SII-SWORD/CoKE huggingface dataset:
Bacterial Potassium Binding (Bact_Kbp)
Type: Family

The protein family includes highly specific potassium binding proteins that are essential for normal growth under high external potassium levels. Members of the family may function as sensors for cytoplasmic potassium concentration, binding potassium ions and undergoing significant conformational changes upon binding. The binding affinity is not exclusive to potassium, as larger alkali metal ions such as rubidium and cesium, as well as ammonium, can also be accommodated. The family is characterized by the presence of BON and LysM domains, which synergistically contribute to potassium binding. The BON domain primarily facilitates the binding, while the LysM domain stabilizes the complex. Some members are uncharacterized, but they share similarity with characterized potassium binding proteins, suggesting a conserved function within the family.
Complex I 49 kDa subunit-like (ComplexI_49kDa-like)
Type: Family

This family of proteins includes subunits of enzyme complexes involved in energy metabolism, such as hydrogenases and NADH-ubiquinone oxidoreductase (complex I). They play roles in redox reactions, coupling these to proton translocation across membranes, which is essential for energy conservation in the form of proton gradients. Some members are involved in the oxidation of carbon monoxide, which is coupled to the reduction of protons by a hydrogenase. The family is characterized by the presence of iron-sulfur (Fe-S) clusters that are crucial for their catalytic activity. These proteins are also involved in the regulation of hydrogen production from protons.
Indolepyruvate Oxidoreductase IorB (IorB_Oxidoreductase)
Type: Family

This family of proteins is involved in the oxidative decarboxylation of arylpyruvates. Members of this family function as enzymes that facilitate the ferredoxin-dependent conversion process, which is a key step in the metabolic pathway. The enzymatic activity is crucial for the catabolism of aromatic compounds, where it contributes to the breakdown and utilization of these molecules for energy production and biosynthesis.
Myo-inositol 1-phosphate synthase (MIPS)
Type: Family

This family of proteins includes enzymes that are key in the biosynthesis of myo-inositol, a molecule with various cellular functions including as a precursor for inositol phospholipids and inositol phosphates. Members of this family catalyze the NAD-dependent conversion of glucose 6-phosphate to 1D-myo-inositol 3-phosphate. This reaction is the first and rate-limiting step in the production of myo-inositol. In addition to their central role in myo-inositol production, these enzymes also contribute to oxidative stress resistance by providing the precursor for the synthesis of the protective antioxidant mycothiol.
Protoporphyrinogen IX dehydrogenase (Protoporphyrinogen_IX_DH)
Type: Family

This family of proteins catalyzes the 6-electron oxidation of protoporphyrinogen IX to protoporphyrin IX, a key step in the biosynthesis of heme. The reaction is mediated by different electron acceptors depending on the environmental oxygen availability. Under anaerobic conditions, members of this family typically use menaquinone as an electron acceptor, while under aerobic conditions, ubiquinone is used. The activity of these enzymes is crucial for cellular respiration as it is linked to electron transfer across the cell membrane, contributing to ATP synthesis. Some family members have shown the ability to transfer electrons to various reductases and oxidases, highlighting their role in the electron transport chain.
Leucine-rich repeat-containing regulator of pluripotency (LRR-containing_regulator)
Type: Family

This family of proteins includes members that are highly expressed in stem cells and may play a role in the regulation of pluripotency. They are implicated in maintaining the normal expression of key pluripotency regulators such as POU5F1/OCT4 and KLF4. Additionally, these proteins are important for the expression of marker genes indicative of ectodermal and endodermal lineage commitment, such as NES and GATA4, respectively. They may also promote stem cell proliferation in vitro, suggesting a role in stem cell maintenance and possibly differentiation.
Yeast Metabolic Pathway Regulatory Proteins (Yeast_MetPath_Reg)
Type: Family

This family of proteins includes transcriptional regulators that interact with various elements of cellular machinery to control gene expression. Members of this family are involved in the regulation of metabolic pathways, such as the pyrimidine and purine utilization pathways, by acting as positive regulators of gene expression. Some proteins within this family bind to specific DNA sequences to mediate gene induction, while others interact with protein complexes like SIN3 or protein kinases such as SNF1 to exert their regulatory functions. Additionally, certain family members are implicated in the negative regulation of drug resistance genes by modulating the expression of ABC transporter genes. The diverse regulatory roles suggest that these proteins are key modulators of cellular response to metabolic needs and stress conditions.
GHMP Kinase-Related Enzymes (GHMP_Kinase-Related)
Type: Family

This family of proteins includes enzymes that are involved in the salvage pathways of various sugars. Members of this family exhibit kinase activity, where they catalyze the phosphorylation of specific sugar substrates using ATP or GTP. Some members are bifunctional, having both kinase and pyrophosphorylase activities, specifically converting L-fucose to GDP-L-fucose. Others are involved in the phosphorylation of D-glycero-alpha-D-manno-heptose 7-phosphate to form a bisphosphate product. The activities of these enzymes are crucial for the reutilization of sugars from the degradation of oligosaccharides, contributing to the metabolic processes within the cell.
PpiC/parvulin rotamase (PpiC/parvulin_rotamase)
Type: Family

The PpiC/parvulin rotamase family is characterized by its peptidyl-prolyl cis-trans isomerase (PPIase) activity, which plays a crucial role in accelerating the folding of proteins. Members of the family exhibit a preference for substrates with hydrophobic side chains, such as leucine and phenylalanine, at the P1 position. While the family generally contributes to protein folding, one member is noted for not being inhibited by immunosuppressive drugs cyclosporin A or FK506, suggesting a regulatory mechanism distinct from other PPIases. The family's function is essential for various cellular processes, as proper protein folding is critical for maintaining cellular function and homeostasis.
Flagellar biosynthesis and adherence (FliO/MopB)
Type: Family

The FliO/MopB family is involved in bacterial motility and virulence, with members playing roles in flagellar biosynthesis and adherence. Proteins in the family may assist in the localization and assembly of flagellar components and adhesins on the bacterial surface, which are crucial for movement and host interaction. The family includes proteins that are required for both motility and virulence, indicating a dual function that is essential for the pathogenicity of some bacteria.
All-trans-retinol saturase (Retinol_saturase)
Type: Family

This family of proteins includes enzymes that are involved in the metabolism of vitamin A. They catalyze the saturation of all-trans-retinol, converting it to all-trans-13,14-dihydroretinol, a step in the vitamin A metabolic pathway. These enzymes do not show activity towards all-trans-retinoic acid or various cis-isomers of retinol. Beyond their enzymatic role, they may also influence liver metabolism and adipocyte differentiation, with potential regulatory functions upstream of MLXIPL/ChREBP. One member is noted to be inactive, while others have additional functions such as regulating adipocyte differentiation and possibly affecting liver metabolism.
Max-like/E-box-binding transcription factors (Max-like/E-box_TFs)
Type: Family

The protein family in question is involved in transcriptional regulation, with members forming sequence-specific DNA-binding complexes that recognize the E box motif 5'-CACGTG-3'. These complexes can act as transcriptional repressors or activators, depending on the context and interacting partners. Family members are implicated in various biological processes including glycolytic gene regulation, fat oxidation, mitochondrial respiration, lifespan maintenance, fertility, body size regulation, autophagy, cell migration, and stress responses. They play roles in modulating longevity in response to multiple signaling pathways and environmental factors, and in the transcriptional regulation of genes encoding extracellular matrix components. Some members are also involved in host-pathogen interactions, influencing the infection by certain pathogens.
DmX-like/RAVE complex component (DmX-like/RAVE_component)
Type: Family

This family of proteins includes members that are involved in various cellular processes. Some proteins in this family may function as scaffold proteins, interacting with other proteins such as MADD and RAB3GA on synaptic vesicles, and are implicated in the regulation of neuronal and endocrine homeostatic processes. Other family members are components of the RAVE complex, which is essential for the stable assembly of the V-ATPase complex, a critical component for vacuolar acidification and membrane transport. These proteins play roles in the brain and are key controllers of homeostasis, as well as being involved in the transport between endosomal compartments and the assembly of vacuolar ATPase.
Adenosylcobinamide Amidohydrolase (CbiZ)
Type: Family

The CbiZ family is involved in the de novo biosynthesis of coenzyme B12. Members of the CbiZ family, such as adenosylcobinamide amidohydrolases, catalyze the conversion of adenosylcobinamide to adenosylcobyric acid, an essential intermediate in this biosynthetic pathway. The function of some members within the family remains uncharacterized, but characterized members play a crucial role in the production of coenzyme B12, which is vital for various cellular processes including DNA synthesis, fatty acid metabolism, and energy production.
Secreted LysM effector LysM1-like (LysM1-like)
Type: Family

This entry represents Secreted LysM effector LysM1 from Trichophyton rubrum and similar sequences mainly found in fungi. LysM1 binds two substrates, chitin and N-linked oligosaccharides associated with human skin glycoproteins . Chitin oligosaccharides are degradation products of fungal cell walls. Members of this family may play a role in modulating the host's immune response during fungal invasion by sequestering these oligosaccharides. The presence of LysM domains suggests a specific binding affinity to chitin and possibly related carbohydrates, which could be a mechanism for attenuating the host defence system .
Cpx two-component system auxiliary protein (Cpx_auxiliary_protein)
Type: Family

This family of proteins includes periplasmic components involved in bacterial stress response and protein quality control. Members act as auxiliary proteins in the Cpx two-component envelope stress response system, modulating the response to various inducers. They bind the periplasmic domain of the sensor histidine kinase CpxA, inhibiting its kinase activity and thus the induction of the stress response in the absence of inducers. Additionally, these proteins exhibit chaperone activity, aiding in the refolding of misfolded proteins and preventing protein aggregation in the periplasm. They can also enhance the stability of periplasmic proteins and protect against inactivation by antimicrobial compounds such as tannins. The family is characterized by a cradle-shaped structure that may interact with substrates and other periplasmic components.
Pleckstrin homology-like domain-containing protein (PH-like_domain)
Type: Family

This family of proteins includes members that contain a Pleckstrin homology (PH) domain, which is known to be involved in binding to phosphoinositides. This interaction is important in cellular signaling pathways and membrane dynamics. Additionally, some members of this family are implicated in the assembly of the postsynaptic apparatus and may contribute to the aggregation of acetyl-choline receptors (AChR) at the postsynaptic membrane, suggesting a role in synaptic function and neurotransmission.
Partitioning defective 3 homolog (PAR3)
Type: Family

The PAR3 family consists of adapter proteins involved in the establishment and maintenance of cell polarity, playing a pivotal role in asymmetrical cell division. Members of the family are central to the formation of epithelial tight junctions and are implicated in various cellular processes, including the targeting of the phosphatase PTEN to cell junctions, Schwann cell peripheral myelination, and the establishment of neuronal polarity and axon formation. The family proteins interact with PARD6B and atypical protein kinase C proteins via GTP-bound Rho small GTPases, influencing tight junction assembly and cell polarization. Some members are also involved in early embryonic development, contributing to cell adhesion, gastrulation, and the establishment of apicobasal and anterior-posterior asymmetries.
Diacylglycerol Lipase-Related (DAG_Lipase-Related)
Type: Family

This family of proteins includes serine hydrolases that are involved in the biosynthesis of the endocannabinoid 2-arachidonoylglycerol (2-AG) by hydrolyzing diacylglycerols (DAGs) containing arachidonic acid. These enzymes preferentially cleave sn-1 fatty acids from DAGs and have minimal activity against other lipid substrates such as monoacylglycerols and phospholipids. They play a crucial role in the central nervous system by regulating 2-AG signaling, which is important for neuronal synapse activity, axonal growth, neurogenesis, and the physiological regulation of anxiety and depressive behaviors. Additionally, they are involved in neuroinflammatory responses and support the metabolic and signaling demands of macrophages by regulating the pools of 2-AG and arachidonic acid for eicosanoid production.
Plant ABC transporter G (Plant_ABCG)
Type: Family

The ABC transporter G family is involved in various transport functions across the plant cell membrane. Members of this family are implicated in the development and maintenance of plant structures such as the cuticle, root suberin, and pollen coat by regulating the transport of lipids, cutin, waxes, and possibly lignin precursors. They play a role in developmental plasticity, stress responses, and vascular development. Some members are also involved in the secretion of cuticular wax, which is crucial for plant interactions with the environment, including response to microbial infection and influencing plant attractiveness to insect vectors. Additionally, a member of the family in Petunia hybrida is responsible for the release of volatile organic compounds that attract pollinators during the evening and night.
CRISPR-associated Csm3 endoribonuclease (CRISPR_Csm3_endoribonuclease)
Type: Family

This family of proteins is associated with the CRISPR adaptive immune system, which protects against mobile genetic elements such as viruses, transposable elements, and conjugative plasmids. Members of this family are involved in the CRISPR mechanism where they act as endoribonucleases targeting single-stranded RNA (ssRNA). They cleave target RNA at regular six nucleotide intervals and are part of the type III-A Csm effector complex. This complex binds CRISPR RNA (crRNA) and exhibits multiple enzymatic activities, including RNA-guided RNase, DNase, and cyclic oligoadenylate synthase functions. The binding of target RNA that is complementary to the crRNA is essential for these activities. Some members also exhibit non-specific single-stranded DNA (ssDNA) nuclease activity, which is regulated by the cleavage of target RNA, suggesting a mechanism to prevent uncontrolled DNA degradation.
Mitochondrial and Peroxisomal Carrier Protein (Mito/Peroxisomal_Carrier)
Type: Family

This family of proteins includes mitochondrial and peroxisomal transporters that are involved in the translocation of various cofactors across the organelle membranes. Members of this family are characterized by their ability to transport molecules such as coenzyme A (CoA), flavin adenine dinucleotide (FAD), flavin mononucleotide (FMN), and nucleotide adenosine monophosphate (AMP), among others. Some proteins in this family are suggested to function through a counter-exchange mechanism, allowing the import of these cofactors into the peroxisomal matrix from the cytosol. Additionally, these proteins lack typical peroxisomal sorting signals and have regions necessary for peroxisome-targeting activity. The family is part of the larger mitochondrial carrier superfamily, which is known for its role in the transport of metabolites and nucleotides across mitochondrial membranes.
Archaeal Preflagellin Peptidase (Preflagellin_Peptidase)
Type: Family

This family of proteins includes enzymes known as preflagellin peptidases, which are responsible for the cleavage of the N-terminal leader peptide from preflagellins. This processing step is crucial for the proper assembly of flagellins into the flagellum structure, a whip-like appendage that enables motility in archaeal cells. Members of this family are characterized by their belonging to the peptidase A24 family, specifically the archaeal preflagellin peptidase subfamily, indicating a conserved mechanism of action across different archaeal species.
DNA Photolyase Class-2 (Photolyase_Class-2)
Type: Family

This family of proteins is involved in the cellular response to ultraviolet (UV) radiation-induced DNA damage. Members of this family catalyze the light-dependent repair of cyclobutyl pyrimidine dimers, which are DNA lesions formed between adjacent pyrimidine bases on the same DNA strand after exposure to UV light. The repair process, known as photoreactivation, involves the monomerization of these dimers, restoring the DNA to its undamaged state. This activity is crucial for maintaining genomic integrity and is necessary for organismal survival under UV-B light. The proteins are not responsible for repairing other types of UV-induced DNA damage, such as (6-4) photoproducts.
Methyltransferase-like protein 25 (METTL25)
Type: Family

The METTL25 family comprises proteins with a putative function as methyltransferases. Members of this family, known as Methyltransferase-like protein 25B and Probable methyltransferase-like protein 25, are characterized by their similarity to other methyltransferases, suggesting a role in the transfer of methyl groups to various substrates. The exact biochemical function and specific substrates for methylation by the METTL25 family members remain to be elucidated. However, the conserved nature of these proteins implies a potential regulatory role in cellular processes through methylation, which is a common post-translational modification influencing protein function and interactions.
SLC35F Solute Transporter (SLC35F_Transporter)
Type: Family

This family of proteins is involved in the transport of solutes across cellular membranes. Members are characterized as putative solute transporters and are part of the SLC35F solute transporter family, which suggests a role in the facilitated or active transport of specific substrates, although the exact substrates and transport mechanisms may vary among family members. The function of these proteins is essential for maintaining cellular homeostasis by regulating the intracellular concentration of various molecules.
Arabidopsis DESIGUAL (DESIGUAL)
Type: Family

The DESIGUAL family is involved in various developmental processes in Arabidopsis thaliana. Members of the family contribute to secondary cell wall biology, particularly in lignin biosynthesis, which is crucial for plant structural integrity and defense. Some members are also implicated in ensuring bilateral symmetry development and early leaf margin patterning, likely through the regulation of auxin and CUC2 distribution. Additionally, they play a role in embryo provasculature development, cotyledon vascular complexity, and connectivity, as well as regulating cell proliferation.
Actin Cytoskeleton Regulatory (Actin_Cytoskeleton_Reg)
Type: Family

This family of proteins is involved in the regulation of the actin cytoskeleton. Members of this family target specific proteins to the actin cytoskeleton and are essential for the modulation of cytoskeletal organization. They play a role in the formation of cellular structures such as stress fibers and rootlets, and are required for processes like cell spreading, cell contraction, and mitotic progression. These proteins interact with RhoA and ROCK1 to regulate the stability of actin fibers, which is crucial for maintaining the structural integrity of muscle cells and neuronal cells. They also possess actin-binding domains, which allow them to bind and stabilize filamentous F-actin, preventing its depolymerization and facilitating the recruitment of additional proteins necessary for actin formation and turnover.
THAP domain-containing protein (THAP_domain_protein)
Type: Family

This family of proteins includes members with sequence-specific DNA-binding activity, suggesting a role in transcriptional regulation. Some members have been shown to function as transcriptional repressors in vitro. Additionally, there is evidence that overexpression of certain family members can lead to cell cycle arrest at the G2/M phase, indicating a potential involvement in cell cycle regulation.
Serine/arginine repetitive matrix (Ser/Arg_repetitive_matrix)
Type: Family

The Serine/arginine repetitive matrix protein family is involved in various pre-mRNA splicing and processing events. Members of this family are integral components of both pre- and post-splicing multiprotein mRNP complexes and play a role in the splicing of U12-type introns as part of the minor spliceosome. They are known to promote splicing activation, both constitutive and ESE-dependent, by connecting sequence-specific splicing factors with basal snRNP components of the spliceosome. Additionally, they can stimulate mRNA 3'-end cleavage independently of exon junction complex formation and have the ability to bind RNA and DNA with low sequence specificity, showing no marked preference for double- or single-stranded substrates.
UPF0332 putative toxin (UPF0332_toxin)
Type: Family

The UPF0332 family includes proteins that are putative toxin components of type VII toxin-antitoxin (TA) systems. These systems typically consist of a stable toxin and a labile antitoxin that can neutralize the toxin's effect. The antitoxins degrade under stress conditions, freeing the toxins to inhibit cell growth or kill the cell. This regulatory mechanism helps the bacteria to survive under adverse conditions. The exact functions of UPF0332 family members are not well characterized, and their roles may vary among different organisms.
Arf-GAP with Rho-GAP domain, ANK repeat and PH domain-containing protein (Arf-Rho-GAP_ANK-PH_domain)
Type: Family

This family of proteins includes GTPase-activating proteins (GAPs) that are involved in the modulation of the actin cytoskeleton. They are activated by binding to specific phosphoinositides, including phosphatidylinositol 3,4,5-trisphosphate and, to a lesser extent, phosphatidylinositol 3,4-bisphosphate. These proteins regulate the activity of ARF and RHO family members, which are small GTPases playing critical roles in actin dynamics, membrane trafficking, and cell signaling. Some family members exhibit specificity towards certain ARF isoforms. Additionally, they may participate in cellular processes such as the internalization of anthrax toxin by influencing the cytoskeletal architecture.