SII-SWORD/CoKE huggingface dataset:
Regulatory protein for polyketide-peptide biosynthesis (Polyketide-peptide_reg)
Type: Family

This family of proteins includes transcription factors that are implicated in the regulation of gene expression for certain biosynthetic processes. Specifically, members of this family are thought to play a role in the control of gene clusters responsible for the biosynthesis of complex molecules. These molecules are composed of a polyketide chain linked to a peptide made up of several amino acids. The activity of these proteins is crucial for the coordinated expression of genes involved in the assembly of these secondary metabolites, which may have important biological functions or applications.
ArsA ATPase-like (ArsA_ATPase-like)
Type: Family

This family of proteins is associated with ATPase activity and is involved in the transport of various substances across cellular membranes. Members of this family are typically characterized by their ability to hydrolyze ATP to drive the active transport of ions, such as arsenite, antimonite, and other substrates, which is crucial for cellular detoxification processes. The ATPase activity is essential for providing the energy required for the transport mechanism. These proteins may play a role in resistance to toxic metals and metalloids, contributing to the survival of organisms in environments with varying levels of these elements.
Eukaryotic RPA34 RNA polymerase subunit (Euk_RPA34_RNAP_subunit)
Type: Family

This family of proteins includes subunits of eukaryotic DNA-directed RNA polymerase I, which are involved in the transcription of DNA into RNA. They play a role in the synthesis of ribosomal RNA precursors and possess intrinsic RNA cleavage activity. Members of this family, such as the heterodimer formed by RPA34 and RPA49, are known to stimulate transcript elongation by RNA polymerase I.
Inactive lipoate--protein ligase 2 (Lipoate-ligase_2_inactive)
Type: Family

The Inactive lipoate--protein ligase 2 family is involved in the mitochondrial lipoylation process, which is essential for the proper functioning of key dehydrogenase complexes involved in metabolic pathways. Specifically, members of this family work in conjunction with LipL1 to facilitate the lipoylation of the E2 components of the branched chain alpha-ketoacid dehydrogenase complex (BCKDH-E2/BCDH) and the alpha-ketoglutarate dehydrogenase complex (KDH). While LipL1 activates lipoate to form lipoyl-AMP, the exact catalytic role of the Inactive lipoate--protein ligase 2 family is not clear. They may transfer lipoyl groups to BCDH and KDH or serve as effector proteins, influencing the lipoylation process without directly catalyzing the reaction.
Serine protease inhibitor (Serpin)
Type: Family

This family of proteins includes inhibitors of serine proteases such as human tryptase, trypsin, and chymotrypsin. These inhibitors are likely involved in modulating host defense mechanisms by blocking the activity of these proteases, which play a role in immune responses and other physiological processes.
Zinc finger protein 7 (Zinc_finger_protein_7)
Type: Family

The Zinc finger protein 7 family is characterized by its role as a negative regulator of abscisic acid signaling during germination and early seedling development. Abscisic acid (ABA) is a plant hormone that plays a crucial role in stress responses and developmental processes. Members of the Zinc finger protein 7 family are involved in modulating the ABA pathway, ensuring proper control of germination and seedling growth under various environmental conditions. By regulating ABA signaling, this family contributes to the plant's ability to adapt and survive in response to abiotic stresses.
Verrucosidin biosynthesis-associated protein (Verrucosidin_biosynth-assoc)
Type: Family

This family of proteins is involved in the biosynthesis of verrucosidin, a neurotoxic compound that disrupts oxidative phosphorylation in mitochondria, leading to neurological diseases. The proteins in this family are part of a gene cluster responsible for the production of verrucosidin's carbon backbone, which is initially synthesized by a highly reducing polyketide synthase and subsequently modified by associated enzymes. Members of this family likely contribute to the modification and assembly of verrucosidin, although their exact biochemical functions may vary.
Woronin body anchoring protein (Woronin_anchor)
Type: Family

This family of proteins includes tethering components that are crucial for the localization and function of Woronin bodies, which are organelles in certain fungi. Members of this family are involved in the cellular response to hyphal damage by facilitating the occlusion of septal pores, thereby compartmentalizing and protecting undamaged sections of the hyphae. The proteins possess an N-terminal domain that interacts with Woronin bodies, anchoring them at the septal pore, and a C-terminal domain that binds to the septal pore itself, ensuring the correct positioning of the Woronin bodies for their role in cellular defense.
L-aspartate--L-methionine ligase (Asp-Met_ligase)
Type: Family

This family of proteins includes L-amino acid ligases that catalyze the ATP-dependent formation of dipeptides, specifically L-aspartyl-L-methionine. They exhibit substrate specificity, showing higher activity with L-aspartate and L-methionine, and reduced activity with other amino acid combinations. These enzymes do not function with L-methionine analogs or when key functional groups on the substrates are modified. They are also nucleotide-specific, requiring ATP and not other nucleoside triphosphates. These proteins play a role in sulfur amino acid metabolism.
Friend virus susceptibility protein 1 (Fv1_restriction_factor)
Type: Family

The Friend virus susceptibility protein 1 family comprises retroviral restriction factors that protect against infection by gammaretroviruses. Members of the family function by binding to the viral capsid protein post-entry into the host cell. This binding is believed to disrupt the viral capsid, leading to inactivation of the viral genome and preventing its integration into the host genome and subsequent replication.
DDT domain-containing protein (DDT_domain)
Type: Family

This family of proteins includes members that contain a DDT domain, which is typically associated with DNA-binding properties. The DDT domain is characterized by a conserved pattern of cysteine and histidine residues that coordinate a zinc ion, facilitating the domain's role in binding to DNA. Proteins with this domain may be involved in various cellular processes, including transcription regulation, DNA repair, and chromatin remodeling. The specific functions can vary widely among family members, depending on the context of the domain within the full-length protein and the presence of additional domains or motifs that modulate activity or specificity.
Serine/threonine/tyrosine-interacting-like protein (STY_interacting-like)
Type: Family

This family of proteins includes catalytically inactive phosphatases that interact with specific binding partners to modulate cellular processes. Members of this family are known to bind to G3BP1, a process that results in the inhibition of stress granule formation. These proteins do not prevent the dephosphorylation of G3BP1 at a specific serine residue. Additionally, they are capable of inhibiting the activity of PTPMT1 phosphatase, which in turn positively regulates intrinsic apoptosis. This regulatory function suggests a role in cell death pathways. Furthermore, these proteins may contribute to neuronal development by influencing the formation of neurites.
Cell_Separation_Timing_Regulator (CST_Regulator)
Type: Family

This family of proteins appears to play a role in the process of cytokinesis, specifically in the timing of cell separation. Members of this family may function either as enzymes involved in the degradation of glucans within the cell wall at the neck region between mother and daughter cells, or as regulatory proteins that control this metabolic step. The presence of intragenic tandem repeats, which can vary among strains, suggests a potential for variability in function or regulation within this family.
Fluconazole resistance-associated protein (Fluconazole_resistance)
Type: Family

This family of proteins is associated with a phenotype resistant to the antifungal drug fluconazole when deleted. The exact molecular function of these proteins remains to be characterized, but the observed resistance suggests a potential role in the cellular mechanisms that contribute to antifungal drug susceptibility. Further research is required to elucidate the biological processes and pathways in which these proteins are involved, and to determine their specific functions within the cell.
Agnestin biosynthesis monooxygenase (Agnestin_monoxygenase)
Type: Family

This family of proteins includes monooxygenases involved in the biosynthesis of agnestins, which are dihydroxy-xanthone metabolites. These enzymes participate in a multi-step pathway that starts with the assembly of atrochrysone thioester and ends with the production of agnestins A and B. The family member described is implicated in a Baeyer-Villiger oxidation step, leading to the formation of monodictyphenone through the cleavage of a specific carbon bond in chrysophanol. Although the exact role of this protein within the biosynthetic pathway remains unassigned, it is hypothesized to be involved in oxidation/reduction processes that are essential for the conversion of intermediates in the pathway. The protein's function is crucial for the structural diversification of the metabolites produced in this biosynthetic cluster.
Mitochondrial DNA mismatch repair MutS (MtDNA_mismatch_repair_MutS)
Type: Family

DNA mismatch repair MutS is involved in the maintenance of mitochondrial genome integrity. Members of this family, such as MSH1 from Arabidopsis thaliana, play a crucial role in controlling mitochondrial genome configuration. They achieve this by suppressing asymmetric recombination at certain repeat pairs, thereby preventing the rearrangement of the mitochondrial DNA . This function is essential for the proper functioning and stability of the mitochondrial genome, which is critical for cellular energy production and overall plant development.
Endomembrane trafficking modulator (Endomembrane_traffic_mod)
Type: Family

This family of proteins is involved in endomembrane trafficking, specifically in the recycling of proteins to the plasma membrane. Members of this family form a complex with other proteins and actin, which is crucial for the modulation of the trans-Golgi network and early endosome functions. These proteins are also implicated in linking post-Golgi traffic with the actin cytoskeleton, playing a role at the intersection of exocytic and endocytic pathways.
Shuttling pre-60S factor ECM1 (Pre-60S_factor_ECM1)
Type: Family

This family of proteins is involved in the nucleocytoplasmic transport process, specifically in the export of the 60S ribosomal subunit from the nucleus. Members of this family function as pre-ribosomal factors that are essential for the proper assembly and maturation of the 60S subunit, which is a critical component of the eukaryotic ribosome. The ribosome is responsible for protein synthesis, and the 60S subunit forms the larger part of the ribosome, where it joins with the 40S subunit to create the functional 80S ribosome during translation. The export of the 60S subunit from the nucleus to the cytoplasm is a key step in ribosome biogenesis, and proteins in this family play a crucial role in this process.
ER membrane protein complex subunit (EMC_subunit)
Type: Family

This family of proteins is involved in the biogenesis and insertion of membrane proteins into the endoplasmic reticulum (ER). Members facilitate the energy-independent integration of newly synthesized proteins into the ER membrane, particularly accommodating those with less hydrophobic or destabilizing transmembrane domains. The family plays a crucial role in the cotranslational insertion of multi-pass membrane proteins, ensuring correct topology by inserting N-terminal transmembrane domains with the N-terminus facing the ER lumen. Additionally, it is essential for the post-translational insertion of tail-anchored proteins into the ER membrane.
Aerolysin-like pore-forming protein (Aerolysin-like_pore-former)
Type: Family

This family of proteins includes pore-forming proteins that may have a role in host defense mechanisms. They are capable of forming dimers and can also oligomerize into octameric structures that span the cell membrane. The oligomerization process is likely initiated by the binding of a jacalin-type lectin domain to specific high-mannose proteoglycans on the cell surface and is facilitated by an acidic pH. These proteins have been observed to bind to yeast mannan and the HIV virus glycoprotein gp120 with high affinity, suggesting a potential role in immune response and pathogen recognition.
Double zinc ribbon domain-containing protein (Double_zinc_ribbon)
Type: Family

This family of proteins includes members that are characterized by the presence of a double zinc ribbon motif. The double zinc ribbon is a type of zinc finger domain that typically binds two zinc ions and is involved in protein-protein and protein-DNA interactions. Proteins with this motif are often involved in transcriptional regulation, DNA repair, and replication. The zinc ribbon domains facilitate the recognition of specific DNA sequences and can also contribute to the structural stability of the proteins. Given the presence of this motif, proteins in this family are likely to play roles in gene expression regulation and maintenance of genomic integrity.
Regulator of G-protein signaling domain-containing protein (RGS_domain-containing)
Type: Family

This family of proteins includes regulators that modulate the activity of G-proteins, which are molecular switches involved in transmitting signals from various stimuli outside a cell to its interior. Their primary function is to inactivate G-proteins by accelerating the hydrolysis of GTP to GDP, thereby terminating the signal transduction event. They play a critical role in a wide range of cellular processes including vision, neural development, and hormonal signaling. Members of this family are characterized by the presence of a conserved domain known as the RGS domain, which is responsible for their GTPase-activating protein (GAP) activity towards G-proteins.
TUNICAMYCIN INDUCED 1 (TUNICAMYCIN_INDUCED_1)
Type: Family

The TUNICAMYCIN INDUCED 1 family is involved in the regulation of pollen surface morphology. It likely plays a role in modulating the secretion of proteins and/or lipids during the development of pollen, which is crucial for the proper formation of the pollen surface and its functions in plant reproduction.
RGS1-HXK1-interacting protein (RGS1-HXK1_interactor)
Type: Family

This family of proteins is involved in sugar signaling pathways. Members of this family facilitate the physical interaction between RGS1 and HXK1, two key components in glucose-regulated gene expression. Through this interaction, they play a crucial role in modulating the growth of roots and inflorescences in response to glucose levels. The proteins in this family are essential for the proper regulation of plant development and metabolism, particularly in adapting to varying sugar availability.
Thylakoid lumenal pentapeptide repeat protein (Thylakoid_lumenal_pentapeptide)
Type: Family

This family of proteins includes thylakoid lumenal components that are characterized by the presence of pentapeptide repeats. The precise biological functions of these proteins remain unclear, but they are known to be susceptible to degradation in their reduced form. The proteins may play a role in the thylakoid lumen of chloroplasts, which is an important site for various processes related to photosynthesis.
Nematode receptor-like srab (Nematode_rcpt-like_srab)
Type: Family

This family of proteins includes receptors that are likely to be involved in chemosensory processes. They are characterized by a serpentine topology, typically with multiple transmembrane domains, which suggests a role in signal transduction. These receptors may be responsible for detecting environmental cues and initiating appropriate physiological responses in nematodes. The specific ligands and signaling pathways associated with this family are not detailed in the provided information, but members are anticipated to contribute to the complexity of sensory perception and behavior in these organisms.
PP2C-like domain-containing protein (PP2C-like_domain)
Type: Family

This family of proteins includes phosphatase 2C-like enzymes, which are characterized by their ability to dephosphorylate serine and threonine residues in target substrates. These enzymes play a crucial role in various cellular processes, including cell cycle regulation, stress response, and signal transduction pathways. They function as Mg2+ or Mn2+-dependent enzymes and are involved in the negative regulation of cellular processes by counteracting the action of kinases. The PP2C-like domain is responsible for the catalytic activity of these proteins.
TRIGALACTOSYLDIACYLGLYCEROL Bridge Protein (TGD_Bridge_Protein)
Type: Family

This family of proteins is involved in lipid trafficking within plant cells, specifically facilitating the movement of lipids from the outer to the inner envelope of plastids. Members of this family play a critical role in the assembly of thylakoid lipids by acting as a bridge between the TGD4 protein and the TGD1,2,3 transport complex. They are essential for the eukaryotic pathway that transports lipids from the endoplasmic reticulum to the plastid, which is a key process in the biogenesis of thylakoid membranes in chloroplasts.
TSET complex member (TSET_complex_member)
Type: Family

This family of proteins is involved in the TSET complex, which is implicated in the transport of transmembrane proteins. Members of this family, such as TstF, are likely to play a role in the assembly or function of this complex, contributing to the intracellular trafficking processes that are essential for cellular function and homeostasis. The specific molecular functions and mechanisms by which TstF and related proteins operate within the TSET complex remain to be fully elucidated, but they are thought to be critical for the proper delivery of proteins to their designated locations within the cell.
Ommatidial differentiation-associated protein (Ommatidial_diff-associated)
Type: Family

This family of proteins is associated with the development of visual structures, particularly playing a role in the formation of the compound eyes found in arthropods. Members of this family are implicated in the proper differentiation of the cells that make up the individual optical units, ensuring the correct assembly and functionality of these complex visual systems.
UBAP1-MVB12-associated domain-containing protein (UBAP1-MVB12_assoc_domain)
Type: Family

This family of proteins includes members that contain a UMA domain, which is associated with the UBAP1-MVB12 complex. The complex is involved in endosomal sorting and trafficking, playing a role in the multivesicular body (MVB) pathway. This pathway is crucial for the sorting of endosomal membrane proteins into vesicles that bud into the lumen of the endosome, leading to the degradation of these proteins in lysosomes. Proteins in this family are implicated in the recognition and sorting of ubiquitinated cargo proteins for incorporation into intralumenal vesicles, a process essential for maintaining cellular homeostasis.
Outer Chloroplast Membrane Kinase (OCM_Kinase)
Type: Family

This family of proteins includes serine/threonine kinases that play a regulatory role in the plastid protein import machinery. They are involved in phosphorylating import receptors, which is essential for the import of preproteins into plastids. This phosphorylation process is crucial for chloroplast biogenesis and the survival of plants during their transition from dark to light conditions, known as de-etiolation. Members of this family are characterized by their kinase activity, which is pivotal for the proper functioning and maintenance of chloroplasts.
RNA-binding PWI domain-containing protein (RBM_PWI_domain)
Type: Family

This family of proteins includes RNA-binding regulators involved in the modulation of alternative pre-mRNA splicing. Members of this family are characterized by the presence of a PWI domain, which is known to bind nucleic acids and is instrumental in the protein's role in splicing regulation. The PWI domain's affinity for nucleic acids is not specific to the form of the RNA, as it can bind both single- and double-stranded species. Additionally, these proteins play a role as negative regulators in plant responses to the hormone abscisic acid, impacting processes including early developmental stages.
Innate immunity regulator (Innate_immunity_reg)
Type: Family

This family of proteins is involved in the innate immune response, likely through interaction with the atf-7 signaling pathway. Members of this family are implicated in providing resistance against pathogenic bacterial infections. Additionally, they may have a regulatory role in determining the lifespan of an organism.
TSET complex member tstB (TSET_member_tstB)
Type: Family

This family of proteins is involved in the formation of the TSET complex, which plays a role in cellular processes. The specific functions of the TSET complex and its member tstB are not fully characterized, but they are believed to be important for the proper functioning of the cell. Proteins in this family may have roles in the assembly or regulation of the TSET complex, potentially impacting various cellular pathways.
Dynactin-associated protein (Dynactin-associated)
Type: Family

This family of proteins is involved in the regulation of cellular proliferation. Members of this family are known to enhance the activation of the AKT1 signaling pathway, which is crucial for various cellular processes including metabolism, growth, and survival. They are also implicated in facilitating the phosphorylation of AKT1 at a specific serine residue, which is a key post-translational modification that activates AKT1.
Sushi domain-containing protein (Sushi_domain_protein)
Type: Family

This family of proteins is characterized by the presence of sushi domains, which are also known as complement control protein (CCP) modules. Sushi domains are found in a variety of extracellular and membrane-bound proteins and are typically involved in protein-protein interactions. They play a role in a wide range of biological processes including the complement system, blood coagulation, cellular adhesion, and immune response. Proteins containing sushi domains may act as regulators of these pathways, participating in the maintenance of homeostasis and modulation of signaling events. The specific functions of individual members of this family can vary widely, reflecting the diverse roles of sushi domain-containing proteins in different physiological contexts.
ASTRA complex-associated WD repeat (ASTRA_WD_repeat)
Type: Family

This family of proteins is involved in the structural organization of chromatin. Members of this family are components of the ASTRA complex, which plays a role in chromatin remodeling. Chromatin remodeling is a dynamic process that allows the regulation of gene expression by altering the chromatin structure, thereby making certain regions of DNA more or less accessible to transcription machinery. Proteins in this family contain WD repeats, which are typically associated with protein-protein interactions and are involved in a variety of cellular processes including signal transduction, RNA processing, gene regulation, and cell cycle control.
Homeobox-like transcriptional regulator (Homeobox-like_regulator)
Type: Family

This family of proteins includes transcriptional regulators that interact with specific DNA motifs to control gene expression. They play a crucial role in the early stages of gametocyte development by binding to distinct DNA sequences, thereby regulating genes vital for the growth of the inner membrane complex, which is essential for cellular development and differentiation.