SII-SWORD/CoKE huggingface dataset:
Ankyrin repeat-containing protein (Ankyrin_repeat-containing)
Type: Family

This family of proteins contains ankyrin repeats, a common protein-protein interaction motif. Ankyrin repeats typically consist of tandemly repeated modules of about 33 amino acids and are known to mediate various functions, including cellular signaling, cytoskeletal integrity, and the regulation of specific protein activities. Proteins with ankyrin repeats are involved in a wide range of cellular processes and can be found in diverse organisms. The presence of ankyrin repeats suggests that members of this family may be involved in mediating interactions with other proteins, possibly contributing to the formation of multiprotein complexes.
Fra a 1-associated (Fra_a_1-associated)
Type: Family

This family of proteins is associated with the allergen Fra a 1, which is a major allergen from strawberries. Members of this family may play a role in the plant's defense mechanisms or stress responses, and they could be involved in the interaction with other proteins or molecules that contribute to the allergenic properties of the Fra a 1 protein. The exact biological function of these associated proteins remains to be fully characterized, but they are likely to be important for the plant's physiology and potentially its interaction with the environment and other organisms, including humans who may exhibit allergic reactions to them.
Axonemal microtubule stabilizer (Axonemal_MT_stabilizer)
Type: Family

This family of proteins is involved in the stabilization of axonemal microtubules. Axonemal microtubules are a component of the cytoskeleton and are found in the axonemes of cilia and flagella, which are hair-like structures on the surface of many eukaryotic cells. These microtubules provide structural support and are essential for the beating movements of cilia and flagella. Proteins in this family play a critical role in maintaining the stability and integrity of these microtubules, ensuring proper ciliary function and motility. Dysfunctional or destabilized axonemal microtubules can lead to a range of ciliary disorders, known as ciliopathies, which can affect multiple organ systems.
Protein KPLCE (KPLCE)
Type: Family

This family of proteins is involved in intracellular signaling pathways. It is characterized by its ability to modulate various biological processes, including cell proliferation, differentiation, and apoptosis. Members of this family typically possess enzymatic activity that is crucial for the transduction of signals from the cell surface to the interior of the cell, influencing cellular responses to external stimuli. The specific functions can vary widely among family members, but they generally contribute to the regulation of cellular homeostasis and are implicated in various physiological and pathological conditions.
Chloroplast Vesiculation Inducer (CV_Inducer)
Type: Family

This family of proteins is involved in the cellular response to stress, particularly in the process of chloroplast degradation. The proteins function by initiating the disassembly of chloroplasts when the plant cell encounters stress. This leads to the formation of specialized vesicles that contain various chloroplast components, such as stromal, envelope membrane, and thylakoid membrane proteins. These vesicles, known as chloroplast-containing vesicles (CCVs), transport the chloroplast constituents to the vacuole, where they are subjected to proteolysis. The activity of these proteins is notable for being independent of the autophagy pathway and senescence-associated vacuoles, highlighting a distinct mechanism for chloroplast breakdown and recycling of its components.
Chloroplast NDH Complex Assembly Protein (Chloroplast_NDH_Assembly)
Type: Family

This family of proteins is involved in the photosynthetic electron transport chain, specifically in the formation and stabilization of the chloroplast NAD(P)H dehydrogenase (NDH) complex. Members of this family are essential for both the assembly of the NDH complex and its activity, potentially working in conjunction with other components to form a subcomplex that serves as an assembly intermediate.
FMRFamide-related peptide receptor (FMRFamide_rcpt)
Type: Family

This family of proteins includes G-protein coupled receptors that interact with specific neuropeptides. They are involved in the regulation of arousal from a sleep-like state during critical developmental transitions. These receptors may signal through the G(q) alpha type of G proteins and play a role in modulating sensory responses, contributing to the coordination of complex physiological processes such as developmental molting.
Plant lipid transfer GPI-anchored (Plant_LTP_GPI-anchored)
Type: Family

This family of proteins is involved in the transfer of lipids across cell membranes. Members of this family are characterized by their ability to bind and transport various lipid molecules, which is a critical function for maintaining cellular lipid homeostasis. These proteins are typically small and abundant in plant tissues, where they play roles in processes such as cuticle formation, defense against pathogens, and adaptation to environmental stresses. The lipid transfer activity of these proteins is facilitated by their structure, which allows them to shuttle lipid molecules between different membranes or to specific sites within a membrane.
Monoglucosyldiacylglycerol epimerase (MGDG_epimerase)
Type: Family

This family of proteins includes enzymes that are key players in the biosynthesis of galactolipids, which are essential components of photosynthetic membranes. Members of this family function as epimerases, catalyzing the isomerization of monoglucosyldiacylglycerol into monogalactosyldiacylglycerol. This reaction is crucial for the formation of galactolipids that are integral to the structure and function of chloroplast membranes in plants and algae. The enzymes belong to the short-chain dehydrogenases/reductases superfamily, known for their roles in the metabolism of steroids, prostaglandins, and xenobiotics.
RAD51-associated protein (RAD51-associated)
Type: Family

This family of proteins is involved in the homologous recombination repair pathway, a critical mechanism for maintaining genomic stability by repairing DNA double-strand breaks. Members of this family are associated with RAD51, a protein that plays a central role in pairing homologous DNA sequences during the repair process. Proteins in this family may function as regulators of RAD51, influencing its ability to form nucleoprotein filaments or mediating interactions with other proteins involved in the repair complex. Their activity is essential for the accurate repair of DNA to prevent mutations, which can lead to cancer and other genetic disorders.
Calcium-regulated actin-bundling protein (Calcium-reg_actin-bundling)
Type: Family

This family of proteins is involved in the regulation of actin dynamics. Members of this family are thought to play a role in the formation and remodeling of actin structures such as filopodia and pseudopodia, which are cellular protrusions that facilitate movement and cell shape changes. The actin-bundling activity of these proteins is regulated by calcium levels, suggesting a mechanism by which intracellular calcium signals can influence the cytoskeletal architecture and, consequently, cellular motility and morphology.
Differentiation-associated signaling protein (Diff-assoc_signaling)
Type: Family

This family of proteins is implicated in cellular differentiation processes and is essential for the initiation of this fundamental biological event. Members of this family are also involved in the transduction of cAMP signaling pathways, which are critical for a variety of physiological responses.
Cysteine-rich Acidic Integral Membrane Protein (CRAM)
Type: Family

This family of proteins is believed to be involved in cellular communication and transport processes. Members are thought to act as cell surface receptors that may play a role in receptor-mediated endocytosis, a mechanism by which cells internalize molecules and particles from their surroundings. The exact molecular function and biological significance of these proteins remain to be fully elucidated.
Putative zinc finger domain-containing protein (Zinc_finger_domain)
Type: Family

This family of proteins includes members that are characterized by the presence of zinc finger motifs, which are small protein structural motifs that are capable of binding to zinc ions. These motifs are often involved in interactions with DNA, RNA, or other proteins, and can play roles in various biological processes including gene expression regulation, DNA repair, and transcriptional activation. Given the putative nature of the protein C02F5.12 from Caenorhabditis elegans, the specific functions of this family may include but are not limited to DNA binding and transcriptional regulation, often associated with zinc finger proteins. The exact biological roles and molecular mechanisms of action for this family remain to be fully elucidated through further experimental studies.
Vulval development negative regulator (Vulval_dev_neg_regulator)
Type: Family

This family of proteins is involved in the regulation of vulval development in certain organisms. Members of this family function as negative regulators, working to counteract the effects of Ras-mediated signaling pathways that promote vulval induction. They perform their regulatory role within the same cells where they are expressed, indicating a cell-autonomous mechanism of action. Through their activity, these proteins help to maintain proper developmental processes and ensure that vulval formation occurs correctly and at the appropriate developmental stage.
Receptor polysaccharide phosphotransferase WefF-like (RPS_phosphotransferase_WefF)
Type: Family

This family of proteins is involved in the biosynthesis of type 2G receptor polysaccharides (RPS), which are critical components of the cell surface. Members of this family are believed to function as transferases, specifically as 1-3GalNAc alpha transferases, which are essential for the production of the host-like Gal beta 1-3GalNAc motif within the RPS. The activity of these enzymes is crucial for the proper assembly and expression of cell surface polysaccharides that may play a role in host-microbe interactions.
Leaf patterning domain-containing protein (Leaf_patterning_domain)
Type: Family

This family of proteins includes transcriptional regulators that play a role in the patterning of leaf proximal and distal regions. Members of this family are capable of interacting with BELL transcription factors, which may be mediated through a specific domain within these proteins. Additionally, they possess a domain that is essential for interactions with KNOX proteins, suggesting a role in complex formation with other regulatory proteins to modulate gene expression during plant development.
Fork-head Transcriptional Regulator (Fork-head_TF_regulator)
Type: Family

This family of proteins includes transcriptional regulators that form complexes with specific partners to control the expression of rRNA and ribosomal protein genes. Members of this family are known to interact with DNA-binding factors to target ribosomal protein genes, thereby playing a crucial role in the regulation of ribosome biogenesis, a fundamental process for cellular growth and proliferation.
Nematode receptor-like (Nematode_rcpt-like)
Type: Family

This family of proteins includes receptors that are structurally related to the nematode receptor-like proteins known as sre. These receptors are typically involved in signal transduction processes and are characterized by their serpentine, or G protein-coupled receptor-like, topology. They play a role in various cellular responses to external stimuli, which may include sensory perception, hormone responses, and other signaling pathways relevant to nematode physiology.
Leucine-rich repeat transmembrane protein (LRR_transmembrane)
Type: Family

This family of proteins includes leucine-rich repeat (LRR) transmembrane proteins, such as CCDC168. LRR motifs are typically involved in protein-protein interactions and are known for their role in the immune response by recognizing pathogen-derived molecules. Transmembrane proteins with LRRs are often implicated in signal transduction processes across the cell membrane. They may participate in cell adhesion, receptor activity, or as part of cell surface receptor complexes. Given the presence of LRR motifs, proteins in this family are likely to contribute to cellular communication and immune system function by interacting with various ligands and participating in signaling pathways.
G-protein alpha subunit activating GEF (G-alpha_activating_GEF)
Type: Family

This family of proteins includes guanine nucleotide exchange factors (GEFs) that specifically activate G-protein alpha subunits. Members of this family possess a GBA motif that allows them to interact with G-protein alpha subunits, facilitating the exchange of GDP for GTP on the G-protein, thereby activating it. Through this activation mechanism, these proteins play a crucial role in the modulation of various signaling pathways mediated by G-proteins, which are involved in a multitude of cellular processes.
Viral Envelope Glycoprotein (Viral_Envelope_Glycoprotein)
Type: Family

This family of proteins includes envelope glycoproteins that function in viral entry into host cells. They have a transmembrane domain that acts as a class I viral fusion protein, which undergoes conformational changes to facilitate membrane fusion. This process is critical for the delivery of the viral nucleocapsid into the host cytoplasm. Additionally, a surface domain of these proteins is responsible for binding to host cell receptors, triggering the fusion process by exposing the fusion peptide. The coordinated action of these domains enables the virus to attach to and fuse with the host cell membrane.
SrfA-induced signaling protein (SrfA-induced_signal)
Type: Family

This family of proteins is induced by the SrfA signaling pathway in the slime mold Dictyostelium discoideum. The specific functions of these proteins are not well characterized, but they are believed to play a role in the cellular response to extracellular signals during development and differentiation processes. The SrfA pathway is known to be involved in the regulation of gene expression in response to environmental stimuli, suggesting that members of this family may be involved in adaptive or stress response mechanisms.
Quorum Sensing Complex Regulator (QS_Complex_Regulator)
Type: Family

This family of proteins includes components of a complex involved in quorum sensing, which is a mechanism that bacteria use to coordinate gene expression according to the density of their population. Specifically, these proteins regulate the expression of discoidin genes, which are important for growth and development. Although individual members of this family do not induce discoidin by themselves, they contribute to the function of the complex in which they are a part.
Involucrin-like (Involucrin-like)
Type: Family

This family of proteins is involved in the formation of the cornified cell envelope (CE) found in stratified squamous epithelia. Members of this family contribute to the structure of the CE, which is a specialized component of the epidermis that provides a barrier against environmental stresses. The CE is composed of insoluble protein complexes that are cross-linked to form a resilient and protective layer.
Vulval toroid morphogenesis-associated protein (Vulval_toroid_morpho-assoc)
Type: Family

This family of proteins includes putative acyltransferases that are implicated in the morphogenesis of specific vulval toroid cells in certain organisms. These proteins are believed to be involved in the structural development of the connection between the vulva and the uterus, although they are not essential for determining the fate of vulval cells. The precise biochemical function of these proteins may involve the transfer of acyl groups to various substrates, contributing to cellular and developmental processes.
Glycine-rich receptor kinase regulator (GRP_receptor_kinase_reg)
Type: Family

This family of proteins includes members that are involved in the regulation of receptor protein kinases. Specifically, they interact with and regulate the function of receptor protein kinases such as WAK1. This interaction is crucial for the phosphorylation of specific target proteins, which is a key step in signal transduction pathways. The C-terminal region of these proteins, which is rich in cysteine residues, plays an essential role in their ability to interact with kinase receptors. Through these interactions, members of this family are implicated in various cellular processes, including response to environmental stimuli.
TCP-1 chaperonin-containing T-complex (TCP-1_chaperonin)
Type: Family

This family of proteins functions as molecular chaperones involved in the folding of other proteins. They are part of a complex known as the chaperonin-containing T-complex (TRiC) or thermosome, which facilitates the correct folding of polypeptides and proteins upon ATP hydrolysis. These proteins are known to assist in the folding of key cellular components such as actin and tubulin, which are crucial for maintaining cell structure and function. They also play a role in various cellular processes including the regulation of telomere maintenance and ciliogenesis, by mediating the assembly of complexes like the BBSome. Additionally, they exhibit ATPase activity, which is essential for their function in protein folding.
UPF0265 domain-containing protein (UPF0265)
Type: Family

This family of proteins is characterized by a shared similarity suggesting a common evolutionary origin. The specific functions of these proteins are not well-defined, but they are grouped together based on conserved features that indicate a potential role in cellular processes. The UPF0265 family designation implies that these proteins have been identified as a conserved family through computational methods, but their biological roles remain to be elucidated through experimental studies. As such, the proteins within this family may participate in a variety of cellular functions, but without further experimental data, their precise roles cannot be confidently assigned.
Serine acetyltransferase (Serine_acetyltransferase)
Type: Family

This family of proteins includes enzymes that catalyze the acetylation of serine using acetyl-CoA to produce O-acetylserine (OAS), a precursor in the biosynthesis of the amino acid cysteine. Members of this family are characterized by the presence of transferase hexapeptide repeats, which are indicative of their enzymatic activity. The activity of these enzymes is regulated by feedback inhibition mechanisms, often involving the end product cysteine or other related metabolites. Some members may also have a role in nitrogen metabolism or in the detoxification process through the production of glutathione.
Iron uptake and transport EfeM/EfeO (Iron_uptake_EfeM/EfeO)
Type: Family

This family of proteins is involved in iron uptake and transport, particularly in the binding and/or electron transfer of ferrous iron (Fe(2+)). Members of this family may contain a Cup-like domain and a peptidase domain, with potential metal-binding sites that could accommodate different metal ions such as Cu(2+) and Fe(3+). Some proteins within this family are known to specifically bind ferric iron (Fe(3+)) after its conversion from Fe(2+) and deliver it to cell membrane permeases for import into the cell. The peptidase domain is implicated in iron binding, and the absence of the Cup-like domain in some members suggests a variation in metal-binding capabilities and functions within the family.
Prenyl diphosphate synthase (Prenyl_diphosphate_synthase)
Type: Family

This family of proteins includes bacterial and plant enzymes that catalyse the synthesis of prenyl diphosphate compounds, which are crucial for the biosynthesis of various terpenoids, including carotenoids, diterpenes, and sesterterpenoids. These enzymes typically perform the trans-addition of multiple isopentenyl diphosphate (IPP) molecules onto a dimethylallyl diphosphate (DMAPP) substrate to form longer-chain prenyl diphosphates such as geranylgeranyl diphosphate (GGPP). The specific reaction catalyzed can vary, with some members producing GGPP by adding three IPP units to DMAPP, while others may use different allylic substrates to produce various prenyl diphosphates. These compounds serve as essential precursors for the production of a wide range of biomolecules with diverse functions, including pigments, hormones, and electron carriers.
D-mannonate dehydratase GalD subfamily (D-mannonate_dehydratase_GalD)
Type: Family

This family of proteins is involved in the dehydration of D-mannonate, a process that converts this sugar acid into a 2-keto acid. Members of this family exhibit low dehydratase activity with D-mannonate and D-gluconate in vitro, suggesting these substrates may not be their main physiological targets. Some proteins within this family have no detectable activity with a broad range of other acid sugars, indicating a high degree of substrate specificity or a potential divergence in function. The family belongs to the broader mandelate racemase/muconate lactonizing enzyme superfamily, specifically the GalD subfamily, which is characterized by a conserved catalytic activity and cofactor binding despite the observed low or undetectable activities with certain substrates.
SbcCD Nuclease Subunit C (SbcCD_Nuclease_C)
Type: Family

This family of proteins is involved in DNA repair and recombination processes. Members of this family exhibit exonuclease and endonuclease activities, specifically targeting DNA hairpin structures that can impede DNA replication. They function as a 3'->5' double-strand exonuclease capable of resolving hairpins and also possess a 5' single-strand endonuclease activity. These activities are essential for maintaining genomic stability by facilitating the proper resolution of DNA secondary structures that may arise during DNA replication or recombination events.
SbcCD nuclease (SbcCD_nuclease)
Type: Family

This family of proteins is involved in DNA repair and recombination processes. Members of this family exhibit nuclease activity that targets DNA hairpin structures, which can impede DNA replication and serve as intermediates in DNA recombination reactions. The proteins function as a 3'->5' double-strand exonuclease with the ability to resolve hairpins, and they also possess a 5' single-strand endonuclease activity. Some members may play a role in the SOS response to DNA damage and are likely part of the SOS regulon.
Bacterial ring-hydroxylating dioxygenase ferredoxin reductase (Ring-hydroxylating_dioxygenase)
Type: Family

This family of proteins is involved in the biodegradation of aromatic compounds. They are components of a multicomponent dioxygenase system that catalyzes the conversion of 3-phenylpropionic acid and cinnamic acid into their respective dihydrodiol products. These enzymes function as ferredoxin--NAD(+) reductases, playing a crucial role in the electron transfer process required for the hydroxylation of the aromatic ring, a key step in the breakdown of these compounds.
Phenol-soluble modulin alpha peptides (PSM_alpha_peptides)
Type: Family

This family of proteins includes peptides that interact with human neutrophils, playing a role in immune response modulation. They are capable of recruiting and activating neutrophils, leading to their lysis and the elimination of this key cellular defense against infection. Additionally, these peptides contribute to the inflammatory response by stimulating the secretion of chemotactic factors such as interleukin-8 (IL-8). Their hemolytic activity and pro-inflammatory effects are significant in promoting virulence and may be involved in the development of disease.