction with HSP70-1, and the linker domain is crucial for the selective recognition of chloroplast precursor complexes, distinguishing it from mitochondrial precursors .
Protein DD3-3 O-glycosylation (Protein_DD3-3_O-glyco)
Type: Family

The Protein DD3-3 family is implicated in the biological process of O-glycosylation. Members of this family are believed to play a role in the enzymatic addition of sugar moieties to oxygen atoms on serine or threonine residues of proteins, a post-translational modification critical for protein stability, localization, and function. The precise mechanisms and the extent of involvement of the Protein DD3-3 family in O-glycosylation, as well as its potential substrates and interacting partners, remain to be fully characterized.
Inositol Polyphosphate 5-Phosphatase Type IV (IPP-5-Phosphatase_Type_IV)
Type: Family

This family of proteins is involved in the regulation of phosphoinositide composition within cellular membranes. Members of this family act as enzymes that modify phosphatidylinositol phosphates by removing a phosphate group. Specifically, they convert phosphatidylinositol 3,4,5-trisphosphate to a bisphosphate form and phosphatidylinositol 4,5-bisphosphate to a monophosphate form. Through these enzymatic activities, they play a crucial role in the modulation of cilia membrane composition in auditory receptor neurons, which is essential for the proper localization of specific proteins and the function of ion channels within the cilia.
Phospholipase A2-like (PLA2-like)
Type: Family

This family of proteins includes enzymes that hydrolyze glycerophospholipids to produce fatty acids and lysophospholipids. Members of this family typically act at the sn-2 position of phospholipids and release arachidonic acid, a precursor of eicosanoids which are potent mediators of cellular signaling involved in inflammation and immune response. These enzymes play a role in various biological processes including membrane remodeling, signal transduction, and cell proliferation. They may also participate in the pathogenesis of diseases related to inflammation and immune function.
UPF0235 domain-containing protein (UPF0235)
Type: Family

This family of proteins may be implicated in early embryonic development and is likely to participate in pre-mRNA splicing processes. Members of this family are characterized by a specific domain that suggests a conserved function across the family, although the exact molecular mechanisms remain to be fully elucidated.
Hydrophobic Surface Structural Protein (Hydrophobic_Surface_Structural)
Type: Family

This family of proteins includes structural components that confer water-repellency to certain surfaces. They play a crucial role in the development of aerial hyphae, which are necessary for filamentous growth in some organisms. The proteins are involved in maintaining surface hydrophobicity, which is essential for the organism's interaction with its environment.
Histone H3 Acetylation Activator (H3-Acetyl_Activator)
Type: Family

This family of proteins is involved in the regulation of gene expression. Members of this family are known to activate transcription by interacting with the histone acetyltransferase HAG1/GCN5. This interaction leads to the acetylation of histone H3 at the promoters of target genes, which is a key epigenetic modification that facilitates the initiation of transcription. Through this mechanism, proteins in this family play a crucial role in controlling the expression of genes that are essential for various biological processes.
G-protein coupled receptor 1-like (GPCR1-like)
Type: Family

This family of proteins includes receptors that are typically part of the G-protein coupled receptor (GPCR) superfamily. GPCRs are characterized by their seven transmembrane domains and are involved in transmitting signals from the extracellular environment to the interior of the cell. They play a pivotal role in various physiological processes, including sensory perception, immune response, and neurotransmission. Upon ligand binding, these receptors activate heterotrimeric G-proteins, which in turn modulate various downstream signaling pathways. The specific functions of individual family members may vary, but they generally contribute to cellular communication and response to external stimuli.
Kinase-Interacting Protein (KIP)
Type: Family

This family of proteins is potentially involved in signal transduction processes mediated by receptor-like kinases. Members of this family may play a role in cellular communication and response mechanisms by interacting with kinase enzymes, which are known to be pivotal in regulating a variety of cellular pathways.
Uro-adherence factor A-like (Uro-adherence_factor_A)
Type: Family

This family of proteins is implicated in bacterial adhesion to urinary tract cells, facilitating colonization and potential infection. Members exhibit the ability to agglutinate sheep erythrocytes and adhere to human bladder carcinoma cells, indicating a role in pathogenicity by mediating host-cell interactions. These properties suggest a function in bacterial virulence, particularly in urogenital infections.
Merozoite Surface-Associated Protein (Merozoite_Surface_Assoc)
Type: Family

This family of proteins is implicated in the process of merozoite invasion of erythrocytes. Members are believed to be involved in the initial attachment of the merozoite to the erythrocyte surface, which is a critical step in the life cycle of the parasite. Additionally, these proteins possess a region at the N-terminus that is suggested to have lipid-binding capabilities, which may play a role in membrane interactions or the formation of complexes necessary for invasion.
Mucin-22-like (Mucin-22-like)
Type: Family

This family of proteins includes mucin-22, which is a type of glycoprotein typically found in the mucus secreted by epithelial tissues. Mucins are characterized by their high carbohydrate content and are responsible for the gel-like properties of mucus, which serves as a protective barrier against pathogens and helps to keep tissues moist. Mucin-22 may play a role in the immune response by trapping pathogens and preventing their entry into the body. It may also be involved in cell signaling and establishing the viscosity and elasticity of mucus. The exact functions of mucin-22 can vary depending on its specific glycosylation patterns and the tissues in which it is expressed.
EGF-like domain-containing protein comC (EGF-like_comC)
Type: Family

The EGF-like domain-containing protein comC family is involved in the regulation of cellular aggregation in the social amoeba Dictyostelium discoideum. Members of the family play a crucial role in the signaling pathway that governs aggregation, interacting with other key proteins such as lagC and tgrD1/lagD. Specifically, the family functions to inhibit the expression of lagC and to activate the expression of lagD, thereby modulating the aggregation process that is essential for the development and survival of these organisms.
Cytochrome b6-f complex subunit 7 (Cytochrome_b6-f_sub7)
Type: Family

The PetM family comprises proteins that are components of the cytochrome b6-f complex, which is crucial for photosynthesis in plants and cyanobacteria. Members of the PetM family play a role in mediating electron transfer between photosystem II and photosystem I, facilitating cyclic electron flow around photosystem I, and contributing to state transitions. These processes are essential for the establishment of the proton gradient across the thylakoid membrane, which drives ATP synthesis during photosynthesis.
Chloroplast Sensor Kinase (Chloroplast_Sensor_Kinase)
Type: Family

This family of proteins is involved in the regulation of photosynthesis in chloroplasts. Members act as sensor kinases that detect changes in the redox state of plastoquinone, which is a key component in the photosynthetic electron transport chain. These proteins play a crucial role in the long-term adaptation of photosystems I and II by modulating the transcription of reaction center genes, as well as in short-term adaptation through the reversible phosphorylation of the light-harvesting complex II. They are capable of autophosphorylation, which is influenced by the redox state of plastoquinone, and are also involved in the repression of certain chloroplast-encoded genes.
Fatty Acid Desaturase CarF-like (Fatty_acid_desaturase_CarF)
Type: Family

This family of proteins includes enzymes that are involved in the biosynthesis of unsaturated fatty acids. Members of this family are characterized by their ability to introduce double bonds into fatty acyl chains, a process that is essential for the production of unsaturated fatty acids. These unsaturated fatty acids are important components of cell membranes and play a role in various cellular processes, including signaling and membrane fluidity. The activity of these enzymes is vital for maintaining the proper balance of fatty acids in the cell, which is crucial for normal cellular function and overall organismal health.
Rhoptry Surface-Associated Protein (Rhoptry_Surface_Assoc)
Type: Family

This family of proteins is involved in the critical process of merozoite invasion into host erythrocytes. Members of this family are associated with the rhoptry, an organelle found in the apicomplexan parasites, and contribute to the proper functioning of rhoptry structures and mechanisms. The activity of these proteins is essential for the parasite's life cycle, particularly in the stage where it infects red blood cells, which is a key step in disease progression in the host.
Autotransporter-2 adhesin (AT-2_adhesin)
Type: Family

This family of proteins is involved in bacterial virulence and adherence to human respiratory epithelial cells. Members possess a signal peptide that directs the protein to the periplasmic space and a C-terminal translocator domain that forms a pore in the outer membrane, allowing the passenger domain to reach the bacterial cell surface. A conserved extended signal peptide region may regulate translocation across the inner membrane.
FAS1 domain-containing protein (FAS1_domain_protein)
Type: Family

This family of proteins includes members that contain a FAS1 domain, which is typically involved in cell adhesion processes. The FAS1 domain is found in a variety of proteins across different species and is known for its role in the formation of adhesive structures. Proteins with this domain may participate in interactions with other cell surface proteins, extracellular matrix components, or may be involved in signaling pathways related to cellular adhesion and migration. The specific functions of individual family members can vary widely, depending on their domain architecture and the context of their expression.
Plant-specific TFIIB-related protein PTF2 (PTF2)
Type: Family

Plant-specific TFIIB-related protein PTF2 is characterised by its unique role in plant development, particularly in pollen germination and embryogenesis. Members of this family, such as PTF2 from Arabidopsis thaliana, are known to interact with TBP2 and RNA polymerase subunits, suggesting a regulatory function in gene expression. These proteins have the ability to bind double-stranded DNA in vitro, which further supports their involvement in transcriptional regulation .
Oxidative Stress Response Globin-like (Oxidative_stress_globin-like)
Type: Family

This family of proteins is characterized by its role in the response to oxidative stress. Members of this family are involved in processes that protect the cell from the damaging effects of reactive oxygen species. They are related to globins, which are typically heme-containing proteins, suggesting that they may bind or transport oxygen or other gaseous molecules as part of their function in managing oxidative stress.
Exosome cofactor and PTGS suppressor (Exosome_cofactor/PTGS_suppr)
Type: Family

This family of proteins includes cofactors of the cytoplasmic exosome, linking it to the SKI complex. Members of this family are involved in post-transcriptional gene silencing suppression, particularly by inhibiting the production of small interfering RNAs from specific loci related to cuticle membrane and wax production, as well as typhine and sporopollenin biosynthesis in pollen.
Photosystem II mRNA-binding protein (PSII_mRNA-binding_protein)
Type: Family

This family of proteins is involved in the regulation of photosystem II (PSII) biogenesis and the formation of grana thylakoids in chloroplasts. Members of this family bind to the 5' UTR of PSII subunit mRNAs in a light-dependent manner, which is mediated by a redox-based mechanism. This interaction facilitates the association of specific proteins with the target mRNAs that encode PSII reaction center proteins, thereby modulating their expression and ribosome loading. This regulatory function is essential for the proper assembly and maintenance of the PSII complex, which plays a critical role in the light-dependent reactions of photosynthesis.
Cyclic AMP-inducible BP74-like (cAMP-inducible_BP74-like)
Type: Family

This family of proteins includes cyclic AMP (cAMP)-inducible proteins such as BP74 from Dictyostelium discoideum. These proteins are typically regulated by cAMP, a key signaling molecule in many biological processes. The cAMP-inducible proteins can be involved in various cellular functions, including but not limited to, gene regulation, metabolic pathways, and cellular response to external stimuli. The exact role of BP74 is not clearly defined, but it is likely to be associated with the cellular response to cAMP signaling during the organism's development and differentiation processes.