SII-SWORD/CoKE huggingface dataset:
Exo-beta-D-glucosaminidase (GLMA)
Type: Family

This family of proteins includes exo-beta-D-glucosaminidase GLMA from archaea which is involved in the degradation of chitin, a natural polysaccharide. Members of this family are capable of cleaving the non-reducing terminal glycosidic bond of chitooligosaccharides, thereby catalysing the hydrolysis of specific substrates to produce glucosamine and N-acetylglucosamine. These enzymes are also able to act on chitosan and various lengths of chitooligosaccharides, playing a crucial role in the biological process of chitin breakdown .
Magnetite Biomineralization Domain-Containing Protein (Magnetite_Biomin-Domain)
Type: Family

This family of proteins is involved in the biomineralization process of magnetite, a type of iron oxide. Members of this family promote the formation of magnetite under iron-rich conditions where magnetite does not form easily. They have the ability to bind both ferrous (Fe(2+)) and ferric (Fe(3+)) ions. These proteins are thought to influence the morphology of magnetite crystals and may work in conjunction with other proteins to regulate magnetosome size and number. A key feature of these proteins is a C-terminal domain that can self-assemble into multimers and bind iron, which may alter the protein's structure. Although they bind iron, their direct role in magnetite crystal formation in vitro can vary, with some studies suggesting they do not affect crystal formation, while others indicate a role in nucleation and controlling crystal size.
Cytochrome P450 119-like (CYP450_119-like)
Type: Family

This family of proteins includes enzymes that are part of the cytochrome P450 superfamily, which are involved in the metabolism of a wide range of substrates through oxidation reactions. Members of this family have not been characterized with a specific endogenous substrate but are known to catalyze various oxidation reactions in vitro. These reactions include the epoxidation of styrene and related compounds, as well as the hydroxylation of fatty acids. They can utilize different electron acceptors such as hydrogen peroxide, cumene hydroperoxide, or tert-butyl hydroperoxide for these oxidation processes.
Sulfomuconolactone Hydrolase (SML-Hydrolase)
Type: Family

This family of proteins is involved in the bacterial degradation pathway of sulfonated aromatic compounds, specifically in the breakdown of 4-sulfocatechol, a key intermediate in this process. Members of this family perform a hydrolytic desulfonation reaction, converting 4-sulfomuconolactone into maleylacetate. This reaction is a critical step in the biodegradation of various sulfonated pollutants, contributing to the detoxification and carbon recycling in the environment. These enzymes are part of the metallo-dependent hydrolases superfamily and are characterized by their dependence on metal ions for activity, although they are known to be inhibited by certain metal chlorides such as zinc and copper.
Transposase_Tn903 (Transposase_Tn903)
Type: Family

This family of proteins includes enzymes that are essential for the mobilization of transposon Tn903. Members of this family are responsible for catalyzing the movement of the transposon from one location in the genome to another, a process known as transposition. The activity of these proteins is crucial for the propagation of the transposon within the host genome, which can lead to genetic variation and the potential for adaptation and evolution. The proteins typically possess DNA-binding and endonuclease activities that facilitate the cutting and rejoining of DNA strands during the transposition event.
Microcin J25-processing enzyme (McjB-like)
Type: Family

This family of proteins includes enzymes that are involved in the post-translational modification of peptide antibiotics, specifically the microcin J25. Members of this family work in conjunction with other proteins to convert inactive precursor peptides into their active forms, which exhibit antimicrobial activity. These proteins play a crucial role in the biosynthesis of microcin J25, a peptide antibiotic produced by certain strains of Escherichia coli, by processing the precursor peptide McjA into its mature, bioactive form.
RNA-guided DNA endonuclease TnpB-like (RNA-guided_endonuclease_TnpB)
Type: Family

This family of proteins includes RNA-guided DNA endonucleases that are part of insertion sequence elements. They are characterized by a C-terminal domain related to the transposase 35 family and an N-terminal domain associated with the transposase 2 family. These endonucleases are guided by small RNAs derived from the right-end element of their insertion sequence to cleave DNA at specific sites downstream of a transposon-associated motif. The cleavage occurs in a staggered manner, producing 5'-overhangs. These proteins also bind to a specific RNA molecule that is approximately 150 nucleotides in length, which includes sequences from the 3' end of their gene, the right end of the insertion sequence, and adjacent downstream sequences. They may play a role in homology-directed repair by cleaving at the donor joint to restore the integrity of the insertion sequence after excision. Additionally, they can inhibit the transposition activity of certain IS elements and are not required for the transposition of their own IS element.
Oligopeptide Permease AppC-like (Oligopeptide_permease_AppC)
Type: Family

This family of proteins is involved in the transport of oligopeptides across the cell membrane. They are part of a binding protein-dependent transport system, specifically adapted to recognize and translocate oligopeptides rather than tripeptides. These proteins play a crucial role in various cellular processes, including sporulation and genetic competence, by substituting for other peptide transport systems when necessary. Their primary function is to facilitate the movement of substrate molecules through the membrane, contributing to the cell's nutrient uptake mechanisms.
Aerial hyphae-associated peptide synthase (Aerial_hyphae_peptide-synth)
Type: Family

This family of proteins includes enzymes that are likely involved in the biosynthesis of small peptide molecules with roles in morphological development. Specifically, the family is associated with the synthesis of a molecule necessary for the formation of aerial hyphae in certain bacteria. Members of this family are thought to process a precursor molecule into its mature form, which is essential for the structural development that allows the organism to grow above the surface of its growth medium. The proteins in this family are part of the larger protein kinase superfamily, suggesting that they share evolutionary history and possibly mechanistic features with kinase enzymes, which are known for their role in transferring phosphate groups to various substrates.
Bacterial Sortase Class D (Sortase_D)
Type: Family

This family of proteins functions as transpeptidases that anchor surface proteins to the bacterial cell wall. They recognize and cleave a specific C-terminal sorting signal in their substrates, forming a covalent intermediate via a thioester bond. This intermediate is subsequently attached to the cell wall. Members of this family typically recognize a Leu-Pro-Asp-Thr-Ser/Ala motif and are involved in modifying proteins such as YhcR and YfkN. They are categorized under the bacterial sortase class D subfamily.
5-oxoprolinase catalytic subunit (5-oxoprolinase_subunit)
Type: Family

This family of proteins includes enzymes that are involved in the metabolic breakdown of 5-oxoproline, an intermediate in the gamma-glutamyl cycle. Members of this family function to catalyze the conversion of 5-oxoproline to L-glutamate, a process that is coupled with the hydrolysis of ATP to ADP and inorganic phosphate. This reaction is a key step in the pathway that recycles glutathione and contributes to the regulation of cellular redox balance and detoxification.
Tetrathionate-responsive sensor kinase (Tetrathionate_sensor_kinase)
Type: Family

This family of proteins includes sensor histidine kinases involved in two-component regulatory systems, specifically for the regulation of tetrathionate reductase synthesis. These proteins are typically autophosphorylated in response to environmental signals such as tetrathionate and subsequently transfer the phosphate group to a response regulator, facilitating adaptive responses. In certain bacteria, this signaling mechanism provides a competitive advantage in specific niches, such as the inflamed gut during infection, by enabling the utilization of tetrathionate as an electron acceptor.
Thiolase-like Beta-ketothiolase (Thiolase-like_BktB)
Type: Family

This family of proteins includes enzymes that are involved in the biosynthesis of polyhydroxyalkanoates, which are biodegradable polyesters. Members of this family function by catalyzing the Claisen condensation of acetyl-CoA with propionyl-CoA to produce beta-ketovaleryl-CoA, as well as the condensation of two molecules of acetyl-CoA to yield acetoacetyl-CoA. These reactions are crucial steps in the production of poly(beta-hydroxybutyrate-co-beta-hydroxyvalerate), a type of biopolymer with industrial and medical applications due to its biocompatibility and biodegradability.
Peptidase M23B (Peptidase_M23B)
Type: Family

This family of proteins includes peptidases that are part of the M23B subfamily. Members of this family are typically involved in the cleavage of peptide bonds in specific substrates. They may play a role in bacterial cell wall metabolism by cleaving the peptide cross-links between glycan chains, which is crucial for cell wall remodeling, maintenance, and during cell division. The enzymatic activity of these proteins is dependent on the presence of a zinc ion in the active site, which is characteristic of metallopeptidases. Proteins in this family may also be involved in defense mechanisms against competing bacteria or in the regulation of autolytic processes.
Bacterial ABC transporter arginine-binding (ABC_transporter_arg-binding)
Type: Family

This family of proteins includes components of the ABC transporter complex that are involved in the transport of arginine. Members of this family have a high affinity for binding L-arginine, a key amino acid in various metabolic processes. These proteins are integral to the proper functioning of the ABC transporter system, which is responsible for the uptake of essential nutrients and the export of various molecules across the cell membrane.
RCS-specific HTH-type transcriptional activator (RCS-HTH_transactivator)
Type: Family

This family of proteins includes transcriptional activators that respond to oxidative stress conditions. They are characterized by the presence of a helix-turn-helix (HTH) motif specific to the RCS system, which is involved in the regulation of their DNA-binding activity. The proteins in this family play a crucial role in the cellular defense against reactive chlorine species (RCS), particularly hypochlorous acid (HOCl). They regulate the expression of genes essential for RCS stress resistance, including their own gene, by undergoing a conformational change upon oxidation. This change is mediated by the formation of an intramolecular disulfide bond, which stabilizes the protein in its active form, thus enhancing its ability to upregulate target gene expression under stress conditions.
Reactive Chlorine Species Resistance Protein (RCS_Resistance)
Type: Family

This family of proteins is implicated in the cellular response to oxidative stress, specifically in the defense against reactive chlorine species (RCS). Members of this family are thought to play a role in the resistance mechanism that protects the cell from the damaging effects of RCS, which can include modifications to cellular components like DNA, proteins, and lipids. The precise molecular function and mechanism of action of these proteins in RCS stress resistance, however, remain to be fully elucidated.
HTH-type transcriptional regulator YgbI-like (HTH-type_regulator_YgbI-like)
Type: Family

This family of proteins includes transcriptional regulators that feature a helix-turn-helix (HTH) motif. The HTH motif is a common DNA-binding domain that enables the protein to interact with specific DNA sequences, typically in the promoter regions of genes, to regulate transcription. As transcriptional regulators, these proteins play crucial roles in controlling gene expression in response to various environmental and cellular signals. The precise function of the YgbI-like regulators remains to be characterized, but they are likely involved in the regulation of genes pertinent to bacterial physiology and stress responses.
Tetrathionate response regulator (Tetrathionate_resp_reg)
Type: Family

This family of proteins includes transcriptional regulators that are part of two-component systems, typically comprising a sensor kinase and a response regulator. Members of this family are involved in the regulation of operons responsible for the reduction of tetrathionate. They function as activators of gene transcription, positively influencing the expression of genes such as those in the ttrBCA operon. These proteins play a crucial role in the utilization of tetrathionate as an electron acceptor, which can confer a competitive advantage to certain bacteria within the inflamed gut during infection.
HTH-type transcriptional regulator Lrp (HTH_trans_regulator_Lrp)
Type: Family

This family of proteins includes transcriptional regulators characterized by a helix-turn-helix (HTH) motif. Members of this family are involved in the regulation of a variety of genes, which encode enzymes for amino acid synthesis, elements of central metabolism, and various transport systems. Additionally, they regulate other transcriptional regulators. These proteins can function as both activators and repressors of gene transcription, depending on the context and target genes involved.
Lasso peptide isopeptidase (Lasso_peptide_isopeptidase)
Type: Family

This family of proteins includes isopeptidases that specialize in the hydrolysis of lasso peptides, such as Astexin-2 and Astexin-3. These enzymes recognize and bind to the unique knotted structure of lasso peptides, particularly focusing on the loop structure. Upon binding, they facilitate the opening of the lasso peptides, making the isopeptide bonds accessible for cleavage and converting the cyclic peptides into linear forms. The interaction with substrates involves a limited number of specific contacts, highlighting a specialized recognition mechanism for the lasso peptide structure.
DNA-guanine Transglycosylase (DNA-guanine_TGase)
Type: Family

This family of proteins is involved in the modification of DNA by inserting 7-deazaguanine derivatives. Members of this family are implicated in the synthesis of modified nucleosides such as 7-cyano-7-deazaguanine (preQ0) and 2'-deoxy-7-cyano-7-deazaguanosine (dPreQ0) in DNA. These modifications are carried out through a transglycosylation reaction that requires the cooperative action of proteins within this family. The process is essential for the production of nucleosides with altered electronic properties, which can have various biological implications.
UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-L-glutamate epimerase (MurL_epimerase)
Type: Family

This family of proteins is involved in bacterial cell wall biosynthesis. Members of this family are responsible for the epimerization of the terminal L-glutamate residue in the precursor UDP-N-acetyl-alpha-D-muramoyl-L-alanyl-L-glutamate. This epimerization step is crucial for the proper assembly and structure of the peptidoglycan layer, which is a key component of the bacterial cell wall providing rigidity and protection. The activity of these enzymes is essential for maintaining cell shape and integrity during growth and division.
Scyllo-inosose Dehydrogenase (Scyllo-inosose_DH)
Type: Family

This family of proteins includes enzymes that are involved in the degradation pathway of myo-inositol. Members of this family are responsible for the NAD(+)-dependent oxidation of scyllo-inosose to 3-dehydro-scyllo-inosose. They play a crucial role in the catabolism of inositol compounds, which are important for various cellular processes. These enzymes are characterized by the presence of a zinc-binding motif, which is typical for the zinc-containing alcohol dehydrogenase superfamily. They exhibit specificity for scyllo-inosose and do not act on other inositol isomers such as myo-inositol, D-chiro-inositol, or 1-keto-D-chiro-inositol.
Bisanhydrobacterioruberin Hydratase (BABR_hydratase)
Type: Family

This family of proteins is involved in the biosynthesis of bacterioruberin, an acyclic C50 carotenoid. Members of this family function as enzymes that catalyze the introduction of hydroxyl groups at specific positions on the precursor molecule bisanhydrobacterioruberin, leading to the formation of bacterioruberin. The enzymatic activity is essential for the production of this carotenoid, which is known for its significance in the cellular processes of certain microorganisms.
Polyprenyl diphosphate synthase (Polyprenyl_diphosphate_synth)
Type: Family

This family of proteins is involved in the biosynthesis of polyprenyl diphosphates, which are key precursors for the synthesis of isoprenoids, a diverse class of biological molecules. Members of this family function as enzymes that catalyze the condensation of isopentenyl pyrophosphate (IPP) with allylic diphosphates such as geranyl diphosphate (GPP) and farnesyl diphosphate (FPP) to produce longer chain prenyl diphosphates. These reactions are critical for the production of various isoprenoids, including quinones and certain side chains of chlorophylls. The enzymes typically contain conserved aspartate-rich motifs that coordinate divalent magnesium ions, facilitating substrate binding and catalysis. They may also exhibit specificity in determining the chain length of the product.
Diadenylate Cyclase DacZ (Diadenylate_Cyclase_DacZ)
Type: Family

This family of proteins includes enzymes known as diadenylate cyclases, which are responsible for the synthesis of cyclic di-AMP (c-di-AMP) from ATP. Cyclic di-AMP acts as a second messenger in various cellular processes, including osmoregulation. Members of this family are crucial for the survival of certain organisms and play a role in regulating cell viability. The activity of these enzymes is tightly controlled, as imbalances in c-di-AMP levels can be detrimental to the cell. These proteins are characterized by their inability to utilize GTP as a substrate, distinguishing them from other nucleotide cyclases.
Bacterial Reverse Transcriptase (Bacterial_RT)
Type: Family

This family of proteins includes reverse transcriptases that are part of bacterial antiviral defense systems known as retrons. These enzymes are responsible for the synthesis of multicopy single-stranded DNA (msDNA), which is a branched molecule consisting of RNA linked to single-stranded DNA. The retron-encoded RNA serves as both primer and template for msDNA synthesis. Members of this family are characterized by an N-terminal reverse transcriptase domain and a C-terminal region essential for msDNA synthesis, which may possess nuclease activity. These proteins confer protection against specific bacteriophages and are capable of using various retron elements as substrates. They can also synthesize DNA from DNA templates in vitro, albeit with lower activity compared to RNA templates.
HMG-CoA Synthase-like (HMG-CoA_Synthase-like)
Type: Family

This family of proteins includes enzymes that are responsible for a key step in the mevalonate pathway, which is crucial for the biosynthesis of isoprenoids. These enzymes catalyze the formation of 3-hydroxy-3-methylglutaryl-CoA from acetyl-CoA and acetoacetyl-CoA. Isoprenoids are vital components of archaeal membrane lipids and other cellular functions. Members of this family are characterized by their resistance to feedback inhibition by acetoacetyl-CoA, which distinguishes them from their bacterial and eukaryotic counterparts. However, their activity can be inhibited by specific compounds, highlighting their importance in the survival and propagation of certain archaeal species.
Enoyl-CoA Hydratase-like (Enoyl-CoA_hydratase-like)
Type: Family

This family of proteins is involved in the biosynthesis of specific nonproteinogenic amino acids that are crucial components of certain antibiotics, such as vancomycin and teicoplanin. Members of this family function by catalyzing the addition of water to enoyl-CoA thioesters, resulting in beta-hydroxyacyl-CoA thioesters. This reaction is a key step in the formation of (S)-3,5-dihydroxyphenylglycine (Dpg), which is incorporated into the antibiotic structure. The proteins may also facilitate the dehydration process that contributes to the formation of aromatic compounds in the biosynthetic pathway. They are characterized by their similarity to other members of the enoyl-CoA hydratase/isomerase superfamily, which are known for their role in fatty acid metabolism and other diverse metabolic pathways.
Nre DNA repair-associated (Nre_DNA_repair)
Type: Family

This family of proteins is involved in the cellular response to DNA damage, particularly in the repair mechanisms that address lesions caused by mitomycin C, a DNA damaging agent. Members of this family function in concert with the UvrABC repair system to correct DNA damage, ensuring genomic integrity and cell survival following genotoxic stress.
Multiheme cytochrome c menaquinone reductase (Multiheme_cyt_c_menaq_reduct)
Type: Family

This family of proteins includes components of the respiratory Qrc complex, which are involved in the electron transfer process essential for sulfate respiration. They facilitate the reduction of the menaquinone pool, utilizing electrons from reduced periplasmic cytochrome c3. These proteins are likely crucial for microbial growth on substrates such as H(2) or formate, as they interact with primary electron donors like periplasmic hydrogenases or formate dehydrogenases.
Chemotaxis signal transducer CheY (CheY_signal_transducer)
Type: Family

This family of proteins is involved in the relay of sensory signals to cellular motility apparatus. Members of this family act as intermediaries that communicate environmental cues from sensory receptors, which detect changes in chemical gradients or light, to the machinery responsible for locomotion, such as flagellar motors in motile cells. This signal transduction process is essential for organisms to respond and adapt to environmental stimuli by altering their movement patterns.
NrfD menaquinone reductase subunit (NrfD_menaquinone_reductase)
Type: Family

This family of proteins is involved in the electron transport chain, specifically in the reduction of menaquinone, which is a key component of bacterial respiration. Members of this family function as integral membrane components of the respiratory Qrc complex, which is responsible for transferring electrons from reduced periplasmic cytochrome c3 to the menaquinone pool. This process is likely crucial for bacterial growth under certain conditions, such as when utilizing hydrogen or formate as electron donors. The proteins in this family play a role in anchoring the Qrc complex to the membrane and may interact with the quinone pool to facilitate electron transfer.
Cyclic nucleotide synthase CD-NTase (CD-NTase)
Type: Family

This family of proteins includes cyclic nucleotide synthases involved in the synthesis of cyclic oligonucleotides, which function as second messengers within bacterial CBASS antiviral systems. These enzymes catalyze the formation of 3',3',3'-cyclic AMP-AMP-AMP and other cyclic nucleotides, which activate effectors that lead to bacterial cell death and prevention of phage infection. The activity of these proteins is modulated by various factors, including pH and protein-protein interactions, with specific proteins activating or deactivating the enzyme complex. They possess two domains that are conformationally responsive to ATP binding.