SII-SWORD/CoKE huggingface dataset:
EMX/VAX/Noto Homeobox Transcription Factors (EMX-VAX-Noto_Homeobox_TFs)
Type: Family

The EMX homeobox family comprises transcription factors involved in the development of the central nervous system, particularly in specifying cell fates and regional identities within the brain. Members of the family, such as EMX1 and EMX2, cooperate to delineate boundaries in the developing brain, like the division between the roof and archipallium. VAX1 and VAX2 proteins contribute to dorsoventral specification of the forebrain, optic nerve differentiation, and eye development. NOTO proteins play a role in notochord formation, cilia formation in the posterior notochord, and left-right patterning. The family is characterized by the presence of a homeobox domain, indicative of their role in gene regulation during embryonic development. They are also involved in major tract formation in the forebrain, regulation of Wnt signaling, and axial polarization in the retina.
Pro-opiomelanocortin-derived peptides (POMC-derived_peptides)
Type: Family

This family of proteins includes precursors to various hormones that are involved in a wide range of physiological functions. They play a crucial role in the regulation of stress responses and environmental adaptation. Members of this family are involved in increasing skin pigmentation by stimulating melanin production in melanocytes. They also participate in the modulation of appetite through orexigenic and anorexigenic peptides. Additionally, these proteins are involved in the endocrine system, where they stimulate the adrenal glands to release cortisol, a hormone essential for stress response and metabolism regulation. Furthermore, some peptides derived from these precursors act as endogenous opiates, which can influence pain and immune responses.
Acyltransferase 3 (Acyltransferase_3)
Type: Family

The Acyltransferase 3 family comprises enzymes responsible for acyl group transfer reactions across a diverse range of biological processes. Members of this family are involved in the modification of antibiotics, such as midecamycin and carbomycin biosynthesis, by acylating sugar moieties. They also play a role in bacterial cell wall integrity and resistance to lysozyme by O-acetylating N-acetylmuramyl residues in peptidoglycan. Additionally, they contribute to the biosynthesis of bioactive compounds like fusicoccins, which affect plant hormone activity, and squalestatin S1, a cholesterol-lowering agent. Some members regulate bacterial surface properties in response to plant cells, while others are involved in antigenic variation of bacterial O-antigens. The family's broad substrate specificity and involvement in various biosynthetic pathways highlight its functional versatility in acyl transfer reactions.
LL-diaminopimelate aminotransferase (LL-DAP_aminotransferase)
Type: Family

The LL-diaminopimelate aminotransferase family is involved in the biosynthesis of meso-diaminopimelate (m-DAP or DL-DAP), which is essential for both lysine and peptidoglycan production. Members of this family catalyze the conversion of tetrahydrodipicolinate to LL-diaminopimelate, a key step in the synthesis pathway. Some members can also catalyze the reverse reaction or use alternative substrates. This family is characterized by its dependence on pyridoxal-phosphate as a cofactor, typical of class-I aminotransferases. The enzymes in this family are crucial for bacterial cell wall integrity and represent potential targets for antibiotic development.
Prepilin leader peptidase/N-methyltransferase (Prepilin_peptidase/N-MTase)
Type: Family

The Prepilin leader peptidase/N-methyltransferase family is involved in the biogenesis of type IV pili and type II pseudopili, which are critical for bacterial motility, adhesion, and host colonization. Members of the family function by proteolytically cleaving the leader sequence from precursor proteins, a process essential for pilus assembly. Following cleavage, they catalyze the N-methylation of the N-terminal phenylalanine residue of the mature protein. Some family members are also implicated in the type II general secretory pathway, processing substrates necessary for the secretion system's apparatus. The dual enzymatic activity of these proteins underscores their importance in bacterial cell surface structures and secretion systems.
Peptide-N(4)-(N-acetyl-beta-glucosaminyl)asparagine amidase (PNGase)
Type: Family

The PNGase family proteins are involved in the deglycosylation of denatured N-linked glycoproteins within the cytoplasm, aiding in their proteasome-mediated degradation. They cleave the beta-aspartyl-glucosamine of the glycan and the amide side chain of asparagine, converting it to aspartic acid. These proteins prefer substrates with high-mannose over complex type oligosaccharides and target misfolded glycoproteins exported from the endoplasmic reticulum to the cytosol. Deglycosylation by the PNGase family is essential for the degradation of certain misfolded glycoproteins, although not all require this process. Some family members also exhibit oxidoreductase activity and play roles in regulating proteasomal subunit expression.
Cyclic nucleotide phosphodiesterase class-III (CNP_phosphodiesterase-III)
Type: Family

The cyclic nucleotide phosphodiesterase class-III family encompasses enzymes that hydrolyze cyclic nucleotides to their corresponding monophosphates, thus playing a crucial role in regulating intracellular concentrations of cyclic AMP (cAMP) and cyclic GMP (cGMP). These enzymes modulate cAMP-dependent pathways, influencing responses to nutritional stress and virulence factor regulation in various organisms. Some family members exhibit dual specificity for cAMP and cGMP, while others preferentially hydrolyze glycerophosphodiesters, indicating a broader substrate specificity. The activity of these phosphodiesterases is regulated by divalent metal ions such as Ca(2+), Mg(2+), and Mn(2+), with some also being influenced by the presence of transition-metal ions or activated by iron. The family includes enzymes with a C-terminal extension that adjusts substrate alignment in the active site and affects subcellular localization and expression levels.
RNA-binding_regulatory_proteins (RNA-binding_reg)
Type: Family

This family of proteins is involved in various aspects of RNA metabolism, including the regulation of pre-mRNA splicing, mRNA stability, and mRNA translation. Members of this family play key roles in cell fate decisions and differentiation processes, such as myogenic differentiation and embryonic stem cell transition to cardiac cell differentiation. They are characterized by their ability to bind to RNA, often through recognition of specific sequence motifs, and can influence the inclusion of muscle-specific exons in mRNAs. These proteins are also implicated in the cellular response to stress and in the development of embryonic heart and muscle tissues. Some family members are known to interact with viral RNAs, influencing viral replication and protein expression.
Beta-mannosidase glycosyl hydrolases (Beta-mannosidase_GH2)
Type: Family

The Beta-mannosidase family consists of exoglycosidases that cleave the single beta-linked mannose residue from the non-reducing end of beta-mannosidic oligosaccharides. Members of this family are involved in the degradation of various glycoconjugates, including polymeric mannan and galactomannan. They exhibit specificity for different substrates, with some preferring mannobiose and others having activity against mannotriose or galactosylated mannooligosaccharides. The family is part of the glycosyl hydrolase 2 superfamily, with subfamilies A and B showing distinct substrate preferences and activities. Beta-mannosidase A tends to be involved in broader oligosaccharide degradation, while Beta-mannosidase B has a more restricted activity, being inhibited by galactosyl substitutions and showing no activity against polymeric mannan.
Zinc Finger C2H2-type Transcription Regulators (ZnF_C2H2-type_TF)
Type: Family

The Zinc Finger C2H2-type protein family is characterized by its involvement in transcriptional regulation, with members acting as transcriptional activators or repressors depending on the context. These proteins play pivotal roles in various biological processes, including BMP signaling, olfactory neurogenesis, gluconeogenesis regulation, cell fate determination, mRNA translation regulation, and morphogenesis. They interact with different molecules such as SMADs, EBF1, and DNA sequences to exert their functions. The family's versatility is highlighted by its participation in developmental switches, control of cell proliferation and differentiation, and response to oxidative stress. The domain architecture of these proteins typically includes multiple C2H2-type zinc fingers, which are key to their DNA-binding and protein-interaction capabilities.
Dendritic Spine Regulation and Scaffold (Dendritic_Spine_Reg/Scaffold)
Type: Family

The protein family is involved in various cellular functions, including the regulation of dendritic spine distribution and maintenance, acting as scaffolding proteins in dendritic spines, and participating in the ubiquitination and proteasomal degradation of target proteins. Members of the family are also implicated in translational fidelity, presynaptic neurotoxin activity, and endosome-to-plasma membrane trafficking. The family includes proteins that may serve as scaffold components in the postsynaptic density and are involved in the recruitment of vesicles to dendritic spines. Additionally, some members are associated with the inhibition of kinase activity under specific conditions and may lack ubiquitin-protein ligase activity in vitro.
Phosphotransferase system EIIA component (PTS_EIIA_component)
Type: Family

The protein family consists of phosphotransferase enzyme IIA components that are integral to the phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS), a key carbohydrate active transport system. Members of the family catalyze the phosphorylation of sugar substrates while facilitating their translocation across the cell membrane. Typically, the EIIA domain within these proteins is phosphorylated by phospho-HPr on a histidine residue, which then transfers the phosphoryl group to the EIIB domain. This process is crucial for the transport of glucose and potentially other sugars, playing a significant role in cellular metabolism and regulation. Some family members are also involved in the regulation of other sugar uptake systems and may influence the activity of adenylate cyclase when phosphorylated.
TatD-type Metallo-dependent Hydrolase (TatD-type_Hydrolase)
Type: Family

This family of proteins includes enzymes with endonuclease and exonuclease activities, capable of incising double-stranded DNA and excising DNA from the 3'-to 5'-end. Members of this family preferentially act on single-stranded DNA and RNA substrates. They are implicated in DNA damage repair, particularly in response to oxidative stress. Additionally, some family members are involved in the decatenation of kinetoplast DNA, which is essential for chromosomal segregation and cell cycle progression, especially in eye development. The proteins belong to the metallo-dependent hydrolases superfamily and share a common TatD-type hydrolase domain.
ADP-ribose derivative metabolism enzymes (ADP-ribose_metab_enzymes)
Type: Family

This family of proteins includes enzymes that are involved in the metabolism of ADP-ribose derivatives. Members of this family exhibit phosphatase activity, specifically hydrolyzing ADP-ribose 1''-phosphate (Appr1p) which is a byproduct of tRNA splicing. Some proteins in this family also display glycohydrolase activity, reversing ADP-ribosylation modifications on DNA or proteins. This modification and its reversal are part of a toxin-antitoxin system, with implications for bacterial survival under stress conditions. Additionally, certain members are capable of removing mono-ADP-ribose from glutamate residues on proteins, but are inactive towards poly-ADP-ribose. The family also includes proteins that can deacetylate O-acetyl-ADP-ribose, a signaling molecule, thus participating in the regulation of post-translational modifications.
Sugar Phosphotransferase System (PTS) (Sugar_PTS)
Type: Family

The Phosphoenolpyruvate-dependent Sugar Phosphotransferase System (sugar PTS) is a major carbohydrate active transport system that catalyzes the phosphorylation of incoming sugar substrates concomitantly with their translocation across the cell membrane. The PTS consists of several components, including the EIIC type-2 domain which forms the translocation channel and contains the substrate-binding site, the EIIA type-2 domain which is phosphorylated by phospho-HPr on a histidine residue and transfers the phosphoryl group to the EIIB type-2 domain, and the EIIB type-2 domain which is phosphorylated by phospho-EIIA on a cysteine residue and transfers the phosphoryl group to the sugar substrate. The family is involved in the transport of specific sugars such as D-mannitol and fructose, with some variations in the requirement for HPr among different systems.
Iron uptake system component EfeM/EfeO (EfeM/EfeO_iron_uptake)
Type: Family

The EfeM/EfeO family proteins are involved in iron uptake, particularly in the transport of Fe(2+). Members of this family may function as iron-binding and/or electron-transfer components. The EfeO proteins typically contain an N-terminal Cup-like domain and a C-terminal peptidase domain, with potential metal-binding sites that may preferentially bind Cu(2+) and Fe(3+). In contrast, EfeM proteins lack the Cup-like domain but include a peptidase M75 domain with metal binding sites, and are known to specifically bind Fe(3+), delivering it to the cell membrane permease EfeU as part of the iron transporter system efeUOB/M. Some family members also bind Zn(2+) and Cu(2+) in vitro.
XK-related phospholipid scramblase (XK-related_scramblase)
Type: Family

This family of proteins is involved in the externalization of phosphatidylserine on the surface of apoptotic cells, which is a key signal for their recognition and engulfment by phagocytes. Members of this family are phospholipid scramblases, a type of protein that facilitates the bidirectional movement of phospholipids across the lipid bilayer. The exposure of phosphatidylserine on the cell surface is a hallmark of apoptosis, and these proteins are essential for the clearance of dying cells by the immune system. Some members are known to be activated by caspase cleavage during apoptosis, and they may also play roles in cell differentiation and survival. Additionally, certain members are implicated in microbial infections, where they are hijacked to promote viral particle uptake by host cells.
Mitochondrial lipid metabolism GTPase (Mito_lipid_metab_GTPase)
Type: Family

This family of proteins is characterized by members that are involved in various cellular processes related to GTP binding and hydrolysis. They belong to the TRAFAC class YlqF/YawG GTPase family, indicating a role in the dynamic regulation of molecular interactions through GTPase activity. Some members of this family are specifically implicated in mitochondrial lipid metabolism, suggesting a specialized function within mitochondrial membranes. This activity is important for maintaining mitochondrial integrity and function, which is essential for energy production and other metabolic pathways. Additionally, certain proteins within this family are noted to genetically interact with prohibitins, which are proteins involved in maintaining mitochondrial morphology and function. This interaction further emphasizes the role of this family in mitochondrial health and suggests a broader involvement in cellular homeostasis.
SMAUG/VTS1 RNA-binding (SMAUG/VTS1_RNA-bind)
Type: Family

The SMAUG/VTS1 family includes RNA-binding proteins that play a role in post-transcriptional regulation, including translational repression and transcript degradation. Members of the SMAUG subfamily, such as Smaug homologs, act as translational repressors by binding to SRE-containing messengers, thereby inhibiting their translation. They are known to regulate the translation of specific mRNAs by interacting with their 3'-UTRs, often through a SAM domain. The VTS1 subfamily members are involved in transcript degradation, contributing to the regulation of gene expression at the RNA level. Some members have been shown to bind to SMG-recognition elements (SREs) in mRNAs. Collectively, the SMAUG/VTS1 family is involved in the intricate control of gene expression, ensuring proper cellular function and response to various regulatory signals.
Plant acyltransferase (Plant_acyltransferase)
Type: Family

The plant acyltransferase family is involved in a variety of biosynthetic processes related to plant metabolism and defense. Members of this family function as enzymes that catalyze the transfer of acyl groups from activated acyl-CoA donors to various acceptor molecules, producing esters and amides. These enzymes contribute to the synthesis of volatile esters that give fruits their characteristic flavors, the production of alkaloids and other secondary metabolites with pharmacological activities, the modification of cell wall components such as arabinoxylan, and the formation of lignin precursors and spermidine-based phenolamides. Some family members are also implicated in the biosynthesis of taxol, an important anticancer compound. The activities of these acyltransferases are essential for plant growth, development, and defense against pathogens.
DDRGK domain-containing protein (DDRGK_domain-containing)
Type: Family

This family of proteins serves as substrate adapters for ufmylation, a post-translational modification involving the covalent attachment of the ubiquitin-like modifier UFM1 to target proteins. Members of this family play a crucial role in reticulophagy, also known as ER-phagy, particularly in response to endoplasmic reticulum stress. They facilitate the recruitment of the E3 UFM1-protein ligase UFL1 to the endoplasmic reticulum membrane, which mediates the ufmylation of proteins, promoting the degradation of endoplasmic reticulum components. This process is vital for maintaining cellular homeostasis under stress conditions and is implicated in various biological processes, including hematopoiesis, inflammatory response, and cartilage development. Some family members are involved in regulating transcription through the ufmylation of transcriptional regulators, and may also play a role in NF-kappa-B-mediated transcription by influencing the phosphorylation and degradation of NFKBIA.
Transposase IS3/IS150/IS904 (Transposase_IS3/IS150/IS904)
Type: Family

The transposase IS3/IS150/IS904 family includes enzymes that are primarily involved in the transposition of insertion sequences. These proteins facilitate the movement of DNA segments within genomes, a process that can lead to genetic variation and the evolution of new gene functions. Members of this family are characterized by their ability to recognize specific DNA sequences and catalyze the cutting and rejoining of DNA strands, thereby inserting the mobile elements into new genomic locations. The activity of these transposases is crucial for the mobility of insertion sequences, which are short DNA sequences capable of changing their position within the genome. This mobility can have significant impacts on gene expression and genome stability, influencing the adaptability and evolution of the host organism.
Binding-protein-dependent ABC transporter permease (BP-dep_ABC_trans_perm)
Type: Family

The binding-protein-dependent transport system permease family is involved in the import of various substrates across the cellular membrane through ABC transporter complexes. Members of the family, such as MalG, MdxG, GanQ, DasC, SugB, and others, are primarily responsible for the translocation of sugars and oligosaccharides like maltose, maltodextrin, trehalose, galactooligosaccharides, and N,N'-diacetylchitobiose. These permease proteins are integral to the function of their respective ABC transporter complexes, which are highly specific for their substrates and are essential for processes such as nutrient uptake, bacterial virulence, and possibly antibiotic secretion. The family plays a crucial role in bacterial metabolism and survival by facilitating the uptake of essential nutrients from the environment.
ABC Transporter Solute-Binding (ABC_Transporter_SBP)
Type: Family

The protein family is involved in the transport and binding of various substrates through ABC transporter complexes. Members of the family function as solute-binding proteins that capture and deliver ligands to their respective transporters. Some proteins within the family specialize in heme scavenging, binding Fe(2+) and Fe(3+) heme with a preference for Fe(2+), and play a role in transporting heme-iron to permeases. Others are involved in the import of vitamin B12 or cobalamin, binding the vitamin and presenting it to the transporter surface. Additionally, some members bind molybdate and tungstate, contributing to the import of these oxyanions. The family includes proteins with both high and low affinity for their substrates, and some exhibit a decrease in affinity with increasing substrate and nucleotide concentrations.
Bacterial Chemotaxis Protein Methyltransferase (Bact_Chemotaxis_MeTrfase)
Type: Family

The protein family consists of chemotaxis protein methyltransferases that are primarily involved in the post-translational modification of membrane-bound methyl-accepting chemotaxis proteins (MCPs). These enzymes catalyze the methylation of MCPs to form gamma-glutamyl methyl ester residues, a modification that is crucial for the chemotactic response and adaptation in various bacterial species. The methylation process modulates the signaling pathways that govern bacterial movement towards favorable environments or away from repellents. Some family members are also implicated in biofilm formation and may have specific targets such as the McpS and McpB chemoreceptors. Additionally, one member is involved in the aggregation of cells during fruiting body formation in Myxococcus xanthus, indicating a role in complex multicellular behavior.
Cell adhesion and biosynthesis-related protein (Adhesion/Biosynth-related)
Type: Family

This family of proteins is involved in various biological processes including cell adhesion, cell attachment and spreading, and immune responses. Members of this family play roles in enhancing the incorporation of certain enzymes into the extracellular matrix, mediating proteolytic activation of other proteins, and converting toxic heme into non-toxic forms. Some proteins within this family are also implicated in the biosynthesis of toxins and pigments by catalyzing the formation of complex polyketides, which involves multiple enzymatic steps including polyketide extension, cyclization, methylation, and oxidative coupling. Additionally, certain members act as cell surface adhesion or glycolipoproteins, and may be involved in cytokine secretion and innate immunity responses.
Plant disease resistance NBS-LRR (Plant_NBS-LRR)
Type: Family

This family of proteins is involved in plant defense mechanisms against a variety of pathogens, including bacteria and oomycetes. Members of this family are typically characterized by the presence of nucleotide-binding site (NBS) and leucine-rich repeat (LRR) domains. These domains are thought to play a role in pathogen recognition and the specificity of the immune response. The proteins are known to mediate defense responses by recognizing specific pathogen effectors, which can trigger a hypersensitive response to restrict pathogen growth. Some family members are regulated by kinase cascades and may interact with other proteins to initiate signaling pathways that lead to resistance. The family includes both characterized disease resistance proteins with known targets and putative resistance proteins whose specific functions and pathogen targets may not be fully elucidated.