SII-SWORD/CoKE huggingface dataset:
Type IV Methyl-Directed Restriction Enzyme (Type_IV_Methyl-Rstrct_Enzyme)
Type: Family

This family of proteins includes Type IV methyl-directed restriction enzymes such as EcoKMrr from E. coli. These enzymes play a crucial role in bacterial defense mechanisms by recognizing and restricting foreign DNA that is methylated. They are capable of targeting DNA that contains methylated adenine or cytosine bases, thereby providing protection against invading genetic elements such as phages and plasmids that may be detrimental to the bacterial cell. The specificity and activity of these enzymes are important for maintaining the integrity of the bacterial genome by preventing the incorporation and propagation of foreign DNA sequences.
Beta-lactamase/esterase domain-containing protein (Beta-lactamase/esterase)
Type: Family

This family of proteins exhibits enzymatic activities associated with the hydrolysis of ester and beta-lactam bonds. Members of this family are characterized by their ability to act as esterases, preferentially cleaving short-chain p-nitrophenol esters, as well as beta-lactamases, targeting substrates with a beta-lactam ring such as nitrocefin and ampicillin. These proteins play a role in bacterial defense mechanisms by degrading beta-lactam antibiotics, and they may also participate in various physiological processes through their esterase activity. The activity of these enzymes is subject to inhibition by specific active site residue modifiers, indicating a level of regulatory control over their function. Additionally, at least one member is known to function as an immunogen, eliciting both humoral and cell-mediated immune responses.
AP-4-A phosphorylase (AP-4-A_phosphorylase)
Type: Family

This family of proteins is involved in the catabolism of diadenosine polyphosphates. Specifically, they catalyze the breakdown of diadenosine 5',5'''-P1,P4-tetraphosphate (Ap4A) into adenosine diphosphate (ADP) and adenosine triphosphate (ATP). These enzymes prefer substrates that are dinucleoside polyphosphates with four or five phosphate residues. They are characterized by their inability to perform the reverse reaction, which is the synthesis of Ap4A from ADP and ATP.
Transposase_6_like (Transposase_6_like)
Type: Family

This family of proteins includes enzymes that function as transposases, which are pivotal components in the movement of DNA segments known as insertion sequences. Transposases catalyze the cutting and rejoining of DNA strands, thereby facilitating the insertion of these sequences into new genomic locations. This mobility can result in gene disruption, alteration of gene expression, or the creation of genetic diversity within a genome. Members of this family are characterized by their ability to recognize specific DNA sequences and perform the necessary DNA cleavage and strand transfer reactions that are essential for transposition.
ABC Transporter and Purine-Binding (ABC-Purine-Binding)
Type: Family

This family of proteins includes ABC transporter components and purine-binding proteins. Members are involved in the import of glucose and purines such as adenine and guanine, suggesting a role in nutrient uptake. Some family members are part of ABC transporter complexes, which are critical for transporting various molecules across cellular membranes. Others have a specific affinity for purines, indicating a specialized function in nucleobase transport. The diversity of ligands suggests that these proteins may contribute to a range of cellular processes, including metabolism and homeostasis.
Corrinoid activation enzyme (Corrinoid_activation_enz)
Type: Family

This family of proteins is involved in the metabolic process of quaternary amine degradation, specifically L-proline betaine and L-carnitine. They function as part of a corrinoid-dependent methyltransferase system, which facilitates the transfer of a methyl group from these amines to tetrahydrofolate, producing methyl-THF. This reaction is a crucial step in the Wood-Ljungdahl pathway of acetogenesis. Members of this family are not directly responsible for the methyl transfer but enhance the reduction of the associated methyltransferase component in its cobalt-containing active site, as well as the overall rate of THF methylation.
UPF0111 domain-containing protein (UPF0111_domain)
Type: Family

This family of proteins may play a role in the transport of orthophosphate across the cell membrane. Members of this family are characterized by a conserved domain, denoted as UPF0111, which suggests a common structural framework or evolutionary origin. The precise biological functions of these proteins, beyond the potential involvement in phosphate transport, remain to be fully elucidated. The family is defined by sequence similarity and the presence of the UPF0111 domain.
Glycopeptide antibiotic resistance protein (Glycopeptide_resist_protein)
Type: Family

This family of proteins includes those involved in antibiotic resistance, specifically resistance to glycopeptide antibiotics such as vancomycin. The family member VanW is known to confer resistance to vancomycin by an as yet not fully elucidated mechanism, which is believed to involve the remodeling of cell wall precursors that vancomycin targets. Another member, YoaR, is currently uncharacterized, but its association with the family suggests a potential role in bacterial response to environmental stress or antibiotic pressure. The exact functions and mechanisms of action for this family remain to be fully characterized, and they may vary among different family members.
Aldehyde Oxidoreductase Iron-Sulfur Subunit (Aldehyde_Oxdr_Iron-Sulfur)
Type: Family

This family of proteins includes aldehyde oxidoreductase iron-sulfur-binding subunits that are involved in the oxidation of aldehydes into their corresponding carboxylic acids, with a particular affinity for aromatic aldehydes. These proteins are implicated in the cellular detoxification process, helping to mitigate potential damage caused by aldehydes. The activity of this protein complex is dependent on the presence of an additional component, PaoD, which is required for its enzymatic function.
RNA-splicing ligase RtcB-like (RtcB-like)
Type: Family

This family of proteins includes GTP-dependent RNA ligases that play a crucial role in RNA splicing and repair mechanisms. They are capable of joining RNA molecules with 2',3'-cyclic-phosphate or 3'-phosphate ends to RNA with 5'-hydroxy ends. Additionally, these proteins exhibit versatility by acting as DNA ligases to repair 'dirty' DNA breaks, which are characterized by 3'-phosphate (or cyclic-phosphate) and 5'-hydroxy ends that are not amenable to repair by classical DNA ligases. Their ability to work on both RNA and DNA substrates underscores their importance in cellular maintenance and genome integrity.
Type I Restriction Enzyme MTase Subunit (Type-I_RE_MTase_Subunit)
Type: Family

This family of proteins includes methyltransferase (MTase) subunits of type I restriction enzymes. These enzymes are multifunctional, with the ability to both modify and cleave DNA. The MTase activity involves methylation of adenosines within specific recognition sequences, which serves to protect the DNA from cleavage by the associated restriction enzyme. The methylation typically occurs at A-3 on the top strand and A-2 on the bottom strand, or at adenosines in a different specified sequence. The MTase works in conjunction with the specificity (S) subunit to form a complex that can methylate both strands of the target sequence, acting as a maintenance MTase to preserve the methylation state during DNA replication. In the presence of the restriction (R) subunit, the complex can also function as an endonuclease, binding to the same target sequence but cutting the DNA at a distance from the recognition site. The endonuclease activity is dependent on the methylation state of the DNA, with unmodified DNA being cut and hemimethylated DNA being further methylated. Additionally, these enzymes can translocate DNA in an ATP-dependent manner until a collision event triggers cleavage.
Stress Response and Developmental Protein (Stress-Dev_Protein)
Type: Family

This family of proteins includes members that are implicated in stress response and developmental processes. General stress proteins, such as GS26 from Bacillus subtilis, are typically induced under a variety of stress conditions and may confer protection against environmental stresses by stabilizing cellular proteins or membranes, or by repairing damaged components. On the other hand, proteins like bli-3 from Neurospora crassa are involved in developmental pathways and may play roles in morphogenesis or differentiation. The functions of these proteins can be diverse, reflecting the adaptation of organisms to their specific ecological niches and the evolutionary divergence of protein functions.
Motility and Chemotaxis Regulatory Protein (Motility_Chemotaxis_Reg)
Type: Family

This family of proteins includes members that are involved in the regulation of gene transcription related to motility and chemotaxis. One characterized member functions to modulate the transcription levels of flagellin and chemotaxis-related genes in a temporal manner, suggesting a role in the coordination of locomotion and sensory behaviors. Another member of this family contains WD repeats, which are typically associated with protein-protein interactions, but its specific function remains uncharacterized.
Type II TA system ribonuclease (TA_system_RNase)
Type: Family

This family of proteins includes ribonucleases that function as toxic components within type II toxin-antitoxin (TA) systems. Members of this family are capable of inhibiting translation and colony formation in certain bacterial species. Their RNase activity is typically counteracted by specific antitoxins, which neutralize the toxic effects and allow for normal cellular functions to resume. These proteins are characterized by their membership in the PINc/VapC protein family, indicating a shared structural motif and evolutionary origin.
Potential DNA-binding regulatory protein (DNA-binding_regulatory)
Type: Family

This family of proteins includes members with potential regulatory functions, as suggested by one of its characterized members. However, the full spectrum of activities and roles within the family remains to be elucidated, as another member is currently uncharacterized. The family is likely involved in DNA-binding and may play a role in the regulation of gene expression or other DNA-dependent processes. Further research is necessary to fully understand the functional diversity and biological implications of the protein family.
G-protein Coupled Receptor 1 Superfamily Member (GPCR1_Superfamily_Member)
Type: Family

This family of proteins includes members that are part of the G-protein coupled receptor 1 superfamily. These receptors are typically involved in signal transduction processes and are known for their seven transmembrane helix structure. The family members are characterized by their ability to bind various ligands, which can include hormones, neurotransmitters, and sensory stimuli such as odors. Upon ligand binding, they activate heterotrimeric G-proteins, which then initiate a cascade of intracellular events. Some members of this family are described as probable olfactory receptors, suggesting a role in the detection of odorant molecules, while others are referred to as orphan receptors, indicating that their endogenous ligands have not yet been identified.
Cytidylate Kinase Type 2 (Cytidylate_Kinase-2)
Type: Family

This family of proteins includes enzymes that are involved in nucleotide metabolism, specifically the phosphorylation of cytidine monophosphate (CMP) to cytidine diphosphate (CDP). These enzymes play a crucial role in the synthesis of nucleic acids by maintaining the cellular balance of nucleotides. They are characterized by their ability to transfer a phosphate group from ATP to CMP, a key step in the nucleotide salvage pathways and de novo synthesis of CDP. The family is essential for cellular replication and DNA repair processes.
UPF0718 domain-containing protein (UPF0718)
Type: Family

This family of proteins may be involved in amino acid transport, particularly under low pH conditions. Members of this family could be part of two-component membrane permease systems, which are integral in processes such as acidogenesis, biofilm formation, and survival in acidic environments. The specific roles and mechanisms of these proteins, however, appear to be diverse and not fully characterized.
OsmC/Ohr hydroperoxide reductase (OsmC/Ohr_hydroprdx_reductase)
Type: Family

The OsmC/Ohr family comprises proteins that function as hydroperoxide reductases, which are crucial for cellular defense against oxidative stress. Members of this family are involved in the reduction of both organic and inorganic peroxide substrates, thereby protecting cells from the damaging effects of reactive oxygen species. The enzymatic activity of these proteins is essential for maintaining cellular redox balance and ensuring the survival of the organism under conditions that promote oxidative stress.
Phage Integrase-like Recombinase (Phage_Integrase-like_Recomb)
Type: Family

This family of proteins includes enzymes that catalyze site-specific recombination events. Members are characterized by their ability to recognize and recombine specific DNA sequences, typically involving short conserved sequences. These proteins play key roles in the integration and excision of DNA segments, such as phage genomes into host bacterial chromosomes, and are crucial for the maintenance of genomic stability and the regulation of gene expression. The family is associated with the 'phage' integrase family, indicating a shared evolutionary origin and similar mechanistic functions in DNA manipulation.
Metallo-beta-lactamase domain-containing protein (Metallo-beta-lactamase_dom)
Type: Family

This family of proteins includes enzymes that belong to the metallo-beta-lactamase superfamily and are involved in the biosynthesis of cofactors. Specifically, they catalyze the condensation of 6-hydroxymethyl-7,8-dihydropterin pyrophosphate with 4-(beta-D-ribofuranosyl)-aminobenzene-5'-phosphate to form a precursor in the biosynthesis of tetrahydromethanopterin. Additionally, they can catalyze the formation of related compounds using different arylamine substrates. These enzymes are characterized by their ability to bind and utilize metal ions to facilitate catalysis.
DCC thiol-disulfide oxidoreductase (DCC_oxidoreductase)
Type: Family

This family of proteins includes thiol-disulfide oxidoreductases that are involved in the formation, isomerization, and reduction of disulfide bonds. These enzymatic activities are crucial for protein folding and stability, and they play a significant role in various cellular processes including signal transduction, redox homeostasis, and the response to oxidative stress. Members of this family are characterized by their ability to catalyze thiol-disulfide exchange reactions, which are essential for maintaining the redox environment of the cell.
Uncharacterized desiccation-related membrane-associated (Desiccation-related_membrane)
Type: Family

This family of proteins includes uncharacterized members that are predicted to be associated with the membrane, as indicated by one of its members, YhaH from Bacillus subtilis. Another member, YtxH, also from Bacillus subtilis, shares similarity with a desiccation-related protein from Craterostigma plantagineum, suggesting a potential role in cellular response to stress conditions such as desiccation. However, the specific functions of these proteins within the family remain to be elucidated through experimental studies.
RNase H-like EbsB-related (RNase_H-like_EbsB-rel)
Type: Family

This family of proteins includes members that are related to the RNase H family, specifically the EbsB subfamily. The proteins in this family are implicated in cellular processes involving the cell surface, such as the expression of receptors that facilitate mating aggregate formation. Although they share a common ancestry with ribonucleases, the actual enzymatic activity of these proteins may vary, with at least one member lacking RNase H activity. Instead, they may have roles in the synthesis or assembly of cell wall components or function as cell wall hydrolases, influencing the structural dynamics of the bacterial cell envelope.
Type VII TA system antitoxin MntA (TA_antitoxin_MntA)
Type: Family

This family of proteins functions as antitoxins within type VII toxin-antitoxin (TA) systems. They neutralize the effects of cognate toxins through post-translational modifications, specifically by AMPylating the toxins. The AMPylation involves the addition of AMP to specific tyrosine residues on the toxins, which can occur as di- or tri-AMPylation. These proteins are also capable of binding to their own promoter regions, suggesting a role in autoregulation of their expression. The antitoxin activity is crucial for the stability of certain plasmids, especially when expressed in bacterial systems like E. coli. Structural elements such as alpha-helices are important for their interaction with the toxins, and deletions in these regions can significantly reduce antitoxin function.
Prophage regulatory DNA-binding activator (Prophage_regulatory_activator)
Type: Family

This family of proteins includes transcriptional activators involved in the regulation of gene expression within cryptic prophage elements. Members of this family are known to positively regulate specific genes, such as the slpA gene, and can influence phenotypes related to capsule production and UV sensitivity. They are associated with the control of prophage excision through interaction with integrase enzymes. Additionally, these proteins can impact the trans-translation process by inactivating upstream genes when overexpressed.
OprB Porin (OprB_Porin)
Type: Family

This family of proteins includes substrate-selective channels that facilitate the diffusion of compounds across cellular membranes. Members of this family are typically involved in the transport of small molecules, such as sugars and potentially other compounds with hydroxyl groups. Specific functions include the transport of glucose, mannitol, fructose, glycerol, quinate, and shikimate. These proteins play a role in the uptake of nutrients necessary for the growth and metabolism of certain bacteria.
DNA Protection and Modification (DNA_Protect_Modify)
Type: Family

This family of proteins includes members that are involved in the protection of DNA from host restriction-modification systems. They appear to function by preventing the degradation of DNA, particularly viral DNA, by host enzymes that recognize and cleave foreign DNA. Some family members are similar to type I restriction system adenine methylases, suggesting a role in DNA modification, potentially to evade host defense mechanisms. Others are related to helicases, indicating a possible involvement in DNA processing or repair mechanisms. The exact functions may vary among family members, but they collectively contribute to the survival of genetic material in the face of host defense strategies.
Methylated DNA Recognition and Restriction Enzymes (Methyl-DNA_Rec/Restrict_Enz)
Type: Family

This family of proteins includes enzymes involved in the recognition and processing of methylated DNA. Members of this family are capable of binding to DNA that contains methylated cytosines, which can be produced by various DNA methylases. Some proteins within this family recognize specific DNA sequences with methylated cytosines and may cleave the DNA at these sites, although the exact cleavage patterns can vary. These proteins play a role in the restriction-modification systems of bacteria, providing defense against foreign DNA such as that from bacteriophages. They can also participate in regulating gene expression through epigenetic modifications. The family includes enzymes that recognize methylated cytosines preceded by a purine residue and enzymes that recognize specific double-stranded DNA sequences.
Mg(2+)-dependent Phosphatidate Phosphatase (Mg2+_PAP)
Type: Family

The protein family includes Mg(2+)-dependent phosphatidate phosphatases that play a role in lipid metabolism by catalyzing the dephosphorylation of phosphatidate (PA) to produce diacylglycerol (DAG). This reaction is central to the synthesis of triglycerides and phospholipids. Members of the family may also be involved in vesicular trafficking, particularly at cortical actin patches, through their phosphatidate phosphatase activity. The family's enzymes can also act on diacylglycerol pyrophosphate and lyso-PA, albeit with lower specificity compared to PA. The catalytic activity of these enzymes is characterized by the presence of a DXDXT motif and is subject to inhibition by N-ethylmaleimide.
Jasmonate Hydroxylase-like (Jasmonate_Hydroxylase-like)
Type: Family

This family of proteins includes enzymes with monooxygenase activity that are involved in the modification of jasmonate, a plant hormone. Specifically, these proteins are capable of hydroxylating jasmonate to produce 12-hydroxyjasmonate, also known as tuberonic acid. This modification can influence plant innate immunity, potentially playing a role in the interaction between pathogens and host plants. Members of this family may also be associated with a secondary metabolism gene cluster, suggesting a possible involvement in the synthesis of other metabolites, including efflux substrates and polyketides.
Inner membrane integral protein (Inner_membrane_protein)
Type: Family

This family of proteins is involved in the structural integrity and function of the inner membrane in bacteria. Members of this family are typically integral membrane proteins that may play a role in various cellular processes, including the transport of molecules across the membrane, signal transduction, or interactions with other proteins within the membrane. The specific functions of these proteins, however, may vary between different bacterial species and could be influenced by the unique cellular context in which they are found.
23S rRNA Guanine-N(1)-Methyltransferase RlmA (23S_rRNA_MeTrnsfrase_RlmA)
Type: Family

The RlmA family consists of enzymes that are involved in the post-transcriptional modification of bacterial ribosomal RNA. Members of this family are 23S rRNA methyltransferases, which specifically methylate guanosine at position 745 (G745) in 23S rRNA. This methylation is important for the proper function of the ribosome, potentially affecting the accuracy of protein synthesis. The methyltransferase activity of these enzymes is crucial for the maturation and function of the ribosome, which is the cellular machinery responsible for protein synthesis. The RlmA family is part of the larger methyltransferase superfamily, indicating that these proteins share a common mechanism for transferring a methyl group from S-adenosylmethionine to their substrate rRNA.
Carbohydrate Esterase 6 (Carb_Esterase_6)
Type: Family

This family of proteins includes enzymes that are involved in the modification and metabolism of carbohydrates. Members of this family are characterized by their ability to catalyze reactions involving ester linkages in carbohydrate molecules. The functions of these enzymes are diverse, ranging from the hydrolysis of acetyl groups in specific carbohydrate structures to broader roles in the processing of carbohydrate moieties. These activities are crucial for various biological processes, including the degradation of complex carbohydrates, the modification of glycoconjugates, and the utilization of carbohydrate sources for growth and development in different organisms.