SII-SWORD/CoKE huggingface dataset:
Outer Membrane Peptidase A26 (OMP_A26_sf)
Type: Homologous_superfamily

This superfamily of proteins includes outer membrane proteases with diverse functions, such as acting as receptors for bacteriophages, activating plasminogen in mammalian hosts, and cleaving various substrates including T7 RNA polymerase, ferric enterobactin receptor protein, and antimicrobial peptides. Members of this superfamily exhibit specificity for paired basic residues and are involved in processes like fibrinolysis and bacterial cell migration. Some proteins in this superfamily are regulated by factors such as bacterial lipopolysaccharides, which can activate the protease, or zinc, which can inhibit protease activity. The proteolytic activity of some members contributes to bacterial motility by maintaining a polar localization of surface proteins.
CRISPR-associated Cas5 (CRISPR_Cas5_sf)
Type: Homologous_superfamily

This superfamily of proteins is involved in the CRISPR adaptive immune system, which provides a defense mechanism against mobile genetic elements such as viruses, transposable elements, and conjugative plasmids. Members of this superfamily are associated with the processing of CRISPR clusters into CRISPR RNA (crRNA), which contains sequences that are complementary to those of invading nucleic acids, thereby targeting them for degradation or interference. These proteins play a crucial role in the transcription and subsequent processing of the CRISPR clusters, ensuring the proper function of the CRISPR system in immunity.
Bacterial Lectin Domain-Containing Protein (Bacterial_Lectin_Domain_sf)
Type: Homologous_superfamily

This superfamily of proteins includes bacterial lectins that exhibit specificity for high mannose N-glycans, recognizing the branched structures within these glycans. They do not interact with other types of N-glycans or monosaccharides. Members of this superfamily are involved in cell differentiation and may have roles in agglutinating erythrocytes and inhibiting viral replication, such as that of HIV, by binding to viral envelope glycoproteins. Some members also display mitogenic activity on lymphocytes and do not require metal ions for their activity.
HPA decarboxylase small subunit superfamily (HPA_decarboxylase_ss_sf)
Type: Homologous_superfamily

This superfamily of proteins is involved in the enzymatic decarboxylation of phenylacetates, particularly those with a hydroxyl group in the para position. The proteins function as components of a larger enzymatic complex known as HPA decarboxylase, which plays a crucial role in the catabolism of aromatic amino acids, such as tyrosine. The enzymatic activity results in the formation of metabolites like 4-methylphenol and 4-methylcatechol, which confer metabolic toxicity and can suppress competing microbes. This activity may provide a competitive advantage to the producing organisms in their respective ecological niches. The small subunit of the proteins within this superfamily is essential for the catalytic function of the HPA decarboxylase complex and is also implicated in regulating the complex's oligomeric state and overall catalytic activity.
Alginate Permeability Channel-forming (Alginate_Permeability_Chnl)
Type: Homologous_superfamily

This superfamily of proteins is involved in the transport of alginate, a biopolymer produced by certain bacteria. Members of this superfamily are characterized by their ability to form channels in the bacterial membrane that facilitate the permeation of alginate. These channels are distinct from classical porins as they do not adopt a porin-like structure, indicating a unique mechanism of action for alginate translocation across the membrane.
MAD2L1-binding domain-containing protein (MAD2L1BP_domain_sf)
Type: Homologous_superfamily

This superfamily of proteins is involved in the regulation of the spindle checkpoint during mitosis. Members of this superfamily are known to interact with the MAD2L1 protein, particularly after its dissociation from the MAD2L1-CDC20 complex. Through this interaction, they may contribute to the silencing of the spindle checkpoint, facilitating the progression of mitosis from metaphase to anaphase. The precise mechanism of this regulatory function and the broader biological roles of these proteins may vary among different organisms and require further characterization.
Multidrug Efflux Pump Accessory AcrZ (MEP_Accessory_AcrZ)
Type: Homologous_superfamily

This superfamily of proteins is involved in the efflux of a broad range of substrates across the cell membrane, contributing to multidrug resistance. Members of this superfamily interact with components of a protein complex that actively transports various compounds out of the cell. The presence of these proteins is essential for the selective export of certain substrates, indicating a role in modulating the specificity of the efflux system. The complex they associate with is typically composed of several proteins that together facilitate the removal of drugs and other substances, thereby providing a mechanism for the cell to resist toxic compounds.
Fimbrial Structure-Associated Virulence Factor (Fimbrial_Virulence_Factor)
Type: Homologous_superfamily

This superfamily of proteins is involved in the formation of fibrillar structures that are components of fimbriae, which are hair-like appendages on the surface of bacteria. These structures are implicated in bacterial virulence as they play a crucial role in the adherence to host cells, colonization, and evasion of the host immune response. The presence of these proteins is associated with the pathogenicity of certain bacterial serotypes, indicating their significance in the disease-causing mechanism of these organisms.
Fimbrial Assembly Component (Fimbrial_Assembly_Comp)
Type: Homologous_superfamily

This superfamily of proteins includes components that are integral to the structure of fimbriae, also known as pili. These hair-like appendages extend from the bacterial cell surface and are critical for adherence to host epithelial cells, facilitating colonization and persistence within host tissues. The superfamilies' members are involved in the assembly of these filamentous structures, which can be several micrometers in length and are present in large numbers on bacterial cells. The fimbriae are key virulence factors, particularly in the context of pathogenic bacteria, where they play a central role in the establishment of infections by mediating attachment to host surfaces.
Heme Transport and Utilization Superfamily (Heme_Transport_Util_sf)
Type: Homologous_superfamily

This superfamily of proteins is involved in the transport and management of heme, an essential cofactor in various biological processes. Members of this superfamily are responsible for binding heme and facilitating its transfer to other proteins, such as heme-degrading enzymes. They play a crucial role in the binding-protein-dependent transport system for hemin, which is a ferric form of heme. The proteins within this superfamily exhibit specific protein-protein interactions that are critical for the proper functioning of heme transport and utilization pathways in bacterial organisms.
Bacteriophage Head-Tail Connecting Superfamily (Phage_Head-Tail_Connect_sf)
Type: Homologous_superfamily

This superfamily of proteins is involved in the assembly of viral particles, specifically in the process of connecting the head and tail components of bacteriophages. The proteins function at the final stage of morphogenesis, ensuring the proper attachment of the DNA-containing head to the pre-assembled tail structure. They interact with various other proteins that are part of the virion assembly pathway, including those that close the capsid and the tail terminator protein.
Type III TA system endoribonuclease (Type_III_TA_endoRNase)
Type: Homologous_superfamily

This superfamily of proteins includes endoribonucleases that function as toxic components within type III toxin-antitoxin (TA) systems. These proteins typically cleave specific RNA sequences, leading to growth inhibition in a bacteriostatic manner without causing cell lysis. The endoribonuclease activity is neutralized by cognate RNA antitoxins, which are characterized by multiple nearly identical nucleotide repeats that can fold into structures such as pseudoknots to bind and inhibit the toxin. These TA systems are implicated in plasmid maintenance through a plasmid addiction mechanism and can confer resistance to bacteriophages by causing abortive infections. The toxins are capable of self-regulation in complex with their antitoxins and can negatively regulate their own operon expression.
Metallocarboxypeptidase Inhibitor Domain-containing Protein (MCP_Inhibitor_Domain_sf)
Type: Homologous_superfamily

This superfamily of proteins consists of inhibitors that specifically target metallocarboxypeptidases, a type of metalloprotease. Members of this superfamily are capable of inhibiting a range of metallocarboxypeptidases from different species, including bovine CPA1, human CPA1, CPA2, CPA4, CPB1, CPB2, and porcine CPB1. They do not inhibit carboxypeptidase D from Drosophila melanogaster, nor do they affect proteases from other mechanistic classes such as serine proteases (e.g., trypsin, chymotrypsin, subtilisin), cysteine proteases (e.g., papain), or aspartyl proteases (e.g., pepsin). Some members have been reported to exhibit antiplasmodial activity against Plasmodium falciparum without cytotoxic effects on human cells, suggesting a potential role in defense mechanisms.
Type II TA System Toxin (Type_II_TA_Toxin)
Type: Homologous_superfamily

This superfamily of proteins includes components of type II toxin-antitoxin (TA) systems. Members of this superfamily function as toxins that can inhibit cell growth and protein synthesis by interacting with ribosomal subunits and phosphorylating elongation factors. These toxins are counteracted by specific antitoxins, which neutralize their toxic effects and regulate their activity. The balance between the toxin and antitoxin can affect gene expression and is involved in the cellular response to stress, contributing to the stabilization of certain genetic elements such as plasmids within bacterial cells. Additionally, these proteins may play a role in the regulation of cellular metabolism by linking catabolic and anabolic processes.
Lambda phage major capsid assembly (Lambda_capsid_assembly)
Type: Homologous_superfamily

This superfamily of proteins is involved in the assembly of icosahedral capsids, which are geometric structures composed of proteins that encapsulate the genetic material of certain viruses. Members of this superfamily are characterized by their structural role in forming the protective shell that is critical for the stability and infectivity of the virus particles.
Bacteriocin Immunity Domain-containing Protein (Bact_Immunity_Domain_sf)
Type: Homologous_superfamily

This superfamily of proteins includes members that are involved in providing immunity to certain types of bacteriocins, which are antimicrobial peptides produced by bacteria. The proteins within this superfamily are responsible for protecting host bacterial cells from the lethal action of these peptides. By binding to or neutralizing the bacteriocins, these immunity proteins ensure the survival of the producer strain, which can be advantageous in competitive microbial environments. The specific interactions and mechanisms of immunity can vary among different family members and the bacteriocins they target.
Type III Secretion System Pilotin (T3SS_Pilotin)
Type: Homologous_superfamily

This superfamily of proteins is involved in the assembly and operation of the type III secretion system (T3SS), a complex bacterial apparatus that facilitates the injection of effector proteins into eukaryotic host cells. Members of this superfamily function as pilot proteins, essential for the correct placement and stabilization of secretin components within the bacterial outer membrane. These proteins are crucial for the formation of the T3SS's injectisome structure, playing a key role in bacterial pathogenicity and host interaction. They exhibit a beta-sandwich fold and may interact with membranes through a region rich in basic residues.
Serine and fungal protease inhibitor (Ser_Fungal_Prot_Inhib_sf)
Type: Homologous_superfamily

This superfamily of proteins includes members that function as inhibitors of various serine proteases, such as trypsin, and fungal proteases. These proteins exhibit specificity in their inhibitory activity, as they do not inhibit a range of other proteases, including chymotrypsin, subtilisin Carlsberg, proteinase K, porcine pancreatic elastase, and certain toxin proteases. The members of this superfamily are involved in protective mechanisms against protease-mediated damage, potentially playing a role in defense against pathogens by targeting their proteolytic enzymes.
Fungal Immunomodulatory Lectin (Fungal_ImmunoLectin_sf)
Type: Homologous_superfamily

This superfamily of proteins includes lectins that have a specificity for complex cell-surface carbohydrates and exhibit immunomodulatory activities. Members of this superfamily can stimulate lymphocyte mitogenesis, suppress systemic anaphylaxis reactions and edema, and enhance the transcription of cytokines such as IL-2, IFN-gamma, and TNF-alpha. They are also capable of hemagglutinating red blood cells, indicating a role in cell-cell or cell-matrix interactions. These proteins are found in fungi and are known for their roles in immune system modulation.
CRISPR system Cmr7 complex component (CRISPR_Cmr7_comp)
Type: Homologous_superfamily

This superfamily of proteins is involved in the CRISPR adaptive immune system, which provides a defense mechanism against mobile genetic elements such as viruses, transposable elements, and conjugative plasmids. Members of this superfamily are associated with the processing of CRISPR RNA (crRNA) and the subsequent targeting and degradation of complementary RNA sequences. The CRISPR RNA-guided CMR complex, to which these proteins belong, is responsible for cleaving target RNA within specific dinucleotide contexts, producing defined ends. The activity of this complex is dependent on certain structural features of the crRNA and the target RNA, and is also ATP-stimulated. Additionally, the complex has been observed to cleave the guide crRNA under some conditions.
UDG Inhibitor phi29likevirus (UDG_Inhib_phi29likevirus)
Type: Homologous_superfamily

This superfamily of proteins is involved in the inhibition of host uracil-DNA glycosylase (UDG), an essential enzyme in the base excision repair pathway that removes uracil from DNA. Members of this superfamily interact with UDG to prevent it from binding to DNA, thereby protecting viral genomes that contain uracil, which can be incorporated by viral DNA polymerases. The inhibition of UDG by these proteins is crucial for the virus to evade host DNA repair mechanisms that could otherwise compromise the integrity of the viral genome.
Viral Tail Completion Superfamily (Viral_Tail_Comp_sf)
Type: Homologous_superfamily

This superfamily of proteins is involved in the assembly of viral structures, specifically by capping the tail of bacteriophages. Members of this superfamily function to ensure the proper attachment of the tail to the capsid, which is a critical step in the virus assembly process. They achieve this by interacting with other viral components, such as the connector proteins, to form a stable and functional virion. The action of these proteins is essential for the completion of the virus particle, enabling it to infect host cells effectively.
Viral Head-Tail Connector Assembly Factor (Viral_HT_Connector_Assembly)
Type: Homologous_superfamily

This superfamily of proteins is involved in the assembly of viral components, specifically participating in the formation of a structural interface between the viral head and tail. Members of this superfamily are characterized by their ability to form a central channel that is crucial for the DNA ejection process during viral infection. They interact with other viral proteins, such as the portal protein and additional head completion proteins, to facilitate the correct assembly of the virus and ensure the proper function of the DNA ejection mechanism.
Fluorescence Recovery Regulator (Fluoresc_Recovery_Reg)
Type: Homologous_superfamily

This superfamily of proteins is involved in the photoprotection mechanism of photosynthetic organisms. Members of this superfamily interact with a specific form of the orange carotenoid protein, facilitating its conversion to a different state. This interaction is crucial for the regulation of a process known as non-photochemical quenching, where excess light energy is dissipated as heat to prevent damage to the photosynthetic apparatus. The proteins in this superfamily play a role in restoring fluorescence in the light-harvesting complexes after this energy dissipation event, by affecting the binding of the carotenoid protein to the phycobilisome core, which is a part of the photosynthetic machinery.
Host DNA Degradation Endonuclease (Host_DNA_Degrad_Endo)
Type: Homologous_superfamily

This superfamily of proteins includes enzymes that are involved in the degradation of host DNA, which is a process that facilitates the recycling of nucleotides for the synthesis of viral DNA. Members of this superfamily exhibit sequence-specific endonuclease activity, cleaving the bottom strand of double-stranded DNA at specific motifs. The cleavage typically occurs adjacent to recognized DNA sequences, allowing these enzymes to make precise cuts in the DNA. The specificity of these enzymes is such that they do not cleave their own viral DNA, which is modified to prevent self-digestion. This modification usually involves the presence of modified bases, such as 5-hydroxymethylcytosine, in place of the typical cytosine found in host DNA.
Bacterial toxin-antitoxin system-associated superfamily (TA_system-associated_sf)
Type: Homologous_superfamily

This superfamily of proteins includes members that are typically involved in bacterial toxin-antitoxin systems. These proteins are often encoded by operons and function as toxins that can inhibit various cellular processes, such as DNA replication, transcription, and translation, leading to cell growth arrest or death. The antitoxin counterparts neutralize the toxic effects, allowing for the regulation of cell growth and death in response to environmental stresses. The superfamily may play a role in maintaining genomic stability, mediating programmed cell death, and contributing to antibiotic resistance. The specific functions of individual members can vary widely, and some may have evolved additional or alternative roles beyond the canonical toxin-antitoxin system.
Programmed Cell Death 10 Homolog (PDCD10_Homolog)
Type: Homologous_superfamily

This superfamily of proteins is involved in various cellular processes including the maintenance of cellular structures and the regulation of vesicle transport. Members of this superfamily are implicated in the elongation of excretory canals during developmental stages, suggesting a role in morphogenesis. They are also associated with the stabilization of the Golgi apparatus and the integrity of the endoplasmic reticulum. Additionally, these proteins are involved in the regulation of small GTPases, such as cdc-42, which are critical for various aspects of cell signaling and dynamics. The functions of this superfamily contribute to essential physiological processes, including fertility in organisms.
Viral Major Capsid Assembly (Viral_Major_Capsid_sf)
Type: Homologous_superfamily

This superfamily of proteins includes structural components of viral capsids. The major capsid protein is essential for the assembly and stability of the capsid, which is the protein shell of a virus that encloses its genetic material. These proteins are typically characterized by their ability to form the protective outer layer of the virus, which is critical for viral integrity, infectivity, and interaction with host cells. The superfamily may exhibit variations in structure among different viruses, reflecting the diversity of viral shapes and sizes, but all share the common function of forming the capsid structure.
Small archaeal modifier domain-containing protein (SAM_domain_containing)
Type: Homologous_superfamily

This superfamily of proteins is involved in post-translational modification of substrate proteins through a process known as sampylation. Members of this superfamily function by covalently attaching to lysine residues on target proteins via an isopeptide bond formed with the C-terminal glycine carboxylate of the modifier protein. This modification can signal for proteolytic degradation by proteasomes. Additionally, these proteins can form polymeric chains with themselves, akin to ubiquitin and other ubiquitin-like proteins, and also act as sulfur carriers in the process of tRNA thiolation.
Ribonuclease N1/T1-like (RNase_N1/T1-like_sf)
Type: Homologous_superfamily

This superfamily of proteins is involved in the catalysis of RNA molecules. Members of this superfamily are characterized by their enzymatic activity, which includes the cleavage of phosphodiester bonds within RNA, yielding 3'-nucleoside monophosphates. The enzymatic process proceeds through the formation of 2',3'-cyclophosphate intermediates. These proteins play a crucial role in RNA metabolism, including the degradation of RNA polymers into smaller units, which can be a part of various cellular processes such as the regulation of gene expression, RNA turnover, and the defense mechanism against RNA viruses.
Oligomannose-binding and Chitinase-activity Domain-containing Protein (OligoMan_bind_ChitinaseAct_sf)
Type: Homologous_superfamily

This superfamily of proteins encompasses carbohydrate-binding entities that recognize and interact with specific oligosaccharides, such as oligomannosides. Members of this superfamily are characterized by their ability to bind to a specific tetrasaccharide core found in N-linked oligomannosides with high affinity. They exhibit hemagglutinating activity, which can be inhibited by certain polysaccharides like yeast mannan. Additionally, these proteins possess a unique enzymatic function, with one of the binding sites demonstrating weak beta-1,4-glycosidase activity, capable of cleaving chitin oligomers. This catalytic activity is distinct and limited to certain oligosaccharides, and does not extend to all substrates. The dual functionality of binding and catalysis within the same protein is a notable feature of this superfamily.
Contact-dependent growth inhibition immunity (CDI_immunity_sf)
Type: Homologous_superfamily

This superfamily of proteins encompasses immunity components within toxin-immunity modules, specifically functioning in contact-dependent growth inhibition (CDI) systems. These systems are utilized by bacteria to interact with and suppress the proliferation of closely related bacteria through direct contact. Members of this superfamily confer protection to bacterial cells by neutralizing the ribonuclease activity of cognate toxin proteins that target the 16S rRNA. However, they do not provide immunity against non-cognate toxins with similar ribonuclease activity from different bacterial strains.
Toxin-specific immunity effector (Toxin_immunity_effector)
Type: Homologous_superfamily

This superfamily of proteins includes immune effectors involved in bacterial competition. Members function by binding to and inhibiting the activity of cognate toxins, thereby providing a defense mechanism against toxin-mediated cell damage. The interaction between these immune proteins and their target toxins is highly specific, often involving the occlusion of the toxin's active site to prevent its premature activation and subsequent cellular harm.