SII-SWORD/CoKE huggingface dataset:
Glyceraldehyde dehydrogenase medium chain (Glyceraldehyde_DH_medium)
Type: Family

This family of proteins includes enzymes that participate in the nonphosphorylated Entner-Doudoroff pathway. They are responsible for the oxidation of D-glyceraldehyde, producing glycerate. These enzymes exhibit a broad substrate specificity when artificial electron acceptors are used, capable of oxidizing various aldehydes including glyceraldehyde-3-phosphate, formaldehyde, acetaldehyde, propionaldehyde, and isobutyraldehyde. The preferred in vivo electron acceptor for these enzymes remains unidentified. Their activity is highest with D-glyceraldehyde among the tested substrates.
Bacterial phytochrome-like (Bacterial_phytochrome-like)
Type: Family

This family of proteins functions as photoreceptors that can exist in two different light-responsive forms. The red-absorbing form (Pr) is induced by far-red light, while the far-red-absorbing form (Pfr) is favored in the dark or under red light. These proteins are involved in regulating virulence in certain bacteria, potentially by modulating gene expression in response to ambient light levels or spatial cues. The Pr form is associated with a reduction in virulence, while the Pfr form, prevalent in the dark, is linked to increased biofilm and xanthan production, making the bacteria more virulent. These photoreceptors contain multiple domains that contribute to their light-sensing function and dimerization, including PAS, GAF, and PHY domains, with a mobile tongue domain within the PHY domain playing a role in chromophore interaction.
Chemotaxis signal transducer CheA (CheA_signal_transducer)
Type: Family

This family of proteins plays a crucial role in bacterial chemotaxis, the movement towards or away from chemical stimuli. Members of this family are responsible for processing signals from sensory receptors, which can be either chemoreceptors or photoreceptors. Upon receiving a signal, these proteins undergo autophosphorylation and subsequently transfer the phosphate group to other proteins involved in the signaling pathway, such as CheY and potentially CheB. This phosphorylation event is a key step in the signal transduction process that ultimately controls the direction of flagellar motor rotation and, consequently, the movement of the bacterium.
Betaine reductase complex component B subunit beta (Betaine_reductase_B_beta)
Type: Family

This family of proteins is involved in the reductive deamination process, where the substrate is initially bound to a component via a Schiff base intermediate. A selenol anion then nucleophilically attacks the activated substrate, leading to the formation of a carboxymethylated selenoether and the release of the respective amine. In subsequent steps, acetyl phosphate is produced, and an oxidized component is restored to its reduced state by the thioredoxin system, enabling the catalytic cycle to continue. The proteins play a role in the betaine reductase complex, contributing to the metabolism of compounds that include betaine.
Glyceraldehyde dehydrogenase small chain-like (Glyceraldehyde_DH_small)
Type: Family

This family of proteins includes enzymes that participate in the nonphosphorylated Entner-Doudoroff pathway, a metabolic route distinct from glycolysis. Members of this family are responsible for the oxidation of D-glyceraldehyde, producing glycerate. These enzymes exhibit a broad substrate specificity in the presence of artificial electron acceptors, being able to oxidize various aldehydes such as glyceraldehyde-3-phosphate, formaldehyde, acetaldehyde, propionaldehyde, and isobutyraldehyde. The most efficient substrate is D-glyceraldehyde. The natural electron acceptor used by these enzymes in vivo remains unidentified.
Cytochrome c (Cytochrome_c)
Type: Family

This family of proteins is typically involved in electron transport processes. Members of this family are known to participate in redox reactions, which are crucial for various biological energy conversion pathways. Specifically, they may play a role in anaerobic respiration mechanisms, such as iron respiration, where they could facilitate the transfer of electrons to iron as a terminal electron acceptor under oxygen-limited conditions. The presence of a heme group is characteristic of these proteins, which allows them to perform their electron transfer function.
Flagella basal body rod (Flagellar_basal_body_rod)
Type: Family

This family of proteins is involved in the formation of the bacterial flagellum, which is a complex structure responsible for motility in many bacteria. Members of this family are typically components of the basal body rod, a crucial part of the flagellar apparatus that provides a scaffold for the flagellum and is essential for its assembly and function. The flagellar hook protein, such as FlgE, plays a key role in connecting the basal body to the filament and is critical for the proper functioning of the flagellum, enabling bacteria to swim and navigate their environment.
FAD-dependent oxidoreductase 2/FRD/SDH (FAD-oxidoreductase_2/FRD/SDH)
Type: Family

This family of proteins includes flavoprotein subunits that are part of the 8-methylmenaquinol:fumarate reductase complex, which is involved in anaerobic metabolism. These proteins are responsible for the enzymatic reduction of fumarate to succinate, using 8-methylmenaquinol-6 as the electron donor. The family members contain a site for dicarboxylate reduction and are characterized by their similarity to FAD-dependent oxidoreductases within the FRD/SDH subfamily. They do not exhibit succinate oxidation activity.
Sarcosine Reductase Complex Component (Sarcosine_Reductase_Comp)
Type: Family

This family of proteins is involved in the reductive deamination of sarcosine. The proteins function as components of a sarcosine reductase complex, which catalyzes the transformation of sarcosine into a carboxymethylated selenoether and the respective amine. This process involves the formation of a Schiff base intermediate, nucleophilic attack by a selenol anion, and the production of acetyl phosphate. The proteins in this family work in concert with other components of the complex and are regenerated through a reduction by the thioredoxin system, enabling continuous catalytic cycles.
Cytochrome b-type electron transport (Cytochrome_b-type_ET)
Type: Family

This family of proteins includes members that are involved in electron transport by binding to heme groups. Each protein within this family can bind two distinct heme groups, which are integral to the protein's function but are not covalently attached. These heme groups play a critical role in the protein's ability to transfer electrons within the mitochondrial respiratory chain, particularly within the context of oxidative phosphorylation where they contribute to the establishment of a proton gradient across the mitochondrial membrane. This, in turn, is essential for the production of ATP, the energy currency of the cell. Members of this family are characterized by their similarity in structure and function, and are key components in the bioenergetic processes of the cell.
Cytochrome c-554-like (Cytochrome_c-554-like)
Type: Family

This family of proteins is involved in the biological process of ammonia oxidation. Members of this family are capable of accepting electrons from the enzyme hydroxylamine oxidoreductase, which is a key step in the conversion of ammonia to nitrite. This electron transfer is essential for the energy metabolism of organisms that perform nitrification, a part of the global nitrogen cycle.
Retron Ec48 antiviral membrane protein (Retron_Ec48_antiviral)
Type: Family

This family of proteins includes membrane components of the Retron Ec48 antiviral defense system. These proteins are associated with a non-coding RNA and a reverse transcriptase to form a complex that protects bacteria against various bacteriophages. The N-terminal transmembrane region of these proteins is essential for this protective function. When the bacterial RecBCD enzyme is compromised by viral proteins, the effector protein of this family is likely activated, leading to an abortive infection and halting bacterial growth. This defense mechanism is effective against several phages and can result in different outcomes depending on the multiplicity of infection, ranging from normal growth to growth stasis and membrane permeabilization without lysis.
ABC transporter glucose import ATPase (ABC-Glucose_import_ATPase)
Type: Family

This family of proteins is involved in the active transport of glucose across the cell membrane. Members function as part of an ABC transporter complex, which typically includes additional components for substrate specificity and translocation. These proteins utilize the energy derived from ATP hydrolysis to drive the import of glucose into the cell. The ATPase activity is an intrinsic characteristic of these proteins, even in the absence of the full transporter complex. The family is characterized by a conserved ABC-ATPase domain, which is essential for ATP binding and hydrolysis, and is linked to a C-terminal domain whose function is not well-defined. Proteins in this family are unified by their membership in the larger ABC transporter superfamily, known for their role in the transport of various molecules across cellular membranes.
Alkane Uptake OmpP1/FadL-like Protein (Alkane_Uptake_OmpP1/FadL)
Type: Family

This family of proteins is implicated in the process of alkane utilization, playing a crucial role in the growth of organisms on alkanes. Members are likely involved in the transport of alkanes into the cell, facilitating their uptake by interacting with micelle-solubilized alkanes. The family is characterized by its similarity to the OmpP1/FadL family, which is known to include proteins that function as transporters for various hydrophobic substrates across the outer membrane of Gram-negative bacteria.
Protein-lysine N-methyltransferase (Lysine_N-MTase)
Type: Family

This family of proteins includes enzymes that function as protein-lysine N-methyltransferases. They are involved in the post-translational modification of lysine residues in target proteins by transferring methyl groups from S-adenosyl-L-methionine (SAM) to the amino group of lysine side chains. These modifications can affect the function, interaction, or localization of the target proteins. Members of this family exhibit broad substrate specificity and can methylate various proteins, including chromatin-associated proteins and other cellular substrates, often in a sequence-independent manner.
SbcD nuclease (SbcD_nuclease)
Type: Family

This family of proteins is involved in DNA repair and recombination processes. Members of this family are characterized by their ability to cleave DNA hairpin structures, which can pose obstacles to DNA replication and are formed as intermediates during DNA recombination events. The proteins exhibit a 3'->5' double-strand exonuclease activity, enabling them to unwind and process hairpin structures. Additionally, they possess a 5' single-strand endonuclease activity, which contributes to their role in maintaining genomic stability by resolving problematic DNA structures.
Mandelate racemase/muconate lactonizing enzyme-like (MR_MLE-like)
Type: Family

This family of proteins is involved in the epimerization of specific dipeptides, which is a type of isomerization where the stereochemistry of an amino acid within a peptide is altered. Members of this family are capable of catalyzing the conversion of L-Ala-D-Glu to L-Ala-L-Glu, a reaction that is likely important in the metabolism of murein peptides, components of bacterial cell walls. Additionally, these enzymes can perform the reverse reaction and are able to epimerize a variety of dipeptides, showing the highest efficiency with substrates such as L-Ala-D/L-Phe, L-Ala-D/L-Tyr, and L-Ala-D/L-His. Their broad substrate range suggests a versatile role in cellular metabolism, potentially including the modification of signaling peptides or the degradation of misfolded proteins.
CRISPR-associated Cas12b endonuclease (Cas12b_endonuclease)
Type: Family

This family of proteins is involved in the CRISPR adaptive immune system, which provides defense against mobile genetic elements such as viruses and plasmids. Members of this family function as endonucleases that cleave double-stranded DNA complementary to CRISPR RNA (crRNA) sequences. These proteins require a crRNA, which is derived from CRISPR clusters, and a trans-encoded small RNA (tracrRNA) for activity. The crRNA-tracrRNA complex guides the protein to the target DNA, which is then endonucleolytically cleaved, resulting in staggered DNA breaks with short overhangs. These proteins also recognize a short motif adjacent to the target sequence, known as the protospacer adjacent motif (PAM), which is crucial for distinguishing between self and non-self DNA and is necessary for catalytic activity.
F(420)H(2) dehydrogenase complex subunit I (F420H2_dehydrogenase_I)
Type: Family

This family of proteins is involved in the energy-conserving processes of methylotrophic methanogens, particularly during growth on methanol or methylamines. Members of this family are components of the F(420)H(2) dehydrogenase complex, which is crucial for the oxidation of methanophenazine to dihydromethanophenazine. They facilitate the transfer of electrons from reduced coenzyme F(420) to methanophenazine, through FAD and iron-sulfur centers. This action is coupled with proton translocation across the cytoplasmic membrane, thereby conserving the energy of redox reactions in the form of a proton gradient. Additionally, these proteins can oxidize F(420)H(2) with various quinones, playing a significant role in the membrane-bound electron transfer system.
Lignin-Degrading GST-like Enzyme (Lignin-Degrading_GST-like)
Type: Family

This family of proteins includes enzymes that are capable of degrading lignin-derived compounds. Specifically, they perform a reductive cleavage of arylglycerol-beta-aryl ether linkages, which are prevalent in lignin. These enzymes are part of the glutathione S-transferase (GST) superfamily, which is known for its role in detoxification processes by conjugating glutathione to a wide range of substrates, facilitating their solubility and excretion. The activity of these proteins is important in the biological breakdown and utilization of lignin, which is a major component of plant biomass and a potential source of renewable chemicals and fuels.
Complex I 30 kDa subunit-like (Complex_I_30kDa_subunit-like)
Type: Family

This family of proteins includes components of the F(420)H(2) dehydrogenase complex, which is integral to the energy-conserving systems in methylotrophic methanogens. These proteins are involved in the oxidation of reduced coenzyme F(420)H(2), transferring electrons through FAD and iron-sulfur centers to methanophenazine, an electron carrier within the membrane. This process is coupled with the translocation of protons across the cytoplasmic membrane, thereby conserving the energy of the redox reaction in the form of a proton gradient. Additionally, these proteins can oxidize F(420)H(2) with various quinones, playing a crucial role in the metabolism of organisms that utilize methanol or methylamines.
Complex I subunit 6-like (Complex_I_subunit_6-like)
Type: Family

This family of proteins includes components of the F(420)H(2) dehydrogenase complex, which is crucial for the energy metabolism in certain methanogenic archaea. These proteins are involved in the oxidation of reduced coenzyme F(420)H(2) and transfer electrons to methanophenazine, a membrane electron carrier. They contain FAD and iron-sulfur (Fe-S) centers that facilitate this electron transfer. The process is coupled with proton translocation across the cytoplasmic membrane, contributing to the creation of a proton gradient that is used for energy conservation. Additionally, these proteins can oxidize F(420)H(2) with various quinones, indicating a broader role in electron transfer processes.
Succinate dehydrogenase/fumarate reductase iron-sulfur subunit (SDH/FR_iron-sulfur_subunit)
Type: Family

This family of proteins includes iron-sulfur subunits of enzymes like 8-methylmenaquinol:fumarate reductase (MFR), which are involved in the anaerobic metabolism. These proteins catalyze the reduction of fumarate to succinate, using electron donors such as 8-methylmenaquinol-6. Despite being related to succinate dehydrogenase/fumarate reductase iron-sulfur proteins, members of this family specifically lack succinate oxidation activity. Their role is crucial in the electron transport chain, particularly under anaerobic conditions where alternative electron acceptors are utilized.
Sensor Histidine Kinase MalK-like (Histidine_kinase_MalK-like)
Type: Family

This family of proteins includes sensor histidine kinases like MalK, which are part of two-component regulatory systems. They are involved in the response to specific environmental stimuli, such as the presence of malate. These proteins typically function by activating response regulators, such as MalR, through phosphorylation. This activation can lead to the regulation of genes associated with metabolic processes, exemplified by the activation of genes like maeA, maeN, and yflS. The phosphorylation event is a key step in signal transduction, allowing the cell to adapt to varying environmental conditions.
F(420)H(2) dehydrogenase complex component (F420H2_dehydrogenase_comp)
Type: Family

This family of proteins includes components of the F(420)H(2) dehydrogenase complex, which is crucial for the energy metabolism in certain methanogenic archaea. Members are involved in the oxidation of reduced coenzyme F(420)H(2) to its oxidized form, transferring electrons to methanophenazine or other quinones. This process is coupled with the translocation of protons across the cytoplasmic membrane, thereby generating a proton gradient that can be harnessed for energy production. The protein family contains FAD and iron-sulfur (Fe-S) centers that play a role in the electron transfer mechanism.
Glycogen_Phosphorylase (Glycogen_Phosphorylase)
Type: Family

This family of proteins includes allosteric enzymes involved in carbohydrate metabolism. Members catalyze the phospholytic cleavage of maltodextrins to produce glucose-1-phosphate. They exhibit a preference for maltodextrins with a minimum of five glucose residues, while showing lower activity with shorter chains and no activity with disaccharides like maltose. These enzymes do not effectively process very long maltodextrins, amylose, or starch compared to maltoheptaose. Their role is crucial in the mobilization of glucose units from polysaccharides for energy production and metabolic processes.
ADP-dependent Ribose-1-phosphate Kinase (ADP-R1P_Kinase)
Type: Family

This family of proteins is involved in the metabolic pathway of nucleoside degradation. Members of this family are enzymes that catalyze the phosphorylation of ribose 1-phosphate to ribose 1,5-bisphosphate using ADP as the primary phosphate donor. They are also capable of phosphorylating deoxyribose 1-phosphate, albeit with lower activity compared to ribose 1-phosphate. The enzymes exhibit a preference for ADP, but can also utilize GDP and UDP as phosphate donors. These proteins are characterized by their similarity to the PfkB family of carbohydrate kinases, which are known for their role in various carbohydrate metabolism processes.
Aliphatic Nitrilase (Aliphatic_Nitrilase)
Type: Family

This family of proteins includes enzymes that exhibit nitrilase activity, catalyzing the hydrolysis of aliphatic nitriles into corresponding monoacid mononitriles. They are regioselective, preferring substrates such as malononitrile and fumaronitrile, and do not act on nitriles bound to aromatic rings or amino acids. The biological role of these enzymes is not clearly defined. Their enzymatic activity is subject to inhibition by various substances, including acetone, methanol, and certain metal ions, as well as thiol reagents, but is not affected by EDTA. They are part of the carbon-nitrogen hydrolase superfamily.
SMC SbcC-like nuclease (SMC_SbcC-like_nuclease)
Type: Family

This family of proteins is involved in DNA repair and maintenance. Members of this family function to resolve DNA hairpin structures that can pose a barrier to DNA replication and recombination processes. They exhibit a 3'->5' double-strand exonuclease activity that enables them to unwind and cleave these hairpins. Additionally, they possess a 5' single-strand endonuclease activity, further contributing to their role in maintaining genomic stability by processing various DNA structures that arise during cellular metabolism.
PCNA-interacting regulator (PCNA-interact_regulator)
Type: Family

This family of proteins interacts with the DNA polymerase sliding clamp, known as proliferating cell nuclear antigen (PCNA), and is involved in the regulation of DNA replication and repair processes. Members of this family are capable of binding to PCNA and disrupting its trimeric ring structure. This action results in the inhibition of PCNA-dependent DNA synthesis and repair activities, including those mediated by DNA polymerase PolB and flap endonuclease 1 (FEN-1). The regulatory function of these proteins is crucial for maintaining genomic integrity by controlling the activity of key enzymes during the cell cycle.
GHMP Kinase PoK-Type (GHMP_kinase_PoK-type)
Type: Family

This family of proteins is involved in the biosynthesis of coenzyme A (CoA), a fundamental molecule for various biochemical reactions. Members of this family catalyze the phosphorylation of (R)-pantoate, converting it into (R)-4-phosphopantoate, which is a critical step in the CoA biosynthesis pathway. These enzymes exhibit a broad nucleotide specificity, being capable of using ATP, GTP, UTP, and CTP with similar efficiency. The enzymatic activity is known to be moderately enhanced by the presence of potassium ions, while it is inhibited by high concentrations of pantoate. CoA or acetyl-CoA does not influence the activity of these enzymes. They are characterized by their membership in the GHMP kinase superfamily, specifically within the PoK subfamily.
Glyceraldehyde-3-phosphate:ferredoxin oxidoreductase (GAPOR)
Type: Family

This family of proteins includes glycolytic enzymes that substitute for both glyceraldehyde-3-phosphate dehydrogenase and phosphoglycerate kinase in the glycolysis pathway. They are involved in anabolic gluconeogenesis, a metabolic pathway that results in the generation of glucose from non-carbohydrate carbon substrates. Members of this family are regulated by various compounds, with activity being modulated positively or negatively by specific metabolites and conditions. They are sensitive to oxygen and their activity is influenced by the presence of different ions and molecules, suggesting a role in cellular energy metabolism under varying environmental conditions.
tRNA N1-methyltransferase (tRNA_N1-methyltransferase)
Type: Family

This family of proteins includes enzymes that function as tRNA methyltransferases. Members of this family are responsible for the methylation of guanine(9) and adenine(9) at the N1 position in tRNA molecules. They utilize S-adenosyl-L-methionine as the methyl donor for this modification. The methylation of nucleotides at this position is crucial for the stability and function of tRNA, impacting its overall structure and interaction with other molecules during protein synthesis. The enzymatic activity of these proteins is essential for the proper decoding of genetic information and the fidelity of protein translation.