SII-SWORD/CoKE huggingface dataset:
Fungal Meroterpenoid Biosynthesis Methyltransferases (Meroterpenoid_MTases)
Type: Family

This family of proteins includes methyltransferases involved in the biosynthesis of various fungal meroterpenoids. These enzymes typically catalyze the transfer of methyl groups from S-adenosyl-L-methionine (SAM) to specific substrates, which are often intermediates in the production of secondary metabolites with diverse biological activities. The reactions they facilitate are essential steps in the formation of complex chemical structures, such as those found in antitumor agents, mycotoxins, and other bioactive compounds. The proteins in this family share a similarity in that they belong to the class I-like SAM-binding methyltransferase superfamily, indicating a common mechanism of action and structural fold.
FAM161 (FAM161)
Type: Family

The FAM161 family is associated with cellular structures known as cilia, which are hair-like projections on the cell surface. Members of the FAM161 family are involved in the process of ciliogenesis, which is the formation and maintenance of cilia. Cilia play crucial roles in motility, sensory perception, and signaling pathways. Defects in ciliogenesis can lead to a variety of human diseases, collectively known as ciliopathies.
LEM domain-containing (LEM_domain)
Type: Family

The LEM domain-containing protein family is associated with the nuclear lamina and the inner nuclear membrane, playing critical roles in maintaining nuclear structure, chromosome segregation, and cell division. Members of the family are involved in organizing the distribution of nuclear components such as lamins, nuclear pore complexes, and chromatin. They participate in nuclear envelope reformation post-mitosis and may influence DNA replication initiation. Some family members interact with BANF1 and are implicated in muscle cell attachment and sarcomere organization. The family also includes thymopoietins, which have immunomodulatory effects on T-cell development and function. Additionally, they may be involved in DNA damage repair and transcriptional regulation.
RNF168/RNF169 E3 ubiquitin-protein ligase (RNF168/RNF169_E3_ubiq-ligase)
Type: Family

This family of proteins includes E3 ubiquitin-protein ligases that play a crucial role in DNA damage response. They are involved in the accumulation and regulation of repair proteins at sites of DNA damage, particularly double-strand breaks (DSBs) and interstrand cross-links (ICLs). These proteins function by recognizing and binding to ubiquitinated histones, amplifying histone ubiquitination, and promoting the formation of 'Lys-63'-linked ubiquitin conjugates. This activity is essential for the recruitment of other repair factors and complexes to DNA lesions, thereby facilitating proper repair pathway utilization. Some family members also participate in transcriptional silencing near DSBs to prevent transcription-repair conflicts and are implicated in immune system processes such as class switch recombination. The family is characterized by the presence of MIU and UMI motifs, which mediate specificity for different types of ubiquitin chains through their juxtaposition with LR motifs.
Ubiquitin-like domain-containing CTD phosphatase 1 (UBLCP1)
Type: Family

Ubiquitin-like domain-containing CTD phosphatase 1 (UBLCP1) is characterised by an ubiquitin-like domain that mediates interactions with proteasomes. Members of this family are involved in the regulation of proteasome activity by dephosphorylating 26S nuclear proteasomes, which results in a decrease in their proteolytic activity . These proteins are recruited to the 19S regulatory particle of the 26S proteasome, where they target components such as PSMC2/RPT1, impairing ATPase activity and disrupting proteasome assembly . Some reports also suggest that members UBLCP1 can stimulate the proteolytic activity of the 26S proteasome, indicating a complex role in proteasome regulation .
Serine Protease S1 Domain-Containing Protein (Serine_Protease_S1-Domain)
Type: Family

This family of proteins includes serine proteases with diverse biological functions. Some members, known as thrombins, play a crucial role in the coagulation cascade by converting fibrinogen to fibrin, which is essential for blood clot formation. They also activate several coagulation factors and protein C, contributing to blood homeostasis, inflammation response, and wound healing. These proteins are regulated by inhibitors such as SERPINA5. Other members of this family, although classified as serine proteases, are inactive and may be involved in the regeneration of skeletal muscle. The family is characterized by a similarity to the peptidase S1 family, indicating a shared structural domain that typically confers protease activity.
BPI fold-containing BPI/LBP (BPI_fold-BPI/LBP)
Type: Family

This family of proteins is involved in the recognition and binding of specific odorant molecules. They may function as carrier molecules, transporting odorants across the mucus layer to olfactory receptors. Additionally, they may play a role in mucosal defense by identifying and removing harmful odorants or pathogenic microorganisms, as well as clearing excess odorants to facilitate the detection of new stimuli.
Actin filament dynamics regulator (Actin_filament_regulator)
Type: Family

This family of proteins is involved in the organization and regulation of the cytoskeleton, particularly in actin filament dynamics and microtubule organization. Members of this family play crucial roles in various cellular processes including cytokinesis, cell polarity, and cell shape maintenance. They are characterized by their ability to nucleate actin filaments, cap the barbed ends of actin filaments, and interact with profilin to regulate actin polymerization. Some members are also involved in recruiting and activating the Arp2/3 complex, leading to actin polymerization. Additionally, these proteins are implicated in the positioning and movement of the spindle during cell division, and some have been associated with virulence in pathogenic organisms.
H2.0 Homeobox Neural Patterning (H2.0_Homeobox_NeuralPatt)
Type: Family

The H2.0 homeobox family is involved in the patterning and differentiation of the central nervous system during embryogenesis. Members of the family, such as DBX1 and DBX2, play crucial roles in regulating the phenotypic features that distinguish ventral interneurons, V0 and V1 neurons. They are responsible for determining transcription factor profiles, neurotransmitter phenotypes, migratory paths, and axonal trajectories. Additionally, some members may inhibit neuronal differentiation within certain progenitor populations, influencing the identity of cells in the developing spinal cord and hindbrain.
C-type lectin and Tetranectin domain-containing protein (CLec_Tetranectin-domain)
Type: Family

This family of proteins includes members that are involved in various biological processes such as cell adhesion, osteogenesis, and possibly exocytosis. Some family members promote cell adhesion by interacting with extracellular matrix components like laminin and fibronectin. Others are implicated in bone health by stimulating the differentiation of mesenchymal progenitors into osteoblasts, which are essential for bone repair and maintenance. Additionally, certain proteins within this family may bind to plasminogen and could play a role in the packaging of molecules for exocytosis, as well as contributing to retinal function.
MYND-type zinc finger domain-containing protein (MYND-type_zinc_finger)
Type: Family

This family of proteins includes MYND-type zinc finger domains and is involved in the regulation of morphogenesis and polarized growth. Members of this family play a crucial role in the onset of polarized growth, branching regulation in hyphae, and spore formation. In yeast, they are also implicated in the ubiquitin-dependent degradation of specific proteins, contributing to cellular protein homeostasis.
Adrenomedullin-regulatory peptide (Adrenomedullin-reg_peptide)
Type: Family

This family of proteins includes regulatory peptides with a role in cardiovascular and gastrointestinal bioactivity modulation. Members of this family are known to be potent hypotensive and vasodilatory agents, with some acting as hormones in circulation control. They are involved in the physiological control of fluid and electrolyte homeostasis, with functions including diuretic and natriuretic effects, inhibition of aldosterone secretion, and suppression of basal ACTH secretion. Their actions are mediated through receptor complexes, particularly involving CALCRL and RAMPs, and they activate the cAMP-dependent pathway. Some family members may have non-functional remnants or exhibit both peripheral vasodepressor and central vasopressor effects.
Seminal Plasma Capacitation Regulator (SP_Capacitation_Regulator)
Type: Family

This family of proteins is involved in the reproductive process, specifically in the binding and capacitation of sperm. Members of this family have been shown to interact with spermatozoa, promoting their fertilizing capacity and potentially playing a role in the sperm's ability to fertilize the egg. Some proteins in this family have been noted to bind to high density lipoproteins (HDLs), heparin, and gelatin, which may facilitate the capacitation process. Additionally, certain members may influence the release of pituitary gonadotropins, indicating a regulatory function in reproductive hormone signaling. The binding activities to various substances, including glycosaminoglycans, phospholipid liposomes, and phosphorylcholine, suggest a multifaceted role in sperm maturation and interaction within the female reproductive tract.
Archaeal ATPase domain-containing protein (Archaeal_ATPase_domain)
Type: Family

This family of proteins is involved in ATP binding and hydrolysis, which are fundamental processes in cellular energy transactions and signaling. Members of this family are characterized by their ability to bind ATP, a common molecular currency of energy in cells. The hydrolysis of ATP by these proteins is often coupled to various cellular activities, including molecular transport, signal transduction, and mechanical work. Given the broad role of ATPases in cellular functions, proteins in this family may be implicated in a variety of biological processes specific to archaeal organisms. However, the precise functions of these uncharacterized ATP-binding proteins within the archaeal ATPase family remain to be elucidated through further experimental studies.
Autophagy-related protein 33 (ATG33)
Type: Family

This family of proteins is involved in the selective degradation of mitochondria via autophagy. Autophagy is a cellular process that occurs during starvation and at post-log phase, where it plays a critical role in maintaining cellular homeostasis by recycling cellular components. Members of this family are essential for proper vegetative growth, asexual and sexual reproduction, and contribute to the virulence of certain species by participating in the biosynthesis of specific virulence determinants.
Immune Modulating & Transcription Coactivator (Immune_Mod/Transcr_Coactivator)
Type: Family

This family of proteins includes cell surface receptors that modulate innate and adaptive immune responses, with a general inhibitory function on immune cells. They are involved in regulating macrophage activation, promoting immunological tolerance, and attenuating T-cell receptor-induced signaling. These proteins serve as receptors for certain ligands, potentially influencing T-cell responses and phagocytosis of apoptotic cells. They also interact with components of the immune system to regulate cytokine production and innate immune responses. Additionally, they are implicated in the transcriptional regulation of RNA polymerase II-dependent genes, acting as coactivators that bridge gene-specific regulatory proteins with the basal transcription machinery.
TNF and chemokine receptor-like (TNF_chemokine_rcpt-like)
Type: Family

This family of proteins includes receptors that interact with tumor necrosis factor (TNF) and chemokines. They are involved in modulating the immune response by binding to these signaling molecules in the extracellular space, which inhibits the host's immune defense mechanisms. Some members mimic host TNF receptors and can bind TNF with high affinity, potentially preventing TNF from reaching its cellular targets and dampening its antiviral effects. The family also includes viral proteins that can bind host chemokines, thereby interfering with chemokine-mediated immune responses.
CYSTM1 Heavy Metal Tolerance (CYSTM1_HM_Tolerance)
Type: Family

The CYSTM1 family proteins are involved in conferring resistance to various heavy metal ions. They achieve this by chelating the ions at the plasma membrane of root cells, which prevents the ions from entering the cells and reduces their accumulation within the organism. Members of the CYSTM1 family have been shown to interact with metals such as cadmium, copper, and aluminium. The chelation process is crucial for the detoxification and tolerance of these potentially toxic ions, allowing organisms to survive in environments with high concentrations of heavy metals.
Single-stranded-DNA-specific exonuclease RecJ (SSDNA_exonuclease_RecJ)
Type: Family

The RecJ family comprises single-stranded-DNA-specific exonucleases that play a crucial role in various recombinational DNA repair events. Members of this family are required for the processing of DNA during repair and recombination, with some acting in a 5' to 3' direction. The necessity of RecJ family proteins can vary depending on the type of recombinational event and the availability of other recombination gene products. Some members are implicated in RecA thread formation during DNA double-strand break repair. The family includes both well-characterized exonucleases and putative proteins suggested to have similar functions based on sequence similarity.
Malate Decarboxylating Enzymes (Malate_Decarboxylase)
Type: Family

This family of proteins includes enzymes that are primarily involved in the decarboxylation of malate to pyruvate, a key step in the tricarboxylic acid cycle. Some members also exhibit malolactic enzyme activity, converting malate to lactate, particularly in the presence of NADPH. These enzymes can use either NAD or NADP as a cofactor, although there is a preference for NADP in certain members. The family is characterized by a C-terminal domain that may be involved in oligomerization and is associated with regulatory functions, including inhibition by acetyl-CoA and activation by various metabolites. Additionally, some members are bifunctional, with the ability to decarboxylate oxaloacetate. The enzymes play crucial roles in metabolic processes such as nitrogen fixation in bacteria and maintaining cellular NADPH balance.
Endonuclease/exonuclease/phosphatase family domain-containing protein 1 (Endo/Exo/Phosphatase_dom_1)
Type: Family

The Endonuclease/exonuclease/phosphatase family domain-containing proteins are involved in DNA processing, with a specific role in the uptake of transforming DNA. Although not directly responsible for DNA binding, they are essential for DNA transport into the cell and may indirectly influence DNA binding. Their function is crucial in genetic transformation processes, where exogenous DNA is incorporated into a recipient cell, leading to genomic alteration and diversification.
UPF0053 domain-containing protein (UPF0053_domain)
Type: Family

This family of proteins is characterized by the UPF0053 domain, which is a conserved domain found in a wide range of bacteria. The exact function of this domain is not well understood, but it is thought to be involved in metal ion transport or binding, possibly playing a role in maintaining metal homeostasis within the cell. Proteins containing the UPF0053 domain are typically small and may be involved in cellular processes that are essential for survival in various environmental conditions. Further research is required to elucidate the specific biochemical pathways and mechanisms in which these proteins are involved.
AfsR/DnrI/RedD regulatory protein (AfsR-DnrI-RedD_regulator)
Type: Family

This family of proteins includes transcriptional regulators that are involved in the control of various biosynthetic pathways, such as antibiotic production and molybdopterin biosynthesis. Members of this family are characterized by their ability to bind DNA and activate the transcription of specific operons or genes. Some proteins in this family are part of two-component regulatory systems, while others may have additional enzymatic activities, such as ATPase and GTPase. They play crucial roles in the regulation of secondary metabolite formation and the response to environmental stimuli.
Aminoglycoside Phosphotransferase Enzymes (AGP_Transferase)
Type: Family

This family of proteins is involved in the inactivation of aminoglycoside antibiotics through phosphorylation, which confers resistance to these antibiotics. The phosphorylation process targets the hydroxyl groups of the aminoglycoside molecules, thereby preventing their interaction with bacterial ribosomes and subsequent inhibition of protein synthesis. Members of this family are known to confer resistance to various aminoglycosides, including kanamycin, amikacin, and hygromycin, among others. The activity of these enzymes is a common mechanism of antibiotic resistance in bacteria, which is a significant concern in the treatment of bacterial infections.
Divalent Anion Sodium Symporter-Related Transporters (DASS-Related_Transporters)
Type: Family

This family of proteins includes transporters involved in the translocation of various substrates across biological membranes. Members of this family are primarily associated with the transport of anions such as sulfate, as indicated by the presence of sodium/sulfate cotransporters that exhibit varying affinities for sulfate. These cotransporters are part of the divalent anion:Na+ symporter (DASS) superfamily, suggesting a role in the electrogenic symport of sulfate ions in exchange for sodium ions. Additionally, some members are implicated in the transport of basic amino acids and may influence metabolic pathways such as the glyoxylate shunt. Other proteins within the family are uncharacterized but are related to known transporters, hinting at potential roles in cellular responses to nutrient availability or environmental stress.
ATP-dependent Glutamate--Cysteine Ligase Type 2 (ATP-dep_Glu-Cys_Ligase-2)
Type: Family

This family of proteins includes ATP-dependent carboxylate-amine ligases with a weak activity as glutamate--cysteine ligases. Members of this family are involved in the catalysis of the ligation of glutamate and cysteine, a key step in the biosynthesis of glutathione, although the activity appears to be weak. The family is part of the YbdK subfamily, which suggests a conserved function or structural domain within this group.
Serine/Threonine Kinases and Pseudokinases (Ser/Thr_Kinases-Pseudokinases)
Type: Family

This family of proteins includes both active serine/threonine kinases and pseudokinases. The active kinases are involved in various cellular processes such as signal transduction pathways, stress responses, and regulation of gene expression. They may function in defense mechanisms, potassium homeostasis, and viral egress. The pseudokinases, despite lacking catalytic activity, play crucial roles in programmed cell death processes like necroptosis. They are activated by phosphorylation and binding to specific inositol phosphates, leading to cellular events such as membrane localization and plasma membrane damage. Some family members are also involved in the regulation of nuclear envelope integrity in response to viral infection.
Mitochondrial Persulfide Dioxygenase (Mito_Persulfide_Diox)
Type: Family

This family of proteins includes enzymes that are involved in hydrogen sulfide catabolism within the mitochondrial matrix. Members of this family function as sulfur dioxygenases, catalyzing the oxidation of cysteine persulfide residues that are generated from hydrogen sulfide by other enzymes. This oxidation process typically involves the transfer of the persulfide to a thiophilic acceptor such as glutathione. The activity of these proteins is crucial for preventing the accumulation of toxic levels of hydrogen sulfide, which can inhibit cytochrome c oxidase and disrupt metabolic homeostasis. Some members of this family have been implicated in additional cellular processes, including the regulation of apoptosis and cell adherence or biofilm development. The family belongs to the metallo-beta-lactamase superfamily and shares similarities with the Glyoxalase II family.
Enoyl-CoA Hydratase/Isomerase Domain-Containing Protein (Enoyl-CoA_Hydratase/Isomerase)
Type: Family

This family of proteins is involved in various metabolic processes, including the hydration of enoyl-CoA thioesters, isomerization reactions, and the biosynthesis of host-selective toxins and secondary metabolites. Members of this family catalyze crucial steps in the synthesis of compounds such as antibiotics, toxins affecting plant pathogens, and the degradation of complex organic molecules. They are characterized by their ability to act on substrates with different chain lengths and structures, reflecting a broad specificity and functional diversity within the family. The enzymes play roles in cellular defense mechanisms, pathogenicity, and the utilization of environmental resources.
Electron Transfer/Redox Process (Electron_Trans/Redox)
Type: Family

The protein family is involved in various electron transfer and redox processes within cells. Members of the family are implicated in transferring electrons to different types of reductase complexes, such as nitrate reductase, and are predicted to participate in redox signaling pathways. Some proteins within the family form part of membrane-bound complexes that couple cation pumps to redox reactions, while others are required for maintaining repression of gene expression in response to environmental oxygen levels. The family includes both characterized and uncharacterized proteins, suggesting a potential diversity in function and involvement in various aspects of cellular metabolism.
Ycf3/AcsC/BcsC/TPR Multifunctional (Ycf3/AcsC/BcsC/TPR_MFPF)
Type: Family

The Ycf3/AcsC/BcsC/TPR family is involved in various cellular processes. The Ycf3 subfamily members are essential for the assembly of the photosystem I complex, possibly acting as chaperone-like factors for the assembly of PSI subunits. The AcsC/BcsC subfamily is implicated in bacterial cellulose synthesis, playing a crucial role in maximizing the production of this extracellular polysaccharide. Additionally, the family includes proteins with TPR repeats, which are typically involved in protein-protein interactions; however, their specific functions in this context are not detailed.
Outer membrane lipoprotein DolP (Lipoprotein_DolP)
Type: Family

The DolP lipoprotein family is characterized by its role in maintaining the integrity of the outer membrane in various bacteria. Members of the DolP family are known to contribute to the proper folding and function of BamA, particularly under stress conditions affecting the envelope. They exhibit a specific affinity for anionic phospholipids through their BON domains, which is crucial for their localization to the cell division site and their functional role. While initially thought to be regulators of the amidase activator NlpD, later studies have indicated that their influence on cell division and daughter cell separation may not be through direct regulation of NlpD. In some species, such as Salmonella typhimurium, DolP proteins are also implicated in virulence.