SII-SWORD/CoKE huggingface dataset:
Type IV secretion system-coupling protein (T4SS-coupling_protein)
Type: Family

This family of proteins is involved in the conjugative transfer of plasmid DNA between bacterial cells, a process central to the propagation of antibiotic resistance and virulence factors. Members of this family are known to interact with relaxase enzymes and may form a pore-like structure to facilitate the transfer of single-stranded DNA through a type IV secretion system. Some proteins within this family are also implicated in the subversion of human endothelial cell function, leading to various cellular responses such as cytoskeletal rearrangements, pro-inflammatory activation, and inhibition of apoptosis.
S-2-haloalkanoic acid dehalogenase (S-2-haloacid_dehalogenase)
Type: Family

This family of proteins includes enzymes that catalyze the hydrolytic dehalogenation of small (S)-2-haloalkanoic acids, producing the corresponding (R)-2-hydroxyalkanoic acids. These enzymes are active on short-chain acids, ranging from C(2) to C(4), and they operate with inversion of configuration at the second carbon atom. They are specific for the S-isomer of 2-halogenated carboxylic acids, such as 2-chloropropionic acid, converting it to the R-lactate form. Members of this family are part of the HAD-like hydrolase superfamily and are characterized by their ability to perform these dehalogenation reactions, which are important in the metabolism of halogenated compounds.
PTS System Sugar Transport and Nitrogen Regulation (PTS_SugarTrans_NitroReg)
Type: Family

The protein family is involved in the phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS), which is a key carbohydrate active transport system. Members of the family catalyze the phosphorylation of sugar substrates during their translocation across the cell membrane. Specific components of this family are involved in the transport of different sugars such as galactitol and fructose. Additionally, some members are implicated in regulating nitrogen assimilation, possibly through a PTS EIIA type-2 domain that may have a regulatory function via phosphorylation activity. The EIIA domains within this family are typically phosphorylated by phospho-carrier proteins such as phospho-HPr or phospho-NPr on a histidyl residue, which then transfers the phosphoryl group to the EIIB domain of the PTS system.
Hydrogenase-associated cytochrome (Hydrogenase_cytochrome)
Type: Family

This family of proteins includes components involved in electron transfer processes and redox reactions. Members are typically associated with the catalysis of reactions involving hydrogen or thiosulfate, often with a role in energy metabolism. Some proteins in this family function as b-type cytochromes, which are involved in the electron transfer from hydrogenase to oxygen or quinones, and are anchored to the membrane. Others may participate in systems that repair oxidized proteins or catalyze the reduction of thiosulfate to sulfite and hydrogen sulfide. The electron transfer is usually coupled to the generation of a proton motive force across the membrane.
Serine Peptidase S9A Subfamily (Serine_Peptidase_S9A)
Type: Family

This family of proteins includes serine peptidases that exhibit a range of substrate specificities and biological functions. Some members are known to cleave peptide bonds on the C-terminal side of lysyl and argininyl residues, while others do not cleave after arginine or lysine residues. Functions of these proteins include the sequential removal of dipeptide units from the amino termini of peptides and proteins, regulation of trans-Golgi network morphology and sorting, and potentially playing a role in the regulation of synaptic vesicle exocytosis. Activity regulation varies among family members, with some being inhibited by metal ions, serine protease inhibitors, and other specific compounds.
Two-partner secretion system outer membrane transporter (TPS_OM_transporter)
Type: Family

This family of proteins is involved in a two-partner secretion (TPS) system, which is a mechanism for the transport of large proteins across the outer membrane of Gram-negative bacteria. Members of this family function as the outer membrane component, forming a beta-barrel structure that facilitates the translocation of partner proteins such as toxins, hemolysins, and other effector molecules. These transported proteins often play roles in bacterial pathogenesis, host interaction, or interbacterial competition. Some family members are associated with contact-dependent growth inhibition (CDI) systems, where they contribute to the secretion and assembly of toxins that inhibit the growth of competing bacteria upon direct cell contact.
NAD(P)H dehydrogenase (quinone) (NAD(P)H_dehydrogenase_qn)
Type: Family

The NAD(P)H dehydrogenase (quinone) family comprises enzymes that catalyze the two-electron reduction of quinones to hydroquinones. These enzymes utilize NADH or NADPH as electron donors in a ping-pong kinetic mechanism, transferring electrons to a flavin cofactor and then to the quinone, avoiding semiquinone and reactive oxygen species formation. The family plays a crucial role in cellular redox state regulation, primarily through quinone detoxification, and may act as superoxide scavengers. Some family members are involved in biosynthetic processes, such as vitamin K-dependent gamma-carboxylation of glutamate residues in prothrombin synthesis. Additionally, they can activate quinones with antitumor potential or interact with tumor suppressors to inhibit their degradation under oxidative stress.
Class-II Aspartate Ammonia-Lyase (Aspartate_Ammonia-Lyase)
Type: Family

This family of proteins includes aspartate ammonia-lyases, which catalyze the reversible deamination of L-aspartate to fumarate and ammonia, an important reaction in the nitrogen metabolism of cells. Members of this family are involved in the biosynthesis and degradation of amino acids, playing a key role in the metabolic pathways that interconvert amino acids and nucleotide bases. These enzymes are characterized by their membership in the class-II fumarase/aspartase family, specifically within the aspartase subfamily, indicating a shared evolutionary origin and similar structural features that are critical for their enzymatic function.
Tyrosyl-DNA phosphodiesterase 2-like (TDP2-like)
Type: Family

This family of proteins functions primarily in DNA repair, specifically by removing covalent adducts from DNA. They act through hydrolysis of a 5'-phosphodiester bond, resulting in DNA with a free 5' phosphate, which is essential for the repair of DNA double-strand breaks. These proteins can hydrolyze dead-end complexes between DNA and topoisomerase 2, as well as 5'-phosphoglycolates on protruding 5' ends caused by radiation and free radicals. Some members also exhibit 3'-tyrosyl DNA phosphodiesterase activity. Additionally, certain proteins in this family are involved in non-canonical TGF-beta signaling pathways, acting as adapters for specific activation of signaling modules, and may play roles in regulating transcription and ribosome biogenesis under stress conditions.
Glutaredoxin-like Electron Transport (Grx-like_ET)
Type: Family

This family of proteins includes members that are involved in electron transport systems, particularly for the ribonucleotide reductase system NrdEF, which is essential for DNA synthesis. Some proteins in this family function as glutaredoxins, a group of small redox enzymes that use glutathione as a cofactor to catalyze thiol-disulfide exchange reactions. These reactions are crucial for maintaining cellular redox homeostasis and for the reduction of protein disulfides. Additionally, certain members are implicated in a cysteine salvage pathway, catalyzing the reduction of N-acetyl-S-hydroxy-L-cysteine to N-acetyl-L-cysteine, which is likely important in the catabolism of alkylated cysteine residues.
Phosphoenolpyruvate Utilizing Enzyme (PEP_Utilizing_Enz)
Type: Family

The PEP-utilizing enzyme family includes proteins involved in various biosynthetic processes. Members of this family are characterized by their ability to utilize phosphoenolpyruvate (PEP) in enzymatic reactions. The family encompasses enzymes such as phosphotransferases and synthases. Functions of these proteins include the biosynthesis of antibiotics like prodigiosin, the phosphorylation of pyruvate to phosphoenolpyruvate, and the biosynthesis of the O-methyl phosphoramidate group on capsular polysaccharides. The enzymes share common structural features that facilitate the binding and transformation of specific substrates, reflecting the diversity of reactions they catalyze within the cell.
SCF Complex Subunits and Alginate Epimerases (SCF-Subunits/Alg-Epimerases)
Type: Family

This family of proteins includes components of SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complexes, which are involved in the ubiquitination and proteasomal degradation of various target proteins. They play roles in cell cycle regulation, apoptosis, immune response, and differentiation. Some members mediate the degradation of specific substrates, such as BCL6, DTL, and p53, influencing processes like TGF-beta signaling, erythropoiesis, and antiviral responses. Other members are involved in the epimerization of polysaccharides during the synthesis of alginate, contributing to the protection of alginate from degradation and its transport through bacterial cells.
Bacterial autotransporter adhesion (Autotransporter_adhesion)
Type: Family

This family of proteins includes autotransporters, which are involved in bacterial pathogenesis through mechanisms such as adhesion to host cells, invasion, and biofilm formation. They typically possess a signal peptide that directs the protein to the periplasmic space and a C-terminal translocator domain that inserts into the outer membrane to form a pore. This pore facilitates the translocation of the passenger domain, which often contains the functional elements of the protein, to the bacterial cell surface. Some members of this family can mediate cell aggregation and inhibit complement activation, contributing to immune evasion. The functions of these proteins are crucial for bacterial colonization and persistence within the host, playing significant roles in the infection process.
Hexose Phosphate Transport Regulator (HptR)
Type: Family

The protein family comprises transcriptional regulatory proteins that are part of two-component regulatory systems. These systems play a crucial role in the regulation of genes associated with hexose phosphate transport in response to extracellular phosphate levels. Family members such as HptR activate the expression of uhpT, enabling glucose-6-phosphate utilization by binding to its promoter. Additionally, they can counteract the transcription of certain genes regulated by CcpA, affecting antibiotic susceptibility. Some members are uncharacterized but are presumed to be part of similar two-component systems based on their genetic context.
Ran GTPase-activating (Ran_GTPase-activating)
Type: Family

The protein family is involved in critical cellular processes such as chromosome condensation, mitotic spindle assembly, and nucleocytoplasmic transport. Members act as guanine-nucleotide releasing factors, facilitating the exchange of GDP for GTP on the Ran GTPase, which is pivotal for maintaining high levels of GTP-bound Ran in the nucleus. This activity is essential for various nuclear events, including mitotic checkpoint control, chromosome decondensation, mRNA processing and transport, and the assembly of the nuclear pore complex. Some family members also bind to chromatin or DNA, influencing transcriptional control and chromosomal dynamics. Additionally, certain proteins within the family serve as components of the SCF E3 ubiquitin-protein ligase complex, targeting specific proteins for ubiquitination and proteasomal degradation.
Acetyltransferase Eis (Acetyltransferase_Eis)
Type: Family

The acetyltransferase Eis family comprises proteins that function as effectors released into host cells, modulating host immune responses and contributing to bacterial survival. Members of the family possess acetyltransferase activity, acetylating lysine residues of host proteins and multiple amine groups of aminoglycoside antibiotics, leading to drug resistance. Some proteins within the family are known to acetylate and deactivate the cyclic peptide antibiotic capreomycin. They are involved in the negative modulation of inflammation, macrophage autophagy, and cell death through redox-dependent signaling. The acetylation of specific host proteins, such as dual-specificity protein phosphatase 16 (DUSP16)/MKP-7, inhibits JNK-dependent autophagy and ROS generation, enhancing intracellular survival of pathogens like M.tuberculosis. The family's role in immune response includes altering T-cell proliferation and cytokine production, skewing immunity away from a protective T(H)1 response.
Formate Dehydrogenase Electron Transfer Unit (FDH_Electron_Transfer_Unit)
Type: Family

The protein family consists of electron transfer units involved in various respiratory processes. Members of the family participate in the reversible two-electron oxidation of formate to carbon dioxide, functioning as integral components of formate dehydrogenase complexes. These complexes facilitate the use of formate as a major electron donor during both anaerobic and aerobic respiration. In anaerobic respiration, formate dehydrogenase works in conjunction with nitrate reductases, using nitrate as an electron acceptor. During aerobic respiration, the family members transfer electrons from formate to a molybdenum cofactor. The proteins contain iron-sulfur clusters that are essential for their electron transfer activity. Additionally, some members are involved in the electron flow from periplasmic hydrogenase to cytoplasmic enzymes that reduce sulfates. Overall, the family plays a critical role in energy conservation and metabolic versatility, allowing organisms to adapt to varying oxygen levels.
N-terminal and lysine N-acetyltransferase (N-term/lysine_N-AcTrnsfr)
Type: Family

This family of proteins includes N-alpha-acetyltransferases that modify the N-terminus of proteins by acetylating the initiating methionine, a process that is essential for various cellular functions. These proteins exhibit a broad substrate specificity and are involved in critical processes such as sister chromatid cohesion during mitosis. Some family members also possess N-epsilon-acetyltransferase activity, targeting specific lysine residues on proteins. Additionally, certain members are implicated in viral DNA modification, immune response to microbial infection, and regulation of DNA replication and cohesion. The family is characterized by a conserved acetyltransferase domain and includes members from a wide range of organisms, indicating a fundamental role in cellular biology.
NipSnap domain-containing protein (NipSnap_domain)
Type: Family

This family of proteins is characterized by a common structural motif known as the NipSnap domain. Members of this family are implicated in various cellular processes, although their precise biological functions may vary among different organisms and homologs. Some proteins within this family have been suggested to act as positive regulators of L-type calcium channels, which are critical for calcium ion transport across cell membranes and play a significant role in muscle contraction and neurotransmitter release. The functional diversity of this family is reflected in the range of processes they may influence, including vesicular trafficking, metabolism, and cellular signaling pathways.
Metallophosphoesterase Purple Acid Phosphatase (Metallophosphoesterase_PAP)
Type: Family

This family of proteins includes metallophosphoesterases known as purple acid phosphatases (PAPs). Members of this family are involved in various biological processes, including phosphate metabolism and bone resorption. They exhibit phosphatase activity towards a range of substrates, such as nucleotide tri- and diphosphates, and are implicated in the dephosphorylation of osteopontin and bone sialoprotein. Some members are known to be involved in transplacental iron transport and may have a role in protecting against host immune responses during parasite infection. The activity of these enzymes can be regulated by metal ions, phosphate, and molybdate. They are characterized by their resistance to inhibition by tartrate and their ability to function in acidic environments.
Hypoxia-inducible factor prolyl hydroxylases (HIF_prolyl_hydroxylases)
Type: Family

The protein family includes prolyl hydroxylases that function as cellular oxygen sensors, catalyzing the post-translational formation of 4-hydroxyproline in hypoxia-inducible factor (HIF) alpha proteins under normoxic conditions. These enzymes hydroxylate specific proline residues within the oxygen-dependent degradation domains of HIF1A and HIF2A, leading to their proteasomal degradation via the von Hippel-Lindau ubiquitination complex. Under hypoxic conditions, the hydroxylation reaction is reduced, allowing HIFs to avoid degradation, translocate to the nucleus, heterodimerize with HIF1B, and increase the expression of hypoxia-inducible genes. The family plays a critical role in various physiological processes including hypoxia tolerance, apoptosis regulation in cardiac and skeletal muscle, neuronal death, cell cycle regulation, primary cilia formation, and the DNA damage response. Substrate selectivity is attributed to a characteristic Beta(2)beta(3) 'finger-like' loop domain.
MAM domain-containing protein (MAM_domain-containing)
Type: Family

This family of proteins includes members that are involved in various cellular processes, such as sorting and selective transport of receptors and ligands across polarized epithelia, regulation of bile acid synthesis through production and/or transport of fibroblast growth factors, and potential roles in cell-cell interactions. These proteins typically contain MAM domains, which may mediate protein-protein interactions, and some also have LDL-receptor class A domains, which are often involved in ligand binding or cell adhesion. The specific functions of these proteins can vary, but they generally contribute to cellular communication and transport mechanisms.
FRAS1-related extracellular matrix (FRAS1_ECM)
Type: Family

The FRAS1 family proteins are extracellular matrix proteins that play crucial roles in tissue integrity, cell adhesion, and embryonic development. They are involved in the maintenance of the skin and renal epithelia, epidermal differentiation, and adhesion. These proteins are essential for the proper development of eyelids, anterior segment of the eyeballs, and brain organization. They also contribute to the regulation of epidermal-basement membrane adhesion, which is vital for organogenesis. The Calx-beta domains within these proteins bind calcium with high affinity, which induces a significant conformational change, suggesting a role in calcium-mediated signaling or structural stability. Some family members are implicated in cell proliferation, migration, and microvascular morphogenesis, potentially affecting processes like neurite outgrowth, collagen degradation, and plasminogen activation.
Ascorbate-specific PTS system EIIC component (Ascorbate-PTS_EIIC)
Type: Family

This family of proteins is involved in the phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS), which is a major carbohydrate active transport system. These proteins catalyze the phosphorylation of incoming sugar substrates concomitantly with their translocation across the cell membrane. Specifically, they are part of the enzyme II UlaABC PTS system that is responsible for the transport of ascorbate. Unlike classical PTS systems, these proteins do not exhibit the topological features of any recognized enzyme IIC domains that typically form the translocation channel and contain the specific substrate-binding site.
Glycosyl Hydrolase Family 51 (Glycosyl_Hydrolase_51)
Type: Family

The glycosyl hydrolase 51 family is involved in the degradation of plant cell wall components, particularly arabinoxylan, which is a major constituent of hemicellulose. Members of this family act on small linear 1,5-alpha-linked L-arabinofuranosyl oligosaccharides, facilitating the breakdown of complex carbohydrates into simpler sugars. Some enzymes within this family also exhibit activity against other arabinose-containing substrates such as arabinan and may play roles in processes like abscission and secondary cell wall formation in xylem vessels. They are characterized by their ability to hydrolyze terminal alpha-L-arabinofuranosyl residues, with varying specificities for different linkages and substrate types.
Leucine-rich repeat receptor-like kinase (LRR_receptor-like_kinase)
Type: Family

The LRR receptor-like kinase family encompasses proteins with roles in plant growth regulation, immunity, and development. Members act as receptors for various ligands, including defense peptides, CLV3-like peptides, and phytosulfokines, triggering signaling cascades essential for plant cell differentiation, organogenesis, and immune responses. Some proteins within the family possess dual specificity kinase activity, phosphorylating serine/threonine- and tyrosine-containing substrates. Others are involved in the negative regulation of bone mass in mammals. The family includes both active kinases and proteins with predicted inactive kinase domains, suggesting diverse regulatory mechanisms within the family.
Sal C2H2-type zinc-finger (Sal_C2H2-zinc-finger)
Type: Family

The sal C2H2-type zinc-finger protein family comprises transcription factors involved in a variety of developmental processes across different species. Members of the family play crucial roles in organogenesis, such as kidney development and eye formation, and are essential for the maintenance and self-renewal of embryonic and hematopoietic stem cells. Some proteins within this family act as transcriptional repressors, while others are involved in cell-fate regulation, including neuronal, mesodermal, and vulval lineages. They are characterized by their ability to bind to multiple DNA sequence motifs and modulate gene expression, often interacting with other transcription factors. Additionally, they are implicated in the regulation of detoxification pathways and the control of morphogenesis and virulence in certain species.
Connector enhancer of kinase suppressor of Ras (CNKSR)
Type: Family

The CNKSR family proteins function as adapter or scaffold proteins involved in various signaling pathways. They enhance guanine-nucleotide exchange on ARF6, regulate Ras signaling, and are implicated in cell migration and transepithelial sodium transport. The family members coordinate the assembly of protein complexes, such as the ENaC-regulatory complex (ERC), and are involved in the regulation of cell surface expression of channels like ENaC. Their roles are essential in processes like HGF-dependent activation of Arf6 and aldosterone-induced sodium transport, contributing to cellular responses to external stimuli and intracellular signaling.
Unconventional Myosin ATPase (Unconventional_Myosin_ATPase)
Type: Family

The Unconventional Myosin family comprises motor proteins with ATPase activity that interact with actin filaments for intracellular movements. Members of the family have highly divergent tails, which are thought to bind to membranous compartments, facilitating their movement relative to the actin cytoskeleton. These myosins play critical roles in various cellular processes, including the differentiation and organization of epithelial brush borders, the renewal of photoreceptor disks, the distribution of pigment epithelial melanosomes, and the arrangement of stereocilia in hair cells. They are also involved in mechanotransduction in cochlear hair cells, necessary for normal hearing, and in the transport of opsin in retinal photoreceptors. Some family members are involved in the formation of cellular projections and are essential for embryonic and larval viability, as well as for auditory transduction by organizing Johnston's organ.