SII-SWORD/CoKE huggingface dataset:
Immune Signaling and Apoptosis Regulator (Immune_Signaling-Apoptosis_Reg)
Type: Family

This family of proteins includes transmembrane adaptors and mediators that function as scaffolds for Src-family kinases and other signaling proteins in immune cells. They are involved in signaling transduction pathways such as major histocompatibility complex class II (MHC-II) in B cells, enhancing calcium response and ERK activity upon stimulation. These proteins also sustain signaling in dendritic cells after activation by fungal beta-glucans and act as agonist-inducible signaling adapters for various Toll-like receptors, enabling the expression of pro-inflammatory cytokines. Additionally, the family encompasses proteins that are part of the Bcl-2 family, which are involved in the regulation of apoptosis and anoikis through interactions mediated by the BH3 motif. Another member is implicated in meiotic processes, particularly in chromosome synapsis and the formation of double-strand breaks in spermatocytes.
Interleukin enhancer-binding factor 2 (ILF2)
Type: Family

This family of proteins interacts with chromatin and forms stable heterodimers with interleukin enhancer-binding factor 3 (ILF3). They are involved in various biological processes, including transcription, innate immunity, and cell growth. These proteins are crucial for the nuclear reshuttling of ILF3 isoforms and form an RNA-binding complex essential for mitotic progression and cytokinesis by regulating mitotic gene expression. They also compete with STAU1/STAU2-mediated mRNA decay and play a role in inhibiting the replication of certain viruses, such as Japanese encephalitis virus and enterovirus 71. In humans, they have been implicated in stabilizing HIV-1 RNA, thus promoting HIV-1 virus production.
Tumor Necrosis Factor Receptor Superfamily Member 5 (TNFRSF5)
Type: Family

The Tumor Necrosis Factor Receptor Superfamily Member 5 family comprises receptors that bind to TNFSF5/CD40LG. These receptors are pivotal in immune system regulation, particularly in macrophages and B cells. Upon ligand binding, they initiate signaling cascades involving TRAF6 and MAP3K8, which subsequently lead to the activation of ERK. This activation is crucial for the induction of immunoglobulin secretion, a key process in the adaptive immune response. The family plays a significant role in the communication between T cells and B cells, and is essential for the proper functioning of the immune system.
Adipolin/Erythroferrone-related (Adipolin/Erythroferrone-rel)
Type: Family

This family of proteins includes adipokines and iron-regulatory hormones with diverse roles in metabolism, iron homeostasis, and cellular signaling. Members are secreted by adipocytes and erythroblasts, influencing glucose metabolism in liver and adipose tissue, and regulating iron absorption and mobilization. They are involved in the activation of signaling pathways such as PI3K-Akt and MAP kinase, affecting processes like glucose uptake, lipid uptake, and suppression of gluconeogenesis. Some members also play roles in the suppression of apoptosis, inflammation, autophagy, and the differentiation of osteoblasts, with implications for bone resorption and cardiovascular health.
Universal small ribosomal subunit uS15 (uS15_ribosomal)
Type: Family

This family of proteins is involved in the structure and function of the ribosome, which is essential for protein synthesis in all living cells. Members of this family are part of the small ribosomal subunit and play a role in the assembly and stability of the ribosome. One member has been noted to be essential for gut mitochondrial activity and may be involved in tissue-specific growth factor production, suggesting additional specialized functions beyond the general role in ribosome structure.
GATA Zinc Finger Domain-Containing (GATA_ZnFinger_Domain)
Type: Family

The GATA zinc finger domain-containing protein family includes transcriptional regulators that bind specific DNA motifs to modulate various biological processes. Members of this family are involved in chloroplast development, influencing chlorophyll biosynthesis and plant growth. They play roles in cytokinin and gibberellic acid signaling pathways, affecting flowering, greening, germination, senescence, and elongation growth. Additionally, they regulate sugar-sensing genes and contribute to starch content in leaves. Some members also influence biofilm formation, hyphal growth, and virulence in fungi, demonstrating a functional diversity across different organisms.
Methylosome Component WDR77 (Methylosome_Comp_WDR77)
Type: Family

This family of proteins includes non-catalytic components of the methylosome complex, which is involved in the post-translational modification of specific arginines to dimethylarginines in spliceosomal Sm proteins and histones. These modifications are crucial for targeting Sm proteins to the survival of motor neurons (SMN) complex, facilitating their assembly into small nuclear ribonucleoprotein core particles. Additionally, these proteins are implicated in the methylation of Piwi proteins, a process necessary for their interaction with Tudor domain-containing proteins and subsequent localization to the meiotic nuage. Some members also function in the ubiquitination and degradation of immune regulatory GTPases in intestinal cells and may play roles in transcription regulation and the localization of cytoplasmic proteins during cellular processes such as oogenesis.
Developmental Signaling Hedgehog-like (Dev_Signal_Hedgehog-like)
Type: Family

This family of proteins includes members that are essential for various developmental patterning events. They function as intercellular signals that are crucial for proper morphological development. One member is specifically required for cuticle shedding and the formation of normal alae structures, which are vital for larval development. Additionally, several members of this family share a similarity with the hedgehog family of proteins, suggesting a conserved role in signaling and developmental processes.
Calmodulin Regulator PCP4-like (Calmodulin_Regulator_PCP4-like)
Type: Family

This family of proteins functions as modulators of calcium-binding by calmodulin, regulating its activity and the various processes it controls. Members of this family are characterized by an intrinsically disordered nature, with some residual structure primarily in the IQ domain. This domain is responsible for mediating interactions with calmodulin. Through their regulatory role, these proteins may influence neuronal differentiation by modulating calmodulin-dependent kinase signaling pathways.
Mitochondrial Large Ribosomal Subunit bL36m (Mitoribosomal_bL36m)
Type: Family

This family of proteins is involved in the structure and function of mitochondrial ribosomes, which are specialized for the synthesis of proteins encoded by the mitochondrial genome. These proteins are integral components of the large subunit of mitoribosomes and are thought to play a role in the cotranslational integration of newly synthesized proteins into the mitochondrial inner membrane. Additionally, there is evidence suggesting a potential involvement in telomere capping processes.
piRNA biogenesis EXD1-related protein (piRNA_biogenesis_EXD1)
Type: Family

This family of proteins is involved in the piRNA metabolic process, which is crucial for the repression of transposable elements during meiosis. Members of this family form part of the PET complex, a multiprotein assembly essential for piRNA processing during spermatogenesis. These proteins act as RNA adapters within the complex and are associated with the loading of Piwi proteins with piRNAs. Although they possess a 3'-5' exonuclease domain, they lack the critical DEDD residues necessary for catalytic activity, rendering them inactive exonucleases. The family plays a significant role in maintaining germline integrity by preventing the mobilization of transposable elements.
Mediator complex and homeobox domain-containing protein (Mediator/Homeobox_domain)
Type: Family

This family of proteins includes components of the Mediator complex, which are coactivators involved in the transcription regulation of RNA polymerase II-dependent genes. They function as a bridge between gene-specific regulatory proteins and the basal transcription machinery, facilitating the assembly of a preinitiation complex. Members of this family are also involved in various developmental processes, including neuronal differentiation, eye development, and limb morphogenesis. Some proteins within this family may regulate the expression of neural basic helix-loop-helix genes, influencing patterns of neuronal differentiation and development in specific regions of the nervous system.
High-osmolarity-induced transcription (HOT1)
Type: Family

The HOT1 family proteins are involved in the transcriptional response to osmotic stress. They are required for the complete activation of genes that respond to changes in osmotic conditions, ensuring cellular adaptation and survival. Members of the HOT1 family may also interact with other proteins, such as HOG1, to facilitate the recruitment of RNA polymerase II to the promoters of target genes, further enhancing the transcriptional response. Additionally, the family includes proteins that may function as transcriptional activators in various contexts, influencing the expression of genes related to glycolysis, invertase expression, and growth in iron-limiting conditions. Some members are also implicated in the ubiquitination processes at specific DNA motifs, playing a role in protein turnover and stress response regulation.
Phloem protein 2-like/Lectin (PP2-like/Lectin)
Type: Family

Phloem protein 2 (PP2) is one of the most abundant and enigmatic proteins in the phloem sap. PP2 is translocated in the assimilate stream where its lectin activity or RNA-binding properties can exert effects over long distances. PP2-like genes have been identified in many plant species, indicating a wide distribution of PP2 genes in the plant kingdom .

Phloem Protein2-Like A1 and Phloem Protein2-Like A2 are presumed to have roles in phloem function, although their specific functions remain uncharacterised. Some members of the family, like PP2-Like A5, contain a TIR domain which is implicated in NAD(+) hydrolase activity and is essential for self-association required for this activity .

Phloem lectins bind chito-oligosaccharides and may have hemagglutinating activity or be involved in plant defense by binding to the chitin cell wall of pathogens .
Dehydrogenase/reductase SDR family member 7C (SDR_family_member_7C)
Type: Family

The Dehydrogenase/reductase SDR family member 7C proteins are NADH-dependent oxidoreductases involved in the oxidation of all-trans-retinol to all-trans-retinal. They play a crucial role in the regulation of cardiac and skeletal muscle metabolic functions, maintaining Ca(2+) intracellular homeostasis by repressing Ca(2+) release from the sarcoplasmic reticulum in myotubes. These proteins are also implicated in controlling Ca(2+) overload in the cytosol and the sarcoplasmic reticulum. Additionally, they contribute to glucose uptake into skeletal muscles and enhance muscle performance by activating PI3K and mTORC2-mediated AKT1 phosphorylation signaling pathways, potentially through the production of all-trans-retinoic acid. The N-terminal region of these proteins is associated with the sarcoplasmic reticulum membrane, while the C-terminal catalytic domain is oriented towards the myoplasm.
17-beta-hydroxysteroid dehydrogenase type 3-like (17-beta-HSD3-like)
Type: Family

This family of proteins includes members that are structurally related to the short-chain dehydrogenases/reductases (SDR) superfamily, specifically the 17-beta-hydroxysteroid dehydrogenase (17-beta-HSD) type 3 subfamily. These enzymes are typically involved in the metabolism of steroid hormones, which is crucial for various physiological processes including sex differentiation, the development of secondary sexual characteristics, and the regulation of endocrine functions. Although most members of this family are described as inactive, they may still retain roles in the metabolism of steroid hormones or related regulatory pathways.
Methionine-R-sulfoxide reductase B1 (MsrB_Met_sulfoxide_reductase)
Type: Family

The Methionine-R-sulfoxide reductase B1 family comprises enzymes that catalyze the reduction of methionine (R)-sulfoxide to methionine, a reaction that can reverse post-translational modifications or oxidative stress effects. Members of the family are involved in regulating actin assembly by interacting with MICAL proteins to promote actin filament repolymerization. Additionally, they play a role in innate immunity by restoring oxidized actin to its reduced state, facilitating actin repolymerization in macrophages.
Complex I LYR motif-containing protein (Complex_I_LYR)
Type: Family

This family of proteins contains the LYR motif, which is indicative of a role in mitochondrial complex I assembly or function. Members of this family are likely involved in the biogenesis and maintenance of the mitochondrial respiratory chain, specifically complex I, which is responsible for the initial step of electron transport. The LYR motif is known to mediate interactions with iron-sulfur cluster assembly proteins, suggesting a role in the incorporation of iron-sulfur clusters into complex I subunits. As such, these proteins may be essential for cellular energy metabolism and mitochondrial function.
Multicopper oxidase LPR1/LPR2 (LPR1/LPR2)
Type: Family

Multicopper oxidase LPR1 and LPR2 are involved in copper homeostasis and oxidative stress response, particularly in the context of root growth and inorganic phosphate homeostasis in plants. Members of the family function in a common pathway that modulates root meristem activity in response to phosphate availability . LPR1 may contribute to the oxidative stress response by oxidizing various substrates, as shown with 2,2'-azinobis-(3-ethylbenzthiazoline-6-sulphonate) in vitro, suggesting a broader role in plant metabolism and environmental stress adaptation . LPR1 is involved in the regulation of the auxin response to Pi starvation and function in opposite ways in regulating the root growth response to Pi starvation in the endoplasmic reticulum compared to LPR2 .
DEVIL/RTFL Small Polypeptides (DVL/RTFL_small_peptides)
Type: Family

The DVL/RTFL small polypeptides family consists of regulatory molecules that play a crucial role in coordinating cellular responses essential for plant differentiation, growth, and development. Members of this family are involved in modulating processes such as polar cell proliferation in lateral organs and the recruitment and differentiation of socket cells at trichome sites. They are implicated in determining leaf shape, pedicule elongation, inflorescence organization, and fruit maturation, ensuring proper plant form and reproductive success.
Keratin-associated protein type 2-like (KRTAP_type_2-like)
Type: Family

Keratin-associated protein type 2 (KRTAP2) is involved in the structural integrity of hair. Members of this family are hair keratin-associated proteins (KRTAPs) that play a crucial role in the hair cortex. They are part of an interfilamentous matrix that embeds hair keratin intermediate filaments. These proteins are essential for creating a rigid and resistant hair shaft by forming extensive disulfide bond cross-linking with the cysteine residues of hair keratins . The matrix proteins are characterised by high-sulfur and high-glycine-tyrosine content, contributing to the durability and resilience of hair.
Bacterial biofilm regulation/maintenance (Biofilm_reg_signaling)
Type: Family

This family of proteins is involved in the regulation of bacterial biofilm formation and maintenance . Members of this family function in signaling cascades that control the transition between cellular states, such as motility and adhesion. Key activities include the synthesis and degradation of cyclic-di-GMP (c-di-GMP), a secondary messenger that modulates the expression of biofilm-related genes . Some proteins in this family act as diguanylate cyclases, catalyzing the formation of c-di-GMP , while others function as phosphodiesterases, breaking down c-di-GMP . This regulatory mechanism influences the biosynthesis of curli and the architecture of biofilms, impacting the three-dimensional structure and biomass accumulation within the biofilm matrix.
Branched-Chain Amino Acid Transport ATP-binding Protein LivF (BCAA_Transport_ATP-bd_LivF)
Type: Family

The LivF protein family is involved in the transport of branched-chain amino acids (BCAAs) such as leucine, isoleucine, and valine. Members of this family function as components of high-affinity transport systems that do not require sodium ions for activity. These systems are specialized for the uptake of BCAAs, which are essential nutrients in the cell. Some members are also capable of transporting alanine and threonine. The family belongs to the larger ABC transporter superfamily, which is characterized by the presence of ATP-binding domains that power the transport process.
Branched-chain amino acid transport system permease (BCAA_transport_permease)
Type: Family

The LivHM family is involved in the high-affinity transport of branched-chain amino acids (BCAAs) such as leucine, isoleucine, and valine. Members of this family function as part of a binding-protein-dependent transport system, which is likely responsible for the translocation of BCAAs across the cell membrane without the need for sodium ions. This system is specific not only for BCAAs but also for alanine and threonine, indicating a broader substrate specificity within the amino acid transport process. The permease proteins of the LivHM family play a crucial role in the uptake of essential amino acids, which are vital for protein synthesis and metabolic processes in the cell.
Isonitrile Hydratase and Quaternary Amine Regulator (INH-QAR)
Type: Family

This family of proteins includes enzymes and transcriptional regulators. The enzymes catalyze the hydration of isonitriles to formamides, likely playing a role in detoxification processes. They are sensitive to thiol and oxidizing reagents. The transcriptional regulators are involved in the metabolism of quaternary amines, such as choline and carnitine, by activating the transcription of genes involved in their catabolism and transport. These regulators are critical for the induction of specific genes in response to various metabolites and may be important for bacterial interactions with eukaryotes.
Bacterial competence-related DNA uptake protein (Competence_DNA_uptake)
Type: Family

This family of proteins appears to be involved in bacterial competence for transformation, a process where bacteria take up extracellular DNA from their environment. Members of this family may function as part of a membrane-bound pore complex known as the transformasome. They are likely to play roles in the binding, uptake, and internalization of transforming DNA, potentially acting as transporters or interacting directly with the DNA during translocation. Some members are essential for natural transformation, indicating a critical role in horizontal gene transfer and genetic diversity in bacterial populations.
Gypsy Retrotransposon Integrase-like (Gypsy_RT_Integrase-like)
Type: Family

This family of proteins includes integrase-like enzymes that are typically encoded by gypsy retrotransposons. These enzymes are responsible for integrating the retrotransposon DNA into the host genome, a process that is crucial for the replication and mobilization of these mobile genetic elements. The integrase-like proteins share similarities with integrases from retroviruses, possessing domains that facilitate the recognition of specific DNA sequences and the catalysis of the strand transfer reaction necessary for integration. The activity of these proteins is essential for the propagation of gypsy retrotransposons within the genome, which can have significant impacts on genome structure and function.
Mycobacterial Acyl-CoA Dehydrogenase (Mycobact_Acyl-CoA_DH)
Type: Family

The Acyl-CoA dehydrogenase family is involved in the beta-oxidation of cholesterol catabolism, contributing to the virulence of Mycobacterium tuberculosis by increasing the efficiency of this metabolic pathway. Members of this family catalyze the dehydrogenation of various CoA esters, including those with steroid side chains, playing roles in different cycles of side chain dehydrogenation. Specific functions include the conversion of 3-oxo-4-pregnene-20-carboxyl-CoA to 3-oxo-4,17-pregnadiene-20-carboxyl-CoA, the dehydrogenation of 5OH-HIP-CoA to 5OH-HIPE-CoA, and the transformation of (25S)-3-oxo-cholest-4-en-26-oyl-CoA to (24E)-3-oxo-cholest-4,24-dien-26-oyl-CoA. Some members also show activity with other steroyl-CoA substrates, indicating a broader substrate specificity within the family.
Two-component sensor kinase/Photoreceptor (Sensor_kinase/Photoreceptor)
Type: Family

This family of proteins includes sensor kinases and photoreceptors that are part of two-component regulatory systems, which are typically involved in environmental response and signal transduction. Members of this family are known to play roles in processes such as methyl sulfide metabolism, methanogenesis, and photoreception, with some acting as heme-binding sensors. They can exist in different forms that are interconvertible by light, absorbing in the red and far-red regions of the spectrum. Additionally, some members may be involved in the synthesis of quorum sensing signal molecules and the regulation of cellular morphology and metabolic fluxes. Others are implicated in nodulation and may function as protein kinases that phosphorylate response regulators in response to environmental signals.
Diguanylate Cyclase/Regulatory Protein (DGC-Regulatory_Protein)
Type: Family

This family of proteins includes diguanylate cyclases and regulatory proteins involved in the synthesis of cyclic-di-GMP (c-di-GMP) and the regulation of nitrogen fixation. Diguanylate cyclases catalyze the formation of c-di-GMP from GTP, a signaling molecule that controls bacterial cell surface-associated traits, such as biofilm formation, motility, and cell division. These proteins are part of signaling systems that respond to environmental cues, such as oxygen levels and reductive stress, to modulate cellular processes. Regulatory proteins in this family are involved in controlling the activity of other proteins, such as NifA, in response to oxygen and nitrogen levels, which is crucial for nitrogen fixation in bacteria. The activity of diguanylate cyclases is tightly regulated by interactions with other proteins and domains, ensuring precise control of c-di-GMP levels in the cell.
Anthracycline and Secondary Metabolite Biosynthesis Protein (Anthracycline_SecMetBiosynth)
Type: Family

This family of proteins includes enzymes involved in various biosynthetic pathways, including the production of anthracyclines, which are aromatic polyketide antibiotics with significant cytotoxicity used in cancer chemotherapy. Members of this family participate in key steps of the anthracycline biosynthesis, such as hydroxylation and conversion of precursor compounds into active antibiotics like carminomycin and daunorubicin. Some proteins within this family are also implicated in the detoxification of methylglyoxal, suggesting a role in cellular defense mechanisms. Additionally, certain members are involved in immune modulation, specifically in the maturation of dendritic cells and the induction of Th1-polarized immune responses through TLR2-dependent pathways. The family also includes proteins with a glyoxylase-like domain that are part of gene clusters mediating the biosynthesis of secondary metabolites with potential roles in microbial competition and pathogenicity.