SII-SWORD/CoKE huggingface dataset:
Archaeal Glycosyltransferase 16-like (AGL16-like)
Type: Family

This family of proteins includes glycosyltransferases that are involved in the final step of N-glycan biosynthesis. Members of this family are characterized by their enzymatic activity, which involves the transfer of sugar moieties to specific acceptor molecules, thus playing a crucial role in the formation of glycoproteins. The proper function of these enzymes is essential for the correct folding, stability, and function of many proteins, as well as for cell-cell interactions and cellular signaling. The family is part of the glycosyltransferase group 1 and falls within the Glycosyltransferase 4 subfamily, indicating a shared structural domain and evolutionary history.
L-rhamnose 1-dehydrogenase (NADP(+)) (L-rhamnose_1-dehydrogenase)
Type: Family

This family of proteins is involved in the catabolism of L-rhamnose, a sugar commonly found in plant cell walls. Members of this family function as enzymes that catalyze the first step in the non-phosphorylated metabolic pathway of L-rhamnose degradation. Specifically, they oxidize L-rhamnose to produce L-rhamnono-1,4-lactone. These enzymes exhibit substrate flexibility, being capable of oxidizing other sugars such as L-lyxose and L-mannose. They are characterized by their exclusive use of NADP as a cofactor for the oxidation reaction. The proteins belong to the short-chain dehydrogenases/reductases superfamily, which is known for its members' involvement in various metabolic processes through the catalysis of oxidation-reduction reactions.
Glycosyl Hydrolase 2 (GH2)
Type: Family

This family of proteins includes enzymes that catalyze the hydrolysis of beta-galactosides into monosaccharides. Members of this family are characterized by their ability to break down lactose into glucose and galactose, a critical step in the metabolism of this sugar in organisms that can digest lactose. These enzymes are essential for the proper utilization of lactose as a carbon source and play a significant role in various biological processes, including the dairy industry where they are used to produce lactose-free products. The enzymes in this family share a common evolutionary origin and exhibit a conserved active site that is responsible for their catalytic activity.
DnaJ-like chaperone (DnaJ-like_chaperone)
Type: Family

This family of proteins includes molecular chaperones that are part of the DnaJ, or Hsp40, family. They are characterized by the presence of a J-domain and play a crucial role in the heat shock response. These proteins typically function by stimulating the ATPase activity of Hsp70s, which are another type of heat shock proteins, thereby facilitating the folding of nascent polypeptides and the refolding of denatured proteins. They are involved in various cellular processes, including protein trafficking, signal transduction, and the degradation of misfolded proteins. The DnaJ-like proteins are also implicated in the response to environmental stresses and may have a role in the assembly and operation of protein complexes within the cell.
S-layer large protein (S-layer_large)
Type: Family

This family of proteins is involved in the formation of the highly ordered outer sheath of certain archaeal cells. Members of this family are characterized by their large size and are thought to play a role in providing structural support and protection, potentially contributing to the cell's shape and integrity under extreme environmental conditions.
Abortive phage resistance AbiGi-like (AbiGi-like)
Type: Family

This family of proteins is involved in providing resistance to bacterial phages. The resistance mechanism is characterized by abortive infection, which is believed to function by disrupting the synthesis of phage RNA. The proteins in this family do not target the synthesis of phage DNA, indicating a specific interaction with the phage replication process that is RNA-dependent.
Sulfolobales S-layer anchor (SlaB_anchor)
Type: Family

This family of proteins is involved in the formation of the S-layer, a part of the cell envelope found in Sulfolobales archaea. Members of this family are believed to play a role in anchoring the S-layer complex to the cell membrane, which is crucial for maintaining cell shape and protecting the cell from its environment. The S-layer is composed of proteinaceous subunits that self-assemble into a two-dimensional crystalline array, and this family includes smaller proteins that may interact with other components of the S-layer or the cell membrane to facilitate attachment and stability of the layer.
Isocitrate/Homoisocitrate Dehydrogenase (ICDH/HICDH)
Type: Family

This family of proteins includes enzymes that are involved in the oxidative decarboxylation of isocitrate to 2-oxoglutarate and homoisocitrate to 2-oxoadipate. They play a crucial role in central metabolic pathways, such as the tricarboxylic acid (TCA) cycle and the lysine biosynthesis pathway. These enzymes exhibit a preference for NAD(+) as a cofactor over NADP(+), highlighting their specificity in redox reactions. Their dual substrate specificity suggests a versatile function in cellular metabolism, contributing to the production of key metabolic intermediates.
Acyl-CoA synthetase (ADP-forming) alpha/beta (Acyl-CoA_synthetase_A/B)
Type: Family

This family of proteins is involved in the reversible conversion of various acids into their corresponding acyl-CoA esters, with a preference for aryl acids such as indoleacetate and phenylacetate over acetate. These enzymes are key in the degradation pathway of aryl-CoA esters, converting them back to the respective acids. They also play a role in the catabolism of branched-chain amino acids through the processing of branched-chain-acyl-CoA esters. The enzymatic activity of these proteins is dependent on the presence of divalent metal cations.
Dapdiamide Synthase (Dapdiamide_Synthase)
Type: Family

This family of proteins is involved in the biosynthesis of dapdiamide antibiotics. Members of this family catalyze the ligation of N-beta-fumaramoyl-DAP with branched-chain amino acids such as valine, isoleucine, or leucine to produce dapdiamides A, B, or C. Additionally, these enzymes can catalyze the formation of dapdiamide E through the ligation of N-beta-epoxysuccinamoyl-DAP and valine. These reactions are crucial steps in the production of dapdiamide compounds, which exhibit antibiotic properties.
Glycosyl Hydrolase 39 (GH39)
Type: Family

This family of proteins includes enzymes with alpha-rhamnosidase activity, specifically involved in the degradation of ulvan, a major polysaccharide found in the cell walls of green seaweed. Members of this family are characterized by their ability to cleave alpha-1,4-L-rhamnosidic linkages in ulvan. The enzymatic action results in the breakdown of ulvan into smaller oligomers and dimers, facilitating the utilization of this polysaccharide as a carbon source. The smallest degradation products produced by these enzymes are typically dimers consisting of xylose and sulfated rhamnose units.
L-lysine 4-chlorinase BesD (BesD)
Type: Family

This entry represents a very small family of proteins which includes L-lysine 4-chlorinase BesD, a protein involved in the biosynthesis of terminal alkyne-containing amino acids such as L-propargylglycine (Pra) and L-beta-ethynylserine, that are produced as antibiotics by S.cattleya .
Terminal Alkyne Amino Acid Synthase (Alkyne_AA_Synthase)
Type: Family

This family of proteins is involved in the production of unique amino acids with antibiotic properties, synthesized by certain bacterial species. Members of this family are enzymes that catalyze the oxidative cleavage of specific lysine derivatives to produce amino acids with terminal alkyne groups. These reactions result in the formation of compounds such as L-propargylglycine and L-beta-ethynylserine, as well as the by-products formaldehyde and ammonia. The enzymatic activity includes the conversion of 4-chloro-L-lysine into 4-chloro-allyl-L-glycine, a process significant in the natural biosynthesis of antibiotic substances.
Abortive phage resistance AbiGii-like (AbiGii-like)
Type: Family

This family of proteins is involved in providing resistance to bacterial phages. Members of this family are known to disrupt the process of phage infection in a manner that results in the premature termination of the infection cycle. The mechanism of action appears to target the synthesis of phage RNA, thereby preventing the successful replication and proliferation of the phage within the host. The activity of these proteins does not influence the synthesis of phage DNA, suggesting a specific interaction with the phage's RNA-related processes.
Sarcosine/dimethylglycine N-methyltransferase (SDMT)
Type: Family

This family of proteins includes enzymes that function as methyltransferases, specifically catalyzing the transfer of methyl groups from S-adenosylmethionine to sarcosine and dimethylglycine, resulting in the production of dimethylglycine and betaine, respectively. These enzymes exhibit strict substrate specificity for sarcosine and dimethylglycine. The activity of these enzymes can be regulated by certain compounds, with p-chloromercuribenzoate partially inhibiting their activity, and S-adenosylhomocysteine providing complete inhibition.
L-propargylglycine--L-glutamate ligase (LpgL-glutamate_ligase)
Type: Family

This family of proteins is involved in the biosynthesis of unique amino acids with terminal alkyne groups, which serve as antibiotics. These proteins catalyze the ATP-dependent formation of dipeptides by ligating L-propargylglycine with L-glutamate, resulting in L-gamma-glutamyl-L-propargylglycine. The enzyme exhibits specificity for L-propargylglycine, with a preference over other similar amino acids, although L-cysteine can also be a substrate to a lesser extent. The biosynthetic activity of these proteins contributes to the production of antibiotic compounds in certain bacteria.
Acetophenone carboxylase alpha subunit-like (APC_alpha_subunit-like)
Type: Family

This family of proteins includes enzymes that are involved in the anaerobic catabolism of ethylbenzene, catalyzing the carboxylation of acetophenone to produce 3-oxo-3-phenylpropanoate, also known as benzoylacetate. Members of this family can also carboxylate propiophenone and 4-acetyl-pyridine, albeit at different rates. The activity of these enzymes is subject to inhibition by certain compounds, including zinc ions and specific ATP analogs. They play a role in the breakdown of aromatic compounds, contributing to the metabolic versatility of microorganisms that can utilize such substrates under anaerobic conditions.
UPF0637 domain-containing protein (UPF0637_domain_sf)
Type: Homologous_superfamily

This superfamily of proteins is characterized by a shared domain architecture that suggests a potential role in various cellular processes. However, the specific functions of these proteins are not well-defined and may vary across different members of the superfamily. Research into individual family members is required to elucidate their biological roles and mechanisms of action.
Eukaryotic Ribosomal Large Subunit eL42 (Ribosomal_LSU_eL42)
Type: Homologous_superfamily

This superfamily of proteins is involved in the fundamental process of protein synthesis within the cell. Members of this superfamily are integral components of the ribosome, which is a large ribonucleoprotein complex. Specifically, they are associated with the large ribosomal subunit (LSU) and play a role in the catalytic activity of peptide bond formation. The ribosomal proteins bind to ribosomal RNA and contribute to the structural stability and function of the ribosome. They participate in the translation of messenger RNA (mRNA) into polypeptide chains, with the nascent chains exiting through a tunnel in the LSU. These proteins also interact with factors that assist in the enzymatic processing, targeting, and membrane insertion of the newly synthesized polypeptides.
Eukaryotic Ribosomal Protein eS24 (eRP_eS24_sf)
Type: Homologous_superfamily

This superfamily of proteins is involved in the structure and function of the ribosome, specifically the small ribosomal subunit. Members of this superfamily are essential for protein synthesis within the cell. They participate in the processing of precursor ribosomal RNA and the maturation of the 40S ribosomal subunits. These proteins are components of the small subunit processome, which is the initial precursor to the small eukaryotic ribosomal subunit. In the nucleolus, they work alongside ribosome biogenesis factors, RNA chaperones, and other ribosomal proteins to facilitate RNA folding, chemical modifications, structural rearrangements, and cleavage. They also contribute to the targeted degradation of pre-ribosomal RNA by the RNA exosome, ensuring the proper assembly and function of the ribosome.
Arylamine N-acetyltransferase domain-containing protein (Arylamine_NAT_domain_sf)
Type: Homologous_superfamily

This superfamily of proteins is involved in the detoxification of various compounds, including drugs and plant-produced toxins. Members of this superfamily are characterized by their ability to transfer acetyl groups from acetyl-CoA to various substrates, a process known as acetylation. This modification can lead to the inactivation of toxic substances, making them less harmful and easier to excrete. Some members are also involved in the bioactivation of carcinogens, potentially contributing to chemical carcinogenesis. Additionally, certain proteins within this superfamily participate in the biosynthesis of complex natural products, such as antibiotics, by catalyzing key steps in their assembly. Overall, the superfamily plays a crucial role in cellular defense mechanisms and metabolic processes.
Lentiviral Vpx-associated factor (Lentiviral_Vpx_assoc_factor)
Type: Homologous_superfamily

This superfamily of proteins is involved in the viral infection process of non-dividing cells. They facilitate the nuclear translocation of the viral pre-integration complex, which is essential for the integration of viral DNA into the host genome. Additionally, these proteins interact with the host's ubiquitin-proteasome system by binding to a specific E3 ligase complex, altering its substrate specificity. This interaction leads to the targeted degradation of host proteins that are otherwise involved in the innate immune response against the virus. The depletion of such host proteins enables viral replication, particularly in myeloid cells, by preventing the hydrolysis of deoxynucleoside triphosphates, which are necessary substrates for viral reverse transcription.
Bacterial Cell Division Activator (Bac_CellDiv_Activator)
Type: Homologous_superfamily

This superfamily of proteins acts as activators of bacterial cell division. They are known to inhibit the GTPase activity of the FtsZ protein, which is a key regulator in the assembly of the bacterial cytoskeleton. By inhibiting FtsZ GTPase activity, these proteins promote the polymerization of FtsZ into protofilaments, which are essential for the formation of the Z ring at the site of cell division. The Z ring serves as a scaffold for the division machinery and is crucial for the cytokinesis process. These proteins are typically recruited to the mid-cell early in the cell division process, although they are not considered essential for the division to occur.
Bacterial Outer Membrane Channel Superfamily (Bact_OM_Channel_sf)
Type: Homologous_superfamily

This superfamily of proteins includes outer membrane channel proteins that facilitate the transport of specific solutes across the bacterial outer membrane. Members of this superfamily are involved in the uptake of compounds such as N-acetylneuraminic acid, small sugars, and oligogalacturonides, which are essential for bacterial nutrition and virulence. These proteins can form high-conductance channels with varying selectivity, including weak anion selectivity, and are known to operate at low membrane potentials. Some members may also play a role in bacterial signal transduction pathways.
Isomerization and Racemization Enzyme Superfamily (Iso_Racemase_Enz_sf)
Type: Homologous_superfamily

This superfamily of proteins includes enzymes that catalyze isomerization and racemization reactions. Members of this superfamily are involved in the conversion of maleate to fumarate, a reaction that involves the cis-trans isomerization of a double bond. Other members are responsible for the racemization of hydantoins, which is a reversible isomerization process that converts one enantiomer of a compound into the other, facilitating the production of L-amino acids from racemic mixtures. These enzymes exhibit specificity for substrates such as maleate and various substituted hydantoins, and their activity can be modulated by metal ions and other chemical agents.
Glycosyl Hydrolase 4 Enzyme Superfamily (GH4_Enzyme_sf)
Type: Homologous_superfamily

This superfamily of proteins includes enzymes that catalyze the hydrolysis of glycosidic bonds in various oligosaccharides and polysaccharides. Members of this superfamily are characterized by their ability to act on alpha-linked sugar moieties, with specificities that include but are not limited to alpha-galactosidase and alpha-glucosidase activities. These enzymes are involved in the breakdown of complex carbohydrates into simpler sugars, which can then be utilized by the organism for energy and as building blocks for other biological processes. The superfamily exhibits a broad range of substrate specificities, with some members capable of hydrolyzing bonds in di-, tri-, and oligosaccharides, while others are more restricted in their action. They are also subject to regulation by various inhibitors, including metal ions and chelating agents such as EDTA.
Flagellar assembly and chemotaxis effector (Flag_assembly_chemotaxis_eff)
Type: Homologous_superfamily

This superfamily of proteins includes components involved in bacterial flagellar assembly and chemotaxis. Members of this superfamily are implicated in the formation and function of the flagellum, a lash-like appendage that enables motility in various bacterial species. These proteins play a role in the response to chemotactic stimuli, which are environmental signals that guide the movement of an organism towards or away from a chemical source. The superfamily is also associated with the secretion machinery of certain virulence factors in pathogenic bacteria, indicating a role in the translocation of effector proteins during infection processes.
Mercury resistance MerB lyase (MerB_lyase_sf)
Type: Homologous_superfamily

This superfamily of proteins is involved in the detoxification process of organomercurials by breaking the carbon-mercury bond. The enzymatic action results in the release of Hg(2+), which is then further detoxified. The members of this superfamily share a common function in mercury resistance mechanisms across various bacterial species, providing protection against the toxic effects of mercury compounds by converting them into less harmful forms.
Insecticidal knottin-like domain-containing protein (Insecticidal_knottin-like_sf)
Type: Homologous_superfamily

This superfamily of proteins includes members that exhibit insecticidal properties. They are characterized by their ability to inhibit insect voltage-gated sodium channels, leading to partial blockade of the channel pore. This action results in flaccid paralysis and eventual death when administered to certain insect larvae. Some members of this superfamily are also known to be orally active against various insect pests when fused with other molecules such as snowdrop lectin. Structurally, these proteins are defined by a 'disulfide through disulfide knot', a feature that classifies them as knottins.
Lipogenesis and Microtubule Stabilization Superfamily (Lipogen_MT_Stabilize_sf)
Type: Homologous_superfamily

This superfamily of proteins is involved in the regulation of lipid metabolism, particularly lipogenesis. Members of this superfamily are known to up-regulate enzyme activity associated with the biosynthesis of various lipids, including triacylglycerol, diacylglycerol, and phospholipid. They are also implicated in the stabilization of microtubules. Some members may function as transcriptional coactivators and modulate the activity of specific transcription factors. The superfamily plays a significant role in liver lipid metabolism and in the mammary gland during lactation, where it is important for the production of medium-chain fatty acids.
Proteasome Assembly Chaperone (Psm_Assembly_Chaperone)
Type: Homologous_superfamily

This superfamily of proteins is involved in the assembly and regulation of the 20S proteasome, a key component of the ubiquitin-proteasome system responsible for protein degradation. Members of this superfamily function as chaperones that facilitate the correct folding and assembly of proteasome subunits. They may work in conjunction with other specific chaperone proteins to ensure the proper formation of the proteasome's alpha-ring structure, which is crucial for its proteolytic activity. The superfamily plays a significant role in maintaining cellular homeostasis by participating in the degradation of misfolded or damaged proteins and the regulation of various protein pathways.
Fimbrial Adhesin Regulatory Protein (Fimbrial_Adhesin_Reg)
Type: Homologous_superfamily

This superfamily of proteins includes transcriptional regulators that modulate the expression of genes associated with the biosynthesis of various types of fimbriae and adhesins. These proteins are involved in both positive and negative regulation of gene transcription, with some acting as trans-acting factors. They play crucial roles in the biogenesis of fimbrial structures, which are important for bacterial adhesion to host cells. The regulatory mechanisms may involve differential binding to distinct sites within operons, influencing the transcription of genes responsible for the assembly and function of adhesive pili. Collectively, these proteins contribute to the control of bacterial virulence factors, impacting host-pathogen interactions.
Curli assembly CsgC/AgfC domain-containing protein (Curli_assembly_CsgC/AgfC)
Type: Homologous_superfamily

This superfamily of proteins is involved in the formation of extracellular fibrous structures known as thin aggregative fimbriae, which are important for cell adhesion and biofilm formation. The proteins facilitate the assembly of a major structural subunit, promoting the formation of these fibers through a process that may include both extracellular nucleation-precipitation and intracellular pathways. The assembly is a coordinated effort that may require additional proteins for efficient fiber formation and stabilization in the extracellular environment.
Secretoglobin Domain-Containing (Secretoglobin_Domain_sf)
Type: Homologous_superfamily

This superfamily of proteins is characterized by their involvement in various biological processes, primarily related to the transport and sequestration of small hydrophobic molecules. Members of this superfamily are typically small, secreted proteins that can bind to a range of ligands, including hormones, pheromones, and other signaling molecules. They play a crucial role in modulating the availability and activity of these ligands, thereby influencing physiological responses such as inflammation, immune responses, and cellular communication. The structure of these proteins often includes a compact fold that allows for the stable binding of hydrophobic molecules, which is essential for their function as carriers and modulators in diverse biological pathways.