SII-SWORD/CoKE huggingface dataset:
Metalloprotease Desampylase (Metalloprotease_DSAMP)
Type: Family

This family of proteins includes metalloproteases with a specific desampylase activity, which involves the cleavage of ubiquitin-like small archaeal modifier proteins (SAMPs) from their protein conjugates. These proteins are responsible for regulating the process of sampylation, controlling the availability of 'free' SAMPs for further protein modification. The activity of these enzymes is characterized by their specificity, as they do not act on a broad range of unmodified proteins. Their function is crucial for maintaining cellular processes that rely on protein modification by SAMPs. They are sensitive to inhibition by agents such as EDTA and N-ethylmaleimide.
Menaquinone reductase iron-sulfur cluster-binding subunit (Menaquinone_reductase_QrcC)
Type: Family

This family of proteins is involved in the electron transfer process within the respiratory Qrc complex, which is responsible for the reduction of menaquinone. These proteins are crucial for the utilization of electrons from reduced periplasmic cytochrome c3 during sulfate respiration. They play a key role in energy metabolism, especially when the organism grows on hydrogen or formate, as they interact with periplasmic hydrogenases or formate dehydrogenases. The family includes subunits that contain iron-sulfur clusters, facilitating electron transfer to the membrane quinone pool.
Glucosyl-dolichyl phosphate glucuronosyltransferase (GDP_glucuronosyltransferase)
Type: Family

This family of proteins is involved in the N-glycosylation pathway, which is essential for the proper folding and function of many proteins. Members of this family function as enzymes that catalyze the addition of a glucuronate residue to a glucose residue already linked to dolichol phosphate. Dolichol phosphate acts as a lipid carrier for glycans in Archaea. The enzyme activity contributes to the assembly of an N-linked pentasaccharide, which is a component of the glycan coat found on surface-layer glycoproteins and flagellins. The family is characterized by its glycosyltransferase activity, specifically transferring glucuronate to a glycosylated dolichol phosphate.
Glyceraldehyde dehydrogenase-related (Glyceraldehyde_dh-related)
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 to produce glycerate. These enzymes exhibit a broad substrate range when using artificial electron acceptors, such as 2,6-dichlorophenol-indophenol, and can act on various aldehydes including glyceraldehyde-3-phosphate, formaldehyde, acetaldehyde, propionaldehyde, and isobutyraldehyde. The preferred in vivo electron acceptor for these enzymes is not clearly established. They are related to the xanthine dehydrogenase enzyme family, suggesting a potential for catalytic versatility and involvement in various metabolic processes.
Type II topoisomerase GyrA/ParC (Topoisomerase_II_GyrA/ParC)
Type: Family

This family of proteins includes type II topoisomerases, specifically the GyrA/ParC subunit, which are essential enzymes that modify the topology of double-stranded DNA. These proteins are involved in introducing negative supercoils into DNA, which is crucial for various cellular processes such as replication, transcription, recombination, and repair, as these processes require the DNA strands to be separated. They function by breaking and rejoining DNA strands in an ATP-dependent manner, allowing for the interconversion of DNA topological isomers, including catenanes and knotted rings. The activity of these enzymes can be inhibited by certain fluoroquinolone antibiotics.
Glycosyl hydrolase 13 alpha-amylase (GH13_alpha-amylase)
Type: Family

This family of proteins includes alpha-amylases that are involved in the initial stages of starch degradation. They function as endo-acting enzymes, preferentially hydrolyzing linear polysaccharides over branched ones by cleaving alpha-1,4 glucosidic bonds. Members of this family exhibit transglycosylation activity and are characterized by their ability to remain stable and active across a wide range of salt concentrations. They show varying degrees of activity against different substrates such as amylose, soluble starch, amylopectin, and glycogen, with no significant activity against cyclodextrins.
Molybdopterin-binding Qrc complex component (Molybdopterin-Qrc_component)
Type: Family

This family of proteins includes components of the respiratory Qrc complex, which is involved in the reduction of the menaquinone pool using electrons from reduced periplasmic cytochrome c3. These proteins are likely crucial for growth on H(2) or formate as they interact with periplasmic hydrogenases and/or formate dehydrogenases, which serve as primary electron donors to the Qrc complex. Although the specific role of these proteins within the complex is not well-defined, they are thought to provide structural support for the assembly and proper function of other subunits.
Type IV secretion system Dot/Icm subcomplex protein (T4SS_Dot/Icm_subcomplex)
Type: Family

This family of proteins is involved in a type IVB secretion system (T4BSS), specifically the Dot/Icm system, which is essential for the delivery of bacterial effector proteins into host eukaryotic cells. Members of this family form part of a subcomplex that is responsible for the recruitment and delivery of these effector proteins to the core transmembrane components of the T4BSS, facilitating the bacterial infection process.
Polyferredoxin (Polyferredoxin)
Type: Family

This family of proteins includes polyferredoxins such as FwdF, which are involved in electron transfer processes. Polyferredoxins typically contain iron-sulfur clusters that facilitate their role in redox reactions. These proteins are often associated with metabolic pathways, particularly those related to the energy conversion in organisms. They can act as electron carriers, transferring electrons between different proteins or molecular complexes within a cell. The specific function of FwdF suggests a role in methanogenic archaea, where it may participate in the reduction of coenzyme F420, an essential step in the methanogenesis pathway. The precise mechanism and the full scope of interactions and reactions that FwdF is involved in may vary and are subject to further research.
Hyi sugar epimerase/isomerase (Hyi_epimerase/isomerase)
Type: Family

This family of proteins includes enzymes that are involved in the reversible epimerization of various sugars, playing a role in myo-inositol degradation pathways. They are capable of catalyzing the C3-epimerization of L-ribulose to L-xylulose, D-ribulose to D-xylulose, D-psicose to D-fructose, and D-tagatose to D-sorbose, preferring ketopentoses over ketohexoses. Additionally, they can perform aldose-ketose isomerization from D-erythrose or D-threose to D-erythrulose. These enzymes are characterized by a broad substrate specificity and are known to be inhibited by EDTA. They do not exhibit activity for C4-epimerization of D-tagatose to D-fructose.
UDP-N-acetylglucosamine 3-dehydrogenase (UDP-GlcNAc_3-dehydrogenase)
Type: Family

This family of proteins includes enzymes that are involved in the NAD(+)-dependent oxidation of UDP-N-acetylglucosamine (UDP-GlcNAc). They exhibit a high degree of substrate specificity, as they do not act on similar compounds such as UDP-glucose, UDP-N-acetylgalactosamine, N-acetylglucosamine, or glucosamine. The enzymatic activity of these proteins can be modulated by the presence of certain nucleotide sugars, with UDP and its derivatives being capable of reducing the oxidoreductase activity. These proteins do not require metal ions for their activity, indicating that they rely on different cofactors or intrinsic structural elements for their function.
3-Hydroxyacyl-CoA Dehydrogenase-like (3-Hydroxyacyl-CoA_DH-like)
Type: Family

This family of proteins is involved in the metabolic breakdown of vitamin B(6), specifically in the degradation pathway of pyridoxine. Members of this family function as enzymes that catalyze the oxidation of a specific intermediate compound in the pathway, using NAD(+) as an electron acceptor to produce a distinct oxidized product. Additionally, these enzymes have the capability to catalyze the reverse reaction, reducing the same intermediate by utilizing NADH as an electron donor to produce a reduced form of vitamin B(6). The enzymatic activity of these proteins is crucial for maintaining the proper levels of vitamin B(6) derivatives, which are important for various cellular functions.
Glycerol-responsive transcriptional regulator (Glycerol_resp_trans_regulator)
Type: Family

This family of proteins includes transcriptional regulators that function as repressors for genes involved in fructose and glucose metabolism. They are particularly active during growth on glycerol, inhibiting the expression of enzymes such as phosphofructokinase and 2-keto-3-deoxy-D-gluconate kinase. These proteins play a crucial role in the regulation of metabolic pathways by modulating the transcription of specific genes based on the available carbon source, ensuring optimal energy utilization and metabolic efficiency.
Sensor kinase FixL-like (Sensor_kinase_FixL-like)
Type: Family

This family of proteins includes sensor proteins like FixL, which are involved in the regulation of kinase activity through a heme moiety. Members of this family function as putative oxygen sensors and play a role in modulating the activity of transcriptional activators involved in nitrogen fixation genes. They likely possess kinase activity that is responsible for phosphorylating other proteins such as FixJ, which is crucial for the transcriptional activation of genes like fixK that are essential for nitrogen fixation processes.
Glycosyl Hydrolase 78 (GH78)
Type: Family

This family of proteins includes enzymes with alpha-L-rhamnosidase activity, capable of hydrolyzing alpha-L-rhamnopyranoside linkages. They play a role in the degradation of complex molecules, such as citrus flavonoids and arabinogalactan-proteins, releasing L-rhamnose. These enzymes are characterized by a carbohydrate-binding module that specifically recognizes L-rhamnose, a specificity influenced by the stereochemistry of the sugar and dependent on the presence of calcium for ligand binding.
4'-Phosphopantetheinyl Transferase (P-Pant_transferase)
Type: Family

This family of proteins includes enzymes that are responsible for the post-translational modification of certain proteins by attaching a 4'-phosphopantetheine moiety from coenzyme A to a serine residue. This modification is crucial for converting apo-proteins to their active holo-forms, particularly in the activation of acyl-carrier proteins involved in fatty acid and polyketide synthesis. Members of this family are characterized by their role in the activation of carboxylic acid reductase and potentially other proteins that require phosphopantetheine for their function.
Cytochrome c-550-like (Cytochrome_c-550-like)
Type: Family

This family of proteins is involved in the respiratory process of bacteria, particularly under oxygen-limited conditions. They are essential for the transfer of electrons during the process of denitrification, which is a part of the nitrogen cycle where nitrate is reduced and ultimately produces nitrogen gas under anaerobic conditions. These proteins contribute to the energy metabolism of bacteria by participating in the electron transport chain, which is crucial for the survival of bacteria in environments where oxygen is scarce.
F(420)H(2) dehydrogenase complex subunit (F420H2_dehydrogenase_subunit)
Type: Family

This family of proteins is involved in the energy-conserving process of methylotrophic methanogens, particularly when they metabolize methanol or methylamines. Members of this family function as components of the F(420)H(2) dehydrogenase complex, which is crucial for the oxidation of methanophenazine to dihydromethanophenazine. These proteins facilitate the transfer of electrons from reduced coenzyme F(420) to methanophenazine, through FAD and iron-sulfur centers. This electron transfer is coupled with the translocation of protons across the cytoplasmic membrane, thereby conserving energy in the form of a proton gradient. Additionally, these proteins can oxidize F(420)H(2) with various quinones, contributing to the broader metabolic network within these archaeal organisms.
Tungstate uptake ABC transporter ATPase (Tungstate_ABC_transporter)
Type: Family

This family of proteins is involved in the transport of tungstate across cellular membranes. Members of this family are part of an ABC transporter complex, which is characterized by its high affinity for tungstate, an oxyanion of tungsten. These proteins are likely to play a crucial role in the energy-dependent uptake of tungstate, utilizing ATP hydrolysis to translocate the substrate across the membrane. The family is a member of the larger ABC transporter superfamily, which is known for its diverse functions in transporting a variety of substrates across membranes in all forms of life.
Small Heat Shock Protein (HSP20) (sHSP/HSP20)
Type: Family

This family of proteins includes molecular chaperones that are likely involved in preventing the aggregation of misfolded proteins under stress conditions, such as elevated temperatures. Members of this family are characterized by their small molecular weight and are part of the small heat shock protein (HSP20) group. They are thought to maintain protein homeostasis and protect cells during stress by binding to and stabilizing unfolded or partially folded proteins, thereby facilitating proper folding or refolding.
Heterodisulfide Reductase Subunit B (HdrB)
Type: Family

This family of proteins is involved in the energy metabolism process of methanogenic archaea, specifically in the reversible reduction of heterodisulfide compounds. The proteins function as part of a complex that facilitates the conversion of CoM-S-S-CoB into its thiol-coenzyme forms, H-S-CoM and H-S-CoB, which are essential for the methanogenesis pathway. The activity of these proteins is crucial for organisms that rely on methylotrophic methanogenesis, a process where methane is produced from methylated substrates. However, they are not implicated in aceticlastic methanogenesis, where methane is generated from acetate.
Membrane-stabilizing protein A (MspA)
Type: Family

This family of proteins is involved in a variety of cellular processes including the production of toxins, defense against host immune responses, and the regulation of iron within the organism. Members of this family are characterized by their role in membrane stabilization, which is crucial for maintaining the integrity and functionality of cellular membranes under various conditions.
Major Facilitator Superfamily Drug Efflux Pump (MFS_Drug_Efflux_Pump)
Type: Family

This family of proteins includes members that function as energy-dependent efflux pumps. They are involved in the active transport of various antimicrobial agents out of the cell, thereby contributing to increased resistance against certain drugs. These proteins are part of the major facilitator superfamily, which is characterized by facilitating the movement of small solutes across cellular membranes in response to chemiosmotic gradients.
Cytoplasmic Filament Component (Cyto_Filament_Comp)
Type: Family

This family of proteins includes components of cytoplasmic filaments that are situated just beneath the cytoplasmic membrane, extending along the length of the cell. These proteins play a structural role in maintaining cellular integrity and potentially participate in intracellular transport processes.
Retron Ec78 HNH endonuclease (Retron_Ec78_HNH_endo)
Type: Family

This family of proteins includes putative HNH endonucleases that are part of an antiviral defense system known as retron Ec78. The system is composed of a non-coding RNA, a reverse transcriptase, a probable ATPase, and the HNH endonuclease. These proteins are implicated in providing protection against bacteriophage infections, specifically bacteriophage T5. When expressed, they enable bacterial cultures to endure and survive phage attacks by slowing down growth or entering a state of growth stasis, depending on the intensity of the infection. The mechanism by which this protection is conferred is not fully described but is likely related to the endonuclease activity of the HNH protein component.
Ribonuclease HI-like (RNase_HI-like)
Type: Family

This family of proteins includes nucleases that specialize in degrading the RNA component of RNA-DNA hybrids. They play a crucial role in DNA replication by endonucleolytically removing RNA primers from Okazaki fragments on the lagging strand. These enzymes can function independently but also exhibit activity in the presence of divalent metal ions such as manganese or cobalt, where they can cleave RNA-RNA hybrids, albeit with significantly lower efficiency compared to their primary RNase H activity. They are essential for maintaining genomic stability and can rescue certain bacterial mutants deficient in RNase H function.
Trans-sulfuration enzyme (Trans-sulfuration_enzyme)
Type: Family

This family of proteins includes enzymes that are involved in the trans-sulfuration pathway, which is crucial for the metabolism of sulfur-containing amino acids. Members of this family catalyze the cleavage of cystathionine to produce homocysteine, a reaction that is central to the conversion of methionine to cysteine. Additionally, these enzymes possess the ability to carry out secondary reactions, such as the transformation of cystathionine to methionine and the conversion of methionine to methanethiol, albeit with lower efficiency. The enzymatic activity of these proteins is subject to regulation by various compounds, including some that are found in sweat, as well as by the substrate cystathionine at higher concentrations.
UDP-sulfoquinovose synthase (UDP-sulfoquinovose_synthase)
Type: Family

This family of proteins includes enzymes that are involved in the biosynthesis of UDP-sulfoquinovose, which is a crucial component for the assembly of the S-layer N-glycans in certain organisms. Members of this family function by transferring sulfite to UDP-glucose, a process that is likely facilitated by NAD(+)-dependent oxidation, dehydration, enolization, and sulfite addition. In the absence of sulfite, these enzymes can also convert UDP-D-glucose to UDP-D-glucose-5,6-ene through an intermediate UDP-4-keto-D-glucose. This enzymatic activity is part of a metabolic pathway that contributes to the synthesis of sulfolipids, which are important for various cellular functions including the integrity of the cell membrane.
3-Hydroxypropionate/Butyrate CoA Ligase (3HP/4HB_CoA_Ligase)
Type: Family

This family of proteins is involved in a modified autotrophic carbon fixation pathway known as the hydroxypropionate/hydroxybutyrate (HP/HB) cycle, which is characteristic of certain archaeal organisms. Members of this family function as enzymes that catalyze the ATP-dependent ligation of CoA to various organic acids, including 3-hydroxypropionate and 4-hydroxybutyrate, although they exhibit a preference for the former. The enzymatic reaction results in the production of the corresponding acyl-CoA derivatives, ADP, and phosphate. Despite being able to process a range of substrates, these enzymes are most efficient with 3-hydroxypropionate. Structurally, the proteins in this family are composed of two distinct sections, each showing similarity to different subunits of acetate CoA ligases, suggesting a bifunctional role.
4-hydroxybutyrate--CoA ligase [ADP-forming] (4-HB-CoA_ligase_ADP-forming)
Type: Family

This family of proteins is involved in a modified autotrophic hydroxypropionate/hydroxybutyrate cycle, which is central to the metabolism of certain archaeal organisms. Members of this family are enzymes that catalyze the ATP-dependent ligation of 4-hydroxybutyrate with coenzyme A to form 4-hydroxybutyryl-CoA, releasing ADP and phosphate in the process. Although they exhibit optimal activity with 4-hydroxybutyrate, these enzymes can also act on other short-chain carboxylic acids such as acetate, propionate, and butyrate, albeit with lower efficiency. The family includes proteins with two distinct regions that are homologous to the alpha and beta subunits of acetate CoA ligases, indicating a bifunctional nature and a possible evolutionary relationship with these ligases.
4'-Phosphopantetheinyl Transferase HetI-like (P-Pant_Transferase_HetI-like)
Type: Family

This family of proteins is involved in the activation of acyl carrier protein (ACP) domains within certain biosynthetic enzymes. Members of this family are responsible for the post-translational modification of ACP domains by transferring the 4'-phosphopantetheinyl moiety from coenzyme A to a serine residue on the ACP. This modification is crucial for the activation of ACP domains, which are essential for the synthesis of various biomolecules. The activity of these proteins is important for maintaining vegetative growth in certain organisms and may interact with regulatory pathways to inhibit differentiation processes.
Homoaconitase small subunit LeuD type 2 (Homoaconitase_LeuD_type2)
Type: Family

This family of proteins includes hydro-lyases with a broad substrate specificity, acting on cis-unsaturated tricarboxylic acids. They are capable of catalyzing the reversible dehydration of (R)-homocitrate to cis-homoaconitate, as well as the hydration of cis-homoaconitate to homoisocitrate. Additionally, they can hydrate longer chain substrates such as cis-homo(2)-aconitate and cis-homo(3)-aconitate. These enzymatic activities are integral to the biosynthesis pathway of coenzyme B, which is essential for various metabolic processes.
ROK family beta-glucoside kinase (ROK_beta-glucoside_kinase)
Type: Family

This family of proteins is involved in the ATP-dependent phosphorylation of various beta-D-glucosides, resulting in the formation of 6-phospho-beta-D-glucosides. Members of this family are capable of processing substrates such as cellobiose, gentiobiose, cellobiitol, salicin, and arbutin, but they do not act on alpha-D-glucosides. The enzymatic activity suggests a role in carbohydrate metabolism, possibly in the utilization of specific sugars as a carbon source. Additionally, these proteins may function in the regulation of gene expression, specifically in the transcriptional control of operons associated with carbohydrate uptake and metabolism. They are subject to inhibition by certain chemicals, although ATP can mitigate this inhibition.
RecJ exonuclease (RecJ_exonuclease)
Type: Family

This family of proteins includes single-stranded-DNA-specific exonucleases, which are enzymes that catalyze the removal of nucleotides from the ends of single-stranded DNA (ssDNA). These proteins play a crucial role in DNA repair and maintenance by processing ssDNA regions that can arise during DNA replication, recombination, and repair processes. The precise function may vary among family members, but typically involves the hydrolysis of DNA to remove potentially deleterious or mismatched nucleotides, thereby contributing to the fidelity of DNA replication and the overall genomic stability of the cell.
3-beta-Hydroxysteroid Dehydrogenase-like (3-beta-HSD-like)
Type: Family

This family of proteins is involved in the biosynthesis of olefins, a class of hydrocarbons. Members of this family function as enzymes that catalyze the NADPH-dependent reduction of 2-alkyl-3-oxoalkanoic acids to their corresponding 2-alkyl-3-hydroxyalkanoic acids. This reaction is reversible and stereospecific. The enzymatic activity is crucial for the production of certain olefins, such as 3,6,9,12,15,19,22,25,28-hentriacontanonaene, which may play a role in cellular adaptation to environmental changes, such as temperature fluctuations.