SII-SWORD/CoKE huggingface dataset:
Myb-related transcriptional repressor (Myb-related_repressor)
Type: Family

This family of proteins includes transcriptional repressors that interact with DNA through a specific core sequence recognition. Members of this family are characterized by their ability to bind to a consensus DNA motif, which is essential for their function as transcriptional repressors. The interaction with profilin, through a proline-rich region, is noted to modulate the DNA-binding activity of these proteins, suggesting a regulatory mechanism that influences their repressor function. The family is involved in gene expression regulation through these DNA-protein and protein-protein interactions.
V-set and immunoglobulin domain-containing protein (V-set/Ig_domain)
Type: Family

This family of proteins includes members that are characterized by the presence of V-set and immunoglobulin domains, which are typically involved in cell adhesion, recognition, and signaling processes. These domains are commonly found in proteins that participate in immune responses, although their exact functions can vary widely. The proteins in this family may play roles in intercellular communication and the modulation of immune system activity. However, without additional specific information about the individual proteins or the family as a whole, it is difficult to provide a detailed description of the functions these proteins may have.
Environmental Stress Response Regulator (ESR_Regulator)
Type: Family

This family of proteins includes members that are implicated in plant responses to environmental stresses such as cold and drought conditions. They are thought to play roles in the plant's resistance mechanisms by possibly participating in cellular processes that mitigate the effects of these stresses. Some family members are inducible by abscisic acid, a plant hormone that regulates growth and development, and is especially involved in responses to environmental stress.
HEAT repeat-containing protein 9 (HEATR9)
Type: Family

This family of proteins is characterized by the presence of HEAT repeats, which are tandemly repeated units of approximately 37 to 47 amino acids that are found in a number of cytoplasmic proteins. These repeats are thought to be involved in intracellular transport processes and are implicated in the regulation of a variety of cellular functions, including mRNA transport, protein trafficking, and signal transduction. Members of this family are likely to play a role in these processes through their ability to mediate protein-protein interactions. The exact function of the HEATR9 protein within this family is not well characterized, but it is presumed to participate in cellular mechanisms that are consistent with the general functions attributed to HEAT repeat-containing proteins.
Sperm-binding zona pellucida regulatory protein (Sperm-ZP_regulatory)
Type: Family

This family of proteins includes members that are involved in reproductive processes and cell regulation. Specifically, they are implicated in the migration of sperm into the oviduct and are essential for male fertility, as they influence the binding of sperm to the zona pellucida. Additionally, some family members may have roles in cellular growth. Beyond reproductive functions, there is evidence to suggest involvement in regulatory pathways, such as those associated with apoptosis or cell-cycle control in response to DNA damage, potentially under the influence of the tumor suppressor p53/TP53.
CRISPR-associated endoribonuclease (CRISPR_assoc_ribonuclease)
Type: Family

This family of proteins is involved in the CRISPR adaptive immune system, which provides defense against mobile genetic elements such as viruses, transposable elements, and conjugative plasmids. Members of this family are associated with the processing of CRISPR RNA (crRNA) and the subsequent targeting and degradation of invading nucleic acids complementary to the crRNA. Some proteins in this family are endoribonucleases activated by cyclic oligoadenylates, such as cyclic tetraadenylate (cA4), to degrade linear RNA. The RNase activity of these proteins is regulated by the levels of cyclic oligoadenylates, highlighting a sophisticated mechanism of activity modulation in response to cellular signals.
Insect Developmental Hormone Regulators (Insect_Hormone_Regulators)
Type: Family

This family of proteins includes secretory polypeptides primarily involved in the regulation of insect development. They act as hormonal messengers, stimulating the production and release of ecdysone, a critical steroid hormone for insect growth and metamorphosis. The proteins are synthesized in the brain and are known to influence the prothoracic glands. Some members of this family may also have additional, yet unidentified, physiological or developmental roles, as suggested by the presence of post-translationally cleaved peptides with unknown functions.
Lamin Tail Domain-Containing Protein (Lamin_tail_domain)
Type: Family

This family of proteins includes members that are involved in the structural organization of the nuclear lamina, which is a dense fibrillar network inside the nucleus of eukaryotic cells. These proteins play a crucial role in maintaining the integrity of nuclear structures and providing mechanical support to the nucleus. They may also be involved in chromatin organization, DNA replication, and cell division. The presence of a lamin tail domain suggests that these proteins may interact with other lamina components or nuclear elements to perform their functions.
Keratin-associated matrix protein (KRTAP_matrix)
Type: Family

This family of proteins is involved in the structural integrity of hair. They are part of the interfilamentous matrix in the hair cortex, where they interact with hair keratin intermediate filaments. These proteins are crucial for hair shaft formation, providing rigidity and resistance by forming extensive disulfide bond cross-linking with keratin's cysteine residues. They are characterized by high levels of sulfur and the amino acids glycine and tyrosine.
Dictyostelium Spore Germination and Stalk Formation (Dd_Spore_Germination_Stalk)
Type: Family

This family of proteins includes members that are specific to the spore germination and stalk formation stages in the life cycle of the slime mold Dictyostelium discoideum. One member is characterized by an internal repeat motif that is indicative of its role in spore germination. Other members are associated with the stalk formation process, suggesting a functional specialization in the developmental transition from spore to multicellular organism. The exact molecular functions of these proteins are not fully elucidated, but their stage-specific expression implies a role in the regulation of cellular differentiation and morphogenesis during the life cycle of D. discoideum.
Nematode Receptor-Like Serpentine Class Gamma (NRL-Serpentine_Class_Gamma)
Type: Family

This family of proteins includes receptors that are part of a larger group known as the serpentine receptor class gamma. These receptors are characterized by their serpentine structure, which typically involves multiple transmembrane domains that allow them to function as signal transducers. They are involved in various signal transduction pathways, responding to external stimuli and initiating a cascade of cellular responses. The specific functions of these receptors may include sensing environmental signals, regulating development, or modulating neural communication, which are critical for the organism's interaction with its environment and for maintaining homeostasis. The exact ligands and signaling mechanisms, however, may vary among family members and require further investigation.
Keratinocyte Proline-Rich (Keratinocyte_PR)
Type: Family

This family of proteins is involved in the structural organization of keratinocytes, which are the predominant cell type in the epidermis, the outermost layer of the skin. They are characterized by a proline-rich region that suggests a role in protein-protein interactions. These interactions are crucial for the formation of the cytoskeleton and cell-cell adhesion structures, contributing to the integrity and barrier function of the skin. The proteins may also be involved in the regulation of keratinocyte proliferation and differentiation.
EZH Inhibitory Protein (EZH_Inhibitor)
Type: Family

This family of proteins includes inhibitors of the PRC2 complex, which consists of EED, EZH1, and EZH2 components. Members of this family negatively regulate the methyltransferase activity of EZH1 and EZH2, leading to decreased levels of histone H3 trimethylation at lysine 27 (H3K27me3). This action is thought to occur through the modulation of PRC2 cofactors such as AEBP2 and JARID2, which normally stimulate the complex's activity. The inhibition of H3K27me3 deposition by these proteins plays a crucial role during the development of gametes, specifically in spermatogenesis and oogenesis.
Hisactophilin (Hisactophilin)
Type: Family

This family of proteins may function as intracellular pH sensors that are potentially involved in linking chemotactic signals to the cytoskeletal system. They are implicated in the regulation of actin dynamics, either by initiating the polymerization of actin or by maintaining the stability of actin filaments. These activities suggest a role in cellular responses to environmental cues, possibly by modulating the structure of the microfilament system in response to changes in pH.
Vacuolar Import and Degradation Regulator (VID_Regulator)
Type: Family

This family of proteins is involved in the regulation of metabolic processes, specifically in the negative regulation of gluconeogenesis. Members of this family are implicated in the transport of certain enzymes into vesicles for degradation, playing a role in the maintenance of cellular metabolic balance. The characterized member from yeast suggests an indirect mechanism of action through the import of enzymes into vacuolar import and degradation vesicles, which may be a conserved function within the family.
Dictyostelium Calcium-Dependent Adhesion Molecules (Dictyostelium_CAD)
Type: Family

The Dictyostelium CAD family is characterized by its role in mediating calcium-dependent cell-cell adhesion, which is crucial during the early stages of development. Members of the family are involved in the formation of cell assemblies by adhering to one another in a calcium-dependent manner. The adhesive function is attributed to the N-terminal segment of the proteins, which is responsible for cell binding, while the C-terminal domain is important for anchoring the proteins to the cell membrane. The family is part of a larger group of calcium-dependent adhesion molecules that facilitate cellular interactions and communication, playing a vital role in the structural organization and function of multicellular organisms.
Linker Cell Survival and Transcription Coactivator/Chloroplast RNA Splicing Factor (LCS_TC/CRSF)
Type: Family

The protein family encompasses diverse functions, including the promotion of linker cell survival and its non-apoptotic death in nematodes, acting as a coactivator in the transcription of RNA polymerase II-dependent genes in slime molds, and involvement in chloroplast RNA splicing in green algae. In nematodes, the family is implicated in nuclear envelope dynamics during specific cell death processes. In slime molds, it is essential for the starvation-induced gene expression pathway. In green algae, it is crucial for the trans-splicing of chloroplast-encoded mRNA, suggesting a role in chloroplast RNA stability and processing.
FLYWCH-type zinc finger-containing protein (FLYWCH-type_ZF)
Type: Family

This family of proteins includes transcription factors characterized by their ability to bind DNA and repress the expression of target genes, which notably include micro-RNA genes. Members of this family are known to act redundantly with at least one other family member in their biological context. They recognize specific DNA sequence motifs in the promoters of their target genes to exert their regulatory function. The redundancy within this family suggests a potential for compensatory interactions or a division of labor among the different members in regulating gene expression.
Proline-rich region-containing protein 9 (PRR9)
Type: Family

This family of proteins describes proline-rich protein 9 found in mammalian organisms.

Small proline-rich proteins (SPRRs) are a family of proteins primarily involved in maintaining epithelial barrier integrity and antimicrobial defence. They are critical components of the cornified cell envelope, where they function as crosslinking proteins to enhance structural stability. SPRRs are categorized into four main types :

SPRR1:
Found in squamous epithelia and associated with tissues requiring flexibility.

SPRR2:
Includes subtypes like SPRR2A and SPRR2B, which are involved in epithelial differentiation and antimicrobial defense.

SPRR3:
Plays a role in epithelial cell differentiation.

SPRR4:
Less studied but contributes to similar structural functions.
C. elegans Fungus-Induced Response (Celegans_Fungus-Induced_Rsp)
Type: Family

The protein family, which includes Fungus-induced-related protein 15, Fungus-induced protein 3, and Fungus-induced-related protein 16, is characterized by a potential role in the organism's response to fungal infection. Members of the family may be involved in the hypoxia response, suggesting a function related to cellular adaptation to low oxygen conditions, which could be a part of the broader immune or stress response mechanisms triggered by fungal presence.
Sea Urchin Spicule Matrix (SM50_spicule_matrix)
Type: Family

The SM50 family comprises major matrix proteins found in sea urchin embryos' spicules. These proteins are essential for biomineralization, a process where they direct the growth of calcite crystals in specific orientations while inhibiting growth in others. The presence of a repetitive domain within these proteins suggests a role in providing a calcite binding matrix, which is crucial for the structural integrity and formation of the spicule. By controlling crystal growth, the SM50 family plays a pivotal role in the development of the sea urchin's endoskeleton, ensuring proper shape and strength.
DNA-3-methyladenine glycosylase (DNA-3mA_glycosylase)
Type: Family

This family of proteins is involved in the repair of damaged DNA. Members of this family are enzymes that recognize and excise 3-methyladenine, a non-bulky alkylated base, from the DNA helix. This is achieved through the hydrolysis of the deoxyribose N-glycosidic bond. The excision of this lesion is crucial for maintaining the integrity of the genetic material and preventing mutations that could lead to cell death or oncogenesis. The enzymatic activity of these proteins is subject to regulation, with product inhibition being a reported mechanism to control their function.
Nucleic_acid-targeting_endonuclease (NA-targeting_endonuclease)
Type: Family

This family of proteins includes enzymes involved in nucleic acid modification and interaction. One member functions in the CRISPR adaptive immune system, utilizing guide RNAs to identify and cleave foreign DNA sequences in a sequence-specific manner, which is essential for the defense against invading genetic elements like viruses and plasmids. It contains two distinct endonuclease domains that cleave opposite strands of the target DNA. Another member is a restriction enzyme that specifically targets and cleaves DNA containing methylated or hydroxymethylated cytosines within a particular recognition sequence. These activities are crucial for processes such as bacterial immune defense and restriction-modification systems.
Two-component system response regulator (TCS_response_regulator)
Type: Family

This family of proteins includes members that are part of two-component regulatory systems, which are typically involved in response to environmental stimuli. These proteins function as response regulators that receive signals from associated sensor kinases and effect changes in gene expression, typically to adapt to varying conditions. The family encompasses proteins that regulate processes such as methanogenesis, a biological pathway in certain microorganisms that produce methane, as well as other cellular responses to environmental changes.
AsmA-related (AsmA-related)
Type: Family

This family of proteins is implicated in the process of outer membrane protein assembly. One member is specifically involved in preventing the assembly of defective versions of the OmpF protein, suggesting a quality control role in the biogenesis of membrane components. The broader function of the family appears to be associated with the assembly or maintenance of outer membrane structures in bacteria.
Heterokaryon Regulation/Transcriptional Modulator (HetReg/Transcr_Mod)
Type: Family

This family of proteins is involved in diverse cellular processes including non-self-recognition and growth regulation in fungi. Members of this family play a role in restricting heterokaryon formation by recognizing genetic differences at specific loci, which is crucial for maintaining organismal integrity during asexual growth. Additionally, some proteins in this family may influence gene expression indirectly through protein-protein interactions rather than direct DNA binding or possessing typical transcriptional activation motifs. These interactions can modulate the suppression of mutations in promoters induced by transposable elements.
Gamma-glutamyltransferase-like enzyme (GGT-like_enzyme)
Type: Family

This family of proteins includes enzymes that are structurally related and share a common evolutionary origin, as suggested by their membership in the gamma-glutamyltransferase family. Members of this family are involved in various biochemical processes. One characterized member is implicated in the uric acid degradation pathway, where it facilitates the conversion of oxamate to oxalate, an important step in purine catabolism. Another member, although initially thought to be a glutathione hydrolase, has been reported not to hydrolyze glutathione when overexpressed with an N-terminal His tag. This raises questions about the enzyme's substrate specificity and the potential impact of protein tags on its activity. The exact functions of these enzymes may vary, and their activities could be influenced by post-translational modifications or the presence of protein tags in recombinant constructs.
Secondary metabolite biosynthesis hydrolase (Sec-Metab_Biosynth_Hydrolase)
Type: Family

This family of proteins includes alpha/beta hydrolases from bacteria and fungi, involved in complex biosynthetic pathways for the production of secondary metabolites with diverse biological activities. Members of this family function as epimerases, esterases, and dehydrogenases, participating in the synthesis of compounds such as meroterpenoids and squalene-based molecules. Their activities include the modification of intermediate compounds through oxidation, reduction, methylation, and lactonization reactions, contributing to the structural diversity and bioactivity of the metabolites produced.

Among its members is the probable hydrolase R7 catalyses key steps in the formation of structurally intricate products like novofumigatonin and squalestatin S1, which have potential pharmacological applications . Alpha/beta hydrolase nvfD mediates the biosynthesis of novofumigatonin, a heavily oxygenated meroterpenoid containing a unique orthoester moiety . Carbendazim hydrolyzing esterase, also included in this entry, catalyses the hydrolysis of the fungicide carbendazim (methyl-1H-benzimidazol-2-ylcarbamate or MBC) to 2-aminobenzimidazole (2-AB) .
Acyl-CoA dehydrogenase 10-like (ACAD10-like)
Type: Family

This family of proteins includes acyl-CoA dehydrogenases that are specifically active with R- and S-2-methyl-C15-CoA substrates. These enzymes play a crucial role in the metabolism of fatty acids, participating in the beta-oxidation pathway by introducing a double bond between the alpha and beta carbon atoms of acyl-CoA substrates. The activity of these proteins is essential for the breakdown of fatty acids, a process that provides energy for cellular functions.
Class-I DAHP synthase (Class-I_DAHP_synthase)
Type: Family

This family of proteins includes enzymes that catalyze the first step in the shikimate pathway, which is the condensation of phosphoenolpyruvate (PEP) and D-erythrose-4-phosphate (E4P) to produce 3-deoxy-D-arabino-heptulosonate-7-phosphate (DAHP). This reaction is a key regulatory point in the biosynthesis of aromatic amino acids. Members of this family are subject to feedback inhibition by various end products of the pathway, such as L-phenylalanine and L-tyrosine.
Phospholipid Metabolizing Enzymes (Phospholipid_Metab_Enz)
Type: Family

This family of proteins includes enzymes with diverse catalytic activities, primarily involved in the metabolism of phospholipids. Members of this family are capable of catalyzing the hydrolysis of phospholipids, releasing phosphatidic acid and an alcohol. Additionally, they can perform a transphosphatidylation reaction in the presence of primary alcohols and high concentrations. Some members also exhibit phosphatase activity towards specific phosphate esters. The proteins are regulated by various mechanisms, including calcium binding and proteolytic cleavage, which can modulate their enzymatic activity. The family is characterized by a catalytic domain typically located in the N-terminal region, while the C-terminal region is associated with regulatory functions.
Bacterial transglutaminase-like (Bact_TGase-like)
Type: Family

This family of proteins includes enzymes with transglutaminase activity, which is typically found within a periplasmic domain. These enzymes play a crucial role in the viability of certain bacteria, potentially contributing to essential functions related to cell wall processes. The transglutaminase activity involves the post-translational modification of proteins by catalyzing the formation of isopeptide bonds between glutamine and lysine residues, impacting the stability and function of protein assemblies.
ABC-2 integral membrane transporter (ABC-2_transporter)
Type: Family

This family of proteins is involved in the transport of specific substrates across cellular membranes. Members are likely part of an ABC transporter complex that confers resistance to certain compounds, such as the antibiotic doxorubicin. These proteins are thought to play a key role in the translocation process of the substrate, moving it from one side of the membrane to the other, which is a critical function in the resistance mechanism.
Acyl-CoA dehydrogenase-like protein (Acyl-CoA_dehydrogenase-like)
Type: Family

This family of proteins includes enzymes that are involved in the metabolism of fatty acids and potentially in DNA repair mechanisms. Members of this family are characterized by their ability to bind to and modify fatty acids or to interact with DNA. They may participate in adaptive responses to environmental stresses, such as elevated temperatures or the presence of alkylating agents. These proteins typically have dehydrogenase activity, which is often associated with a flavin adenine dinucleotide (FAD) cofactor, and may also possess DNA-binding capabilities. The diverse functions of these proteins reflect their involvement in various cellular processes, including lipid metabolism and the maintenance of genomic stability.
L,D-transpeptidase YkuD-like (LD-transpeptidase_YkuD-like)
Type: Family

This family of proteins includes L,D-transpeptidases that are likely involved in the synthesis of bacterial cell walls by catalyzing the formation of a specific type of cross-link between peptidoglycan strands. These enzymes are characterized by their ability to generate meso-diaminopimelyl-3 to meso-diaminopimelyl-3 cross-links, which are essential for maintaining cell wall integrity and shape in certain bacteria. Members of this family share structural similarities and are related to the YkuD family, suggesting a conserved mechanism of action across different bacterial species.