SII-SWORD/CoKE huggingface dataset:
Teicoplanin resistance-associated protein (Teicoplanin_resist-assoc)
Type: Family

This family of proteins is associated with a specific function related to antibiotic resistance. Members of this family have been implicated in providing low-level resistance to the glycopeptide antibiotic teicoplanin. The mechanism by which this resistance is conferred is not fully understood, but it is believed that these proteins may interact with components of the cell wall or membrane to reduce the effectiveness of teicoplanin, which targets the cell wall synthesis pathway in bacteria. The study of this family is important for understanding antibiotic resistance mechanisms and potentially developing strategies to overcome or mitigate resistance in pathogenic bacteria.
Ribonuclease H-like (RNase_H-like)
Type: Family

This family of proteins includes enzymes that are putative ribonucleases H (RNases H), which are known to catalyze the hydrolysis of RNA in RNA/DNA hybrids. These proteins play a crucial role in DNA replication, repair, and recombination by removing RNA primers from Okazaki fragments and during the process of retroviral replication. The presence of the RNase H domain suggests that these proteins may have similar enzymatic activity, although the specific functions in different organisms and contexts can vary.
Probable Hydrolase YcaC-like (Hydrolase_YcaC-like)
Type: Family

This family of proteins includes enzymes that are likely to function as hydrolases. Hydrolases are a broad class of enzymes that catalyze the hydrolytic cleavage of chemical bonds, such as ester, glycosidic, peptide, and other bonds. The specific substrates and reactions catalyzed by this family are not detailed in the provided information. However, based on the probable function as hydrolases, members of this family may be involved in diverse metabolic and regulatory processes within the cell, including the degradation of biomolecules, the recycling of cellular components, and the regulation of metabolic pathways. The precise biological role and the mechanism of action of the YcaC-like proteins would require further experimental validation.
APC Superfamily Potassium Transporter (APC_K+_Transporter)
Type: Family

This family of proteins includes high-affinity potassium transporters that function as K(+)/H(+) symporters. They facilitate the uptake of potassium ions into cells, a process which is enhanced at lower external pH levels. The activity of these transporters is sensitive to changes in proton motive force, as demonstrated by the inhibition of potassium uptake in the presence of proton ionophores. Additionally, these proteins can bind cyclic di-AMP, a nucleotide second messenger, which negatively regulates their potassium transport activity. Members of this family are part of the amino acid-polyamine-organocation (APC) superfamily, indicating a broad role in the transport of a variety of substrates across cellular membranes.
Cyclic di-AMP regulator (c-di-AMP_regulator)
Type: Family

This family of proteins enhances the enzymatic activity of diadenylate cyclases upon coexpression. Specifically, they can stimulate the production of cyclic di-AMP, a molecule that serves as a second messenger in various cellular processes including growth, DNA repair, and cell wall maintenance. However, an overabundance of cyclic di-AMP can be detrimental to the cell.
F-pilin assembly protein TraC (F-pilin_assembly_TraC)
Type: Family

This family of proteins is involved in the formation of bacterial appendages known as F pili. Members of this family play a crucial role in the assembly process by facilitating the incorporation of mature F-pilin subunits into the structure of the pilus. These pili are filamentous projections on the bacterial surface that are essential for processes such as bacterial conjugation, which is a mechanism of horizontal gene transfer between bacteria.
Type VI secretion system TssM-like (T6SS_TssM-like)
Type: Family

This family of proteins includes core components of the type VI secretion system (T6SS), which is involved in the secretion of effector molecules that target a variety of cells, including both eukaryotic and prokaryotic organisms. Members of this family are crucial for the stabilization of the TssK1 structure, which is necessary for the proper localization and function of the T6SS at the cellular membrane. The T6SS is a complex apparatus that contributes to bacterial competitiveness and virulence by delivering toxic proteins to competitor cells and host tissues.
Sterol Uptake Control Transcription Regulator (Sterol_Uptake_Regulator)
Type: Family

This family of proteins includes transcription factors that are key regulators of anaerobic gene expression, particularly for genes encoding cell wall mannoproteins. They are known to bind specific anaerobic response elements in the promoters of target genes. Additionally, these proteins play a crucial role in the uptake and regulation of sterol biosynthesis by interacting with sterol regulatory elements in the promoters of enzymes involved in sterol metabolism. They may also participate in the down-regulation of certain cell wall proteins during anaerobic adaptation.
Type 1 Capsular Polysaccharide Biosynthesis Protein CapK (CapK_Type1_Caps_Biosynth)
Type: Family

The CapK protein family is involved in the biosynthesis of type 1 capsular polysaccharide. Capsular polysaccharides are critical components of the bacterial cell envelope, often contributing to pathogenicity and immune evasion by forming a protective layer around the cell. Members of the CapK family are essential enzymes that catalyze steps in the synthesis of these complex sugar molecules, enabling bacteria to establish infections and persist in hostile environments.
Hybrid Signal Transduction Histidine Kinase (Hybrid_Histidine_Kinase)
Type: Family

This family of proteins participates in signal transduction pathways as receptor histidine kinases. They are characterized by an ATP-dependent autophosphorylation on a conserved histidine residue within the kinase core. Following autophosphorylation, a phosphoryl group is transferred to a conserved aspartate residue in the receiver domain. Members of this family exhibit an atypical domain architecture, including a STYKc/AAA module coupled with a histidine kinase/receiver module. They are part of the protein kinase superfamily and are related to serine/threonine protein kinases.
Major Facilitator Superfamily DHA3 Transporter (MFS_DHA3_Transporter)
Type: Family

This family of proteins includes members that are part of the major facilitator superfamily (MFS), which are known to facilitate the transport of a variety of substrates across cellular membranes. Specifically, this family is associated with the Drug:H(+) antiporter-3 (DHA3) group within the MFS, indicating a role in the antiport of drugs and protons across the membrane. This transport activity is typically driven by a proton motive force and is important for the cellular efflux of toxic compounds, contributing to multidrug resistance in bacteria.
Ulvan-degrading glycoside hydrolase (Ulvan_degrading_GH)
Type: Family

This family of proteins includes glycoside hydrolases that are implicated in the degradation of ulvan, a major polysaccharide found in the cell walls of green seaweed from the Ulvales order. Members of this family are characterized by their ability to cleave the glycosidic linkages within ulvan, which is composed of disaccharide units that include 3-sulfated rhamnose linked to various sugars such as D-glucuronic acid, L-iduronic acid, or D-xylose. The enzymatic activity of these proteins facilitates the breakdown of this complex carbohydrate, suggesting a role in the utilization or recycling of ulvan in the environment.
DnaD (DnaD)
Type: Family

This entry represents DnaD proteins in bacteria.

The DnaD protein is a component of the PriA primosome. The PriA primosome functions to recruit the replication fork helicase onto the DNA . Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria . DnaD consists of two domains with distinct activities: an N-terminal domain with oligomerisation activity and a C-terminal domain with DNA-binding activity and a second DNA-induced oligomerisation activity .
HTH-type transcriptional regulator Rgg-like (HTH-type_regulator_Rgg)
Type: Family

This family of proteins includes transcriptional regulators that feature a helix-turn-helix (HTH) motif. Members of this family are involved in the regulation of gene expression, specifically controlling the synthesis of enzymes such as glucosyltransferases. These proteins play a key role in the modulation of bacterial carbohydrate metabolism by influencing the production of enzymes that are responsible for the biosynthesis of polysaccharides. The activity of these transcriptional regulators is crucial for the proper response to environmental changes and for the regulation of virulence factors in pathogenic species.
IS1016-like transposase (IS1016-like_transposase)
Type: Family

This family of proteins includes transposase-like elements that are similar to the insertion element IS1016 transposase. Transposases are enzymes that catalyze the movement of transposable elements (TEs) within the genomes of bacteria and other organisms. These proteins play a key role in the mobility of TEs, enabling them to cut and rejoin DNA sequences, which can lead to genetic variation and the potential for adaptation and evolution. The activity of transposases is tightly regulated as uncontrolled transposition can be harmful to the host organism. The IS1016-like transposases are likely involved in the recombination and movement of specific insertion elements, contributing to genomic rearrangements and horizontal gene transfer.
HSI-I assembly protein Hcp1 (HSI-I_assembly_Hcp1)
Type: Family

This family of proteins is involved in the assembly of a protein secretion system known as HSI-I. Members of this family are actively secreted and play a role during chronic infections, such as those occurring in cystic fibrosis patients. They are essential components of the machinery required for the secretion of effector proteins that may contribute to the pathogenicity and persistence of infections.
UPF0718 putative permease (UPF0718_permease)
Type: Family

This family of proteins includes putative permeases that may be involved in the transport of molecules across cellular membranes. The specific substrates and mechanisms of transport for the UPF0718 family members are not well characterized. However, as permeases, they likely play a role in the uptake or efflux of essential nutrients, ions, or other compounds, contributing to the cell's homeostasis and interaction with its environment. The functional details and biological significance of these proteins may vary among different organisms and could be subject to further experimental validation.
Late-developmental Spore Coat Component (Spore_coat_component)
Type: Family

This family of proteins includes late-developmental spore coat components. Members are involved in the formation of the protective layer that surrounds spores, which are a dormant form of the organism that can survive in harsh conditions. The protein contributes to the resilience and viability of the spore during periods when the organism is not actively growing.
Glutamic endopeptidase (Glutamic_endopeptidase)
Type: Family

This family of proteins includes glutamic endopeptidases known for their ability to cleave peptide bonds preferentially on the C-terminal side of proline residues, although they can also target bonds on the C-terminal side of alanine residues with lower efficiency. Unlike many proline-cleaving enzymes, they can degrade proteins of various sizes. These enzymes are characterized by their moderate inhibition by pepstatin and EPNP, while being unaffected by POP inhibitors or denaturants like urea. Their presence in certain viscoelastic fluids suggests a role in the digestion of prey.
Meiotically Up-regulated Gene Protein (MUG_Protein)
Type: Family

This family of proteins is involved in the regulation of meiotic processes. Members of this family are implicated in the cellular events that occur during meiosis, which is a specialized type of cell division necessary for sexual reproduction in eukaryotes. These proteins may play a role in various stages of meiosis, including the pairing of homologous chromosomes, recombination, and segregation of chromosomes into gametes.
Negative transcriptional regulator (Transcription_regulator)
Type: Family

This family of proteins is implicated in the regulation of gene transcription. Members of this family are believed to function as negative regulators, potentially influencing the expression of various genes including those involved in DNA repair, fatty acid biosynthesis, and stress response. The precise regulatory mechanisms and the full spectrum of target genes remain to be elucidated.
Viral Tip Attachment Protein (Viral_Tip_Attach_Protein)
Type: Family

This family of proteins is involved in the attachment of virions to host receptors, specifically initiating the process of viral DNA ejection. They play a crucial role in the assembly of the distal tail tip of the virus by interacting with other viral proteins. Additionally, these proteins are responsible for the irreversible binding to the host receptor, which triggers structural changes in the viral tail, culminating in the injection of viral DNA into the host cell through the receptor's trimeric pore.
Tn903 transposase-like (Tn903_transposase)
Type: Family

This family of proteins includes transposases that are essential for the movement of transposon Tn903 within a genome. Transposases are enzymes that catalyze the cutting and rejoining of DNA strands, thereby enabling the transposition process. The transposition mechanism typically involves the recognition of specific DNA sequences by the transposase, followed by the cleavage of DNA at these sites and the integration of the transposon into a new location. Members of this family are characterized by their role in facilitating the mobility of genetic elements, which can have significant impacts on genome structure and function.
Class I-like SAM-binding MTase (SAM-binding_MTase)
Type: Family

This family of proteins includes enzymes that are likely involved in the methylation of various substrates, potentially including large hydrophobic molecules with aromatic structures. Members of this family are characterized by a two-domain architecture, with one domain implicated in dimerization and the other exhibiting the class I methyltransferase fold, which is indicative of S-adenosylmethionine (SAM) binding. These proteins are part of the class I-like SAM-binding methyltransferase superfamily, suggesting a role in transferring methyl groups from SAM to their substrates.
UDP-2,3-diacylglucosamine pyrophosphatase (LpxI)
Type: Family

This family of proteins is involved in the biosynthesis of lipid A, a critical component of the lipopolysaccharide that forms the outer membrane of certain bacterial cells. Members of this family act as enzymes that specifically hydrolyze the pyrophosphate bond of UDP-2,3-diacylglucosamine, yielding 2,3-diacylglucosamine 1-phosphate and UMP. This reaction is a key step in the formation of lipid A. The enzymes possess two domains: an N-terminal domain that binds lipid X and a C-terminal catalytic domain. The binding of the substrate induces a conformational change that facilitates the enzymatic reaction. The activity of these proteins is regulated by metal ions and can be inhibited by agents such as EDTA.
DHMBA Cluster Regulating Transcription Factor (DHMBA_Reg_Transcription_Factor)
Type: Family

This family of proteins includes transcription factors that are involved in the regulation of gene clusters responsible for the biosynthesis of certain antibiotics. Members of this family are known to specifically enhance the expression of genes related to the production of the antibiotic 2,4-dihydroxy-3-methyl-6-(2-oxopropyl)benzaldehyde (DHMBA) and its derivatives. One of the key genes positively regulated by these transcription factors encodes a FAD-dependent oxidoreductase enzyme, which plays a crucial role in the biosynthetic pathway of DHMBA.
Type VI secretion system TssE1-like (T6SS_TssE1-like)
Type: Family

This family of proteins includes core components of the type VI secretion system (T6SS), specifically the H1-T6SS variant. Members are involved in the secretion of toxins that can target a range of organisms. They play a crucial role in the assembly and stability of the TssB1-sheath structure, which is essential for the function of the T6SS. These proteins operate downstream of TssK1 and are key in preventing the premature disassembly or detachment of the TssB1-sheath. They facilitate the binding of the sheath to TssB1 and serve as a docking point for the recruitment of ClpV1, which is necessary for the disassembly of the sheath during the T6SS cycle.
ADP-glucose phosphorylase (ADP-glucose_phosphorylase)
Type: Family

This family of proteins includes enzymes that are involved in carbohydrate metabolism, specifically in the synthesis of sugar nucleotides. Members of this family are responsible for catalyzing the formation of glucose-1-phosphate from ADP-glucose, releasing ADP in the process. This reaction is a key step in the biosynthesis of glycogen and starch, serving as a glucose donor for the polymerization reactions. The enzymatic activity is crucial for energy storage in various organisms, as it regulates the conversion of glucose for storage as a complex carbohydrate. Despite sharing a name with galactose-1-phosphate uridylyltransferase, these proteins do not exhibit that specific enzymatic function.
Osmoadaptation-associated protein (Osmoadaptation_assoc)
Type: Family

This family of proteins is implicated in the cellular process of osmoadaptation, which is the ability of an organism to adjust to changes in osmotic pressure in its environment. These proteins may play a role in sensing osmotic stress or in the regulatory pathways that manage the cellular response to maintain homeostasis under varying osmotic conditions. The specific mechanisms by which these proteins contribute to osmoadaptation are not detailed in the provided information.
LINE-1 ORF2p reverse transcriptase/endonuclease (LINE-1_ORF2_RT/EN)
Type: Family

This family of proteins includes enzymes with reverse transcriptase and endonuclease activities, essential for the retrotransposition of LINE-1 elements. The reverse transcriptase function is critical for synthesizing DNA from the LINE-1 mRNA, a key step in the integration of these elements into the genome. Additionally, the endonuclease activity enables these proteins to introduce nicks into chromosomal DNA, facilitating the insertion of LINE-1 sequences. These proteins recognize and cleave DNA at AT-rich regions, with target DNA conformation being a significant factor for sequence-specific recognition. The proteins also feature a flexible loop region that influences DNA nicking patterns, and a C-terminal segment that binds RNA non-specifically but with high affinity.
Calcium-binding acidic-repeat (Ca-binding_acidic-repeat)
Type: Family

This family of proteins is implicated in calcium ion binding. Members are believed to have a role in cellular processes that are regulated by calcium levels. The exact biological functions may vary among family members, but the common characteristic is the ability to interact with calcium ions, which suggests a potential role in signaling, regulation, or structural stability of the proteins where calcium is a key factor.
EcdB-like transcription regulator (EcdB-like_regulator)
Type: Family

This family of proteins includes putative transcription factors, such as ecdB from Aspergillus rugulosus. Members of this family are believed to be involved in the regulation of gene expression by interacting with specific DNA sequences, thereby influencing the transcription of genes. The exact DNA-binding mechanisms and regulatory roles may vary among family members and could be essential for various cellular processes, including development, metabolism, and response to environmental stimuli. The functional characterization of these proteins typically requires further experimental validation to confirm their transcription factor activity and to elucidate their specific target genes and regulatory pathways.
Putative transcriptional regulator YobU-like (YobU-like_regulator)
Type: Family

This family of proteins includes putative transcriptional regulators. The characterized member, YobU from Bacillus subtilis, is annotated as a putative transcriptional regulator, suggesting that proteins in this family may be involved in the regulation of gene expression. Transcriptional regulators are typically involved in the response to environmental stimuli, cellular growth, and differentiation by modulating the transcription of target genes. The specific mechanism of action and the target genes for YobU-like proteins, however, remain to be elucidated through experimental studies.
Alkali-sensitive linkage protein (ASL1)
Type: Family

This family of proteins is involved in cellular processes that are sensitive to changes in alkaline conditions. The proteins may play a role in the response to environmental pH shifts, potentially participating in the regulation of pH homeostasis or in signaling pathways that are activated under alkaline stress. The specific functions of these proteins could include modifications of other proteins or interactions with various cellular components to facilitate adaptation to alkaline environments.
FeoA-like (FeoA-like)
Type: Family

This family of proteins is implicated in the cellular uptake of iron ions, specifically ferrous iron (Fe(2+)). Members of this family are thought to play a role in the transport mechanism that allows iron ions to enter the cell, which is a critical process for cellular function and metabolism, as iron is a vital cofactor for many enzymes. The precise mechanism of iron uptake and the regulation of these proteins in response to iron availability may vary among different organisms and cell types.
SET domain-containing protein (SET_domain_protein)
Type: Family

This family of proteins includes enzymes that share a SET domain, which is typically involved in the methylation of lysine residues on histone proteins. This post-translational modification is crucial for the regulation of gene expression and can affect chromatin structure and function. Members of this family are likely to function as methyltransferases, utilizing S-adenosyl methionine (SAM) as a methyl donor to modify histones, thus playing a role in the epigenetic control of gene activity. Given the broad implications of histone methylation in processes such as DNA repair, replication, and transcriptional regulation, these proteins may be integral to cell cycle control, development, and differentiation.
Quercetin 2,3-dioxygenase-related (QDO-related)
Type: Family

This family of proteins includes members that are thought to function as quercetin 2,3-dioxygenases. These enzymes are involved in the degradation of flavonoids, a class of plant secondary metabolites with various biological activities. Quercetin 2,3-dioxygenase catalyzes the cleavage of quercetin, a specific flavonoid, to produce carbon monoxide and 2-protocatechuoylphloroglucinol carboxylic acid. The family is related to the pirin proteins, which are characterized by a conserved pirin domain. Pirin proteins have been implicated in various cellular processes, including as transcriptional regulators and in response to stress conditions. The exact biological role of the putative quercetin 2,3-dioxygenases within this family may vary among different organisms and requires further investigation to confirm their enzymatic activity and physiological functions.