SII-SWORD/CoKE huggingface dataset:
Glutaredoxin-like YDR286C (Glutaredoxin-like_YDR286C)
Type: Family

This family of proteins is characterized by a conserved domain that suggests a role in redox reactions, specifically through the catalysis of thiol-disulfide exchange reactions which are fundamental to cellular redox homeostasis. Members of this family are likely to function in the reduction of protein disulfides and in the regulation of cellular processes through redox signaling. They may also participate in the defense against oxidative stress by maintaining a reduced environment in the presence of reactive oxygen species. The presence of a glutaredoxin-like domain indicates that these proteins may have glutathione-dependent oxidoreductase activity, acting on substrates including ribonucleotide reductase, which is crucial for DNA synthesis and repair.
Non-lysosomal glucosylceramidase (Non-lysos_glucosylceramidase)
Type: Family

The non-lysosomal glucosylceramidase family encompasses enzymes that catalyze the hydrolysis of glucosylceramides to glucose and ceramide, playing a crucial role in the metabolism of glycosphingolipids. These glycosphingolipids are involved in various cellular processes including growth, differentiation, adhesion, signaling, and membrane dynamics. Family members also exhibit transglucosylation activity, transferring glucose from glucosylceramides to cholesterol, affecting its solubility and function. Additionally, they can reverse this process under certain conditions. The enzymes are also capable of hydrolyzing and forming bile acid-glucose conjugates, and they can act on galactosylceramides with lower efficiency. Their activity is lipid-dependent and subject to regulation by various factors, including metal ions and specific inhibitors.
Organophosphonate Dioxygenase (OP_Dioxygenase)
Type: Family

This family of proteins is involved in the degradation of various organophosphonates, which are compounds containing carbon-phosphorus (C-P) bonds. Members of this family catalyze the oxidative cleavage of C-P bonds in specific substrates, resulting in the formation of inorganic phosphate and other products such as formate, glycine, or glycine betaine. These enzymatic activities are crucial for the utilization of organophosphonates as phosphate sources or for their detoxification. The proteins exhibit specificity for different substrates, including hydroxymethylphosphonic acid, aminoethylphosphonic acids, and N-trimethylated phosphonates. Some family members are known to be inhibited by chelating agents like EDTA.
Polyketide Synthase and Fatty Acid Synthase (PKS-FAS_Synthase)
Type: Family

The protein family is involved in the biosynthesis of various polyketide-derived compounds, including pigments and polyunsaturated fatty acids (PUFAs). One member catalyzes the formation of a yellow pigment in conidia by condensing acetate units into a heptaketide naphthopyrene. Another is implicated in the production of the red antibiotic prodigiosin, facilitating the formation of a bipyrrole precursor. The remaining members are part of a PUFA synthase complex that synthesizes essential fatty acids like DHA and DPA through an anaerobic polyketide synthase pathway, distinct from the conventional fatty acid synthase pathway for saturated fatty acids. The family showcases a variety of enzymatic domains, including ketosynthase, acyl-carrier protein, and malonyl-CoA:ACP transacylase domains, which are involved in the elongation and modification of polyketide and fatty acid chains.
Flagellar FliJ (FliJ)
Type: Family

This family of proteins is involved in the structure and function of bacterial flagella, which are essential for motility and chemotaxis. Members of this family play a role in the assembly and operation of the flagellar apparatus, influencing the bacterial cell's ability to move towards or away from chemical stimuli. Mutations in these proteins can disrupt chemotactic responses, indicating their importance in the sensory and adaptive systems of flagellated bacteria.
Mitochondrial RNA Methyltransferase (Mt_RNA_Methyltransferase)
Type: Family

This family of proteins includes mitochondrial S-adenosyl-L-methionine-dependent RNA methyltransferases, which are likely involved in the methylation of mitochondrial rRNA. This modification is essential for the stabilization of the mitochondrial small ribosomal subunit (mt-SSU), a critical component for the assembly and functionality of the mitochondrial ribosome. Consequently, these proteins play a significant role in ensuring proper protein translation within the mitochondria. Despite the absence of protein methyltransferase activity, their function in RNA methylation underscores their importance in maintaining mitochondrial gene expression.
UPF0153 domain-containing protein (UPF0153_domain)
Type: Family

This family of proteins is characterized by the UPF0153 domain. The specific functions of these proteins are not well characterized. However, proteins with the UPF0153 domain are typically small and conserved across various bacterial species, suggesting a fundamental role in bacterial physiology. The domain's function has not been definitively established, and further research is needed to elucidate the biochemical activities and biological roles of these proteins. They may be involved in processes such as stress response, metabolism, or regulation of gene expression, but these are speculative roles that have not been confirmed for the UPF0153 protein family.
DnaJ homolog subfamily C member 28 (DnaJ_C_subfamily_28)
Type: Family

The DnaJ homolog subfamily C member 28 family includes proteins that are potentially involved in protein folding or may function as chaperones. These proteins are likely to assist in the correct folding of other proteins or in the stabilization of unfolded or partially folded proteins, preventing their aggregation. The family is represented by members in both mouse and human, indicating a conserved role across these species. However, the exact functions of some family members, such as those from bacteria, remain uncharacterized.
Cell Division and Infection-Related Protein (CDIRP)
Type: Family

This family of proteins is involved in various cellular processes including cell division, infection mechanisms, and cellular adhesion. Members of this family play roles in organizing microtubule structures, facilitating mitotic exit, and shaping membranes during cell division or sporulation. Some proteins within this family are also implicated in pathogenic infection, acting as adhesins that enhance bacterial adherence to host cells. They may participate in signaling pathways that coordinate cellular and nuclear division, and their activity can be regulated in a host-dependent manner.
Small subunit processome component 20 (SSU_processome_comp_20)
Type: Family

This family of proteins is involved in the early stages of ribosome assembly, particularly in the processing of pre-18S ribosomal RNA within the nucleolus. Members of this family are components of the small subunit (SSU) processome and associate with U3 small nucleolar RNA (snoRNA). They contribute to the folding, modification, rearrangement, and cleavage of pre-rRNA, and are also implicated in the targeted degradation of pre-ribosomal RNA by the RNA exosome. These activities are essential for the proper formation of the small eukaryotic ribosomal subunit.
Amino Acid Transporter-Related (AA_Transporter-Related)
Type: Family

This family of proteins includes members that are involved in the transport of amino acids across cellular membranes. One characterized member functions as a glutamine transporter, suggesting a role in amino acid uptake and metabolism. Other members are uncharacterized but are predicted to have similar membrane-associated transport functions based on their homology to the characterized transporter.
VWA7 (VWA7)
Type: Family

This entry represents the VWA7 and related proteins.

The von Willebrand factor is a large multimeric glycoprotein found in blood plasma. Mutant forms are involved in the aetiology of bleeding disorders
. In von Willebrand factor, the type A domain (vWF) is the prototype for a protein superfamily. The vWF domain is found in various plasma proteins: complement factors B, C2, CR3 and CR4; the integrins (I-domains); collagen types VI, VII, XII and XIV; and other extracellular proteins . Although the majority of VWA-containing proteins are extracellular, the most ancient ones present in all eukaryotes are all intracellular proteins involved in functions such as transcription, DNA repair, ribosomal and membrane transport and the proteasome. A common feature appears to be involvement in multiprotein complexes. Proteins that incorporate vWF domains participate in numerous biological events (e.g. cell adhesion, migration, homing, pattern formation, and signal transduction), involving interaction with a large array of ligands . A number of human diseases arise from mutations in VWA domains.
Phosphatidylinositol Transfer CRAL-TRIO Domain-Containing Protein (PI_Transfer_CRAL-TRIO)
Type: Family

This family of proteins is involved in the transfer of phosphatidylinositol between different membrane compartments, which is crucial for the regulation of the phospholipid composition of plasma- and endomembranes. By modulating the lipid composition, these proteins may play a role in mechanisms of multidrug resistance. They are also implicated in the activation of phospholipase D1 and the inhibition of phospholipase B1, contributing to the turnover of phospholipids. Some family members form complexes with enzymes such as phosphatidylserine decarboxylase, which is essential for maintaining specific phospholipid levels in organelles like vacuoles. Additionally, they are involved in sterol biosynthesis regulation and may regulate the release of fatty acids from lipid droplets, indicating a broader role in lipid metabolism.
Zinc finger SWIM domain-containing protein (Zinc_finger_SWIM)
Type: Family

This family of proteins contains a SWIM-type zinc finger domain, which is known to mediate protein-protein interactions. Members of this family are involved in various cellular processes, including regulation of transcription, DNA repair, and ubiquitination. The SWIM domain may function by binding to other proteins or specific DNA sequences, thereby influencing the activity of target genes or the stability of other proteins. The exact roles of individual family members can vary, but they generally contribute to the regulation of gene expression and maintenance of genomic integrity.
Probable Lipid Hydrolase (Lipid_Hydrolase)
Type: Family

This family of proteins appears to be involved in lipid metabolism, specifically in the hydrolysis of lipid substrates. The members of this family are characterized by their probable function as lipid hydrolases, which suggests that they may play a role in breaking down complex lipids into simpler molecules. This activity is essential for various biological processes, including membrane remodeling, energy production, and signaling pathways. The proteins in this family are uncharacterized, indicating that while their function as lipid hydrolases is predicted, further experimental validation is required to confirm their specific roles and mechanisms of action within the cell.
tRNA-dihydrouridine synthase-like (tRNA-DUS-like)
Type: Family

This family of proteins includes enzymes that catalyze the NAD(P)H-dependent synthesis of dihydrouridine, a modified base commonly found in the D-loop of tRNAs. Members of this family specifically modify uridine at position 20 in cytoplasmic tRNAs, contributing to the structural and functional diversity of tRNA molecules. Some family members are also capable of modifying certain mRNAs, which can influence their translation. Additionally, certain members of this family are involved in cellular regulatory mechanisms, such as the negative regulation of EIF2AK2/PKR activation, which is a protein kinase involved in the response to viral infection and other cellular stresses.
ATP-dependent Helicase/E3 Ubiquitin Ligase (ATP-helicase/E3_Ub-Ligase)
Type: Family

This family of proteins includes ATP-dependent helicases and E3 ubiquitin-protein ligases. Members are involved in pathways that maintain genomic integrity and are implicated in DNA repair processes. The ATP-dependent helicases likely unwind DNA or remodel chromatin, which is crucial during DNA replication, repair, and transcription. The E3 ubiquitin-protein ligases in this family specifically modify PCNA with non-canonical poly-ubiquitin chains linked through 'Lys-63', a post-translational modification that is important for DNA damage tolerance pathways. Additionally, these ligases accept ubiquitin from certain E2 complexes, highlighting their role in the ubiquitin-proteasome system.
Pre-mRNA Spliceosomal U2 snRNP Complex Component (U2_snRNP_Complex_Component)
Type: Family

This family of proteins is involved in the splicing of pre-mRNAs, a critical step in gene expression where introns are removed from transcribed pre-mRNAs. Members of this family are essential components of the spliceosome, particularly the 17S U2 snRNP complex, which is crucial for early spliceosome assembly and the recognition of the intron branch site. They facilitate the stable binding of U2 snRNP to the branchpoint sequence in pre-mRNA and are necessary for the assembly of the 'A' complex. Additionally, these proteins may play a role in the assembly of the 'E' complex and participate in the splicing of U12-type introns as part of the minor spliceosome. Some members may also be involved in cellular responses to temperature changes and potentially in the endoplasmic reticulum-associated protein degradation pathway.
Lipid raft-associated zinc-type alcohol dehydrogenase (Lipid_raft_assoc_Zn_ADH)
Type: Family

This family of proteins includes members that are associated with lipid rafts and are involved in the targeting and transport of specific proteins from the Golgi to the plasma membrane. Some family members may also facilitate the clustering of these target proteins, which is important for their incorporation into lipid rafts and subsequent transport to the cell surface. Additionally, certain proteins within this family are characterized by the presence of a zinc-containing alcohol dehydrogenase domain, suggesting a role in enzymatic activities related to quinone oxidoreductase functions within the mitochondrial context.
Activating signal cointegrator 1 complex subunit 2 (ASCC2)
Type: Family

The ASCC2 family comprises ubiquitin-binding proteins that play a crucial role in DNA repair and the ribosome quality control (RQC) pathway. Members of the family are involved in the rescue of stalled ribosomes and the degradation of nascent peptide chains during problematic translation. They function as part of the ASCC complex, recruiting other components such as ASCC3 and ALKBH3 to sites of DNA damage by binding to proteins with 'Lys-63'-linked polyubiquitin chains. Additionally, they are implicated in enhancing the transactivation of NF-kappa-B, SRF, and AP1. The family is characterized by the presence of a CUE domain that specifically binds RPS20/uS10 ubiquitinated by ZNF598, which is essential for the recruitment of the RQT complex on stalled ribosomes, leading to their disassembly.
TELO2-interacting protein 1 homolog (TELO2-interacting_protein_1)
Type: Family

This family of proteins is involved in the regulation of cellular responses to nutrient availability and the DNA damage response. Members function as components of complexes such as TORC1, TORC2, and the TTT complex, playing roles in cell growth, survival, and chromatin remodeling. They are essential for the stabilization of phosphatidylinositol 3-kinase-related protein kinase family proteins and may assist in their proper folding in conjunction with HSP90. These proteins are also crucial for the assembly and maintenance of mTORC1 and mTORC2 complexes, which are key regulators of cellular metabolism.
Kelch domain-containing protein (Kelch_domain_protein)
Type: Family

This family of proteins includes members that contain Kelch motifs, which are typically involved in protein-protein interactions. The Kelch motif is a sequence of approximately 50 amino acids that forms a beta-propeller structure. Proteins with Kelch domains are known to participate in a variety of cellular functions, including but not limited to cytoskeleton organization, cellular morphology, and signal transduction. They often act as scaffolds that bring together other protein complexes or as substrate-specific adaptors in ubiquitination processes. Given the diversity of Kelch domain-containing proteins, the specific functions of this family may vary between members and could include roles in cell division, maintenance of cell shape, and response to oxidative stress.
Arf-GAP with dual PH domain-containing protein (Arf-GAP_dual-PH_domain)
Type: Family

This family of proteins includes GTPase-activating proteins (GAPs) for the ADP ribosylation factor family. Members are involved in modulating the activity of ADP ribosylation factors by accelerating the hydrolysis of GTP to GDP, thereby inactivating the GTPase function of these factors. These proteins are characterized by the presence of dual pleckstrin homology (PH) domains and exhibit lipid-binding properties. They interact with a variety of phosphoinositides, including phosphatidylinositol 3,4,5-trisphosphate (PtdInsP3) and inositol 1,3,4,5-tetrakisphosphate (InsP4), with some members also binding other phosphoinositides at lower affinities. The binding to InsP4 typically occurs with a stoichiometry of two binding sites per protein, both having identical affinity.
Stress and Virulence-Associated Domain-Containing Protein (Stress/Virulence-Domain)
Type: Family

This family of proteins includes members that are involved in various cellular responses to environmental stimuli. Some proteins in this family are implicated in adaptive responses to nutrient deprivation, potentially playing a role in cellular survival mechanisms under stress conditions. Other members are suggested to be involved in the regulation of virulence factors, including the production of compounds that contribute to pathogenicity in certain bacteria. The family is characterized by the presence of conserved domains, which may be associated with their functional roles in stress response and virulence regulation.
Probable calcium-binding protein CML21-like (CML21-like)
Type: Family

This entry represents a family of proteins mainly found in plants, including Probable calcium-binding protein CML21 from Arabidopsis thaliana, which is probably involved in calcium-dependent signalling processes.
LRR Receptor-like Kinase (LRR-RLK)
Type: Family

This family of proteins includes receptor-like kinases that are implicated in various cellular processes. Members of this family are characterized by the presence of leucine-rich repeat (LRR) domains, which suggest a role in protein-protein interactions, and kinase domains that indicate a function in phosphorylation signaling pathways. The kinases in this family are predominantly serine/threonine-specific, although one member is a tyrosine-specific kinase. These proteins are likely involved in the regulation of cell proliferation, growth, and development, particularly in vascular tissues. The diversity of the kinase domain specificity within this family points to a broad range of potential substrates and functions.
Microtubule-associated AKAP9-binding protein (MT-associated_AKAP9-binding)
Type: Family

This family of proteins is involved in the regulation of microtubule dynamics and cellular architecture. Members of this family function as scaffolding proteins that anchor key signaling molecules, particularly those involved in the cAMP-dependent pathway, to specific cellular structures like the Golgi apparatus and centrosomes. They play a crucial role in promoting microtubule assembly and are implicated in various cellular processes such as directed cell migration, mitotic spindle orientation, and cell-cycle progression. These proteins are capable of forming complexes with other proteins, such as AKAP9, CAMSAP2, EB1/MAPRE1, and CDK5RAP2, to facilitate the nucleation and extension of microtubules from the centrosome towards the cell periphery, which is essential for maintaining cell polarity and ensuring proper cell division.
J domain-containing protein (J_domain-containing_protein)
Type: Family

This family of proteins includes J domain-containing proteins that function as molecular co-chaperones. They are involved in the assembly of histones onto DNA, which is a critical step in the formation of nucleosomes and chromatin structure. These proteins form complexes with histone H3-H4 heterodimers and other chaperones to facilitate nucleosome assembly. They also interact with the HSP70 family of heat shock proteins to maintain histone structural integrity during stress conditions. Additionally, they may recruit various histone chaperones to assist in histone management and chromatin dynamics.
Leucine-rich repeat-containing protein 69/Receptor-like (LRRC69/RLP)
Type: Family

The LRRC69/RLP family is involved in the perception and response to extracellular signals that regulate meristem maintenance and root growth. Members of the family, such as CLV2 in Arabidopsis, are receptor-like proteins that detect CLV3 and CLV3-like peptides. These peptides are crucial for controlling stem cell population size in apical meristems and during organ development. Some family members contribute to plant defense by recognizing nematode-secreted effector proteins, which mimic plant CLE signaling peptides, thus playing a role in the development of nematode feeding structures and infection success. Additionally, the family includes proteins with a predicted inactive kinase domain, suggesting diverse functional roles and regulatory mechanisms within the family.
Activating Molecule in BECN1-Regulated Autophagy (AMBRA1_autophagy)
Type: Family

The AMBRA1 family proteins are substrate-recognition components of the DCX E3 ubiquitin-protein ligase complex, playing a pivotal role in cell cycle control and autophagy. They mediate polyubiquitination and degradation of various target proteins, including BECN1 and cyclin-D, thereby regulating the G1 to S phase transition and maintaining genomic integrity. The AMBRA1 family also modulates the BECN1-PIK3C3 complex, essential for autophagosome nucleation and protein turnover, particularly during neuronal development. Additionally, these proteins are involved in mitophagy, either by interacting with PRKN and LC3 proteins or by acting as cofactors for ubiquitination enzymes. They contribute to Treg differentiation by promoting FOXO3 dephosphorylation and are implicated in intracellular trafficking and transcription regulation. The family's interaction with dynein light chains and protein phosphatase 2A highlights its role in cytoskeletal tethering and signal transduction.
Immunoglobulin superfamily CEA-related (IgSF_CEA-related)
Type: Family

This family of proteins is part of the immunoglobulin superfamily and is involved in cell adhesion processes. Members of this family are characterized by the presence of immunoglobulin-like domains, which are typically responsible for mediating interactions between cells or between cells and the extracellular matrix. These proteins may play roles in cellular signaling, immune response, or the maintenance of tissue integrity. Given the reference to carcinoembryonic antigen-related cell adhesion molecules, they may also be implicated in cancer biology, either in tumor progression or as markers for certain types of cancer.