SII-SWORD/CoKE huggingface dataset:
Cadmium-induced response protein (Cadmium-induced_rsp)
Type: Family

This family of proteins includes cadmium-induced proteins that are suggested to be involved in the cellular response to cadmium exposure. The proteins in this family are indicated to have similarity to bacterial proteins, which may imply a role in metal ion binding or detoxification processes. However, the specific functions of these proteins are not clearly defined based on the provided information. The uncharacterized nature of one of the proteins suggests that the family may have diverse functions or that the full range of activities has not been fully elucidated.
Leucine-rich repeat-containing protein (LRR-containing)
Type: Family

This family of proteins contains leucine-rich repeat (LRR) motifs, which are typically involved in protein-protein interactions. The LRR motifs consist of 20-30 amino acids and are rich in leucine residues. Proteins with LRRs are known to participate in a variety of cellular processes including signal transduction, cell adhesion, DNA repair, recombination, transcription, and immune response. Given the presence of LRR motifs, members of this family are likely to be involved in one or more of these processes, although the exact functions may vary among individual proteins and species. The specific roles of these proteins could include involvement in the formation of protein complexes, acting as scaffolds for the assembly of multiprotein complexes, or mediating specific ligand-receptor interactions.
Electron Transfer Ferredoxin (ET_Ferredoxin)
Type: Family

This family of proteins includes iron-sulfur proteins that are involved in electron transfer across a range of metabolic processes. One member of this family is known to participate as a phosphodonor to cytochrome P450 BioI, indicating a role in biosynthetic pathways. The electron transfer function is fundamental to various cellular reactions, highlighting the importance of these proteins in maintaining cellular redox balance and energy metabolism.
Meiotic Drive Suppressor Kinase (Meiotic_Drive_Suppr_Kinase)
Type: Family

This family of proteins is involved in the regulation of meiotic drive, a process that biases the transmission of alleles to progeny. Members of this family function as a poison/antidote system, where they may act as a DNA nuclease that leads to the killing of spores that do not inherit the allele, while also possessing a kinase activity that confers resistance to this nuclease activity. Some members are known to suppress the meiotic drive of other proteins within the same family, indicating a complex regulatory mechanism of allele transmission during meiosis.
NADPH:quinone oxidoreductase MdaB (NADPH-QR_MdaB)
Type: Family

This family of proteins includes NADPH-specific quinone reductases that are most active with quinone derivatives and ferricyanide as electron acceptors. They can utilize menadione, 1,4-naphthoquinone, and 1,4-benzoquinone as substrates. Members of this family may operate in conjunction with other proteins to form a quinone redox cycle, which is essential for various cellular processes including the regulation of oxidative stress and electron transport.
Ubiquitin carboxyl-terminal hydrolase 53/54 (Ubiquitin_hydrolase_53/54)
Type: Family

This family includes ubiquitin carboxyl-terminal hydrolases 53 and 54 that, despite their classification in the peptidase C19 family, do not exhibit peptidase activity. Instead, certain members of this family are associated with tight junctions and are implicated in the survival of auditory hair cells and hearing. They may contribute to this biological process by modulating the barrier properties and mechanical stability of tight junctions.
Phage Baseplate Assembly Protein (Phage_Baseplate_Assmbl_Protein)
Type: Family

This family of proteins includes components typically associated with bacteriophage baseplates, suggesting a role in phage assembly or function. Members are likely involved in the structural formation of the phage tail, which is critical for the phage's ability to infect host bacteria. The presence of these proteins in diverse bacterial species indicates a conserved function related to phage biology, possibly in the assembly of the baseplate structure that facilitates host recognition and DNA injection.
Zn(2)-C6 fungal-type transcription factor (Zn2-C6_fungal_TF)
Type: Family

The Zn(2)-C6 fungal-type transcription factor family is involved in the regulation of various biosynthetic pathways in fungi. Members of this family act as transcription factors that bind to specific DNA sequences to regulate gene expression. They are involved in the positive regulation of ergosterol biosynthesis, mediating the expression of genes such as CYP51A/B and ERG6A/B, which are crucial for sterol production. Some members also regulate sterol uptake and sterol biosynthetic genes by binding to sterol regulatory elements (SREs). Additionally, this family includes proteins that are part of gene clusters responsible for the biosynthesis of secondary metabolites, such as fumihopaside A and orsellinic acid, as well as the cathepsin K inhibitors F9775 A and B. These transcription factors play roles in enhancing thermotolerance, UV resistance, and triggering pyroptosis in macrophages.
Calcium-regulated OB-fold (Ca-regulated_OB-fold)
Type: Family

This family of proteins includes members that are involved in intracellular calcium homeostasis and protection against oxidative stress. Some proteins within this family are uncharacterized, but annotations suggest a potential similarity to proteins in other species, indicating a possible conserved function across different organisms. The characterized member is known to play a role in cell protection and calcium regulation.
ADCK protein kinase (ADCK_kinase)
Type: Family

The ADCK protein kinase family is part of the larger protein kinase superfamily. Members of the ADCK family are characterized by the presence of an aarF domain and are typically associated with mitochondrial functions. Although the precise biochemical activities of these kinases are not fully understood, they are believed to be involved in the mitochondrial import of CoQ precursors, which is essential for muscle mitochondrial function and fatty acid beta-oxidation. The exact substrates for their kinase activity, whether they phosphorylate serine, threonine, or tyrosine residues, remain to be determined.
LINC complex-associated protein (LINC-complex_assoc)
Type: Family

This family of proteins is involved in the LINC complex, which connects the nuclear lamina to the cytoskeleton, facilitating the transmission of mechanical forces across the nuclear envelope and playing a role in nuclear movement and positioning. Members of this family are likely to serve as anchoring proteins, tethering the nucleus to the cytoskeleton and interacting with components such as PLEC and the intermediate filament system. They are implicated in cellular processes like the regulation of cell morphology, centrosome polarization, and directional migration in response to mechanical stimuli. Some family members also contribute to the spatial organization of myonuclei in muscle fibers and the anchoring of cellular organelles to structural components within the cell.
SPP1-like small terminase (SPP1-like_terminase)
Type: Family

The SPP1-like small terminase family is involved in the packaging of viral DNA into the procapsid of bacteriophages. Members of this family recognize specific DNA packaging sequences and regulate the ATPase activity of the terminase large subunit. The small terminase subunit, in conjunction with the large subunit, forms a complex that docks on the portal protein, creating a packaging machine. This complex facilitates the cleavage of viral genome concatemers and the subsequent packaging of DNA into the capsid. The process continues until the capsid is full, at which point the terminase complex is replaced by neck proteins to complete the assembly of the viral particle.
Mitochondrial Translation Release Factor (Mito_Transl_Release_Factor)
Type: Family

This family of proteins is involved in the quality control of mitochondrial translation. Members of this family function as part of a mitoribosome-associated pathway that addresses interruptions during elongation. They form heterodimers with MTRES1 to facilitate the ejection of incomplete nascent chains and peptidyl transfer RNA (tRNA) from stalled ribosomes. The presence of a GGQ domain suggests an interaction with the peptidyltransferase center of the large ribosomal subunit, triggering hydrolysis of the nascent chain. Additionally, these proteins may have roles in mitoribosome rescue, as indicated by the recruitment of mitoribosome biogenesis factors to quality control intermediates.
Chromatin Remodeling Complex Component (Chromatin_Remodeling_Comp)
Type: Family

This family of proteins is involved in chromatin remodeling, which is a critical process in the regulation of gene expression. Members of this family participate in altering DNA-nucleosome topology, thereby affecting transcriptional activation and repression of specific genes. They are components of various chromatin remodeling complexes, such as SWI/SNF and RSC, and are essential for the stability and targeting of these complexes to particular genomic loci. Functions attributed to these proteins include the transfer of histone octamers, DNA translocation, and nucleosome repositioning, which are necessary for proper transcription regulation, chromosome segregation, and cellular response to stress. Some family members are also implicated in the regulation of cardiac genes and the organization of the cellular cytoskeleton.
BTB/POZ domain-containing protein 9 (BTB_POZ_domain_cont_9)
Type: Family

This family of proteins includes BTB/POZ domain-containing proteins that are implicated in the regulation of sleep and motor activity. They are believed to play a role in maintaining homeostasis in these processes, potentially by influencing dopamine biosynthesis, which is a critical neurotransmitter involved in the control of movement and the sleep-wake cycle. The presence of the BTB/POZ domain suggests that these proteins may also be involved in protein-protein interactions, which could be important for their regulatory functions.
Exonuclease MUT-7-like (Exonuclease_MUT-7-like)
Type: Family

This family of proteins includes exonucleases with a role in RNA interference and miRNA processing. Members are involved in the repression of transposon activity, possibly through the degradation of transposon-specific RNA. They are also implicated in the 3'-5' exoribonuclease activity required for the maturation of miRNAs, particularly in the 3'-end trimming of AGO1-bound miRNAs. Some family members are associated with germline gene regulation, affecting processes such as sperm development, X chromosome loss, and gene silencing mechanisms including cosuppression and antisense RNA oligomer-induced silencing.
Myosin-III family with kinase activity (Myosin-III_kinase_activity)
Type: Family

The Myosin-III family comprises actin-based motor proteins with protein kinase activity, playing a crucial role in sensory functions. Members are essential for the development and morphogenesis of cochlear hair bundles, influencing the production and length of stereocilia and limiting microvilli growth, thus contributing to the hair bundle's staircase architecture. They are involved in actin filament elongation at stereocilia tips by transporting actin regulatory factors. Additionally, in photoreceptor cells, they are required for the stability of specific proteins and the normal termination of phototransduction.
Dynein regulatory complex subunit 5 (DRC5)
Type: Family

This family of proteins is involved in the regulation of ciliary and flagellar motility, specifically through the nexin-dynein regulatory complex (N-DRC). Members of this family are essential for maintaining the alignment and integrity of the distal axoneme and for regulating microtubule sliding in motile axonemes. They may also play a role in the assembly of the N-DRC and are implicated in the motility of sperm.
c/mor Transcriptional Regulatory Protein (c-mor_Regulatory_Protein)
Type: Family

This family of proteins includes transcriptional regulators that are involved in the regulation of gene expression in response to various stimuli such as DNA damage and the progression of viral infection. Members of this family typically contain a helix-turn-helix (HTH) motif for DNA-binding and may also have domains for dimerization such as a leucine zipper (bZIP) domain. They are known to regulate the production of enzymes like pectin lyase and activate promoters controlling the expression of viral genes necessary for different stages of the viral life cycle, including the transition from middle to late gene expression. These proteins are essential for the proper timing and regulation of gene expression, ensuring the correct response to environmental cues and the successful replication and assembly of viruses.
Cell Cycle and Developmental Transcription Regulators (CC-Dev_Transcription_Reg)
Type: Family

This family of proteins includes transcription factors that are involved in essential regulatory roles within the cell. Members of this family are necessary for the progression of the cell cycle from G1 to S phase, indicating a role in cell division and proliferation. Additionally, some members function as transcriptional repressors and are crucial for the development of the central nervous system, as well as for the specification of various cell types during embryonic development. They are known to interact with other proteins, such as ATXN1 and ATXN1L, to mediate developmental processes and contribute to patterning in organisms. These proteins also have roles in dorsoventral patterning and the specification of intervein areas during wing development.
SUR7 domain-containing protein (SUR7_domain)
Type: Family

This family of proteins appears to be involved in cellular responses to environmental stress, particularly nitrogen stress, and may play a role in the regulation of amino acid biosynthesis. Members of this family are also implicated in processes such as filamentous growth, cell growth, and cell-cell adhesion. Some proteins within this family may contribute to cell wall organization and biogenesis, suggesting a multifunctional role in cellular structure and signaling pathways.
U3 small nucleolar RNA-associated WD repeat-containing protein (U3_snoRNA-assoc_WDR)
Type: Family

This family of proteins is involved in ribosome biogenesis, particularly in the processing and transcription of pre-18S ribosomal RNA. Members of this family are part of the small subunit (SSU) processome, which is the first precursor of the small eukaryotic ribosomal subunit. They play a role in coordinating the assembly of ribosome biogenesis factors, RNA chaperones, and ribosomal proteins with nascent pre-rRNA to facilitate RNA folding, modifications, rearrangements, and cleavage. Additionally, they are involved in the targeted degradation of pre-ribosomal RNA by the RNA exosome and are essential for maintaining high-level expression of target genes during transcription. These proteins are also required for stem cell pluripotency and embryonic development.
Diphthine methyltransferase (Diphthine_MTase)
Type: Family

This family of proteins catalyzes the demethylation of diphthine methyl ester to form diphthine, an essential step in the biosynthesis of diphthamide, a unique post-translational modification of histidine found in translation elongation factor 2. Diphthamide modification is critical for the function of elongation factor 2 and is the target of ADP-ribosylation by toxins like diphtheria toxin and Pseudomonas exotoxin A. Members of this family are involved in a conserved biosynthetic pathway across different species and play a role in cellular processes such as protein synthesis and potentially in the regulation of the retromer complex, influencing the recycling of plasma membrane proteins.
General transcription factor 3C component (GTF3C_component)
Type: Family

This family of proteins is involved in the transcription process mediated by RNA polymerase III. Members of this family are components of the transcription factor complex TFIIIC, which is essential for the assembly of the transcription initiation complex on tRNA genes and the transcription of 5S rRNA and other stable RNAs. These proteins bind to specific promoter elements within the DNA, facilitating the recruitment and function of RNA polymerase III. Some family members also play a role in stabilizing interactions within the TFIIIC complex and may be involved in nuclear organization by localizing to chromatin insulator sequences.
Dachshund domain-containing protein (Dachshund_domain)
Type: Family

This family of proteins includes transcription factors involved in the regulation of organogenesis. Members of this family appear to regulate the SIX1, SIX6, and possibly SIX5 genes, influencing myogenesis and the proliferation of precursor cells in myoblasts. They are known to act as corepressors or coactivators in these processes, depending on their interaction with other proteins such as EYA3, CREBBP, NCOR1, TBL1, HDAC1, and HDAC3. These proteins are also implicated in the repression of cyclin-dependent kinase inhibitors, including the p27Kip1 promoter, which is key in cell cycle regulation. Some family members inhibit TGF-beta signaling through interactions with SMAD4. They are characterized by a conserved DNA-binding domain known as the DACHbox-N or DD1 domain, which is structurally similar to the forkhead/winged helix domain and is responsible for their DNA-binding activity.
Apolipoprotein B (Apolipoprotein_B)
Type: Family

The Apolipoprotein B family comprises proteins that are key constituents of lipoprotein particles such as chylomicrons, LDL, and VLDL. Members of this family, including Apolipoprotein B-100, play a crucial role in lipid transport and metabolism. They are recognized by the apoB/E receptor, which facilitates the cellular uptake of LDL particles. This process is essential for maintaining lipid homeostasis and is implicated in the pathogenesis of atherosclerosis due to the accumulation of LDL in blood vessels.
5'(3')-deoxyribonucleotidase-like (5_3-deoxyribonucleotidase-like)
Type: Family

This family of proteins is involved in the hydrolysis of nucleotide monophosphates, which is a process of removing a phosphate group from the molecule. Members of this family are known to act on various nucleotide monophosphates and sugar phosphates, suggesting a role in nucleotide metabolism and possibly in the regulation of sugar phosphate pools within the cell. The enzymatic activity observed in vitro indicates that these proteins may participate in the recycling of nucleotides, an essential function for maintaining the balance of nucleotide pools and for providing substrates for nucleic acid synthesis and repair processes in various organisms.
Espin and Espin-like domain-containing protein (Espin/Espin-like)
Type: Family

This family of proteins includes multifunctional actin-bundling proteins that are essential for the organization and dynamics of actin filament-rich structures. They play a pivotal role in the formation and maintenance of stereocilia in inner ear hair cells, which are crucial for hearing. Members of this family are involved in the assembly and stabilization of parallel actin bundles within these cellular protrusions and are necessary for the proper elongation of actin filaments. Additionally, they contribute to the regulation of stereocilia length and diameter, as well as the formation of the characteristic staircase pattern. Some family members are known to bind actin monomers through their WH2 domains, facilitating the assembly of actin bundles, while others bind to actin without promoting cross-linking.
Plant Cell Wall Enzyme Inhibitor (PCW_Enzyme_Inhibitor)
Type: Family

This family of proteins includes inhibitors that target specific enzymes involved in the modification of cell wall components. Members of this family are known to inhibit fructosidases and pectin methylesterases, which are enzymes that play roles in plant development and metabolism. These inhibitors are involved in various physiological processes, such as the regulation of fruit ripening, seed germination, and the growth of pollen tubes. They function by modulating the activity of their target enzymes, thereby affecting the methylesterification of pectin, a key component of the plant cell wall. The presence of an N-terminal alpha-hairpin extension in some family members is critical for their inhibitory activity.
Auxin Signal Transduction Ser/Thr Kinase (Auxin_Ser/Thr_Kinase)
Type: Family

This family of proteins is involved in auxin signal transduction, which is a key process in plant growth and development. Members of this family function as receptor-like kinases and are implicated in the regulation of cell expansion and proliferation. Some proteins within this family form complexes that activate ROP signaling pathways, essential for plant responses to the hormone auxin. Additionally, these proteins may play roles in brassinosteroid-mediated plant growth and development, as well as in microspore and pollen development. The unique structural feature of these proteins is the presence of leucine-rich repeat (LRR) domains that are disrupted by non-LRR regions, forming two LRR solenoid structures that are distinct from the canonical horseshoe structures of LRR proteins.
Erythrocyte Membrane Invagination Regulator (EMIR)
Type: Family

This family of proteins is involved in the structural modification of the erythrocyte membrane. Members of this family are implicated in the alteration of intermolecular interactions within the cytoplasmic domain of band 3, a process that is critical for the formation of the parasitophorous vacuole. This vacuole is essential for the survival and replication of certain parasites within red blood cells. The family includes proteins that may play a role in the invagination of the red cell membrane, which is a prerequisite for vacuole formation. Additionally, some members are suggested to have a continuous role in the structural organization of cellular compartments in plants, indicating a broader functional spectrum.
Kielin/Chordin-like & BMP-binding Regulator (Kielin_Chordin-BMP_Reg)
Type: Family

The Kielin/chordin-like and BMP-binding endothelial regulator protein family is involved in the regulation of bone morphogenetic protein (BMP) signaling pathways. Members of the family enhance BMP signaling in a paracrine manner and are known to inhibit activin-A and TGFB1-mediated signaling pathways. Additionally, they may play a role in the dorsalization of mesoderm during embryonic development and regulate BMP responsiveness in osteoblasts and chondrocytes. This family's regulatory functions are crucial for proper bone and cartilage development and may be involved in embryonic patterning processes.
Uncharacterized MFS-type Transporter (Uncharacterized_MFS-type)
Type: Family

This family of proteins includes uncharacterized members that are predicted to be involved in transport across membranes, as some members are similar to the major facilitator superfamily (MFS). MFS transporters are integral membrane proteins responsible for the movement of a wide variety of substrates across cellular membranes, utilizing the electrochemical gradient. The family may function in the transport of small solutes in a chemiosmotic manner, contributing to various cellular processes.
Plant developmental regulator (Plant_dev_regulator)
Type: Family

This family of proteins includes probable transcriptional regulators involved in various developmental processes in plants. Members of this family are implicated in the regulation of cell proliferation, floral organ development, and maintenance of meristem determinacy. They may act by repressing genes associated with cell division and growth. Some proteins within the family are essential for the development of specific floral whorls, such as petals, and may function downstream of other regulatory proteins. Additionally, these proteins may interact with DNA sequences and mediate responses to plant hormones, contributing to the complex regulation of plant development and growth.