SII-SWORD/CoKE huggingface dataset:
Cell Division Membrane-Interacting Protein (Cell_Div_Membrane-Interact)
Type: Family

This family of proteins is involved in cellular division processes. Members of this family, including CdvA, are known to polymerize between segregating nucleoids during cell division. They form structures that change in size as the cell constricts. Specifically, CdvA is noted for its role in interacting with the cell membrane and recruiting homologs of the ESCRT-III complex to this location. Additionally, these proteins have a domain at the C-terminal end that is crucial for interactions with other cell division proteins, such as CdvB, facilitating the assembly of the cell division machinery.
Cell Division Complex Component (Cell_Div_Complex_Comp)
Type: Family

This family of proteins is involved in the process of cell division. Members of this family, including CdvA, CdvB, and CdvC, form a complex that polymerizes between segregating nucleoids during cell division. This complex plays a crucial role in maintaining the structure that becomes progressively smaller as the cell constricts. Additionally, these proteins possess a winged-helix-like C-terminal extension that is essential for their interaction with other proteins in the complex, particularly CdvA.
Hexaprenyl pyrophosphate synthase (HexPP_synthase)
Type: Family

This family of proteins is involved in the biosynthesis of polyprenyl pyrophosphates, which are key intermediates in the synthesis of isoprenoid compounds. Members of this family function as enzymes that facilitate the E-type condensation reactions between isopentenyl pyrophosphate (IPP) and various allylic substrates, including geranylgeranyl diphosphate (GGPP), farnesyl diphosphate (FPP), or geranyl diphosphate (GPP). The primary reaction catalyzed by these enzymes results in the formation of trans-C30-hexaprenyl pyrophosphate (HexPP), with GGPP being the preferred physiological substrate. These enzymes play a crucial role in the production of isoprenoid lipids, which are essential for various biological processes including the prenylation of proteins, electron transport, and the biosynthesis of quinones.
Glycerate kinase type-1 (Glycerate_kinase-1)
Type: Family

This family of proteins includes enzymes that are responsible for the ATP-dependent phosphorylation of D-glycerate, resulting in the production of 2-phosphoglycerate. Members of this family are capable of using not only ATP but also other nucleotides such as GTP, CTP, UTP, ADP, AMP, or pyrophosphate as phosphate donors. This enzymatic activity is crucial in the metabolic pathway where it participates in the conversion of glycerate into a form that can enter further metabolic processes. The versatility in phosphate donor usage suggests a flexible active site capable of accommodating various nucleotides.
Ced system-associated DNA import protein (Ced-DNA_import)
Type: Family

This family of proteins is associated with the Ced system, which plays a role in the process of DNA import. Members of this family are implicated in the transfer of genetic material into the cell, which is a crucial step for various biological processes including horizontal gene transfer, transformation, and adaptation.
Cell Division Coordination Protein (Cdv_Coordination_Protein)
Type: Family

This family of proteins is involved in cellular division processes. Members of this family are believed to play a role in the coordination of cell division machinery, potentially by interacting with other cell division proteins to ensure proper division of the cell.
DNA Double-strand Break Repair Helicase HerA (DSB_Repair_Helicase_HerA)
Type: Family

This family of proteins is involved in the cellular process of DNA double-strand break (DSB) repair. Members of this family function in conjunction with other proteins, such as NurA, to facilitate the resection of the 5' strand of DNA at the site of damage, which is a critical step in the repair process. The resection results in the formation of a long 3' single-stranded DNA tail that is necessary for the loading of other repair proteins like RadA. Proteins in this family possess DNA-dependent ATPase activity, which is likely important for their function in DNA repair. Additionally, they exhibit DNA helicase activity, which is essential for unwinding the DNA helix, and this activity is known to be enhanced by the presence of NurA.
MfnF synthase (MfnF_synthase)
Type: Family

This family of proteins is involved in the biosynthesis of complex amine-containing compounds. Members of this family are responsible for catalyzing the condensation reaction between 5-(aminomethyl)-3-furanmethanol diphosphate and gamma-glutamyltyramine. The resultant product of this enzymatic reaction is a compound known as APMF-Glu. This specific reaction is a key step in the biosynthetic pathway of certain bioactive molecules that may have physiological relevance. The enzymatic activity exhibited by these proteins is indicative of their role in cellular metabolism, particularly in the formation of specialized metabolites that may be involved in signaling or other cellular functions.
GHMP kinase (GHMP_kinase)
Type: Family

This family of proteins includes enzymes that are involved in the phosphorylation of (R)-mevalonate 5-phosphate to (R)-mevalonate 5-diphosphate. These enzymes play a crucial role in the mevalonate pathway, which is responsible for the production of isopentenyl diphosphate, an essential precursor for the synthesis of isoprenoid compounds, including archaeal membrane lipids.
Geranylfarnesyl diphosphate synthase-like (GFPP_synthase-like)
Type: Family

This family of proteins is involved in the biosynthesis of polyprenyl compounds, which are critical components in various biological processes. Members of this family function as enzymes that catalyze the condensation of isopentenyl pyrophosphate with allylic pyrophosphates, leading to the production of geranylfarnesyl diphosphate. This enzymatic activity is essential for the generation of methanophenazine, an electron carrier that plays a significant role in methanogenesis. The proteins in this family exhibit a preference for geranylgeranyl diphosphate and farnesyl diphosphate as substrates in the biosynthetic pathway.
Thiosulfate dehydrogenase [quinone] large subunit (TQO_large_subunit)
Type: Family

This family of proteins includes thiosulfate dehydrogenase [quinone] large subunits, which are involved in the sulfur oxidation process. They are known to couple the oxidation of sulfur to the reduction of dioxygen, thereby playing a crucial role in the sulfur cycle. These proteins are also responsible for transferring electrons to the electron transport chain's terminal oxidase. The activity of these proteins is regulated by certain sulfur compounds, which can act as inhibitors.
Non-flavoprotein flavin reductase (NFP_flavin_reductase)
Type: Family

This family of proteins is involved in the reduction of free flavins, including FMN, FAD, and riboflavin, using NADH as an electron donor. The reduced flavins are then transferred to a larger component, typically the HpaB component, which is part of the same enzymatic system. These proteins are characterized by their ability to utilize NADH, but not NADPH, for the reduction process and can accept both FAD and FMN as electron acceptors. They play a crucial role in the metabolic pathway involving 4-hydroxyphenylacetate.
Transcriptional Antiterminator BglG (Antiterminator_BglG)
Type: Family

This family of proteins is involved in the regulation of gene expression, specifically in the lactose metabolism pathway. Members of this family function as transcription antiterminators, which means they prevent the premature termination of transcription. By doing so, they enable the continued synthesis of mRNA and subsequent production of enzymes necessary for lactose utilization. These proteins are key regulatory components in the lac operon, a well-studied model system for understanding gene regulation in response to environmental changes, such as the presence or absence of lactose in bacteria.
[5-(aminomethyl)furan-3-yl]methyl phosphate kinase (Furan-3-ylmethyl_P_kinase)
Type: Family

This family of proteins is involved in the biosynthesis of modified nucleotides. Members of this family are known to catalyze the phosphorylation of 5-(aminomethyl)-3-furanmethanol phosphate (F1-P) using ATP to produce 5-(aminomethyl)-3-furanmethanol diphosphate (F1-PP). Additionally, they have adenylate kinase activity, facilitating the transfer of a phosphoryl group from ATP to AMP, which results in the generation of two ADP molecules. The activity of these proteins is sensitive to chelating agents, as evidenced by inhibition by EDTA.
Glycosyl Hydrolase 3 Beta-Xylosidase (GH3_Beta-Xylosidase)
Type: Family

This family of proteins includes enzymes with beta-xylosidase activity, which play a role in the degradation of ulvan, a major polysaccharide in the cell walls of green seaweed. Members of this family catalyze the hydrolysis of xylosides, specifically converting Xyl-Rha3S oligosaccharides into xylose and 3-sulfated rhamnose. These enzymes are also capable of degrading synthetic substrates like 4-methylumbelliferyl-beta-D-xylopyranoside in vitro. They are characterized by their membership in the glycosyl hydrolase 3 enzyme family, which is known for its involvement in the breakdown of glycosidic bonds.
Phosphatase RapA inhibitor (PhrA_inhibitor)
Type: Family

This family of proteins includes signaling molecules that play a role in the regulation of sporulation. They are secreted and subsequently need to be imported into the cell to exert their function intracellularly. Members of this family act as inhibitors of specific phosphatase activities, such as that of RapA, but do not affect others like RapB. The inhibitory function relies on the presence of a free carboxylate group at the C-terminal end of the peptide. These proteins are significantly more active in their free acid form compared to their amide form.
Adenosylcobinamide-phosphate Guanylyltransferase (AdoCbi-P_Guanylyltransferase)
Type: Family

This family of proteins includes guanylyltransferases that are responsible for the synthesis of adenosylcobinamide-GDP from adenosylcobinamide-phosphate and GTP, a key step in the biosynthesis of adenosylcobalamin, also known as coenzyme B12. Members of this family bind GTP specifically and do not utilize other nucleotides such as NTPs or GDP. They also lack adenosylcobinamide kinase activity. Additionally, these proteins can catalyze the formation of (2S)-lactyl-2-diphospho-5'-guanosine from 2-phospho-L-lactate and GTP, although they are less efficient at this reaction compared to the primary enzyme assumed to perform this function in vivo.
Mandelate racemase/muconate lactonizing-like enzyme (MR_MLE-like_enzyme)
Type: Family

This family of proteins is involved in the pentose oxidation pathway, where it functions to convert D-arabinonate into 2-keto-3-deoxy-D-arabinonate by catalyzing a dehydration reaction. Members of this family are characterized by their enzymatic activity in this specific metabolic process, which ultimately leads to the production of 2-oxoglutarate. The activity of these enzymes is known to be inhibited at high substrate concentrations, specifically when levels exceed 8 mM. They share a common evolutionary origin with the mandelate racemase/muconate lactonizing enzymes, indicating a conserved mechanism of action within this group.
Pilus tip thioester-containing adhesin (Pilus_tip_adhesin)
Type: Family

This family of proteins includes adhesins located at the tip of bacterial pili. They play a crucial role in bacterial adherence to host cell surfaces by forming covalent bonds with target molecules. The reactive thioester bonds present in these proteins suggest a mechanism for binding, potentially to lysine residues or carbohydrates that present a free amine group. Although in vitro studies show binding to spermidine, it is not considered the natural target in vivo. The adhesion process is significant for bacterial colonization and pathogenesis, indicating these proteins as potential targets for therapeutic intervention.
Type IV major pilin (Type_IV_major_pilin)
Type: Family

This family of proteins includes major components of type IV pili, which are filamentous structures on the surface of bacterial cells. These proteins are essential for social gliding motility, a process that involves the extension and retraction of pili to enable cell movement. The pilus assembly is orchestrated by a two-component system that regulates the proper formation of these structures. The pili, primarily composed of thousands of copies of a pilin protein, interact with extracellular polysaccharides to mediate cell traction and motility.
Thiosulfate dehydrogenase small subunit (TQO_small_subunit)
Type: Family

This family of proteins includes small subunits of thiosulfate dehydrogenase [quinone], which are involved in the sulfur oxidation process. These proteins are believed to facilitate the transfer of electrons from sulfur compounds to the electron transport chain, ultimately reducing dioxygen. The electron transfer is mediated by specific quinones within the organism. Additionally, the activity of these proteins is known to be inhibited by various sulfur compounds.
Plant RLCK Uridylyltransferase (RLCK_Uridylyltransferase)
Type: Family

This family of proteins includes enzymes that exhibit uridylyltransferase activity, which is implicated in both virulence and avirulence interactions with host plants. These proteins are capable of modifying host receptor-like cytoplasmic protein kinases (RLCKs) by uridylylation, affecting the host's immune signaling pathways. In certain plant ecotypes, this modification can suppress immune responses, facilitating pathogen virulence. Conversely, in resistant plant varieties, the same enzymatic activity can trigger robust immune responses, leading to avirulence. The proteins contain domains such as the LRR and Fic/Fido, which are essential for their function in host-pathogen interactions.
Glucosamine-6-phosphate deaminase (GlcN6P_deaminase)
Type: Family

This family of proteins includes enzymes that are responsible for the reversible isomerization-deamination of glucosamine 6-phosphate into fructose 6-phosphate and ammonium ion. These enzymes play a crucial role in the metabolic pathway of chitin degradation, which is an important process for the recycling of nitrogen and carbon in various organisms. The enzymatic activity is essential for the utilization of chitin as a source of energy and as a carbon and nitrogen reservoir, contributing to the organism's ability to adapt to different nutritional environments.
Trans-sulfuration enzyme-like (Trans-sulfuration_enzyme-like)
Type: Family

This family of proteins includes enzymes that are involved in amino acid racemization and trans-sulfuration processes. They are capable of catalyzing the conversion of L-alanine to D-alanine and L-glutamate to D-glutamate, which are crucial for peptidoglycan synthesis in certain organisms lacking the canonical genes for these pathways. Additionally, these proteins exhibit cystathionine beta-lyase activity, breaking down cystathionine into homocysteine and pyruvate, although this function may not be essential in organisms that have alternative pathways for methionine biosynthesis. They do not, however, participate in the synthesis of cystathionine, indicating the absence of cystathionine gamma-synthase activity.
Glucosyl-3-phosphoglycerate synthase-related (GPGS-related)
Type: Family

This family of proteins is involved in the biosynthesis of specific lipopolysaccharides. Members of this family function as enzymes that facilitate the transfer of a glucose moiety from a nucleotide sugar donor to a phosphate-containing acceptor molecule. The enzymatic activity results in the formation of a glucosylated compound that is a precursor in the biosynthetic pathway of certain bacterial polysaccharides. These proteins are characterized by their glycosyltransferase activity, specifically transferring glucose to 3-phospho-D-glycerate to produce glucosyl-3-phosphoglycerate.
Autotransporter Adhesin (Autotransporter_Adhesin)
Type: Family

This family of proteins includes autotransporter adhesins that play a crucial role in bacterial pathogenesis. Members of this family are involved in mediating bacterial attachment to a wide range of host cells, which is a key step in the infection process. These proteins are known for their ability to promote bacterial aggregation and biofilm formation, which enhances bacterial survival and persistence in the host environment. The proteins are characterized by a signal peptide that directs the precursor to the periplasmic space, followed by the insertion of a C-terminal domain into the outer membrane, allowing the passenger domain to reach the cell surface. The mature protein remains associated with the cell surface, facilitating interactions with host tissues.
DadA oxidoreductase (DadA_oxidoreductase)
Type: Family

This family of proteins includes enzymes that are primarily involved in the oxidation of D-proline to Δ1-pyrroline-2-carboxylate. Members of this family exhibit oxidoreductase activity, acting on the CH-NH2 group of donors with oxygen as the acceptor. While D-proline is the preferred substrate, these enzymes are also capable of processing other D-amino acids, albeit with less efficiency. The enzymatic activity is crucial for the catabolism of D-amino acids, which may serve as nitrogen and energy sources for the organism. The family is characterized by a conserved domain structure that is typical of the DadA oxidoreductase family, indicating a shared evolutionary origin and similar catalytic mechanisms among its members.
Ro 60 kDa domain-containing protein (Ro_60_kDa)
Type: Family

This family of proteins is involved in the cellular response to UV irradiation. Members of this family bind to small RNAs that accumulate as a result of UV damage, contributing to the organism's resistance to such stress. They are characterized by a MIDAS-like motif within a VWFA-like domain that can bind divalent metal cations. Additionally, these proteins possess a TROVE domain, which is composed of helical HEAT-like repeats forming a horseshoe shape, closed by the VWFA-like domain, creating a ring-shaped monomer. This structure allows for the binding of single-stranded RNA within its central cavity, which is positively charged.
Hyperpolarization-activated voltage-gated potassium channel (Hyp-activated_K+_channel)
Type: Family

This family of proteins includes voltage-gated potassium-selective channels that are activated by hyperpolarization. These channels are integral to the control of membrane potential and are characterized by the presence of a voltage-sensor domain, typically containing a series of positively charged amino acids within the S4 segment. The primary function of these channels is to facilitate the selective flow of potassium ions across the cell membrane, which is essential for various physiological processes including the regulation of neuronal excitability and muscle contraction.
Damage-control phosphatase (Damage-ctrl_phosphatase)
Type: Family

This family of proteins includes metal-dependent phosphatases that are thought to play a role in damage control by hydrolyzing oxidatively damaged purine nucleotides or their biosynthetic intermediates. Members of this family are characterized by specific conserved motifs that are critical for their function. These motifs include a CxxC motif near the N-terminus, a GNFE motif close to the C-terminus, and a KC motif also near the C-terminus. The arrangement of these motifs suggests a substrate-binding cleft where the interaction with a metal ion occurs, which is essential for the catalytic activity of these enzymes. Although they bind an iron-containing chromophore, it is not directly involved in the catalytic process. These proteins are part of a larger family known for their role in the hydrolysis of phosphate groups from damaged nucleotides, thereby contributing to the cellular response to oxidative stress.
S-layer A-like (SlaA-like)
Type: Family

This family of proteins includes S-layer large proteins that are likely to contribute to the formation of a highly ordered outer sheath, which may be involved in protecting the cell from environmental factors and in mediating cell adhesion to surfaces.
Arsenate respiratory reductase iron-sulfur subunit (ArrB_iron-sulfur_subunit)
Type: Family

This family of proteins includes subunits that are part of the arsenate respiratory reductase complex, which is involved in the reduction of arsenate to arsenite, a process with implications for energy production and detoxification pathways. Members of this family are likely responsible for electron transfer within the complex. The localization of the complex in the periplasm suggests a role in coupling arsenate reduction to energy production, potentially preventing the need for energy-intensive detoxification processes in the cytoplasm. Additionally, the activity of these proteins is known to be inhibited by phosphate through competitive inhibition.
L-isoleucine 3(1)-dioxygenase-like (Ile_3(1)-dioxygenase-like)
Type: Family

This family of proteins includes enzymes that are involved in the hydroxylation of specific amino acids. Members of this family primarily catalyze the conversion of L-isoleucine to L-4'-hydroxyisoleucine, a reaction that involves the addition of an oxygen atom to the C-4' position of the isoleucine side chain. This modification can impact the biological activity of the amino acid. The enzymes exhibit lower activity with other amino acids such as L-valine and L-methionine. They are characterized by their dependency on iron and ascorbate for oxidoreductase activity, which is a common feature among enzymes that catalyze similar hydroxylation reactions.
Arsenate Respiratory Reductase Molybdopterin-Containing Subunit (Arr_molybdopterin_subunit)
Type: Family

This family of proteins includes arsenate respiratory reductase molybdopterin-containing subunits, such as ArrA. Members of this family are involved in the reduction of arsenate to arsenite, a process that is linked to energy production in prokaryotic organisms. The enzyme complex they form part of is typically located in the periplasmic space, allowing for the immediate reduction of arsenate before its transport into the cytoplasm. This strategic localization helps the cell to avoid the energy-consuming detoxification pathway that would otherwise be necessary. The family is characterized by its ability to bind arsenate and is related to other prokaryotic molybdopterin-containing oxidoreductases.
Zinc-containing ferredoxin (Zinc-ferredoxin)
Type: Family

This family of proteins includes zinc-containing ferredoxins, which are characterized by their ability to transfer electrons in various metabolic processes. They contain iron-sulfur clusters that facilitate their role in electron transfer, participating in redox reactions that are fundamental to cellular metabolism. These proteins are involved in a range of functions, from photosynthesis in plants and bacteria to the electron transport chain in the mitochondria of eukaryotic organisms. The versatility of ferredoxins stems from the different redox potentials of their iron-sulfur clusters, which allow them to interact with a multitude of redox partners, thus playing a key role in the cell's energy conversion mechanisms.
Anti-sigma-F factor NrsF-like (Anti-sigma-F_NrsF-like)
Type: Family

This family of proteins includes anti-sigma factors that specifically interact with extracytoplasmic function (ECF) sigma factors such as sigma-F (SigF). Members of this family play a role in the cellular response to environmental stressors like chromate and cadmium. They maintain ECF sigma factors in an inactive state under non-stress conditions. Upon exposure to specific stress signals, these anti-sigma factors release their cognate sigma factors, thereby activating them to initiate transcription of stress response genes. Overexpression of these proteins can disrupt the stress response, indicating a tightly regulated mechanism for stress adaptation.