SII-SWORD/CoKE huggingface dataset:
Activin-responsive transcriptional regulator (Activin_resp_transcr_regulator)
Type: Family

This family of proteins functions as transcriptional activators, primarily involved in early developmental processes such as gastrulation and mesoderm specification. They recognize and bind to specific DNA sequences, facilitating the transcription of genes responsive to TGF-beta or activin signaling pathways. Members of this family form transcriptionally active complexes with SMAD2 and SMAD4, which are essential for the regulation of target genes during embryonic development. These proteins play a crucial role in the nodal signaling pathway, contributing to the formation of dorsal axial structures and establishing left-right symmetry in developing embryos. They exhibit a preference for binding to phosphorylated SMAD2 within activated SMAD complexes, mediated by a specialized domain known as the FM region.
Forkhead box transcription regulators (FOX_transcription_regulators)
Type: Family

This family of proteins includes transcription factors that can function as both activators and repressors. They are involved in the regulation of genes associated with cellular responses to oxidative stress, such as heat shock chaperones and antioxidant enzymes. Additionally, they play a crucial role in normal brain development by controlling the expression of genes necessary for this process.
Ciliary Microtubule Inner Protein 2C (CIMIP2C)
Type: Family

This family of proteins includes ciliary microtubule inner proteins that are integral components of the dynein-decorated doublet microtubules within the cilia axoneme. They play a crucial role in the beating of motile cilia, which is essential for various physiological processes including fluid movement and cell locomotion.
T-cell immunoglobulin and mucin domain-containing protein (TIM_domain-containing_protein)
Type: Family

This family of proteins includes receptors that play crucial roles in immune regulation and homeostasis. Members are involved in the recognition and binding of phosphatidylserine, facilitating the trafficking of activated T-cells during inflammatory responses and influencing the accumulation of these cells in the central nervous system, potentially affecting the induction of autoimmune diseases. They also contribute to the regulation of B-cell functions, including their generation, expansion, and suppressor activities. Additionally, these proteins are implicated in the regulation of anti-inflammatory cytokine expression and T-cell proliferation. Some family members serve as viral receptors, mediating the entry of various viruses into host cells. They are characterized by an immunoglobulin V-like domain, a mucin domain, and a cytoplasmic tail with a tyrosine phosphorylation motif, indicating a role in signal transduction.
Oxidized LDL receptor 1-like (OxLDL_rcpt1-like)
Type: Family

This family of proteins functions as receptors for oxidatively modified low-density lipoprotein (oxLDL), which is associated with atherosclerosis. They play a role in the internalization and degradation of oxLDL by vascular endothelial cells, leading to pro-inflammatory and pro-oxidative responses, and apoptosis. These proteins are also involved in the activation of NF-kappa-B signaling, reduction of nitric oxide release, monocyte adhesion, and antigen cross-presentation in dendritic cells. Additionally, they serve as receptors for advanced glycation end products, activated platelets, monocytes, apoptotic cells, and bacteria, contributing to the inflammatory process and immune response.
Cystatin family, spermatogenesis-associated (Cystatin_spermatogenesis)
Type: Family

The cystatin family is characterized by its members' ability to inhibit cysteine proteases. These proteins are involved in various physiological processes, including protein catabolism and extracellular matrix remodeling. Some members of the cystatin family, such as Cystatin-12 and Cystatin-14, are suggested to have specialized roles in spermatogenesis, indicating a potential involvement in reproductive functions . The family includes proteins that are likely to share structural similarities and biological functions, although not all members have well-characterized roles.
G8 domain-containing protein comF-like (G8_domain-comF-like)
Type: Family

This family of proteins is characterized by the presence of a G8 domain, which suggests a potential role in signal transduction or protein-protein interactions. Members of this family are implicated in cellular communication processes, although the exact molecular functions and biological roles may vary among individual proteins. The common feature among these proteins is their similarity to the comF family, indicating a shared evolutionary origin and possibly conserved functional elements.
Insulin-like regulatory peptides (Insulin-like_regulatory)
Type: Family

This family of proteins includes insulin-like peptides that are implicated in the regulation of synapse development at neuromuscular junctions and may influence aging processes. They are likely involved in the negative regulation of dauer formation in response to environmental conditions, acting through the daf-2/InsR signaling pathway. Some members also affect chemotaxis responses to high salt concentrations by acting on specific sensory neurons.
MlaD Inter-membrane Phospholipid Transporter (MlaD_Phospholipid_Transporter)
Type: Family

This family of proteins is involved in the maintenance of lipid asymmetry in bacterial outer membranes. Members function as part of an ABC transporter complex, which is essential for the retrograde trafficking of phospholipids from the outer to the inner membrane. These proteins have a high affinity for phospholipids and are implicated in modulating the ATPase activity of the transporter complex, contributing to its energy-dependent transport mechanism. They are characterized by the ability to form hexameric rings with a central hydrophobic pore, which is crucial for their phospholipid binding function.
Satratoxin biosynthesis SC1 cluster protein 4-like (SAT4-like)
Type: Family

The Satratoxin biosynthesis SC1-like family is involved in the biosynthesis of various secondary metabolites with diverse biological activities. Members of the family are typically part of gene clusters that mediate the production of compounds such as wortmanamides, satratoxins, polyenoic acids, tetraketides fugralins and phomoidrides. These metabolites have roles ranging from antihypercholesterolemic agents to potential manipulators of microbiota. The family includes proteins with functions such as polyketide synthases, condensation domains, acetyltransferases, and enzymes for modification and transport. The exact roles of some members within their respective pathways are yet to be elucidated, but they are collectively important for the biosynthesis and functional expression of bioactive compounds. This family includes rhodopsin domain-containing proteins
Transposase_5 (Transposase_5)
Type: Family

This family of proteins includes transposases which are enzymes that catalyze the movement of transposable elements within the genome. Members of this family are responsible for recognizing specific DNA sequences at the ends of transposable elements and facilitating their excision and insertion into new genomic locations. This process can result in spontaneous mutations and has implications for genome plasticity and evolution. The proteins typically act by making double-strand breaks at the transposon ends, which are then repaired and integrated at a target site. The activity of these proteins is crucial for the mobility of transposable elements they are associated with.
Iron-Sulfur Protein Maturation MIP18 (Fe-S_Maturation_MIP18)
Type: Family

The MIP18 family is involved in the maturation of iron-sulfur (Fe-S) proteins, functioning as Fe-S cluster carriers. Members of this family play a crucial role in various cellular processes by assisting in the assembly and repair of Fe-S clusters, which are vital cofactors for many enzymes. The family includes proteins that protect DNA from oxidative damage, assist in the maturation of enzyme complexes, and support the growth of organisms under conditions demanding high levels of lipoic acid or Fe-S clusters. The family's functions are essential for the proper operation of metabolic pathways that depend on Fe-S cluster-containing proteins, such as those involved in respiration and amino acid synthesis.
Ribonuclease Y/Cyclic di-GMP phosphodiesterase (RNase_Y/CdgJ)
Type: Family

The RNase Y family proteins are endoribonucleases that play a crucial role in mRNA decay, initiating the degradation process. Additionally, a member of this family, CdgJ, functions as a phosphodiesterase that hydrolyzes cyclic diguanylate (c-di-GMP), which is involved in the regulation of bacterial motility and biofilm formation. The family appears to be involved in key regulatory processes in bacteria, affecting both gene expression and cellular behavior.
LOG family pyrimidine/purine nucleotide 5'-monophosphatases (LOG_family_nucleotidases)
Type: Family

The LOG family proteins are enzymes that catalyze the hydrolysis of the N-glycosidic bond in various pyrimidine and purine nucleotide 5'-monophosphates, resulting in the production of ribose 5-phosphate and the corresponding nucleobases. The substrates for these reactions include AMP, GMP, IMP, CMP, dTMP, and UMP. The LOG family proteins do not have the capability to perform the reverse synthesis reactions. Their enzymatic activity is crucial for maintaining nucleoside pool homeostasis by breaking down surplus nucleotides and recycling the ribose component into metabolic pathways. This function is essential for optimal bacterial growth, especially in minimal glucose environments.
Mesaconyl-CoA Hydratase/Beta-methylmalyl-CoA Dehydratase (MCH/BMMD)
Type: Family

This family of proteins is involved in various metabolic cycles related to the processing of Coenzyme A (CoA) derivatives. Members of this family catalyze the reversible hydration and dehydration of specific CoA-bound substrates. These enzymes play a role in the methylaspartate cycle, the ethylmalonyl-CoA pathway, and the glyoxylate assimilation cycle. They are responsible for converting mesaconyl-CoA to beta-methylmalyl-CoA and vice versa, which are key steps in these metabolic pathways. The activities of these proteins are crucial for the assimilation of different carbon sources and the regeneration of acetyl-CoA, which is a central metabolite in energy production and biosynthesis.
Diverse Retrotransposon and Effector-Associated Protein (Retrotransposon-Effector_Assoc)
Type: Family

This family of proteins includes diverse elements such as retrovirus-related pol polyproteins, uncharacterized mitochondrial proteins, secreted RxLR effectors, and proteins associated with transposable elements. The retrovirus-related pol polyproteins are likely involved in the replication and mobilization of retrotransposable elements. The mitochondrial protein's function is not specified. The secreted RxLR effector protein is an oomycete effector that is involved in host-pathogen interactions, although it does not suppress host cell death. The transposon-associated protein's role is not clearly defined but is related to mobile genetic elements. Overall, the family appears to be involved in diverse functions including retrotransposition, host-pathogen interactions, and potentially mitochondrial processes.
Transposase-related protein (Transposase-related)
Type: Family

This family of proteins includes members that are related to transposases, which are enzymes that catalyze the movement of DNA segments within the genome. These proteins typically contain domains that facilitate the binding and cleavage of DNA, as well as the integration of the transposable element into new genomic locations. Transposases are key components of mobile genetic elements, such as transposons, and play a significant role in genome rearrangement, evolution, and the regulation of gene expression. The presence of a transposase domain suggests that these proteins may be involved in DNA recombination processes, although the specific functions of the individual proteins within this family have not been fully characterized.
Radiation response metalloprotease (Rad_response_metalloprotease)
Type: Family

This family of proteins includes metalloproteases that are central regulators in DNA repair and protection pathways, particularly in response to radiation stress. They exhibit site-specific proteolytic activity, cleaving and inactivating repressor proteins, which leads to the induction of gene expression necessary for DNA repair and cell survival post-radiation exposure. These proteins are known to regulate the expression of a variety of proteins, including key DNA repair proteins. Structurally, they are characterized by an N-terminal zinc-peptidase domain, a central helix-turn-helix motif indicative of DNA-binding potential, and a C-terminal GAF-type domain. Their protease activity can be modulated by chelating agents such as EDTA.
Protein O-mannosyl-transferase TMTC (O-mannosyl-transferase_TMTC)
Type: Family

The TMTC family consists of O-mannosyl-transferases that catalyze the transfer of mannosyl residues to the hydroxyl groups of serine or threonine residues. Members of the TMTC family are primarily dedicated to modifying the cadherin superfamily with O-linked mannose glycans, with each member having a unique role in the specific regions of cadherin domain decoration. In addition to their primary function with cadherins, some TMTC proteins also exhibit O-mannosyl-transferase activity on other proteins, such as PDIA3, indicating a broader substrate specificity within this family.
Isochorismatase Family Nicotinamidases (Isochorismatase_Nicotinamidase)
Type: Family

The Isochorismatase Family Nicotinamidases are enzymes that catalyze the deamidation of nicotinamide into nicotinate, a key step in the NAD(+) salvage pathway. This reaction is crucial for maintaining cellular NAD(+) levels, which is essential for various metabolic processes. Members of the family are also involved in the regulation of longevity and stress responses in some organisms by modulating the levels of nicotinamide, an inhibitor of sirtuin proteins. Additionally, certain family members can activate the antituberculous drug pyrazinamide by converting it into its active form, pyrazinoic acid. The family is characterized by its similarity to the isochorismatase superfamily and is subject to inhibition by various compounds, including heavy metals and NAD derivatives.
Zinc-dependent_metallopeptidase_M50B (Metallopeptidase_M50B)
Type: Family

This family of proteins includes zinc metalloproteases that are characterized by their ability to hydrolyze peptide bonds in other proteins. Members of this family are typically involved in various cellular processes, including protein degradation, regulation of cell signaling pathways, and the modulation of membrane protein function. The catalytic activity of these proteases is dependent on the presence of zinc ions, which are essential for the stabilization of the protein structure and the coordination of the water molecule necessary for peptide bond cleavage. The peptidase M50B family, to which these proteins belong, is part of a broader group of metallopeptidases that play crucial roles in maintaining cellular homeostasis.
Metallo-dependent Hydrolases Superfamily Enzymes (Metallo-hydrolase_Enzymes)
Type: Family

This family of proteins includes enzymes that are part of the metallo-dependent hydrolases superfamily, which require metal ions for their catalytic activity. Members of this family are involved in various metabolic processes, including the deamination of pterin metabolites and cytosine, as well as the transformation of N-isopropylammelide. These activities contribute to the catabolism of pterin rings, pyrimidine salvage pathway, and the breakdown of triazine derivatives, respectively. Some family members also have the ability to process mutagenic oxidation products of DNA bases and are implicated in the activation of chemotherapeutic precursors. The enzymes are regulated by various inhibitors, including reaction intermediates and excess divalent cations.
Metallo-dependent Lactonases (Metallo-dep_Lactonases)
Type: Family

The Metallo-dependent Lactonases family comprises enzymes that catalyze the hydrolysis of various lactones to the corresponding carboxylate forms, playing a role in carbohydrate degradation pathways. Members of this family exhibit high substrate specificity for lactones derived from sugars such as L-rhamnono-1,4-lactone and L-fucono-1,5-lactone, among others. The enzymatic activity is dependent on metal ions and is inhibited by metal cations like Zn(2+), Fe(2+), and Cu(2+), but not by chelating agents such as EDTA. The family belongs to the metallo-dependent hydrolases superfamily, indicating a reliance on metal ions for catalytic activity. These enzymes are involved in alternative metabolic routes that bypass phosphorylated intermediates, contributing to the versatility of bacterial carbohydrate metabolism.
L-ornithine N(alpha)-acyltransferase (Ornithine_N-alpha-AT)
Type: Family

This family of proteins is involved in the biosynthesis of ornithine lipids, which are a type of phosphorus-free membrane lipid. Members of this family function as enzymes that catalyze the acylation of ornithine with a 3-hydroxyacyl moiety derived from an acyl carrier protein. This enzymatic activity results in the formation of lyso-ornithine lipid (LOL), representing the initial step in the production of ornithine lipids. These lipids play a role in membrane integrity and function in various bacterial species.
Sugar Degradation Dehydratases (Sugar_Degrad_Dehydratases)
Type: Family

This family of proteins includes dehydratases that are involved in the degradation of various sugars and sugar derivatives. Members of this family catalyze the dehydration of specific substrates such as D-xylonate, L-arabinonate, and 6-deoxy-6-sulfo-D-gluconate, leading to the formation of their respective dehydrated products. These enzymes play roles in different metabolic pathways, including the degradation of D-xylose, L-arabinose, and sulfoquinovose, allowing organisms to utilize these compounds as carbon sources. Some family members exhibit broader substrate specificity and can act on multiple related substrates, while others are more specialized. The activity of these enzymes can be modulated by the presence of metal ions such as Mg(2+).
Benzoxazolinone Detoxification Enzymes (Benzoxazolinone_Detox_Enz)
Type: Family

This family of proteins includes enzymes involved in the detoxification of plant-derived benzoxazolinones. These compounds are phytoanticipins produced by certain plants as a defense mechanism and can be toxic to other organisms. The proteins in this family participate in a multi-step degradation process that converts these toxic compounds into non-toxic derivatives. The initial step involves hydrolysis of the cyclic ester bond in benzoxazolinones, followed by N-malonylation of the resulting aminophenols, leading to the formation of malonamic acids. Additional steps in the detoxification pathway may involve hydrolyzing lactone moieties and amidase activity, although the specific roles of some enzymes in this family are not fully characterized. Collectively, these proteins contribute to the ability of certain organisms to survive in environments where benzoxazolinone-producing plants are present.
Bacterial Cell Wall Dynamics Protein (Cell_Wall_Dynamics_Protein)
Type: Family

This family of proteins includes enzymes with roles in bacterial cell wall dynamics and integrity. Members are involved in processes such as peptidoglycan hydrolysis, which is crucial for cell wall lysis, cell viability, and various stages of bacterial life cycle including sporulation and germination. Some proteins in this family may also be associated with pathogenicity due to their involvement in toxin release. Additionally, certain members may have regulatory functions that are influenced by protease activity and can affect cell wall-binding properties. Another possible function within this family is the formation of ionophores, which are molecules that can transport ions across lipid membranes, potentially impacting cellular homeostasis.
Centromere protein V-like (CENP-V-like)
Type: Family

This family of proteins is involved in the structural organization of chromosomes during cell division. Members are essential for the proper distribution of pericentromeric heterochromatin within interphase nuclei. They play a crucial role in the formation and organization of centromeres, which are key to chromosome alignment and segregation. Additionally, these proteins are implicated in the process of cytokinesis, the final step of cell division where the cytoplasm is divided between two daughter cells.
Thiol S-methyltransferase (Thiol_S-MT)
Type: Family

This family of proteins includes thiol S-methyltransferases that catalyze the transfer of a methyl group from S-adenosyl-L-methionine to various thiol-containing substrates. These enzymes are involved in the methylation of small molecules such as hydrogen sulfide and dithiothreitol. Some family members are known to methylate the N6 position of adenosine in long non-coding RNAs, which may influence the transfer of these RNAs into exosomes and affect cell differentiation and survival. Additionally, certain members may play a role in viral life cycles, specifically in the assembly and release of hepatitis C virus. The activity of these proteins can be inhibited by specific chemical compounds.
Orn/Lys/Arg decarboxylase class-I (Orn_Lys_Arg_decarboxylase-I)
Type: Family

The Orn/Lys/Arg decarboxylase class-I family is characterized by its members' enzymatic function in catalyzing the conversion of arginine to agmatine. This reaction is a key step in the biosynthesis of polyamines, which are critical for cell growth and differentiation. The family includes arginine decarboxylases that are widely distributed across different bacterial species. These enzymes play a crucial role in the polyamine biosynthetic pathway by providing the precursor agmatine for subsequent steps leading to the production of spermidine and spermine, which are essential for various cellular functions including DNA stabilization, protein synthesis, and cell signaling.
Aromatic Compound Degradation Hydrolases (Aro_Compnd_Degr_Hydrolases)
Type: Family

This family of proteins includes enzymes involved in the degradation of various aromatic compounds and sulfonated benzenes. Members of this family catalyze hydrolysis and isomerization reactions that are key steps in specific catabolic pathways. These reactions include the hydrolytical desulfonation of 4-sulfomuconolactone, the hydrolysis of 2-pyrone-4,6-dicarboxylate, and the isomerization of D-galactaro-1,5-lactone. The enzymes are characterized by their metallo-dependent hydrolase activity, with some members being inhibited by metal ions such as Zn(2+), Cu(2+), Mn(2+), and Co(2+). The family plays a crucial role in the utilization of various substrates as carbon sources by different microorganisms.
Bacterial HTH-type regulators and antitoxins (HTH-type_reg/antitoxin)
Type: Family

This family of proteins includes transcriptional regulators and antitoxins involved in bacterial toxin-antitoxin (TA) systems. Members of this family function as antitoxins that neutralize the activity of cognate toxins, thereby preventing cell growth cessation and inhibition of cell proliferation. They can bind to DNA and regulate the transcription of various genes, including their own operons. Some members are known to bind to specific promoter regions, influencing processes such as biofilm formation, stress resistance, and cell motility. The transcriptional regulators within this family typically contain a helix-turn-helix (HTH) motif and may be involved in regulating a range of cellular responses.