SII-SWORD/CoKE huggingface dataset:
Xanthocillin Biosynthesis-Associated Protein (Xanthocillin_Biosynth-Assoc)
Type: Family

This family of proteins is involved in the biosynthesis of isocyanide compounds, specifically the compound xanthocillin and its derivatives. The biosynthetic process begins with the conversion of tyrosine into a vinyl-isonitrile intermediate, which is then oxidatively dimerized to form xanthocillin. Members of this family may be responsible for further modifications of xanthocillin, including the introduction of N-formyl and methyl groups, leading to the production of various derivatives. These derivatives can undergo further transformations to produce compounds with potential biological activity. The family includes proteins with functions such as isocyanide synthase activity, cytochrome P450 monooxygenase activity, isonitrile hydratase-like activity, and methyltransferase activity. Some proteins within this family may also be involved in the oxidative and reductive cyclization processes that yield additional bioactive molecules.
SET domain-containing protein SmydA-8 (SET_SmydA-8)
Type: Family

This family of proteins includes SET domain-containing proteins that are part of the class V-like SAM-binding methyltransferase superfamily. These proteins are characterized by the presence of a SET domain, which is associated with lysine methyltransferase activity. Typically, members of this family are involved in the methylation of lysine residues on histone proteins, a post-translational modification that plays a critical role in the regulation of gene expression by affecting chromatin structure and dynamics. The methyltransferase activity of these proteins often requires the binding of S-adenosylmethionine (SAM) as a methyl donor. Through their enzymatic activity, these proteins contribute to the establishment of specific epigenetic marks, which can lead to either the activation or repression of gene transcription depending on the context and specific lysine residues that are methylated.
Dehydrogenase/reductase SDR family member 7 (SDR_family_member_7)
Type: Family

The Dehydrogenase/reductase SDR family member 7 proteins are NADPH-dependent oxidoreductases involved in the reduction of compounds with carbonyl groups, including steroids, retinoids, and xenobiotics. They play a role in the inactivation of 5alpha-dihydrotestosterone, potentially affecting androgen receptor function, and in the conversion of all-trans-retinal to all-trans-retinol. The family's involvement in the reduction of cortisone and various xenobiotics suggests a role in xenobiotic biotransformation. Although dehydrogenase activity has not been observed, these proteins may act as tumor suppressors.
Endoplasmic reticulum-organelle contact domain-containing protein (ER-organelle_contact)
Type: Family

This family of proteins is involved in the establishment of contact sites between the endoplasmic reticulum (ER) and various organelles such as endosomes, mitochondria, and the Golgi apparatus. They interact with proteins that contain conventional and phosphorylated FFAT motifs, which are bound to these organelles, facilitating the formation of these contact sites. Members of this family also play a role in lipid droplet (LD) homeostasis by forming contacts between the ER and LDs. This interaction is mediated through a direct protein-membrane interaction, specifically via an amphipathic helix that targets lipid packing defects on the LD surface. Additionally, these proteins are implicated in the regulation of immune cell migration, promoting the movement of monocytes and neutrophils in response to chemokines.
Lysine Acetyltransferase (LAT)
Type: Family

This family of proteins includes lysine acetyltransferases, which are enzymes that catalyze the transfer of an acetyl group from acetyl-CoA to the epsilon-amino group of a lysine residue on a substrate protein. This modification can affect the protein's function, interactions, stability, or localization. The acetylation reaction is a key post-translational modification and plays a significant role in regulating various biological processes, including gene expression, cell signaling, and metabolism. Members of this family are involved in the lysine degradation pathway, initiating the process by acetylating lysine. The activity of these enzymes can be modulated by specific metabolites, which may serve as inhibitors, reflecting a tight regulation of their function in response to cellular metabolic states.
Cuticle-associated divergent protein (Cuticle_assoc_divergent)
Type: Family

This family of proteins includes members with potential roles in cuticle biosynthesis, although their specific biochemical activities may vary. One member appears to lack serine protease inhibitor activity when tested in vitro, suggesting a divergence in function within the family. The proteins may have evolved distinct biological roles, which could include but are not limited to, involvement in structural aspects of the extracellular matrix.
Pleckstrin homology domain-containing protein M2 (PH_domain-containing_M2)
Type: Family

This family of proteins is involved in intracellular vesicle trafficking, particularly affecting lysosome movement and localization. They act as effectors for small GTPase ARL8B, facilitating the recruitment of kinesin-1 to lysosomes, which in turn promotes their transport along microtubules. These proteins are also key in natural killer (NK) cell function, where they contribute to the polarization of cytolytic granules and microtubule-organizing centers towards the immune synapse during the targeting of cells by NK cells. Additionally, they play a role in maintaining the structural integrity of the Golgi apparatus and may be involved in the formation of membrane tubules.
CTF18-RFC complex component (CTF18-RFC_complex)
Type: Family

This family of proteins includes components of the CTF18-RFC complex, which is involved in sister chromatid cohesion and the fidelity of chromosome transmission. These proteins function as chromosome cohesion factors and play a role in the cell nuclear antigen loader complexes. They are involved in the ATP-dependent loading of PCNA onto primed and gapped DNA, and exhibit weak ATPase activity that is stimulated by primed DNA, RPA, and PCNA. The CTF18-RFC complex is essential for maintaining genome stability during cell division.
Mitochondrial Citrate/Oxoglutarate Carrier (Mito_Cit/Oxoglu_Carrier)
Type: Family

This family of proteins includes mitochondrial antiporters that facilitate the transport of various dicarboxylic acids across the mitochondrial membrane. Members of this family are involved in the exchange of citrate and oxoglutarate, and can also transport other substrates such as oxaloacetate, succinate, fumarate, isocitrate, cis-aconitate, and L-malate, albeit with varying efficiencies. These proteins do not exhibit uniporter activity. They play a role in maintaining cellular metabolic balance, particularly in the regulation of citrate levels and the NADPH/NADP(+) ratio, which is crucial under oxidative stress conditions. Some members may also have a role in mitochondrial DNA maintenance, as suggested by their ability to associate with the mitochondrial nucleoid and bind DNA in vitro.
Elsinochrome Biosynthesis-Associated (Elsinochrome_Biosynth-Asso)
Type: Family

This family of proteins is involved in the biosynthesis of elsinochromes, a group of pigments with a core phenolic quinone structure and various side chains. These pigments exist as interconvertible tautomers and are significant in fungal pathogenesis. The family includes enzymes that participate in the iterative decarboxylation and polyketide chain elongation, cyclization to form aromatic rings, and subsequent modifications to produce the heptaketide backbone of elsinochrome. The symmetrical structure of elsinochrome is formed by the fusion of two identical heptaketides into a dihydrobenzo-perylene ring, which is further modified to yield different elsinochrome derivatives. The family also encompasses proteins that may stabilize biosynthetic enzymes and contribute to the chaperone function necessary for elsinochrome production. However, the complete set of genes for the biosynthesis pathway is not contained within the gene cluster, indicating additional components are involved. The family also includes transporters responsible for exporting elsinochrome out of the fungal cells to prevent toxicity.
GATA zinc finger domain-containing protein (GATA_zinc_finger)
Type: Family

This family of proteins includes transcription factors that are involved in the regulation of morphogenetic cell movements during developmental processes. Members of this family are characterized by the presence of a GATA zinc finger domain, which is typically involved in DNA binding and the control of gene expression. The proteins within this family play a crucial role in the orchestration of cellular behaviors that are essential for the proper formation of tissues and organs during development.
Smr domain-containing protein (Smr_domain_protein)
Type: Family

This family of proteins includes members that contain an Smr domain, which is associated with DNA-binding and endonuclease activities. These proteins are involved in various DNA repair processes, including the repair of interstrand cross-links and the maintenance of genomic stability. The Smr domain facilitates the recognition of DNA mismatches and abnormal DNA structures, which is crucial for the correction of errors that occur during DNA replication and recombination. Members of this family may also play a role in the regulation of other cellular processes through interactions with other proteins and DNA.
Chloroplastic Adenylate Kinase (Chloroplast_ADK)
Type: Family

This family of proteins includes enzymes that are involved in the maintenance of cellular energy homeostasis and adenine nucleotide metabolism. Members of this family are capable of catalyzing the reversible transfer of a phosphate group between ATP and AMP. This reaction is a fundamental process in the energy exchange within cells, helping to regulate the balance of adenine nucleotides. These enzymes are typically located in the chloroplast and play a pivotal role in the energy metabolism of plant cells.
Chloroplast envelope translocon component (Chloroplast_translocon_comp)
Type: Family

This family of proteins is involved in the translocation of protein precursors across the chloroplast envelope. Members of this family are essential components of the inner chloroplast membrane translocon complex (TIC), which works in conjunction with the outer chloroplast membrane translocon complex (TOC) to form a supercomplex. This supercomplex facilitates the import of proteins into the chloroplast stroma. In addition to their role in protein import, these proteins are also implicated in the regulation of starch granule size within amyloplasts, indicating a broader functional scope within the chloroplast.
FLUCTUATING-LIGHT-ACCLIMATION modulator (FLAP_modulator)
Type: Family

This family of proteins is involved in the acclimation of photosynthetic organisms to fluctuating light conditions. Members of this family play a crucial role in maintaining intracellular pH homeostasis by modulating proton transport, which is essential for optimizing photosynthetic activity and balancing photoprotection with photochemical processes. These proteins are responsible for transient pH adjustments in response to changes in light intensity, ensuring efficient photosynthetic growth and the acclimation response to varying light environments.
Fungal Surface Nicotinamide Adenine Dinucleotide Glycohydrolase (Fungal_surface_NADase)
Type: Family

The fungal surface NADase family comprises enzymes that are localized on the conidial surface and are involved in the hydrolysis of nicotinamide adenine dinucleotides. Members of the family cleave NAD(+) and NADP(+) but do not affect their reduced forms, NADH and NADPH. These glycohydrolases lack ADP-ribosyl cyclase and base exchange activities, and thus do not participate in the synthesis of calcium messengers such as cADPR or NAADP. The family plays a role in fungal pathogenicity by depleting the host's NAD(+) pool. Additionally, these enzymes are implicated in the development of aerial hyphae and conidiogenesis in fungi. Regulatory mechanisms include calcium binding in some members, non-competitive inhibition by aliphatic amines, carboxylic acids, and dioxane, as well as auto-ADP-ribosylation leading to self-inactivation.
Mitochondrial ATP Synthase-Associated (Mito_ATP_Synthase-Asso)
Type: Family

This family of proteins is involved in mitochondrial function, specifically in the regulation of mitochondrial respiration. Members of this family are associated with the ATP synthase complex, aiding in ATP synthesis. They may also have a chaperone-like role in the maintenance of mitochondrial complex I, particularly the N-module subunits. These proteins are implicated in the recognition and removal of damaged subunits caused by oxidative stress, thereby supporting the functional efficiency of complex I.
CDC42 guanine nucleotide exchange factor (CDC42_GEF)
Type: Family

This family of proteins includes guanine nucleotide exchange factors (GEFs) that are involved in the regulation of small GTPases, such as CDC42. Members of this family play a crucial role in cell signaling related to morphogenesis, mating, and cell division. They facilitate the exchange of GDP for GTP on CDC42, thereby activating this GTPase to influence cytoskeletal organization and cell polarity. These proteins are also implicated in processes such as septation and the elongation of conjugation tubes, as well as the selection and organization of budding sites in yeast cells.
Angiogenic factor with G patch and FHA domains 1 (AGGF1)
Type: Family

The AGGF1 family is characterized by its role in promoting angiogenesis and endothelial cell proliferation. Members of the family have the ability to bind to endothelial cells, which may suggest an autocrine mechanism of action. The angiogenic factor with G patch and FHA domains, which defines this family, is involved in the physiological process of new blood vessel formation, a critical aspect of various developmental and repair processes in the body. The family's function in angiogenesis highlights its potential significance in both normal vascular development and pathological conditions where angiogenesis is a factor.
Spo0E-like aspartyl-phosphate phosphatase (Spo0E-like_phosphatase)
Type: Family

This family of proteins includes aspartyl-phosphate phosphatases that are involved in the regulation of sporulation initiation. Members of this family are responsible for dephosphorylating the sporulation transcription factor Spo0A-P, which is a key step in the control of the timing of sporulation. By dephosphorylating Spo0A-P, these phosphatases act as negative regulators, ensuring that sporulation occurs at the appropriate time. This regulatory mechanism is crucial for the proper development and differentiation of spore-forming bacteria.
RNA polymerase I-specific initiation factor (RNA_pol_I-specific_init_factor)
Type: Family

This family of proteins includes components of the core factor complex involved in the initiation of ribosomal DNA transcription by RNA polymerase I. Members of this family are essential for the formation of the preinitiation complex, acting subsequent to the binding of upstream activation factors to promoter elements. They are also necessary for the recruitment of transcription initiation factors in a TBP-dependent manner, which is a critical step in the transcription initiation process. The binding of these proteins to the DNA template is contingent upon the prior association of other transcription factors.
Ribosomal biogenesis protein FAF1-like (Ribosomal_biogenesis_FAF1-like)
Type: Family

This family of proteins is involved in the maturation of ribosomes, which are essential cellular machines for protein synthesis. Members of this family are implicated in the processing of precursor ribosomal RNA (rRNA), specifically contributing to the cleavage events that are necessary for the proper formation of the 40S ribosomal subunit. The proteins in this family appear to play a role in the early stages of rRNA processing, participating in the cleavage at specific sites within the precursor rRNA molecule.
Cuticle-associated protein (Cuticle_assoc_protein)
Type: Family

This family of proteins is associated with cuticle structure and integrity. Members of this family are implicated in the proper formation and function of the cuticle, which is an external layer found in some organisms that serves as a protective barrier. These proteins may play a role either directly in the composition and maintenance of the cuticle or indirectly by participating in the regulatory pathways that govern cuticle development and function. The involvement of these proteins is crucial for the normal morphological development of the organism.
Bromo adjacent homology domain-containing protein (BAH_domain-containing)
Type: Family

This family of proteins functions as transcription repressors involved in the formation and maintenance of heterochromatin. Members of this family have the ability to recruit various heterochromatin proteins, including CBX5 (HP1 alpha), HDAC5, and MBD1, to specific genomic regions. They are known to repress the expression of certain genes, such as IGF2, by binding to CpG-rich promoters and facilitating the assembly of heterochromatin. Additionally, these proteins can interact with histone modifications, as their localization is dependent on the presence of H3K27me3, a marker of repressive chromatin.
Androglobin-like (Androglobin-like)
Type: Family

This family of proteins is implicated in the reproductive process, specifically in the development and maturation of male gametes. Members are essential for the formation of the sperm flagellum and the maturation of elongating spermatids, which are critical for male fertility. Additionally, these proteins are involved in proteolytic activities, as evidenced by their role in the calmodulin-dependent cleavage of SEPT10, a process that occurs in vitro. The family is categorized under the peptidase C2 family, indicating a relationship with protease functions.
Glucuronokinase-like (Glucuronokinase-like)
Type: Family

This family of proteins includes enzymes with sugar-1-kinase activity, specifically recognizing D-glucuronic acid and ATP as substrates. Members of this family are involved in the biosynthesis of UDP-glucuronic acid (UDP-GlcA), which is a precursor for nucleotide sugars required in the assembly of cell-wall polymers. Additionally, these proteins may participate in the recycling of glucuronic acid through a salvage pathway.
Mitochondrial GEF domain-containing protein (Mitochondrial_GEF_domain)
Type: Family

This family of proteins functions as guanine nucleotide exchange factors (GEFs) for mitochondrial dynamin-related GTPases, specifically OPA1. They facilitate the activation of OPA1 by promoting the exchange of GDP for GTP, which is crucial for mitochondrial fusion processes, particularly those involving OPA1 and MFN1. Additionally, these proteins are vital for the biogenesis of mitochondrial ribosomes. They form part of a protein-RNA complex that includes RCC1L, NGRN, RPUSD3, RPUSD4, TRUB2, FASTKD2, and 16S mitochondrial ribosomal RNA. This complex is responsible for regulating the abundance of 16S mt-rRNA and is necessary for the intra-mitochondrial translation of core subunits of the oxidative phosphorylation system.
Cell Cycle and DNA Repair Regulator (CellCycle_DNARepair_Reg)
Type: Family

The protein family in question is involved in maintaining genomic stability and proper cell cycle progression. Members of this family are essential for ensuring mitotic fidelity, particularly during the G2 phase, and play a role in chromatin organization. Additionally, they are implicated in the resumption of chromosome replication following DNA damage, especially in the S phase of the cell cycle. Family members are known to be recruited to chromatin in response to stalled replication forks and function as scaffolds during DNA repair processes. These proteins are associated with the regulation of transposition elements and are essential for the integrity of the genome during cell division and in response to genotoxic stress.
Pericyclase pydY-like (Pericyclase_pydY-like)
Type: Family

This family of proteins includes enzymes that are involved in the biosynthesis of complex natural products with antibiotic properties. Members of this family function as pericyclases, which catalyze key steps in the formation of macrocyclic and polycyclic compounds. Specifically, they are implicated in a Diels-Alder cycloaddition reaction that forms a decahydrofluorene core structure. These enzymes are part of gene clusters that orchestrate the assembly of fungal secondary metabolites, such as hirsutellone-like compounds and pyrrocidines. The biosynthetic pathways begin with the synthesis of polyketide-tyrosyl acyl thioester precursors and involve multiple enzymatic transformations, including Knoevenagel condensation, oxidative cyclization, and non-enzymatic hydroxylation, leading to the production of bioactive molecules with potential therapeutic applications.
Receptor-like Plant Defense (RLP_Defense)
Type: Family

This family of proteins is involved in plant defense mechanisms. Members of this family play a role in the recognition of pathogen-associated molecular patterns and are required for basal resistance against specific pathogens, contributing to the plant's immune response.
Cell Polarity and Bud Site Selection Regulator (Polarity_Bud-Selection_Reg)
Type: Family

This family of proteins includes factors involved in the regulation of cell polarity and bud site selection in yeast. Members of this family are essential for the proper localization of cell-end markers and the establishment of cell polarity during the cell cycle. They operate in complex with other proteins to maintain polarity under normal and stress conditions. Additionally, they are implicated in the regulation of actin assembly at cell tips, particularly during the initiation of new growth phases. Some family members also play a role in the regulation of microtubule dynamics at the cortex, possibly by activating specific complexes such as dynein. They may also function as regulatory subunits of phosphatase complexes, influencing processes like bud site selection.
Leucine-rich repeat-containing protein 71 (LRR-containing_protein_71)
Type: Family

This family of proteins contains leucine-rich repeat (LRR) domains, which typically mediate protein-protein interactions and are involved in various cellular processes including signal transduction, cell adhesion, DNA repair, and immune responses. Members of this family are likely to play a role in these biological functions through their LRR domains. The specific functions of the human and mouse leucine-rich repeat-containing protein 71, however, are not well characterized, and further research is necessary to elucidate their precise roles in cellular physiology.
Transglutaminase-like Superfamily Modulators (Transglut-like_Superfamily_Mod)
Type: Family

The Transglutaminase-like Superfamily Protein Family is characterized by proteins that share structural similarity and are involved in various cellular processes. Members of this family, such as Hillarin and LTD-1, are implicated in the modulation of cytoskeletal elements and cellular division. Hillarin is suggested to modulate septin function during cytokinesis in the developing nervous system, indicating a role in neurodevelopment. LTD-1 is associated with the cytoskeleton and may be involved in hypodermal cell development. The common theme in the family's function appears to be the regulation of cytoskeletal dynamics and cellular structure during development and cell division.