SII-SWORD/CoKE huggingface dataset:
SLC43A Amino Acid Transporter (SLC43A_AATransporter)
Type: Family

This family of proteins includes transporters that are part of the SLC43A transporter group, classified under TC 2.A.1.44. Members of this family are involved in the transport of various amino acids across cellular membranes. They are characterized by their ability to transport cationic amino acids such as L-arginine, L-lysine, and to a lesser extent, L-histidine and ornithine. Some family members are selective for L-arginine and do not require other inorganic ions for transport. Others may facilitate the net uptake of L-tyrosine and maintain intracellular pools of aromatic and large neutral amino acids through exchange mechanisms. These transporters play crucial roles in cellular processes such as gametogenesis, amino acid homeostasis, and are essential for parasite survival and virulence.
Nuclear receptor coactivator/corepressor (Nuc_rcpt_coact/corep)
Type: Family

This family of proteins serves as nuclear receptor coregulators, possessing the ability to interact with nuclear receptors and modulate their activity. These proteins contain a conserved Leu-Xaa-Xaa-Leu-Leu (LxxLL) motif, which is crucial for their association with nuclear receptors. They are involved in the coactivation of nuclear steroid receptors, such as estrogen receptors, and can also function as corepressors for certain genes like MYC in response to hormonal signals. Additionally, they may play a role in maintaining adult pluripotent stem cell populations.
Plasmanylethanolamine desaturase (Plasmalogen_desaturase)
Type: Family

This family of proteins includes enzymes that are involved in the biogenesis of plasmalogens within the endoplasmic reticulum membrane. Plasmalogens are a type of glycerophospholipid characterized by a vinyl ether bond at the glycerol sn-1 position. These enzymes exhibit desaturase activity, introducing a double bond into the alkyl chain of plasmanylethanolamine. Plasmalogens play roles in antioxidative and signaling mechanisms. In one member, the enzyme is also implicated in sensing photooxidative stress and participating in light-dependent signaling pathways.
Growth and transcription regulation protein (Growth_transcription_reg)
Type: Family

This family of proteins includes members involved in various cellular processes. Some proteins in this family are necessary for normal growth rates when utilizing specific sugars such as galactose and mannose. Other members are implicated in the regulation of gene expression, potentially acting as coactivators for hormone receptors and mediating the degradation of certain signal transducer proteins. Additionally, these proteins may have a role in intracellular transport, particularly in the retrograde movement of materials from endosomes to the Golgi apparatus and from the Golgi to the endoplasmic reticulum. The family also includes proteins that can bind to viral elements and inhibit transcriptional activation by general transcription factors.
EF-hand calcium-binding domain-containing protein 6 (EFCB6)
Type: Family

This family of proteins is involved in the regulation of the androgen receptor through a negative feedback mechanism that includes the recruitment of a histone deacetylase complex. Members of this family are also implicated in the structural integrity of cilia, specifically as microtubule inner proteins within the axoneme of motile cilia. They are essential for the proper beating of cilia, as they are part of the dynein-decorated doublet microtubules. Additionally, there is an interaction with protein DJ-1, which can counteract the inhibitory effect on the androgen receptor by disrupting the associated complex.
Mitochondrial Tim protein assembly helper (Mito_Tim_assembly_helper)
Type: Family

This family of proteins is involved in mitochondrial protein import and assembly processes. Specifically, they assist in the assembly or recycling of small Tim proteins within the mitochondrial intermembrane space. These proteins play a crucial role in the correct import and insertion of multi-pass transmembrane proteins into the mitochondrial inner membrane, likely by aiding in the formation of disulfide bonds in small Tim proteins.
Fungal transcription regulator (Fungal_trans_regulator)
Type: Family

This family of proteins includes transcription factors that are key regulators of various cellular processes in fungi. Members of this family act as positive regulators of acid phosphatase activity and are crucial for the response to nitrogen and carbon starvation. They play a significant role in vegetative incompatibility, a system for non-self-recognition that leads to programmed cell death. Some members are also involved in meiosis and sporulation, recognizing specific DNA sequences to activate the transcription of genes necessary for these processes. Additionally, they can influence drug sensitivity, hyphal growth, biofilm formation, and virulence by regulating the expression of genes related to ergosterol biosynthesis, cell wall components, and cell separation.
DnaJ domain-containing protein (DnaJ_domain_protein)
Type: Family

This family of proteins includes members that are part of the DnaJ family, which are known to be involved in molecular chaperone activities. These proteins typically contain a J domain and are implicated in the modulation of protein synthesis and folding. They play a crucial role in assisting the Hsp70 chaperone machinery by stimulating ATPase activity, which is essential for the proper folding of nascent polypeptide chains and the refolding of misfolded proteins. Members of this family may also be involved in various cellular processes, including protein transport, degradation, and signaling pathways.
Centrosomal protein 104 kDa-like (CEP104-like)
Type: Family

This family of proteins is involved in the process of ciliogenesis, which is the formation of cilia on the cell surface. These proteins also play a crucial role in maintaining the structural integrity at the ciliary tip, which is essential for the proper function of cilia. Cilia are hair-like structures that extend from the surface of many eukaryotic cells and are involved in various functions, including motility, sensory perception, and signal transduction.
U-box domain-containing protein (U-box_domain_protein)
Type: Family

This family of proteins includes E3 ubiquitin ligases that are involved in the post-translational modification of proteins by attaching ubiquitin molecules. These modifications often target proteins for degradation via the ubiquitin-26S proteasome pathway. Members of this family play roles in various cellular processes, including the regulation of brassinosteroid signaling, prevention of premature senescence, and abscisic acid biosynthesis through the targeted degradation of specific proteins involved in these pathways.
Ribosome Biogenesis Regulator (Ribosome_Biogenesis_Reg)
Type: Family

This family of proteins is involved in ribosome biogenesis and the regulation of the p53/TP53 pathway. Members of this family play a crucial role in the development of hematopoietic stem cells and are also required for the processing of pre-rRNA, which is a fundamental step in the assembly of the 60S ribosomal subunit. These proteins are associated with nucleolar pre-ribosomal complexes, indicating a role in early stages of ribosome assembly.
Basic helix-loop-helix transcription regulator (bHLH_transcription_regulator)
Type: Family

This family of proteins includes transcription factors characterized by the basic helix-loop-helix (bHLH) domain, which is involved in DNA binding and dimerization. Members of this family are known to regulate the expression of various genes and are involved in multiple biological processes. One member is specifically noted to act as a transcription activator, regulating the expression of genes related to the formation of endoplasmic reticulum bodies and symbiotic interactions with endophytic fungi. These proteins play a role in plant development and response to environmental stimuli.
Plant receptor-like kinase with LysM domain-containing protein (Plant_RLK_LysM)
Type: Family

This family of proteins includes receptor-like kinases with a role in plant innate immunity and symbiotic interactions. Members are involved in the perception of microbial signals, such as Nod factors and chitooligosaccharides, which are crucial for initiating plant defense responses and symbiotic nodule formation. Some proteins in this family possess LysM domains that bind chitooligosaccharides, contributing to the recognition of pathogen-associated molecular patterns and microbe-associated molecular patterns. This recognition triggers immune responses and symbiotic processes, including the formation of infection threads and nodule primordia in legumes. Additionally, members of this family are implicated in resistance to various pathogens, including oomycetes and fungi.
Atrial Natriuretic Peptide Clearance Receptor (ANP_Clearance_Receptor)
Type: Family

This family of proteins serves as receptors for natriuretic peptide hormones, including atrial natriuretic peptide (ANP), brain natriuretic peptide (BNP), and C-type natriuretic peptide (CNP). They bind these peptides with similar affinities and are implicated in the clearance of these hormones, thereby regulating their local concentrations and physiological effects. These receptors are involved in the modulation of diuresis, blood pressure, and skeletal development. Notably, they lack guanylate cyclase activity, differentiating them from other natriuretic peptide receptors that possess this enzymatic function.
LicD transferase (LicD_transferase)
Type: Family

This family of proteins includes enzymes that catalyze the transfer of ribitol 5-phosphate from CDP-L-ribitol to a phosphorylated O-mannosyl trisaccharide structure present in alpha-dystroglycan, which is a crucial step in the post-translational modification of this protein. The modification involves the formation of a ribose 5-phosphate tandem repeat, linking the trisaccharide to a ligand-binding domain composed of xylosyl and glucuronic acid repeats. This process is essential for the proper functioning of alpha-dystroglycan, which plays a significant role in cell-matrix interactions and is important for the stability of muscle tissue and neuronal migration.
Cilia-Flagella-Associated Protein 65 (CFAP65)
Type: Family

Cilia-Flagella-Associated Protein 65 (CFAP65) is involved in the structural and functional integrity of cilia and flagella. This protein is implicated in the process of flagellar formation and is essential for proper sperm motility, suggesting a role in reproductive biology. CFAP65's function in flagellar assembly indicates its importance in the motility and sensory functions of cilia and flagella across different species .
Fibroblast growth factor receptor-like (FGFRL)
Type: Family

This family of proteins is characterized by a conserved role in negatively regulating cell proliferation. Members of this family are found across different species, suggesting a conserved biological function in growth control mechanisms. The proteins in this family share a homologous structure that is likely to be involved in the interaction with other cellular components to modulate proliferative signaling pathways, contributing to the maintenance of cellular homeostasis.
SYO1-like (SYO1-like)
Type: Family

SYO1 and HEATR3 are involved in ribosome biogenesis and nuclear import, functioning as adaptor proteins that facilitate the transport of ribosomal components into the nucleus. Specifically, SYO1 acts as a nuclear import adaptor that recruits the functionally and topologically linked ribosomal proteins RPL5 and RPL11 . HEATR3 also contributes to ribosome biogenesis by mediating the nuclear import of the 60S ribosomal protein RPL5, also known as large ribosomal subunit protein uL18 . These proteins are essential for the proper assembly of the ribosome, ensuring the coordinated delivery of RPL5 and RPL11 to the nascent 5S rRNA within the nucleus. In addition to their roles in ribosome assembly, they are critical for erythrocyte maturation, highlighting their broader importance in cellular development and function.
Huntingtin-interacting protein K (Huntingtin-int_K)
Type: Family

The Huntingtin-interacting protein K family comprises components of N-terminal acetyltransferase complexes, specifically inhibiting the N-terminal acetylation activity of the NatA complex. Members of the family exhibit chaperone-like activity that prevents polyglutamine aggregation in neuronal cells, potentially while associated with the NatA complex. Additionally, they may be involved in the NatA complex-mediated N-terminal acetylation of proteins such as PCNP. One member is known to contact the emerging nascent chain on the ribosome, indicating a role in early protein synthesis processes.
Complex I NDUFA12 subunit (ComplexI_NDUFA12)
Type: Family

The NDUFA12 subunit family is involved in the assembly and function of mitochondrial complex I, which is a critical component of the respiratory chain. Members of the family act as molecular chaperones, facilitating the correct assembly of complex I. This complex plays a pivotal role in cellular energy production by transferring electrons from NADH to ubiquinone, initiating a series of redox reactions that ultimately drive ATP synthesis. The family's contribution to the maintenance of the electron transport chain is essential for the generation of metabolic energy in eukaryotic cells.
Bacteriophage lysozyme-like (Phage_lysozyme-like)
Type: Family

This family of proteins includes lysozymes with enzymatic activity that degrade bacterial cell walls by breaking down peptidoglycan. These proteins are involved in bacteriophage-host interactions, facilitating the release of viral particles through host cell lysis. They act in concert with other phage proteins such as holins and spanins to breach the host cell membrane, allowing access to the periplasmic space. Within this space, they perform localized hydrolysis of the cell wall, enabling phage DNA delivery into the host. Additionally, they play roles in phage tail assembly and are essential for the penetration of the tail tube through the bacterial envelope.
ELYS/MEL-28 Nuclear Assembly Factor (ELYS/MEL-28_NucAsmblyFactor)
Type: Family

The ELYS family proteins are essential for the assembly of a functional nuclear pore complex (NPC) on chromatin surfaces as nuclei form post-mitosis. They may initiate NPC assembly by binding to chromatin and recruiting the Nup107-160 subcomplex. Additionally, they play a role in localizing the Nup107-160 subcomplex to the kinetochore during mitosis and are implicated in cytokinesis completion. Some family members are suggested to interact with transcriptionally active chromatin, potentially functioning as transcription factors, particularly in hematopoietic tissues. The N-terminus of these proteins is characterized by a conserved seven-bladed beta propeller structure, which, along with a central alpha domain, mediates anchorage to the Nup107-160 subcomplex. The C-terminus, typically disordered, is responsible for chromatin interactions. In some species, ELYS family proteins may also coordinate nuclear assembly with replication licensing inactivation by interacting with the mcm2-mcm7 complex.
Cell Proliferation and Cornified Envelope Regulator (Cell_Prolif/Cornif_Regul)
Type: Family

The protein family in question appears to be involved in diverse biological processes related to cellular structures and functions. Members of the family are implicated in the regulation of cellular proliferation and differentiation, which are fundamental aspects of cell biology influencing tissue development and homeostasis. Additionally, some family members are suggested to play a role in the assembly or regulation of the cornified envelope, a structure essential for the barrier function of the skin. The LIM domain within these proteins may facilitate specific protein-protein interactions, potentially guiding the localization and function of the family members within cellular compartments.
Glycosyltransferase group 1 domain-containing protein (Glycosyltransferase_G1)
Type: Family

This family of proteins includes enzymes that are part of the glycosyltransferase group 1. Members of this family are characterized by their ability to catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. This process is crucial for the biosynthesis of important biomolecules, including glycoproteins, glycolipids, and polysaccharides. These enzymes play a key role in various biological processes such as cell signaling, cell adhesion, and the immune response. The glycosyltransferase 4 subfamily, to which these proteins belong, suggests a specificity towards certain substrates or a distinct functional role within the broader group 1 glycosyltransferases.
Dynein axonemal assembly factor 5 (DAAF5)
Type: Family

This family includes Dynein axonemal assembly factor 5 (DAAF5). Members of this family are cytoplasmic and play a crucial role in the formation of the dynein inner and outer arms, which are essential for the movement of cilia. These arms are attached to the peripheral outer doublet A microtubule of the axoneme, the core structural component of a cilium .

DAAF5 is a cytoplasmic protein involved in the delivery of the dynein machinery to the motile cilium. It is required for the assembly of the axonemal dynein inner and outer arms, two structures attached to the peripheral outer doublet A microtubule of the axoneme, that play a crucial role in cilium motility .
Cysteine-rich motor neuron 1 (CRIM1)
Type: Family

This family of proteins is implicated in central nervous system (CNS) development, specifically in the differentiation and survival of motor neurons. Members of this family interact with growth factors that are critical for these processes. Additionally, some members are involved in angiogenesis, contributing to capillary formation and maintenance. They also modulate bone morphogenetic protein (BMP) activity by influencing its processing and cellular delivery, which can impact various developmental and physiological pathways.
Chlorophyll b Reductase (Chl_b_Red)
Type: Family

This family of proteins is involved in the degradation of chlorophyll b, a process essential for the proper turnover and recycling of chlorophyll molecules during plant development and stress responses. Members of this family function as chlorophyll(ide) b reductases, enzymes that catalyze the reduction of chlorophyll b to chlorophyll a, which is a key step in the chlorophyll catabolic pathway. These proteins are part of the short-chain dehydrogenases/reductases (SDR) superfamily and are also classified as chlorophyll catabolic enzymes (CCEs). They are localized within the chloroplast and can utilize various chlorophyll b derivatives as substrates.
SWT1 Transcriptional Regulator (SWT1_Regulator)
Type: Family

This family of proteins is involved in transcriptional regulation. Members are likely to function as transcriptional activators, playing a role in the control of gene expression by modulating the transcription process.
von Willebrand factor A domain-containing protein (VWA_domain-containing)
Type: Family

This family of proteins includes members that contain the von Willebrand factor A (VWA) domain, which is typically involved in cell adhesion and migration. These proteins are known to participate in various biological processes including signal transduction, extracellular matrix formation, and possibly in the blood coagulation pathway. The VWA domain mediates interactions with other proteins, and its presence suggests a role in protein-protein interaction networks essential for cellular function and communication.
Cilia- and flagella-associated protein 70 (CFAP70)
Type: Family

This family of proteins is involved in the structural and functional organization of cilia and flagella. Members of this family are axoneme-binding proteins that contribute to the regulation of ciliary and flagellar motility, as well as the determination of cilium length. While the conserved TPR domains within these proteins are not essential for ciliary targeting, the N-terminal region is crucial for proper localization to cilia and/or interaction with the axoneme structure. These proteins are implicated in the regulation of the outer dynein arm, which is a critical component for the movement of cilia and flagella.
Tetratricopeptide repeat protein 17 (TTC17)
Type: Family

The TTC17 family is implicated in the process of primary ciliogenesis, specifically through the modulation of actin polymerization. The proper formation and function of primary cilia are crucial for various cellular signaling pathways, and defects in ciliogenesis can lead to a range of ciliopathies. By influencing actin dynamics, the TTC17 family plays a vital role in the structural organization required for cilia formation, thus contributing to cellular homeostasis and signaling.
Paired homeobox Bicoid subfamily (Paired_homeobox_Bicoid)
Type: Family

This family of proteins includes transcription factors that are characterized by the presence of a homeobox domain, which is indicative of their role in DNA binding and regulation of gene expression. Members of this family are implicated in growth regulation and developmental processes, including the formation of body structures and neural systems that process somatosensory information. Some members may also be involved in heart development. The functions of these proteins are critical for controlling fundamental aspects of growth and development, and they may have specific roles in skeletal patterning and morphogenesis.
MICOS complex subunit Mic19 (MICOS_subunit_Mic19)
Type: Family

This family of proteins is involved in the structural organization of the mitochondrial inner membrane. Members function as components of the MICOS complex, which is essential for the formation and maintenance of crista junctions, the overall architecture of the inner membrane, and the establishment of contact sites with the outer membrane. Some members have been identified to have a dual role, also acting as transcription factors that can influence gene expression, such as repressing the transcription of BAG1. They are critical for maintaining the stability of the MICOS complex and the characteristic morphology of mitochondrial cristae.
GRAM domain-containing protein 2B (GRAM_domain_protein_2B)
Type: Family

This family of proteins includes GRAM domain-containing protein 2B across various species. The GRAM domain is a protein domain that typically binds phosphoinositides, which are important signaling molecules in cells. Proteins with GRAM domains are often involved in membrane-associated processes due to their lipid-binding properties. They may participate in cellular signaling pathways, membrane trafficking, or cytoskeletal organization. The specific functions of GRAM domain-containing protein 2B may include interactions with other proteins or lipids, contributing to cellular homeostasis and signaling networks. As members of this family are found in different organisms, they likely play a conserved role in cellular physiology.
Sperm flagellar development and bone growth associated protein (Sperm_flagellar-bone_growth)
Type: Family

This family of proteins is involved in the structural and functional integrity of sperm flagella, specifically in axoneme development, which is crucial for sperm motility. These proteins are also key for the proper formation of the manchette and sperm head, impacting sperm morphology. Their essential role in male fertility is underscored by their contribution to the localization of intraflagellar transport proteins, such as IFT20, to the manchette, indicating a function in dynein-mediated protein transport during spermatogenesis. Beyond reproductive functions, these proteins are implicated in bone growth, where they appear to be necessary for the differentiation of osteoblasts, the cells responsible for bone formation.