SII-SWORD/CoKE huggingface dataset:
Outer Membrane Factor (OMF) (OMF)
Type: Family

The Outer Membrane Factor (OMF) family proteins are involved in the transport of a wide range of substrates across the bacterial outer membrane. They form the outer membrane component of tripartite efflux systems, which typically include an inner membrane transporter, a periplasmic adaptor protein, and an OMF protein. These efflux pumps confer resistance to various substances, including antibiotics, heavy metals, organic solvents, and toxins. Some family members are involved in the secretion of siderophores for iron acquisition or the expulsion of unwanted metal-siderophore complexes. The efflux systems can be constitutive or inducible and are often driven by a proton gradient. The specificity of the efflux system is not solely determined by the OMF component, which can interact with different inner membrane transporters to export a variety of substrates.
Sulfatase enzyme (Sulfatase)
Type: Family

The sulfatase family encompasses enzymes that hydrolyze sulfate esters from various substrates, including complex carbohydrates, steroids, and aromatic compounds. Members of the family are involved in diverse biological processes such as degradation of glycosaminoglycans, mineralization of sulfates, and conversion of sulfated steroid precursors to active steroids. Some sulfatases are implicated in the degradation of ulvan, a polysaccharide in green seaweed, while others are active towards artificial substrates like 4-methylumbelliferyl sulfate. Arylsulfatases, a subset within the family, hydrolyze sulfate from aromatic compounds, playing roles in cellular processes and environmental sulfate turnover. The family's activity is regulated by factors like phosphate, which can inhibit some members by forming a covalent bond with the active site 3-oxoalanine. The sulfatase family is essential for various organisms, from bacteria to humans, for maintaining sulfate homeostasis and processing sulfated molecules.
Membrane Fusion Protein (MFP)
Type: Family

This family of proteins is involved in the transport and secretion of various molecules across the cell membrane. Members of this family typically function as part of tripartite efflux systems, which are composed of an inner membrane transporter, a periplasmic adaptor protein, and an outer membrane channel. These proteins are responsible for conferring resistance to antibiotics and toxic compounds by actively exporting them out of the cell. Additionally, they play roles in the secretion of bacteriocins, hemolysins, proteases, and other toxins, contributing to bacterial virulence and competition. Some family members are also involved in the biosynthesis of extracellular polysaccharides like alginate, which is important for biofilm formation and pathogenicity in certain bacteria.
Aldehyde Dehydrogenase Superfamily (Aldehyde_DH_Superfamily)
Type: Family

The aldehyde dehydrogenase family is involved in various metabolic pathways by catalyzing the oxidation of aldehydes to their corresponding acids. Members of this family display broad substrate specificity, including but not limited to succinate semialdehyde, glyceraldehydes, and glutarate semialdehyde. They play roles in the degradation of neurotransmitters like gamma-aminobutyric acid (GABA), the utilization of carbon sources such as L-arabinose and sulfoquinovose, and the metabolism of compounds like lactaldehyde, 3,6-anhydro-L-galactose, and trigonelline. The enzymes generally prefer NAD(P)(+) as a cosubstrate and are involved in processes such as stress response in plants and the maintenance of cellular redox states. Activity regulation is often redox-dependent, with inhibition under oxidizing conditions being a common feature.
Acyl-CoA dehydrogenase (Acyl-CoA_dehydrogenase)
Type: Family

The acyl-CoA dehydrogenase family is involved in the first step of mitochondrial fatty acid beta-oxidation, an aerobic process that breaks down fatty acids into acetyl-CoA, facilitating energy production. Members of the family catalyze the dehydrogenation of acyl-CoA to trans-2-enoyl-CoA, with electron transfer flavoprotein (ETF) serving as the electron acceptor. This reaction is crucial for the metabolism of medium-chain fatty acids, typically those with 4 to 16 carbons in length, although some members exhibit specificity for longer chains, such as saturated C22-CoA. The family also includes enzymes like p-hydroxyphenylacetate 3-hydroxylase, which are involved in the hydroxylation of aromatic compounds. Overall, the acyl-CoA dehydrogenase family plays a significant role in energy metabolism and the regulation of fatty acid composition in cellular lipids.
Helicase and Restriction-Modification Enzyme (Helicase_Restrict-Modif_Enz)
Type: Family

The protein family includes helicases and restriction-modification system enzymes. Helicases in the family are involved in processes such as postreplicative transcription termination, ATP-dependent release of nascent RNA, and DNA repair. They form stable complexes with single-stranded DNA and RNA. The restriction-modification enzymes recognize specific DNA sequences and cleave DNA at a distance from the recognition site, requiring both Res and Mod subunits for function. They also exhibit helicase domains and are involved in DNA restriction and modification.
2-oxoacid dehydrogenase family, E2 component (2-oxoacid_DH_E2_comp)
Type: Family

Members of the 2-oxoacid dehydrogenase family are components of multienzyme complexes that catalyze the irreversible oxidative decarboxylation of various 2-oxoacids to form acyl-CoA derivatives and CO2. These complexes play a pivotal role in metabolic pathways, such as the catabolism of branched-chain amino acids and the conversion of pyruvate to acetyl-CoA, which is a key step in the citric acid cycle. The family includes the E2 component, lipoamide acyltransferase, which accepts and transfers acyl groups generated by the E1 component to coenzyme A. The E2 component is essential for the overall function of the complex, working in concert with the E1 decarboxylase and E3 lipoamide dehydrogenase components.
AI-2 Signaling Cycle Isomerase LsrG (AI-2_Isomerase_LsrG)
Type: Family

The LsrG family is involved in the degradation of phospho-AI-2, which terminates the induction of the lsr operon and closes the AI-2 signaling cycle. Members of this family catalyze the isomerization of (4S)-4-hydroxy-5-phosphonooxypentane-2,3-dione (P-DPD) to 3-hydroxy-5-phosphonooxypentane-2,4-dione (P-HPD). This reaction is a key step in the quorum sensing pathway, a mechanism that bacteria use to regulate gene expression in response to changes in cell-population density. Some members of the LsrG family are also putative monooxygenases that may contribute to the degradation of aromatic compounds or may function in redox cycles related to quinone metabolism.
Multifunctional regulatory proteins (Multifunctional_regulatory)
Type: Family

This family of proteins includes a variety of functions, such as modulating neurotransmitter release, regulating gene transcription, and influencing cytoskeletal dynamics. Some members act as neurotoxins that interact with receptors and form pores in membranes, leading to neurotransmitter release. Others are involved in the Wnt signaling pathway, telomere length regulation, and vesicle trafficking through poly-ADP-ribosylation of target proteins. Certain members regulate the growth of actin filaments and inhibit actin-capping protein complexes. Additionally, some proteins in this family may function as regulatory subunits of protein phosphatases or as components of E3 ubiquitin-protein ligase complexes, mediating the ubiquitination and degradation of target proteins.
Dicarboxylate/Amino Acid:Cation Symporter (DAACS)
Type: Family

The dicarboxylate/amino acid:cation symporter family is involved in the sodium-dependent, high-affinity transport of amino acids such as L-glutamate, L- and D-aspartate, and L-cysteine across cell membranes. Members function as symporters, co-transporting amino acids with Na+ ions and a proton, while counter-transporting a K+ ion. They play crucial roles in rapidly clearing glutamate from synaptic clefts, terminating postsynaptic action, and contributing to glutathione biosynthesis and oxidative stress protection. Some members also mediate Cl- flux independent of amino acid transport and exhibit substrate-specific transport regulation.
Mitochondrial chaperone BCS1 subfamily (Mitochondrial_chaperone_BCS1)
Type: Family

The BCS1 subfamily of AAA ATPases functions as mitochondrial chaperones essential for the assembly of mitochondrial respiratory chain complex III. Members of the BCS1 subfamily play a crucial role in maintaining mitochondrial tubular networks, respiratory chain assembly, and the formation of the LETM1 complex. In plants, they are also involved in regulating morphology and anatomy during seed maturation.
Glycosyltransferase 8 domain-containing (Glycosyltrans_8_dom-fam)
Type: Family

The Glycosyltransferase 8 family comprises enzymes involved in the biosynthesis of various polysaccharides and glycoconjugates. Members of this family are known to participate in the synthesis of cell wall components, such as pectin and xylans in plants, and the core oligosaccharide region of lipopolysaccharides in bacteria. They exhibit glucosyltransferase and galactosyltransferase activities, transferring sugar moieties from activated sugar donors like UDP-glucose or UDP-galactose to specific acceptor molecules. Some members are also implicated in the O-glycosylation of serine-rich repeat proteins, contributing to the diversity of bacterial cell surface structures. The family is characterized by the presence of conserved DXD motifs, which are crucial for their catalytic function. These enzymes play essential roles in cell wall integrity, pathogenicity, and stress response across various species.
Glycosyl Hydrolase Family 47 (Glycosyl_Hydrolase_47)
Type: Family

The glycosyl hydrolase 47 family is involved in the maturation of Asn-linked oligosaccharides, a critical process in protein quality control and degradation pathways. Members of this family function as alpha-mannosidases, which progressively trim alpha-1,2-linked mannose residues from Man(9)GlcNAc(2) to produce Man(5)GlcNAc(2). This enzymatic activity is essential for the proper folding and function of glycoproteins. Some family members are also involved in early N-glycan processing, root development, and cell wall biosynthesis. The activity of these enzymes is regulated by inhibitors such as kifunensine and 1-deoxymannojirimycin, highlighting their specificity and importance in cellular metabolism.
Cytosine-specific C5-methyltransferase (C5-MTase)
Type: Family

The C5-methyltransferase family encompasses enzymes that primarily perform methylation of cytosine residues in various biological molecules. Members of the family exhibit specificity for different substrates, including tRNA and DNA. The tRNA-specific methyltransferases target cytosine 38 in the anticodon loop of tRNA(Asp) and sometimes other tRNAs, influencing translation fidelity. DNA-specific methyltransferases within the family recognize specific double-stranded DNA sequences, methylating cytosines to protect DNA from cleavage by restriction endonucleases, thus playing a role in bacterial immune defense and epigenetic regulation. Some members have dual specificity, acting on both tRNA and DNA. The family is characterized by a conserved SAM-binding motif, indicative of their reliance on S-adenosylmethionine as a methyl donor.
Extracellular matrix structural protein (ECM_structural_protein)
Type: Family

This family of proteins is involved in the structural organization and remodeling of the extracellular matrix (ECM). Members of this family play key roles in cell adhesion, migration, and development by interacting with various ECM components, including fibronectin, elastin, and collagen. They contribute to the formation of elastic fibers, basement membranes, and matrix fibers, and are implicated in processes such as blood clotting, tumor suppression, and the regulation of cell shape and adhesion. Some family members are also involved in the activation of growth factor signaling pathways, which can influence cellular proliferation and differentiation. The diverse functions of these proteins reflect their importance in maintaining tissue integrity and facilitating cellular interactions with the ECM.
C2H2-type zinc-finger domain-containing protein (C2H2-ZF_domain)
Type: Family

This family of proteins includes transcription factors that are involved in various developmental and regulatory processes. Members of this family are characterized by the presence of C2H2-type zinc-finger domains, which facilitate DNA binding and allow these proteins to regulate gene expression. Functions attributed to these proteins include roles in embryonic central nervous system development, neuronal fate specification, muscle structure, and transcriptional regulation of specific genes. Some family members are implicated in processes such as cell proliferation, migration, inflammation, and embryonic development. Additionally, certain proteins within this family have been associated with the modulation of signaling pathways and the maintenance of pluripotency in stem cells.
Peptidase M14 domain-containing protein (Peptidase_M14_domain)
Type: Family

This family of proteins includes enzymes that are primarily involved in the post-translational modification of proteins and peptides. They function as carboxypeptidases, which means they cleave C-terminal amino acids from proteins and peptides. Members of this family are involved in various biological processes, such as the regulation of peptide hormone and growth factor activity, modulation of the Wnt signaling pathway, and the processing of prohormones. They play roles in cellular interactions, inflammation, and the immune response by regulating the activity of vasoactive and inflammatory peptides. Some members also have roles in the extracellular matrix organization and may act as transcriptional repressors.
Peptidyl-prolyl cis-trans isomerase FKBP4/5/8-like (FKBP4/5/8-like)
Type: Family

This family of proteins includes immunophilins with peptidyl-prolyl cis-trans isomerase (PPIase) and co-chaperone activities such as Peptidyl-prolyl cis-trans isomerase FKBP4/5 . FKBP4/5 are also involved in the intracellular trafficking of steroid hormone receptors and play a role in maintaining these receptors in the cytoplasm when unliganded . FKBP4/5 regulate Akt/AKT1 activity by promoting interaction with PHLPP1, enhancing Akt/AKT1 dephosphorylation and activation . They also interact with components of the NF-kappaB signaling pathway, influencing kinase activity and IFN production . FKBP4 plays a role in microtubule dynamics, neuronal growth cone regulation, and may protect against oxidative stress in mitochondria . Others are involved in protein folding, cell division, adhesion, elongation, and hormonal control of plant development, such as Peptidyl-prolyl cis-trans isomerase PASTICCINO1 from Arabidopsis . The family is characterised by the presence of TPR repeats and FKBP-type domains.
TRAFAC YlqF/YawG GTPases, Ribosome Maturation (TRAFAC_YlqF/YawG_RiboMat)
Type: Family

The TRAFAC class YlqF/YawG GTPase family is involved in various cellular processes, including the maturation and nuclear export of pre-60S ribosomal subunits, regulation of cellular proliferation, and stabilization of proteins involved in cell cycle regulation and ribosome biogenesis. Members of the family exhibit GTPase activity that is often regulated by ribosomal subunits, particularly the 60S subunit. The family is characterized by a unique circular permutation of GTPase motifs, forming a G4-G1-G3 pattern. Some members are implicated in maintaining stem cell proliferative capacity, stabilizing MDM2 to prevent ubiquitination and proteasomal degradation, and affecting TP53 activity. Others are involved in telomere maintenance by stabilizing TERF1 and promoting cell proliferation. The family also includes proteins that play roles in plant growth, senescence, and development by modulating ribosome biogenesis in the nucleolus.
COP9 signalosome complex subunit 3 (CSN3)
Type: Family

The COP9 signalosome complex subunit 3 (CSN3) family is involved in various cellular and developmental processes. Members of the CSN3 family are essential components of the COP9 signalosome (CSN) complex, which regulates the ubiquitin (Ubl) conjugation pathway. The CSN complex mediates the deneddylation of cullin subunits in SCF-type E3 ligase complexes, modulating their Ubl ligase activity. This action is crucial for maintaining protein homeostasis by controlling the degradation of proteins. The CSN3 family also plays a role in the phosphorylation of key proteins such as p53/TP53 and c-jun/JUN, potentially through association with kinases like CK2 and PKD. This phosphorylation can promote or protect against protein degradation. Additionally, the CSN3 family is implicated in various processes including photomorphogenesis, circadian clock regulation, embryogenesis, oogenesis, and responses to auxin and jasmonate in plants.
Collagen-modifying Glycosyltransferase 25 (Collagen_mod_GT25)
Type: Family

The glycosyltransferase 25 family is involved in the post-translational modification of collagen, a structural protein essential for the integrity of various tissues. Family members include enzymes that hydroxylate lysine residues within collagen sequences, which is a prerequisite for the subsequent glycosylation of these residues. The hydroxylysine sites serve as attachment points for carbohydrate units, crucial for collagen fibril assembly, cross-linking, and stability. Some members exhibit multifunctional activities, catalyzing both hydroxylation and glycosylation, contributing to the formation of the collagen triple helix and the biosynthesis of different collagen types, including type I and IV. Others are involved in cell adhesion processes. The family also includes proteins that, despite sharing sequence similarity, are inactive as glycosyltransferases and may have divergent functions.
Zinc finger protein, C2H2-type (Znf_C2H2-type)
Type: Family

The Zinc finger, C2H2-type protein family is characterized by the presence of one or more zinc finger motifs, which are small protein structural motifs that can coordinate one or more zinc ions to help stabilize their folds. Members of this family are predominantly involved in transcriptional regulation, with some proteins acting as transcriptional repressors or activators. They may play roles in various biological processes including gene silencing, embryonic stem cell maintenance, cell migration and proliferation, angiogenesis, and tumor growth. Some family members are implicated in the regulation of transcriptional repressor activity, erythroid maturation, lymphoid proliferation, and kidney repair. The family is also associated with the recruitment and regulation of several protein complexes involved in histone modification and chromatin remodeling.
Serine proteases and regulators with kringle domains (Serine_protease_kringle)
Type: Family

This family of proteins includes serine proteases and regulators with a variety of biological functions. Members are involved in processes such as tissue remodeling, tumor invasion, inflammation, and blood clot dissolution. They can activate other proteases, degrade extracellular matrix components, and are implicated in cell detachment and apoptosis. Some family members act as growth factors for a wide range of tissues, promoting cell proliferation and survival. Others are involved in lipid metabolism and may serve as ligands for specific receptors. Regulatory proteins in this family can negatively affect phosphatidylinositol 3-kinase activity in the liver. The family is characterized by the presence of kringle domains, which mediate interactions with other proteins, and many members belong to the plasminogen subfamily of peptidase S1.
Period circadian regulator (Period_circadian_regulator)
Type: Family

This family of proteins plays a crucial role in the regulation of circadian rhythms, which are internal biological processes that follow a roughly 24-hour cycle. These proteins function as transcriptional repressors within the molecular circadian clock mechanism, forming a feedback loop that controls gene expression related to various physiological functions, including metabolism, sleep, body temperature, and hormonal levels. They interact with other core clock components to regulate the timing of protein expression, aligning physiological processes with the day-night cycle. Mutations in these proteins can lead to altered circadian rhythms and affect species-specific behaviors.
HD-ZIP Homeobox Leucine Zipper Class II (HD-ZIP_Homeobox_LZ_Class_II)
Type: Family

The HD-ZIP homeobox family, Class II subfamily, consists of proteins that are likely to function as transcription factors. Members of this family are characterized by a homeobox domain paired with a leucine zipper motif, which suggests their role in DNA binding and dimerization. These proteins are involved in various developmental processes in plants, including leaf development, auxin-mediated morphogenesis, and vascular system growth. They typically bind to a conserved DNA sequence, often contributing to the regulation of gene expression in response to developmental cues and environmental factors such as light. Some members have been described as transcriptional repressors, while others may act as transcriptional activators or switches to specify cell fate.
ABC transporter ATP-binding component (ABC_transporter_ATP-binding)
Type: Family

This family of proteins is involved in the transport of various molecules across the cellular membrane using ATP hydrolysis for energy. Members of this family are part of ABC transporter complexes that can export substances such as nodulation factors, antibiotics, and other drugs. Nodulation factors are key for symbiosis and nodulation in certain bacteria. Some proteins in this family are implicated in providing resistance to antibiotics by exporting them out of the cell, thereby reducing their intracellular concentration and effectiveness. The ATP-binding component of these transporters is crucial for the energy-dependent transport process.
CbbQ/NirQ/NorQ/GpvN (CbbQ/NirQ/NorQ/GpvN)
Type: Family

The CbbQ/NirQ/NorQ/GpvN family includes proteins involved in various cellular processes. Some members function as ATPases that enhance gas vesicle formation, which are proteinaceous nanostructures that regulate buoyancy in microbial planktonic organisms. Other members are involved in the post-translational activation and assembly of RuBisCO, an enzyme critical for carbon fixation in photosynthetic organisms. Additionally, certain proteins in the family act as activators of nitrite and nitric oxide reductases, playing a role in the denitrification process. The family also includes proteins that may regulate the formation of active methanol dehydrogenase, which is involved in methanol metabolism. Overall, the CbbQ/NirQ/NorQ/GpvN family encompasses a diverse group of proteins with functions related to gas vesicle formation, enzyme activation and assembly, and metabolic regulation.
Riboflavin Biosynthesis HTP Reductase (Riboflavin_Biosynth_HTPR)
Type: Family

The HTP reductase family is involved in the riboflavin biosynthesis pathway. Members of this family catalyze the NAD(P)H-dependent reduction of the ribose side chain of 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate, producing 2,5-diamino-6-ribitylamino-4(3H)-pyrimidinone 5'-phosphate. This reaction represents an early step in the synthesis of riboflavin, an essential vitamin for many organisms. Some proteins within this family also contain an N-terminal cytidine and deoxycytidylate deaminase domain, which is non-functional in certain members. Additionally, the family includes proteins with a non-functional deaminase domain that can hydrolyze the N-glycosidic bond in riboflavin biosynthesis intermediates, diverting harmful intermediates into less damaging products.