SII-SWORD/CoKE huggingface dataset:
Stomatal Development and Plant Interaction Regulator (StomDev_PlantInt_Reg)
Type: Family

This family of proteins is involved in diverse biological processes including development and interaction with symbiotic organisms. Members of this family play a crucial role in stomatal development, influencing cell fate progression, orientation of spacing divisions, and promoting asymmetric divisions in plant tissues. They are essential for the transition of meristemoids into guard mother cells and for regulating gene expression in differentiating cells. These proteins also form complexes with receptor kinases and are involved in the recognition of regulatory peptides, modulating ligand-receptor activity in developmental pathways. Additionally, some family members are implicated in growth promotion and seed production when interacting with endophytic fungi, suggesting a role in plant-microbe interactions.
Lipopolysaccharide cholinephosphotransferase (LPS_cholinephosphotransferase)
Type: Family

This family of proteins is involved in the modification of lipopolysaccharides (LPS), a major component of the outer membrane of Gram-negative bacteria. Members of this family are responsible for the transfer of phosphorylcholine from choline diphosphonucleoside to LPS. This modification plays a role in bacterial virulence and interaction with the host immune system. The enzymatic activity of these proteins is crucial for the proper assembly and function of LPS, thereby influencing the structural integrity of the bacterial cell envelope.
TMTC O-mannosyl-transferase (TMTC_O-mannosyl-trnsfr)
Type: Family

This family of proteins includes O-mannosyl-transferases that are involved in the post-translational modification of proteins by transferring mannosyl residues to serine or threonine hydroxyl groups. Members of this family primarily modify the cadherin superfamily, adding O-linked mannose glycans in specific regions and thus playing distinct roles in the decoration of cadherin domains. Additionally, they can also mannosylate other proteins, exemplified by their activity on PDIA3.
Sporulation-related (Sporulation_related)
Type: Family

The protein family includes proteins such as the sporulation protein YdcC from Bacillus subtilis, which is required for efficient sporulation. While the function of the protein from Methanocaldococcus jannaschii remains uncharacterized, the presence of a homologous protein in a sporulation-capable bacterium suggests a potential role in cellular development or stress response processes. Further characterization of these proteins may reveal a conserved function within the family.
Mitotic Progression Regulator (Mitotic_Regulator)
Type: Family

This family of proteins includes regulators of mitotic progression. Members of this family are known to interact with kinases involved in the phosphorylation of key mitotic regulators. Through these interactions, they can inhibit kinase activity, which in turn affects the phosphorylation state of proteins that control the transition through the mitotic phase of the cell cycle. The inhibition of kinase activity by these proteins is crucial for maintaining proper control over cell division, ensuring that mitosis occurs at the appropriate time and that genomic integrity is preserved during cell proliferation.
Alkaline pH Cation Antiporter (Alkaline_pH_Ca-Antiporter)
Type: Family

This family of proteins includes cation antiporters that primarily function in the exchange of sodium, potassium, and calcium ions across cellular membranes. Members of this family operate mainly at alkaline pH, where they can export sodium ions and facilitate the exchange of potassium and calcium ions for protons. While the sodium export activity is prominent, these proteins also help cells adapt to potassium salinity stress and maintain potassium homeostasis. The antiporter activity is sensitive to pH levels and is regulated by the presence of magnesium ions, which can inhibit both sodium/proton and calcium/proton exchange. Additionally, the calcium/proton antiporter activity can be inhibited by specific proton ionophores. These proteins are essential for ionic balance and play a role in cellular responses to environmental changes.
Type VI secretion system Hcp1 domain-containing protein (T6SS_Hcp1_domain)
Type: Family

This family of proteins is characterized by the presence of the Hcp1 domain, which is typically associated with a role in bacterial virulence. Members of this family are often involved in the type VI secretion system (T6SS), a mechanism used by Gram-negative bacteria to transport effector proteins into a variety of target cells. The Hcp1 domain-containing proteins are known to form hexameric tubes that can act as conduits for the translocation of effector molecules. These proteins are crucial for the assembly and function of the T6SS apparatus, which plays a significant role in interbacterial competition and pathogenesis in host organisms. The Hcp1 family members may also be involved in other cellular processes related to bacterial secretion systems.
Low temperature-induced all0457 homolog (Low_temp-induced_all0457)
Type: Family

This family of proteins is involved in the response to low temperature stress. The proteins are homologous to the all0457 protein, which suggests a potential role in cold adaptation mechanisms. The exact biological processes and molecular functions of these proteins remain to be characterized. However, based on their association with low temperature-induced expression, they may play a role in maintaining cellular function under cold conditions, possibly through interactions with other proteins or cellular structures, or by acting as chaperones to stabilize other proteins during temperature fluctuations.
Peptide antibiotic immunity-related (PA_immunity-related)
Type: Family

This family of proteins includes members that are involved in providing immunity to certain peptide antibiotics, such as microcin B17, which targets DNA replication in Enterobacteriaceae. The proteins in this family can function in conjunction with others to induce the SOS repair system as a protective mechanism. Some members may also offer protection independently.
CDGSH iron-sulfur domain-containing protein (CISD)
Type: Family

This family of proteins is involved in the transfer of iron-sulfur clusters to apoferrodoxins, specifically FDX1 and FDX2, playing a critical role in mitochondrial iron homeostasis. Members of this family are essential for maintaining appropriate levels of free iron and reactive oxygen species within the mitochondria, which is crucial for normal mitochondrial function and overall cellular health.
Tellurite Resistance Ion Channel (Tellurite_res_ion_channel)
Type: Family

This family of proteins is involved in conferring resistance to potassium tellurite, a toxic compound. Members of this family function as ion channels that facilitate the transport processes associated with tellurite resistance. The activity of these proteins is essential for the survival of organisms in environments containing tellurite. While the exact mechanism of resistance is not fully elucidated, it is known that high copy numbers of these proteins can enhance tellurite resistance in certain bacterial species. The proteins may remain phenotypically silent under conditions where tellurite is not present or when expressed at low levels.
MFS-type Transporter (MFS-Transporter)
Type: Family

This family of proteins includes members that are part of the major facilitator superfamily (MFS), which is one of the largest groups of secondary transporters. Proteins in this family are involved in the transport of a diverse range of substrates across cellular membranes, including sugars, amino acids, ions, and drugs. They function by facilitating the movement of these molecules against their concentration gradient, using the energy derived from the electrochemical potential difference of ions, typically protons or sodium ions, across the membrane. The transport mechanism typically involves conformational changes in the protein structure, alternating between inward-facing and outward-facing states to shuttle the substrate across the lipid bilayer.
Serine-rich & Multicopper Oxidase-related (Ser-rich/MCO-related)
Type: Family

This family of proteins includes extracellular and membrane-anchored components with diverse functions. One member is characterized by a serine-rich extracellular region, suggesting a potential role in interactions with other proteins or cellular structures. Another member is a probable electron transfer copper protein, indicating a role in redox processes. It is likely involved in electron transfer as a direct electron donor, and it is related to the multicopper oxidase family, which is known for its ability to oxidize various substrates while reducing molecular oxygen to water.
GPCR_Ligand_Interaction (GPCR-Ligand_Int)
Type: Family

This family of proteins includes G-protein coupled receptors (GPCRs) that interact with specific ligands to regulate various biological processes. Members of this family are involved in the recognition and response to peptide or pheromone signals, which can influence neuronal excitability, behavior, and developmental pathways. For instance, one receptor in this family responds to FMRFamide peptides, playing a role in the maintenance of neuronal excitability and flight duration in certain species. Another receptor interacts with ascaroside pheromones to control dauer formation and longevity, and is implicated in specific neuronal signaling pathways that affect larval development and reproductive behaviors. These receptors typically function through intracellular signaling cascades, such as calcium signaling or downstream pathways involving other signaling molecules.
UPF0703 two-component membrane permease (UPF0703_membrane_permease)
Type: Family

The UPF0703 family includes proteins that may function in amino acid transport, particularly under low pH conditions. Members of the UPF0703 family are implicated in processes such as acidogenesis, biofilm formation, and survival in acidic environments. Although the specific roles of these proteins can vary, the family generally appears to be associated with two-component membrane permease systems, which are integral in the transport of amino acids across cell membranes.
Mesenchyme-associated surface protein (Mesenchyme-surface_protein)
Type: Family

This family of proteins includes members that may play roles in cellular processes such as migration, adhesion, fusion, or formation of skeletal structures. The specific functions of these proteins are not well characterized, but they are suggested to be involved in the organization and dynamics of mesenchyme-derived tissues. Given the diversity of potential functions, proteins in this family may have a broad impact on cell behavior and tissue development.
Auxin-regulated embryogenesis mediator (Auxin_embryo_med)
Type: Family

This family of proteins is involved in cell fate determination during embryogenesis and plays a crucial role in auxin-dependent cell-fate specification and patterning. Members are essential for proper development of plant structures such as cotyledons, leaves, and roots. They regulate the expression and polarity of PIN-formed (PIN) proteins, which are critical for auxin transport and distribution, thus influencing processes like leaf vascular development, stem cell maintenance in meristems, and cellular patterning.
Interferon-induced PKR regulator (IFN-induced_PKR_regulator)
Type: Family

This family of proteins acts as upstream regulators of interferon-induced serine/threonine protein kinase R (PKR). They are involved in the modulation of PKR activity by potentially interfering with the inhibitory function of DNAJC3, a known regulator of PKR. Through this interaction, these proteins may play a role in controlling kinase activity and consequently influence cell growth suppression.
Inner membrane-associated protein (Inner_membrane_assoc)
Type: Family

This family of proteins is involved in the cellular processes occurring in the inner membrane of bacterial cells. The specific functions of these proteins, however, are not well characterized. They may play a role in various membrane-associated activities, such as transport, signaling, or maintaining the integrity and functionality of the membrane structure. Due to the lack of detailed functional information, the precise biological processes these proteins participate in remain to be elucidated through further experimental studies.
Glucosamine-6-phosphate deaminase-like (GlcN6P_deaminase-like)
Type: Family

This family of proteins includes enzymes that catalyze the reversible isomerization-deamination of glucosamine 6-phosphate to fructose 6-phosphate and ammonium ion. Members of this family are involved in amino sugar metabolism, specifically in the conversion of glucosamine-6-phosphate, a derivative of glucose and an intermediate in the synthesis of various amino sugars and aminoglycans. The activity of these enzymes is critical for the proper functioning of cellular metabolic pathways, including the production of structural polysaccharides and the regulation of nitrogen metabolism.
Oxidoreductase and Kinase-like Enzymes (Oxido-Kinase-like_Enzymes)
Type: Family

This family of proteins includes enzymes with diverse catalytic activities. One member is an oxidoreductase belonging to the short-chain dehydrogenases/reductases (SDR) family, which typically function in the NAD(P)(H)-dependent metabolism of steroids, alcohols, and lipids. Another member is akin to the choline/ethanolamine kinase family, which is involved in the phosphorylation of choline and ethanolamine as part of phospholipid metabolism. These enzymes play crucial roles in various biological processes, including signal transduction, lipid biosynthesis, and metabolism.
Amino Acid Transporter AGT Superfamily (AA_Transporter_AGT)
Type: Family

This family of proteins includes transporters that are involved in the uptake of specific amino acids. Members of this family are characterized by their ability to transport glutamate and serine, with one member being a major transporter for these amino acids under certain growth conditions. Another member of the family is known to facilitate the uptake of L-aspartate along with a proton, and can also transport aspartate hydroxamate and L-glutamate, albeit with lower affinity and efficiency. These proteins are part of the amino acid-polyamine-organocation (APC) superfamily and are categorized within the AGT (TC 2.A.3.11) family, indicating a shared transport mechanism and structural features.
Phosphopantetheine Phosphodiesterase (Pantetheine_PDE)
Type: Family

This family of proteins includes enzymes with phosphodiesterase activity, specifically involved in the hydrolysis of the phosphopantetheine group from holo-carrier proteins. Members of this family are characterized by their role in the modification of carrier proteins, which is a critical step in various metabolic processes. These proteins are part of the metallophosphoesterase superfamily, indicating the presence of a metal ion in the catalytic site that is essential for their phosphodiesterase activity.
Sporulation-related signal maturation (Sporulation_signal_mat)
Type: Family

This family of proteins includes members involved in the maturation of specific signaling peptides and may play a role in cellular processes such as sporulation. One characterized member is essential for the maturation of a signaling peptide, although it is not necessary for the initial steps of signal peptide cleavage, secretion, or disulfide bond formation. The exact functions of other members within this family, including uncharacterized proteins, may vary but could be related to similar cellular signaling and regulatory pathways.
Pigment-associated catalase-like (Pigment-catalase-like)
Type: Family

This family of proteins includes members that are involved in the protection and stabilization of specific pigments. One known function is the facilitation of pigment formation through the condensation of specific aldehydes and amino acids, resulting in compounds with stable imine bonds. These pigments serve as visual attractants for pollinators. Additionally, members of this family exhibit catalase activity, protecting the pigment from degradation by reactive oxygen species by catalyzing the conversion of hydrogen peroxide into water and oxygen.
Beta-lactamase Regulatory Protein (Beta-lactamase_Reg)
Type: Family

This family of proteins includes putative signaling proteins that are implicated in the regulation of beta-lactamase. Members of this family are not believed to directly sense beta-lactams but may play a role in the signaling pathways that control the expression of beta-lactamase, an enzyme responsible for antibiotic resistance to beta-lactam antibiotics. The exact mechanism of action and the pathway in which these proteins operate are not fully elucidated.
Stress Response-Associated Protein (Stress_Response_Assoc)
Type: Family

This family of proteins includes members that are involved in cellular stress response mechanisms. The protein YsnF from Bacillus subtilis is known to be associated with stress response, suggesting a role in the adaptation or protection of the cell under stress conditions. The function of the protein DR_1314 from Deinococcus radiodurans is uncharacterized, but its association with this family implies a potential involvement in similar stress-related processes. Proteins in this family may participate in various cellular pathways that respond to environmental or intracellular stress, contributing to the survival and maintenance of cellular integrity under adverse conditions.
Nucleotide metabolism enzyme (Nucleotide_metab_enz)
Type: Family

This family of prokaryotic proteins includes enzymes involved in nucleotide metabolism. Some members of this family are capable of degrading RNA oligonucleotides, particularly those with a length of five nucleotides, by cleaving them from the 3' to 5' direction. They exhibit a preference for adenine-rich RNA sequences and show reduced activity on shorter oligonucleotides or those with a length of 24 nucleotides . Additionally, some family members possess the ability to hydrolyse cyclic nucleotides such as cAMP and cGMP into their corresponding 5'-monophosphates, without exhibiting phosphohydrolase activity towards phospholipids or phosphorylated sugars . The enzymatic activities of these proteins are crucial for the regulation of intracellular nucleotide levels and the maintenance of RNA turnover.
Threonine-specific kinase-like protein (Thr-specific_kinase-like)
Type: Family

This family of proteins includes members that exhibit kinase activity, with a preference for phosphorylating threonine residues over serine. They may play a role in the regulation of cytoskeletal elements, such as myosin II, particularly during cell division processes like cytokinesis. Some family members are capable of autophosphorylation, which can be enhanced by calcium/calmodulin, indicating a potential regulatory mechanism through calcium signaling. The family encompasses proteins with diverse functions, including those that may impact cell proliferation and developmental progression.
Inner ear hair cell lipoxygenase homology domain-containing protein (Inner_ear_hair_cell_LOXHD)
Type: Family

This family of proteins includes members that are essential for the proper functioning of hair cells in the inner ear, which are critical for the process of hearing. They are characterized by the presence of a lipoxygenase homology domain, which suggests a role in lipid metabolism or signaling pathways related to sensory perception in the auditory system.
Transient receptor potential calcium channel (TRP_calcium_channel)
Type: Family

This family of proteins includes calcium channels that are essential for the regulated release of calcium ions from intracellular stores in response to various stimuli. Members of this family are involved in cellular processes such as response to hyperosmotic shock and stress conditions. They play a crucial role in maintaining cellular homeostasis by contributing to the stability of organelles like mitochondria and vacuoles. These proteins are also implicated in the transcriptional regulation of oxidative stress response genes and are essential for the polarized growth and re-orientation of hyphal tips in certain species, which is a key factor in pathogenicity.
Sacsin chaperone regulator (Sacsin_chaperone_reg)
Type: Family

The Sacsin protein family includes co-chaperones that regulate the Hsp70 chaperone machinery. Members of this family are involved in the processing of proteins linked to ataxia, a neurological disorder affecting coordination. Sacsin proteins contain a functional J domain that stimulates ATPase activity of bacterial dnaK, a homolog of Hsp70, indicating a direct role in chaperone-mediated protein folding. Additionally, they possess a ubiquitin-like domain that mediates interactions with the proteasome, suggesting a role in protein degradation or quality control. The dual functionality of these domains implies a complex role in maintaining cellular proteostasis, particularly in the nervous system where misfolded proteins can lead to disease.
Fungal secondary metabolite regulation transcription factor (Fungal_sec-metab_reg_TF)
Type: Family

This family of proteins includes transcriptional regulators involved in the biosynthesis of secondary metabolites and developmental processes in fungi. Members of this family are known to regulate gene clusters responsible for the production of mycotoxins, such as satratoxins, which can lead to human food poisonings. Additionally, they play a role in the regulation of fungal conidiation and the production of compounds like kojic acid, which has applications in food and cosmetics. These proteins likely function by modulating the expression of key genes within their respective biosynthetic pathways.
Glycosyl Hydrolase 79 Enzymes (GH79_Enzymes)
Type: Family

This family of proteins includes enzymes with beta-glucuronidase activity, which are involved in the hydrolysis of beta-glucuronosyl and 4-O-methyl-beta-glucuronosyl residues of arabinogalactan-protein. These enzymes exhibit very weak hydrolysis of heparan sulfate and no activity on birchwood xylan. They are also capable of catalyzing transglycosylation reactions, transferring glucuronic acid residues to various monosaccharide acceptors, including glucose, galactose, and xylose.
Repressor-like regulatory protein (Repressor-like_regulatory)
Type: Family

This family of proteins includes repressor-like elements that are likely involved in gene regulation. Members of this family may bind to DNA and modulate the transcription of various genes. They could interact with specific DNA sequences, acting as transcriptional repressors or activators depending on the context. These proteins may play a role in the cellular response to environmental changes or stress, contributing to the regulation of genes necessary for adaptation and survival. The exact mechanism of action and the range of target genes may vary among family members, reflecting a potential diversity in function within this protein family.
Scoloptoxin-like (Scoloptoxin-like)
Type: Family

This family of proteins includes neurotoxins known as scoloptoxins. These toxins are typically found in the venom of scorpions and are characterized by their ability to interfere with ion channel function, particularly sodium channels. By binding to these channels, scoloptoxins can disrupt normal neuronal signaling, leading to paralysis and other neurotoxic effects. The proteins in this family share structural similarities that underlie their ability to target and modulate the activity of ion channels, contributing to the venom's overall potency and specificity.