SII-SWORD/CoKE huggingface dataset:
Acyl-CoA N-acyltransferase VerG-like (Acyl-CoA_N-acyltransferase)
Type: Family

This family of proteins includes acyl-CoA N-acyltransferases involved in the biosynthesis of specific neurotoxins, such as verrucosidin, which is a methylated alpha-pyrone polyketide. These enzymes are responsible for the modification of the carbon backbone produced by polyketide synthases, contributing to the production of compounds that can inhibit oxidative phosphorylation in mitochondria, leading to neurological diseases. The activity of these proteins is typically associated with a gene cluster dedicated to the biosynthesis of the toxin.
Pyrrolopyrazine biosynthesis cluster protein F (Pyrrolopyrazine_biosynth_F)
Type: Family

Pyrrolopyrazine biosynthesis cluster protein F, also known as Sulfotransferase ppzF, is involved in the biosynthesis of pyrrolopyrazines, which are secondary metabolites with insecticidal properties . The protein includes a multifunctional non-ribosomal peptide synthetase (NRPS) that synthesises peramine, a simple pyrrolopyrazine . The NRPS contains condensation, methylation, and reduction domains, which facilitate the formation of peptide bonds, N-methylation of arginine, and cyclization to release the product. Oxidation processes are also involved in converting proline into an oxidized derivative for NRPS substrate use.
TRPL channel trafficking regulator (TRPL-trafficking_regulator)
Type: Family

This family of proteins includes GTP-binding proteins involved in the trafficking of ion channels in photoreceptor cells. They play a crucial role in the light-dependent internalization and recycling of specific ion channels, such as the TRPL channel, between the rhabdomere and the cell body. Members of this family are capable of binding to specific phospholipids, including 3-phosphoinositide and phosphatidic acid, which suggests interactions with cellular membranes, particularly early endosomes. Their activity is essential for maintaining photoreceptor cell integrity and preventing degeneration.
Stereospecific Lipase (Stereospecific_Lipase)
Type: Family

This family of proteins is involved in the enzymatic breakdown of triglycerides into their component fatty acids and glycerol, a process known as hydrolysis. Members of this family exhibit a high degree of stereospecificity, meaning they can distinguish between molecularly similar compounds based on their three-dimensional orientation. This specificity is not only crucial for their role in lipid metabolism but also makes them valuable for applications in organic synthesis, particularly in the production of glucolipids which are important for various biological functions including as components of cell membranes and as signaling molecules.
NADH-ubiquinone oxidoreductase subunit (NADH-Q_oxidrdct_subunit)
Type: Family

This family of proteins is involved in the mitochondrial electron transport chain, specifically in the initial stage of transferring electrons from NADH to ubiquinone. Members of this family serve as subunits in the NADH-ubiquinone oxidoreductase complex, also known as Complex I, which is the first enzyme in the respiratory chain. They play a crucial role in the process of oxidative phosphorylation, where the energy from electron transfer is used to generate a proton gradient across the mitochondrial membrane, ultimately leading to the production of ATP, the cell's energy currency.
Transcription regulator galc (Trans_reg_galc)
Type: Family

The Transcription regulator galc family includes transcription factors that play a crucial role in the negative regulation of ochratoxin A biosynthesis, a harmful mycotoxin with various toxic properties. Members of this family are also involved in maintaining cellular redox balance and modulating the cell's response to oxidative stress induced by H(2)O(2). The expression of these regulators is influenced by the presence of carbon sources such as sucrose, glucose, and arabinose, which when present, suppress the family's activity leading to increased production of ochratoxin A and alterations in redox homeostasis.
G-protein coupled receptor LN-TM7 (GPCR_LN-TM7)
Type: Family

This family of proteins includes G-protein coupled receptors (GPCRs) that are part of the LN-TM7 subfamily. GPCRs are a large family of cell surface receptors that respond to a variety of external signals and activate intracellular signal transduction pathways and cellular responses. Being part of the LN-TM7 subfamily, these receptors are characterized by a long N-terminal extracellular domain and seven transmembrane helices. They are involved in cell adhesion and signaling processes. The specific functions of latrophilin receptor-like proteins may include roles in cell-cell communication, neuronal function, and possibly the modulation of synaptic transmission, although the precise physiological roles can vary.
Chloroplastic DnaJ C/III subfamily chaperone (DnaJ_C/III_chloroplastic)
Type: Family

This family of proteins is involved in plant development and is likely important for the structural organization of cellular compartments. Members of this family are characterized by their role as chaperones, which suggests they may assist in protein folding, assembly, translocation, or degradation. As part of the DnaJ family, specifically the C/III subfamily, these proteins share common features that are essential for their chaperone activity, including the presence of a J-domain that typically interacts with Hsp70 heat shock proteins, facilitating ATP hydrolysis and stabilizing protein substrates.
Plasmodium ABRA-related (ABRA-related)
Type: Family

This family of proteins is implicated in the asexual blood stage of a parasitic lifecycle, where they play a role in the invasion of host erythrocytes. They achieve this by interacting with a specific host cell surface protein, which facilitates the entry of the parasite into the red blood cells without the need for sialic acid. The interaction is a critical step in the parasite's ability to proliferate within the host and is essential for its survival and continued infection.
RPM1 Interacting Protein (RPM1_Interactor)
Type: Family

This family of proteins interacts with resistance proteins to enhance plant defense mechanisms against certain bacterial pathogens. Members of this family are involved in promoting resistance to necrotrophic bacteria by positively regulating specific resistance proteins. They play a role in preventing the hypersensitive response controlled by these resistance proteins. Additionally, they are implicated in the process of leaf senescence and cell death, possibly by aiding the nuclear translocation of certain transcription factors. These proteins also have a role in activating reactive oxygen species-related enzymes, contributing to the plant's defense response.
Ser/Thr Protein Kinase (Ser_Thr_kinase)
Type: Family

This family of proteins includes serine/threonine kinases, which are a type of enzyme that modifies other proteins by chemically adding phosphate groups to them. Members of this family are involved in a wide range of cellular processes, including the regulation of cell division, signal transduction pathways, and the response to external stimuli. By phosphorylating their substrates, these kinases play critical roles in the activation or deactivation of various proteins, thereby influencing cellular functions and communication.
Cornifin (Cornifin)
Type: Family

This family of proteins includes members that are involved in the formation of the cross-linked envelope of the epidermis. They act as substrates for transglutaminase-catalyzed reactions, which result in the formation of a proteinaceous barrier. This barrier is essential for protecting the underlying tissues from environmental stress, pathogens, and water loss. The proteins in this family are characterized by their small size and the abundance of proline residues within their sequence, which contribute to their function in the skin's cornified envelope.
Natterin, C-terminal (Natterin_C)
Type: Domain

This entry represents a domain found in Natterin-1 from Thalassophryne nattereri and similar sequences. This protein shows nociceptive, edema-inducing and kininogenase activity with release of kallidin from low molecular weight kininogen. Its proteolytic activity of these proteins specifically targets Met-Lys bonds .
RING-H2 finger domain-containing protein (RING-H2_zinc_finger)
Type: Family

This family of proteins includes members that contain a RING-type zinc finger domain, which is characteristic of a group of E3 ubiquitin ligases. These proteins are involved in the ubiquitination pathway, where they play a role in the transfer of ubiquitin from an E2 ubiquitin-conjugating enzyme to specific substrate proteins. This post-translational modification can lead to various outcomes, including the targeted degradation of proteins via the 26S proteasome, alteration of cellular location, or modulation of activity and interactions of the substrate proteins. The RING-type zinc finger domain is crucial for the interaction with the E2 enzyme and is a defining feature of this protein family.
Dual specificity protein-tyrosine phosphatase (Dual_spec_PTase)
Type: Family

This family of proteins includes dual specificity phosphatases that are involved in the regulation of the cell cycle, particularly during the DNA synthesis phase. Members of this family are characterized by their ability to dephosphorylate serine, threonine, and tyrosine residues, which is a key process in cell signaling and regulation. The enzymatic activity of these phosphatases is crucial for controlling the phosphorylation state of various substrates, thereby influencing cellular processes such as cell growth, division, and differentiation. The family is part of the larger protein-tyrosine phosphatase superfamily, and specifically belongs to the non-receptor class dual specificity subfamily, indicating that these enzymes act within the cell rather than at the cell surface.
VTT domain-containing protein (VTT_domain)
Type: Family

This family of proteins includes members that are integral to cellular membranes and are thought to be involved in various cellular processes. The characteristic feature of this family is the presence of the VTT domain, which was initially thought to be associated with SNARE proteins but was later redefined due to lack of evidence supporting this interaction. The VTT domain is now associated with proteins such as VMP1, TMEM41, and TVP38, and it is implicated in activities related to membrane dynamics and possibly autophagy. The exact functions of these proteins may vary, but they are generally recognized for their role in maintaining cellular homeostasis and may be involved in vesicular transport or membrane remodeling.
NADPH-dependent pterin aldehyde reductase (NADPH_pterin_aldehyde_rdct)
Type: Family

The NADPH-dependent pterin aldehyde reductase family is involved in the salvage of pterin aldehydes during folate turnover. Members of this family are capable of reducing a variety of aromatic and aliphatic aldehydes, including acetaldehyde and benzaldehyde, among others. The family is characterized by its ability to convert pterin-6-aldehyde to 6-hydroxymethylpterin, as well as dihydropterin-6-aldehyde to 6-hydroxymethyldihydropterin. However, it is unable to reduce the pterin ring itself. The family is part of the short-chain dehydrogenases/reductases (SDR) superfamily, which is known for its functional diversity in oxidoreductase activity.
PAM2-like motif domain-containing protein (PAM2-like_domain)
Type: Family

This family of proteins includes members that are known to interact with polyadenylate-binding proteins (PABPs) through a specific motif resembling the PAM2 motif. This motif is typically involved in recognizing and binding to the PABC/CTC domain of PABPs, suggesting a role in mRNA metabolism. PABPs are key regulators of mRNA stability and translation, and their interaction with PAM2-like motif-containing proteins may influence these processes. The exact biological functions of this protein family may vary among its members, but the interaction with PABPs is a common feature that suggests a potential role in post-transcriptional control of gene expression.
Septate junction maturation regulator (SJ_maturation_regulator)
Type: Family

This family of proteins is essential for the development and maturation of septate junctions, which are key structures in the epithelial tissue that contribute to cell adhesion and barrier formation. Members of this family are involved in the localization of core components of septate junctions during late embryogenesis and are specifically required for the formation of tricellular junctions, where three epithelial cells meet. These proteins also play a role in the accumulation of certain proteins at tricellular junctions, indicating a specialized function in cellular contact and communication at these junction points.
Histone deacetylase HD type 1 (HDAC_HD_type_1)
Type: Family

This family of proteins is involved in the removal of acetyl groups from lysine residues at the N-terminal part of core histones, including H2A, H2B, H3, and H4. This action is crucial for epigenetic repression, as it marks the histones for a state that is generally associated with condensed, transcriptionally inactive chromatin. Members of this family are key regulators in the control of gene expression, influencing various cellular processes such as cell cycle progression and development. They function through the assembly of large multiprotein complexes, which are essential for their deacetylase activity.
Mitochondrial Process-Associated (MitoProcess-Associated)
Type: Family

This family of proteins is involved in various cellular processes within the mitochondria. The specific functions of these proteins may include roles in mitochondrial maintenance, energy metabolism, and the regulation of mitochondrial gene expression. They may also participate in the assembly of mitochondrial complexes, the import and export of mitochondrial proteins, and the maintenance of mitochondrial DNA. Given the diverse and essential nature of mitochondrial functions, proteins in this family are likely to be crucial for the normal operation and integrity of the cell's energy-producing organelles.
Nuclear speckle splicing regulatory protein (NS_splicing_regulatory_protein)
Type: Family

This family of proteins is involved in the regulation of pre-mRNA splicing within the cell nucleus. Members of this family are typically localized to nuclear speckles, which are dynamic structures implicated in the storage and modification of splicing factors. Proteins in this family may play a role in the assembly and disassembly of spliceosomes, the complex molecular machines that remove introns from pre-mRNA transcripts. Through their involvement in splicing regulation, these proteins contribute to the control of gene expression and the generation of protein diversity through alternative splicing.
G protein-coupled receptor GPR1/git3-like (GPCR_GPR1/git3-like)
Type: Family

This family of proteins includes G protein-coupled receptors that are involved in the process of conidiation and the regulation of secondary metabolite biosynthesis, such as dihydroxynaphthalene (DHN)-melanin. These receptors function through interactions with G-protein complexes, particularly the alpha subunit, to exert their effects on cellular processes.
Zinc finger MYND domain-containing protein (Zinc_finger_MYND_domain)
Type: Family

This family of proteins includes members that contain a zinc finger MYND-type domain, which is known to mediate protein-protein interactions. These interactions often involve chromatin remodeling complexes, suggesting a role in transcriptional regulation. The MYND domain typically recognizes specific peptide sequences or post-translational modifications, thereby influencing the assembly of protein complexes that are crucial for various biological processes including signal transduction, apoptosis, and development. The exact functions of individual family members can vary, but they generally contribute to the regulation of gene expression and cellular differentiation.
Lachrymatory-factor Synthase (LFS)
Type: Family

This family of proteins is involved in the production of a compound known as the lacrymatory factor, which is responsible for causing tears. The enzyme catalyzes the transformation of 1-propenylsulphenic acid into the lacrymatory factor. The 1-propenylsulphenic acid is an unstable intermediate that is generated from the breakdown of trans-1-propenyl-L-cysteine sulphoxide (PRENCSO) by the enzyme alliinase. This biochemical reaction is significant in the context of plants where it serves as a defense mechanism, particularly noted in species like onions that release a tear-inducing substance when their tissues are damaged.
Glycosyltransferase 77 domain-containing protein (Glycosyltransferase_77)
Type: Family

This family of proteins includes enzymes that are involved in the modification of cell wall components through the process of arabinosylation. Members of this family are responsible for adding arabinose, a sugar molecule, to extensin proteins, which are structural glycoproteins present in plant cell walls. The arabinosylation of extensins is crucial for various plant developmental processes, including cell elongation, root hair cell development, lateral root development, and the growth of root hair tips. The activity of these enzymes is characterized by a conserved DXD motif, which is essential for their catalytic function.
Glycoprotein-specific N-glycanase (N-glycanase)
Type: Family

This family of proteins is involved in the enzymatic process of detaching glycans from glycoproteins. The enzymatic activity is specific to glycosylated asparagine residues that are flanked by polypeptide chains. The cleavage mechanism facilitated by these enzymes ensures the removal of the entire glycan structure, which is essential for various biological processes including protein degradation, quality control, and cellular signaling.
Epithelial-mesenchymal transition regulator (EMT_regulator)
Type: Family

This family of proteins is involved in the regulation of cellular processes that prevent epithelial cells from undergoing a transformation into a mesenchymal cell state. They play a role in maintaining cell polarity and adhesion, thereby inhibiting the increased migratory and invasive capabilities that characterize the mesenchymal phenotype. Their function is crucial in controlling epithelial-mesenchymal transition, a critical event in developmental processes, tissue regeneration, and cancer progression.
Sexual differentiation modulator (Sex_diff_modulator)
Type: Family

This family of proteins is implicated in the modulation of reproductive processes, specifically in the transition from asexual to sexual reproductive modes. Members of this family may play a role in determining the reproductive pathway in their respective organisms.
Small GTPase Arf-like protein (Arf-like_GTPase)
Type: Family

This family of proteins includes members that are part of the small GTPase superfamily, specifically the Arf subfamily. These proteins are involved in various cellular processes including the regulation of vesicular trafficking, actin cytoskeleton organization, and lipid metabolism. They function as molecular switches that cycle between an active GTP-bound state and an inactive GDP-bound state, modulating various downstream effects in the cell. The precise role of ARL9 within this family is less well characterized, but like other Arf proteins, it is likely to be involved in similar regulatory pathways.
Epidermal growth factor-like domain-containing protein (EGF-like_domain)
Type: Family

This family of proteins is involved in the innate immune response by recognizing and binding to lipopolysaccharides on the cell walls of Gram-negative bacteria. They act as pattern recognition receptors, promoting bacterial aggregation and enhancing bacterial clearance. These proteins specifically interact with the inner core oligosaccharides of rough-type LPS and exhibit antibacterial activity against Gram-negative bacteria such as E. coli. However, they do not show activity against Gram-positive bacteria like S. aureus or fungi such as C. albicans.
Kelch repeat-containing protein (Kelch_repeat-containing)
Type: Family

This family of proteins features the kelch motif, which typically forms a beta-propeller structure. These structures are known to mediate a variety of protein-protein interactions. Members of this family are involved in diverse cellular processes, including but not limited to, cytoskeleton organization, cellular morphology, and signal transduction pathways. The kelch repeat-containing proteins may act as scaffolds that assemble key components of a signaling pathway or as regulators of protein degradation. They are also implicated in the response to oxidative stress and in the modulation of transcription factors. Given the presence of the kelch repeats, these proteins may interact with actin and influence the cytoskeleton dynamics.
Cu-only superoxide dismutase (Cu-only_SOD)
Type: Family

This family of proteins includes enzymes that mitigate oxidative stress by catalyzing the conversion of superoxide radicals into less harmful hydrogen peroxide, which can then be further processed into water. These enzymes are characterized by their ability to bind copper ions and function without zinc, which is atypical for superoxide dismutases. Their unique structure allows them to operate effectively in environments where zinc and copper availability is limited, such as at the host-pathogen interface. Additionally, these enzymes play a role in the survival of fungal persisters within biofilms by degrading reactive oxygen species, aiding in evasion of the host's immune response and contributing to antifungal resistance.
Calcium-permeable cation-selective channel (Ca-permeable_cation_channel)
Type: Family

This family of proteins includes calcium-permeable cation-selective channels that play a crucial role in plant immunity. They facilitate the increase of cytosolic calcium levels in root pericycle cells, which is essential for conferring resistance to a broad spectrum of clubroot diseases. These proteins are known to be activated in response to fungal pathogens, such as Plasmodiophora brassicae, and contribute to the induction of defense mechanisms in plants. In addition to calcium, these channels are permeable to sodium ions and potentially other cations, suggesting a versatile role in ion homeostasis and signaling.
Golvesin-related Golgi apparatus protein (Golvesin-related_Golgi)
Type: Family

This family of proteins includes Golvesin, which is known to be involved in the biogenesis and function of Golgi apparatus. Golvesin is a membrane protein that may play a role in the transport of proteins between different compartments of the Golgi or in the maintenance of Golgi structure. It may also be implicated in processes such as protein sorting, vesicle trafficking, or the regulation of Golgi stack assembly. The specific molecular function and biological processes associated with Golvesin and its family members may vary, but they are generally linked to the Golgi apparatus and intracellular protein transport mechanisms.
Heterogeneous nuclear ribonucleoprotein (hnRNP)
Type: Family

This family of proteins is involved in the processing of pre-messenger RNA (pre-mRNA) within the nucleus of eukaryotic cells. Members of this family form complexes with heterogeneous nuclear RNA and other ribonucleoproteins, contributing to the formation of ribonucleosomes. These complexes are essential for the packaging of pre-mRNA into particles known as heterogeneous nuclear ribonucleoprotein (hnRNP) particles. Additionally, these proteins play a role in the transport of polyadenylated mRNA from the nucleus to the cytoplasm and are implicated in the regulation of alternative splicing by potentially influencing splice site selection.