SII-SWORD/CoKE huggingface dataset:
IQ domain-containing protein (IQ_domain_protein)
Type: Family

This family of proteins contains the IQ domain, which is known to be involved in calcium-independent calmodulin-binding. Members of this family are characterized by the presence of this domain, suggesting a role in signal transduction pathways. The IQ motif is typically found in proteins that interact with calmodulin and other members of the EF-hand protein family, without requiring calcium to facilitate this interaction. Proteins with the IQ domain are implicated in a variety of cellular processes, including regulation of cytoskeletal dynamics, enzyme activity modulation, and the mediation of protein-protein interactions. Given the ubiquitous nature of calmodulin in cellular signaling, the exact functions of IQ domain-containing proteins can be diverse and context-dependent, often varying across different cell types and organisms.
Histone-lysine N-methyltransferase ATXR5/ATXR6 (ATXR5/ATXR6)
Type: Family

This family of proteins includes histone-lysine N-methyltransferases that are responsible for the monomethylation of 'Lys-27' on histone H3 (H3K27me1). These enzymes exhibit a preference for nucleosomes containing the H3.1 variant over H3.3 . They play a crucial role in the establishment of constitutive heterochromatin, contributing to the silencing of heterochromatic regions . Additionally, they are involved in the regulation of rRNA gene expression by influencing the expression or silencing of specific rRNA gene variants .
Cyclin-dependent kinase inhibitor (CDK_inhibitor)
Type: Family

This family of proteins includes cyclin-dependent kinase (CDK) inhibitors that are likely involved in the regulation of the cell cycle. Specifically, they are thought to act as repressors of mitosis during the endoreduplication cell cycle, a variant of the normal cell cycle that involves DNA replication without subsequent cell division. This results in an increase in cell size and DNA content without an increase in cell number. Members of this family play a crucial role in controlling cell proliferation and differentiation by modulating the activity of CDKs, which are key regulators of cell cycle progression.
GATA-type Zinc Finger Regulator (GATA-type_Znf_Regulator)
Type: Family

This family of proteins includes transcriptional regulators that are crucial for germ cell development. They are involved in determining the oogenic fate by activating essential genes for the initiation of the oogenic program and the entry into meiotic prophase. These proteins function downstream of bone morphogenetic protein signaling, modulating the expression of genes that are otherwise suppressed by Polycomb group proteins in germ cells that have not yet committed to a sexual fate. They are responsible for the regulation of STRA8, which is a key gene in the meiotic process. These proteins operate independently of retinoic acid signaling. While they are not involved in determining germ-cell sex in males, they are necessary for spermatogonia to progress through meiotic prophase effectively.
Distal Membrane-arm Assembly Complex Protein (DMAC_Protein)
Type: Family

This family of proteins is involved in the mitochondrial respiratory chain, specifically in the assembly of complex I, also known as NADH:ubiquinone oxidoreductase. Members of this family play a crucial role in the formation of the distal membrane arm of complex I, which is essential for the proper function and structure of the enzyme. The activity of complex I is pivotal for the process of oxidative phosphorylation, where it initiates the electron transport chain by transferring electrons from NADH to ubiquinone. The assembly of complex I is a highly regulated process, and these proteins are key to ensuring its correct assembly and maintenance.
Host-Pathogen Interaction Adhesin/Serine-rich (HPI-Adhesin/Ser-rich)
Type: Family

This family of proteins includes members that are involved in host-pathogen interactions. One member functions as a heat-stable antigen that may be present in the sera of infected individuals, suggesting a role in immune response or pathogen detection. Another member is a structural component of fimbriae, contributing to bacterial adherence to host surfaces, such as teeth, in a pH-dependent manner. This adherence is crucial for colonization and persistence of the bacteria in the host environment. The proteins in this family may have domains rich in serine residues, which could be important for their structural stability or interaction with other molecules.
Cubilin domain-containing protein (Cubilin_domain)
Type: Family

This family of proteins functions as endocytic receptors involved in the uptake of various substances including lipoproteins, vitamins, and iron, playing a critical role in their metabolism. They form a complex structure with a long stem and a globular crown, which is essential for their interaction with a range of ligands such as albumin, transferrin, and high-density lipoproteins. Calcium is required for ligand binding. These proteins are also implicated in the internalization of the cobalamin-intrinsic factor complex, contributing to vitamin B12 absorption. They are expressed in absorptive epithelia like the intestine and renal proximal tubules, and are important for the transport of nutrients and other molecules across these tissues. Additionally, they may have a role in embryonic development by mediating the uptake of lipids and proteins at the maternal-fetal interface.
Paraflagellar Rod Component (PFR_Component)
Type: Family

This family of proteins includes components of the paraflagellar rod (PFR), which is a structure found within the flagellum of certain eukaryotic cells. The PFR is composed of highly ordered lattices of fibrous proteins that are oriented in a fixed manner relative to the microtubular axoneme of the flagellum. These proteins play a crucial role in the structural integrity and function of the PFR, contributing to the motility and sensory functions of the flagellum. The precise molecular mechanisms by which these proteins contribute to the PFR's function are essential for the proper movement and signaling of flagellated cells.
Spore Coat Assembly Protein (Spore_Coat_Assembly)
Type: Family

This family of proteins is involved in the formation of protective structures during the developmental stage of spore formation. Members of this family play a role in the assembly of the spore coat, which is crucial for spore viability and resistance. They interact with other components such as cellulose and specific partner proteins to create a triad that is essential for the proper construction of the spore's outer layer. Some family members contain a domain that is necessary for their incorporation into the spore coat, indicating a structural or anchoring function in the spore coat assembly process.
RING finger domain-containing protein (RING_finger_domain)
Type: Family

This family of proteins includes members that contain a RING finger domain, a specialized type of zinc finger that binds two zinc ions. This domain is involved in mediating protein-protein interactions and is commonly found in E3 ubiquitin-protein ligases, which play a critical role in the ubiquitination pathway. Ubiquitination is a post-translational modification process where ubiquitin, a small regulatory protein, is attached to substrate proteins, often targeting them for degradation by the proteasome. However, ubiquitination can also affect protein activity, protein-protein interactions, and protein localization. Members of this family are likely involved in various cellular processes through the ubiquitin-proteasome system, including cell cycle regulation, signal transduction, and immune responses.
Chondroitin Proteoglycan 4-like (CPG4-like)
Type: Family

This family of proteins includes chondroitin proteoglycan 4, which is involved in the formation of proteoglycan aggregates that contribute to the extracellular matrix structure. These proteins play a role in cell adhesion, migration, and proliferation. They are part of the larger group of chondroitin sulfate proteoglycans, which are essential for the proper functioning of various biological processes including the development and maintenance of the nervous system and the modulation of synaptic plasticity.
Notch pathway signaling modulators (Notch_signaling_modulators)
Type: Family

This family of proteins includes secreted factors that are likely involved in Notch signaling pathways. Members of this family are implicated in determining cell fate decisions, particularly in vulval precursor cells, by acting redundantly with other ligands. They are also associated with neuronal functions, contributing to avoidance responses and the regulation of sleep-like quiescence during larval to adult transition. These proteins function through activation of Notch receptors and may operate in conjunction with EGF signaling.
RNA-binding mRNA stabilization regulator (RNA-bd_mRNA_stabilization_reg)
Type: Family

This family of proteins is involved in the post-transcriptional regulation of mRNA stability. Members of this family function by binding to specific mRNA transcripts and enhancing their stability. They achieve this by interacting with other proteins such as MKT1 and PBP1, which are implicated in the stabilization process. These proteins play a crucial role in the cellular differentiation processes by maintaining the stability of mRNAs that are essential for the transition between different cellular forms as well as for the upkeep of those forms. They are particularly important for the stabilization of transcripts that encode mitochondrial and membrane proteins, which are vital for cellular function and integrity.
CD27 antigen receptor (CD27_receptor)
Type: Family

This family of proteins includes receptors that interact with the CD70/CD27L ligand. Members are involved in the regulation of T-cell survival following activation and may influence apoptotic processes through their association with specific adaptor proteins such as SIVA1. These functions are crucial for the immune response, particularly in the context of T-cell mediated immunity.
Chromatin remodeling complex subunit (Chromatin_remod_comp_subunit)
Type: Family

This family of proteins includes components of ATP-dependent chromatin remodeling complexes, which are pivotal in both the activation and repression of gene expression. Members of this family are involved in modifying chromatin structure by altering DNA-histone contacts within nucleosomes. These changes can lead to shifts in nucleosome positioning, thereby modulating the accessibility of transcription factors to DNA and ultimately influencing gene expression. The family is characterized by the presence of GRIP and coiled-coil domains, which may suggest a role in protein-protein interactions and complex assembly.
Cystatin-like inhibitors (Cystatin-like)
Type: Family

This family of proteins includes inhibitors of cysteine proteinases. Members of this family are known to selectively inhibit the activity of specific proteinases, thereby playing a role in protecting tissues from proteolytic damage during various stages of development. The proteins within this family are characterized by their ability to regulate the activity of cysteine proteinases, which are enzymes involved in protein degradation and processing, as well as in various physiological processes including immune responses.
Integrator complex-associated protein (Integrator_complex_assoc)
Type: Family

This family of proteins includes members that are potentially involved in the transcription and processing of small nuclear RNAs (snRNAs), specifically U1 and U2. These proteins may be part of the Integrator complex, which plays a role in snRNA 3'-box-dependent processing. The family also encompasses proteins that are putatively uncharacterized and may contain transmembrane domains, suggesting a diversity of functions and localizations within this family.
ARL14 effector protein-like (ARL14_effector)
Type: Family

This family of proteins includes members that are likely involved in intracellular signaling pathways. They are characterized by their association with the small GTPase ARL14, suggesting a role in modulating the activity of this GTPase. Proteins in this family may participate in the regulation of immune responses, as ARL14 has been implicated in the trafficking of MHC class II molecules to the cell surface in antigen-presenting cells. The exact molecular functions and biological processes these effector proteins-like are involved in remain to be fully elucidated, but they are thought to contribute to the fine-tuning of immune cell signaling and potentially other GTPase-related functions.
Mesendoderm Development Regulator (Mesendoderm_Regulator)
Type: Family

This family of proteins is implicated in the development of the mesendoderm, a germ layer formed during the embryogenesis of some animals. Members of this family are believed to be involved in the regulatory processes that govern the differentiation and development of this layer, which gives rise to both mesodermal and endodermal tissues. The exact molecular function and mechanisms by which these proteins contribute to mesendoderm development remain to be fully elucidated.
Sexual cell fusion glycoprotein (Sexual_fusion_gp)
Type: Family

This family of proteins is involved in the process of sexual cell fusion in the slime mold Dictyostelium discoideum. Members of this family are cell surface glycoproteins that play a crucial role during the sexual phase of the organism's life cycle by mediating cell-to-cell fusion events. These proteins are essential for the formation of multinucleate cells, a key step in the development of the fruiting body of D. discoideum.
RNA-directed DNA polymerase homolog (RNA-dir_DNA_polymerase)
Type: Family

This family of proteins includes enzymes that are responsible for the synthesis of DNA from an RNA template. They are typically found in retroviruses and are essential for the viral replication process. These enzymes exhibit reverse transcriptase activity, which involves the transcription of the viral RNA genome into DNA, a process that is reverse to the usual transcription of DNA into RNA. This DNA is then integrated into the host genome, allowing the virus to hijack the host cell's machinery for its own protein production and replication. Members of this family may also be involved in the replication of certain eukaryotic genomes, particularly in elements such as retrotransposons that use a similar mechanism of replication.
Aldo-Keto Reductase 2 Subfamily Oxidoreductase (AKR2_Oxidoreductase)
Type: Family

This family of proteins includes enzymes that are part of the aldo/keto reductase superfamily. These enzymes are involved in the reduction of aldehydes and ketones into their corresponding alcohols. They play a role in various metabolic processes, including the detoxification of aldehydes and the metabolism of sugars, steroids, and other alcohols. Members of this family are characterized by their ability to utilize NADPH or NADH as a cofactor for the reduction reaction. The specific functions of these enzymes can vary widely among different organisms and tissues, reflecting the diverse substrates they can act upon.
UTP pyrophosphatase-like (UTP_pyrophosphatase-like)
Type: Family

This family of proteins is involved in nucleotide metabolism, specifically catalyzing the hydrolysis of UTP to UMP and diphosphate. The enzymatic activity is highly specific to UTP and does not extend to other nucleoside triphosphates such as ATP, GTP, CTP, dTTP, or ITP. The reaction is a part of the pyrimidine salvage pathway and plays a role in the regulation of intracellular levels of UTP and UMP, which are essential for RNA synthesis and other cellular processes.
Nucleotide-binding leucine-rich repeat (NLR)-like (NLR-like)
Type: Family

This family of proteins includes members with a multi-domain architecture that is involved in nucleotide binding and hydrolysis. Nucleotide-binding leucine-rich repeat (NLR)-like protein from Hyaloscypha variabilis contains a purine nucleoside phosphorylase (PNP) domain at the N-terminal that cleaves the N-glycosidic bond of ATP, and to a lesser extent dATP with very weak activity on adenosine and deoxyadenosine and no activity on (d)ADP or (d)AMP . The C-terminal region is characterised by the presence of TRP repeats, which may be involved in protein-protein interactions.
N-alpha-acetyl-L-2,4-diaminobutyric acid deacetylase (N-alpha-Ac-DABA_deacetylase)
Type: Family

This family of proteins is involved in the degradation of ectoine, a compatible solute that microorganisms use under stress conditions such as high salinity. Members of this family are responsible for the deacetylation step in the ectoine degradation pathway. Specifically, they catalyze the conversion of N-alpha-acetyl-L-2,4-diaminobutyrate to L-2,4-diaminobutyrate, which can then be further processed for use as a carbon and nitrogen source by certain bacteria. This enzymatic activity is crucial for organisms that rely on the catabolism of ectoine to survive in extreme environments.
Putative surface bspA-like protein (Surface_bspA-like)
Type: Family

This family of proteins is implicated in interactions with host tissues. The members of this family may have a role in adherence or invasion processes during the infection cycle, potentially by binding to host cell surfaces or extracellular matrix components. The exact molecular mechanisms and the specific host tissues targeted by these proteins remain to be characterized. Understanding the function of these proteins could provide insights into pathogenic strategies employed by microbes and may have implications for the development of therapeutic interventions.
GDSL lipase Rv0518-like (GDSL_Rv0518-like)
Type: Family

This family of proteins includes enzymes with lipase activity, specifically GDSL lipases. They are characterized by their ability to catalyse the hydrolysis of ester bonds within lipid substrates. Members of this family preferentially act on medium-chain p-nitrophenyl esters, with optimal activity observed for esters with a decanoate chain . They exhibit a broad substrate specificity, also hydrolyzing esters with varying chain lengths, although with lower efficiency for shorter and longer chains. Among its members, this family includes Rv0518 from M.tuberculosis and uncharacterised sequences from bacteria and fungi . The activity of these enzymes is known to be inhibited by serine modifiers such as PMSF, indicating a serine residue's involvement in the catalytic mechanism.
Mycobacterial serine protease inhibitor Rv3364c (Mycobact_SerProt_Inhib_Rv3364c)
Type: Family

This family of proteins includes effectors that interact with host serine proteases such as cathepsin G, located on macrophage cell membranes. They play a role in modulating the host's immune response by inhibiting the enzymatic activity of these proteases. Inhibition of cathepsin G prevents the activation of caspase-1-dependent apoptosis pathways, thereby blocking macrophage pyroptosis. This mechanism is crucial for the survival of certain bacteria within host cells, as it helps them evade the immune system and maintain a persistent infection.
Pyochelin receptor regulatory protein (PchR_regulatory_protein)
Type: Family

This family of proteins includes transcriptional activators that are involved in the regulation of siderophore-mediated iron acquisition systems. Members of this family function as positive regulators, enhancing the expression of genes related to the synthesis and transport of pyochelin, a siderophore that chelates iron, and its associated receptors. These proteins play a crucial role in the microbial iron uptake process, which is essential for survival and pathogenicity in iron-limited environments.
Arylsulfate Sulfotransferase (Arylsulfate_ST)
Type: Family

This family of proteins includes enzymes that are involved in the transfer of sulfuryl groups from donor molecules to acceptor phenolic compounds. These enzymes play a crucial role in various biological processes, including the metabolism of hormones, neurotransmitters, and drugs, by modifying the chemical properties of these compounds through sulfation. Sulfation is a key step in the biotransformation and detoxification pathways, and it also affects the bioavailability and excretion of substances. Members of this family are characterized by their ability to catalyze the sulfuryl group transfer, which is an essential function in cellular homeostasis and signaling.
Putative Acetyltransferase Butenolide Biosynthesis (Acetyltransferase_Butenolide)
Type: Family

This family of proteins includes putative acetyltransferases that are implicated in the biosynthesis of secondary metabolites such as butenolide, a compound with antibiotic properties. These proteins are predicted to contribute to the formation of a 4-acetamido-2-butenoic acid intermediate from glutamic acid. The exact biochemical activities of these enzymes in the butenolide biosynthetic pathway have not been experimentally confirmed, but their roles are consistent with the production of this mycotoxin, which is involved in plant-pathogen interactions but is not a major factor in the spread of head blight in wheat.
AB hydrolase superfamily Esterase 10 (AB_hydrolase_Est10)
Type: Family

This family of proteins exhibits esterase activity, preferentially hydrolyzing short acyl chain esters ranging from C4 to C8. The precise physiological role of these proteins remains unclear. They do not display protease or peptidase activity when tested with common substrates. Members of this family are characterized by their inhibition by specific chemicals, including serine protease inhibitors and histidine modifiers, while being unaffected by chelating agents or reducing agents.
Quercetin 2,3-dioxygenase-like (QDO-like)
Type: Family

This family of proteins is involved in the metabolic breakdown of flavonoids, specifically quercetin. Members of this family are responsible for catalyzing the dioxygenolytic cleavage of the O-heteroaromatic ring in quercetin, leading to the formation of 2-protocatechuoyl-phloroglucinol carboxylic acid and carbon monoxide. This reaction represents a key step in the catabolic pathway of quercetin, a process that is significant for organisms that utilize flavonoids as a carbon source. The enzymatic activity displayed by this family highlights a specialized function in the broader context of microbial degradation of plant-derived compounds.
Heat shock protein HslJ-like (Hsp_HslJ-like)
Type: Family

This family of proteins includes molecular chaperones that are implicated in the response to environmental stress, such as elevated temperatures. They are involved in the folding and unfolding of other proteins, as well as in the assembly and disassembly of protein complexes. These proteins may also play a role in the degradation of misfolded protein species, thus contributing to the cellular quality control system. Their activity is essential for maintaining protein homeostasis, especially under conditions that can lead to protein denaturation and aggregation.
PD-(D/E)XK-like domain-containing protein (PD-DEXK-like_domain)
Type: Family

This family of proteins includes putative nucleases that may play a role in DNA recombination and repair processes. Members are characterized by the presence of a PD-(D/E)XK-like nuclease domain, which suggests they have the ability to interact with and cleave nucleic acid substrates.
Thiamine pyrophosphokinase (TPK)
Type: Family

This family of proteins is involved in the biosynthesis of thiamine pyrophosphate, an essential coenzyme required by all living organisms. Members of this family are responsible for the phosphorylation of thiamine (vitamin B1) to produce thiamine pyrophosphate. This conversion is a critical step in the utilization of thiamine, as the pyrophosphate form is the active coenzyme that participates in various cellular processes, including the metabolism of carbohydrates and branched-chain amino acids. The enzymatic activity of these proteins is vital for the proper functioning of several enzymes that require thiamine pyrophosphate as a cofactor.