SII-SWORD/CoKE huggingface dataset:
Zinc Chaperone and cDPG Synthetase (Zn_Chap_cDPG_Synth)
Type: Family

This family of proteins includes zinc chaperones and cyclic 2,3-diphosphoglycerate synthetases. The zinc chaperones are involved in the direct transfer of zinc cofactors to target proteins, activating them. This transfer occurs from a CXCC motif within the GTPase domain to the zinc binding site of the target proteins and is dependent on GTP hydrolysis. These proteins contribute to optimal growth under zinc starvation conditions. The cyclic 2,3-diphosphoglycerate synthetases catalyze the formation of cyclic 2,3-diphosphoglycerate from ATP, forming an intramolecular phosphoanhydride bond.
NorD/CobT (NorD/CobT)
Type: Family

The NorD/CobT protein family is involved in various aspects of bacterial metabolism. The majority of the family members, such as NorD from different Brucella species, are part of the norEFCBQD operon, which encodes nitric oxide reductase. These proteins are essential virulence factors likely involved in the detoxification of nitric oxide produced by macrophages during the immune response. Another member, CobT from Sinorhizobium, functions as an aerobic cobaltochelatase subunit, catalyzing cobalt insertion into the corrin ring. Additionally, some uncharacterized proteins like PA0525 from Pseudomonas aeruginosa and YojO from Bacillus subtilis are associated with the anaerobic respiratory chain for denitrification, although their precise roles are not well-defined. Collectively, the NorD/CobT family plays a crucial role in bacterial survival and pathogenicity by participating in nitric oxide detoxification, cobalamin biosynthesis, and the denitrification process.
Viral Assembly and Modifier Protease (VirAsm_ModProt)
Type: Family

The protein family encompasses a variety of proteases with distinct functions related to protein modification and processing. Members of the family are involved in the assembly and maturation of viral components, such as the tail tip complex in bacteriophages, indicating a role in viral replication and assembly. Other members display desampylase activity, regulating protein modification by cleaving small archaeal modifier proteins from conjugates, thereby controlling the availability of these modifiers for further protein tagging. Additionally, some proteases in the family are responsible for hydrolyzing specific adducts, such as the CysO-cysteine adduct, to release essential amino acids like L-cysteine. Collectively, the family's activities are crucial for various biological processes, including viral assembly, post-translational modification regulation, and amino acid recycling.
Flavodoxin/Ferredoxin--NADP Reductase (FNR_type-1)
Type: Family

This family of proteins is involved in electron transport, facilitating the transfer of electrons between flavodoxin or ferredoxin and NADPH. Members of this family are crucial for the activation of various enzymes that are essential in metabolic processes, particularly under anaerobic conditions. These enzymes include pyruvate formate-lyase, anaerobic ribonucleotide reductase, and cobalamin-dependent methionine synthase. The proteins exhibit a preference for ferredoxin as the electron transfer partner, both kinetically and thermodynamically.
Serine/threonine-protein kinase PAK 3-like (PAK3-like)
Type: Family

This entry represents human Serine/threonine-protein kinase PAK 3 and similar proteins predominantly found in animals, fungi and actinomycetes. This family also includes a number of predicted serine/threonine and tyrosine kinases, which are key regulators of cell signalling pathways. Members are involved in various cellular processes such as growth, proliferation, differentiation, and apoptosis. They share a conserved kinase domain (

), although some are predicted to be catalytically inactive, suggesting a possible regulatory role. The active kinases transfer phosphate groups from ATP to specific serine, threonine, or tyrosine residues on target proteins, modulating their activity. The family encompasses proteins with diverse functions and regulatory mechanisms, reflecting the complexity of cellular signalling networks.
Bacterial Stress Response Regulators (Bact_StressResp_Reg)
Type: Family

The protein family is involved in the environmental signaling branch of the general stress response in bacteria. Members of the family include blue-light photoreceptors that share spectroscopical features with plant phototropins and are involved in the reversible formation of a blue-shifted photoproduct. This photoproduct is assigned to an FMN-cysteine thiol adduct and plays a role in regulating the activity of the general stress transcription factor sigma-B. Other members, RsbR paralogs (RsbRA, RsbRB, RsbRC, RsbRD), and RsbS, interact with sigma-B through a phosphorylation-dependent mechanism. Non-phosphorylated RsbS and one of the RsbR paralogs sequester RsbT, a negative regulator of sigma-B. Upon phosphorylation, RsbS and the RsbR paralogs release RsbT, which then activates RsbU, leading to the positive regulation of sigma-B in response to stress. The precise functions of some members remain undetermined, and one member is uncharacterized.
Bacterial Resuscitation-promoting factor RpfB (Resuscitation_pf_RpfB)
Type: Family

The RpfB family proteins are known to play a crucial role in the resuscitation of dormant cells, particularly in the context of chronic tuberculosis. They exhibit peptidoglycan hydrolytic activity, which is effective even at picomolar concentrations and does not significantly impact actively growing cells. The enzymatic action of RpfB family members on peptidoglycan results in fragments that may either stimulate dormant bacteria to resume growth or act as substrates for endogenous Rpf proteins, producing compounds that activate resuscitation pathways. Additionally, some family members have been shown to bind specific substrates like N,N',N''-triacetylchitotriose and are regulated by various inhibitors. The RpfB family is part of the broader transglycosylase family, with a particular focus on the Rpf subfamily, which is implicated in cell wall modification and bacterial revival from dormant states.
Bacteriophage Tail Fiber Structural Protein (Phage_Tail_Fiber_Structural)
Type: Family

This family of proteins includes structural components of bacteriophage tail fibers, which are involved in the initial stages of bacterial infection. Members of this family are responsible for recognizing and binding to specific bacterial receptors, determining the host range of the phage. The tail fibers can be divided into proximal and distal halves, with the distal half containing a thin tip that interacts with bacterial lipopolysaccharide receptors. These interactions are crucial for the attachment of the virion to the host cell, facilitating the subsequent injection of viral DNA into the bacterial cell. Some family members are involved in the reversible attachment to host molecules, extending the host range of the virus.
Hydroxysteroid dehydrogenase-like protein 2 (HSDL2)
Type: Family

This family of proteins is part of the short-chain dehydrogenases/reductases (SDR) superfamily. Despite their classification, these proteins are noted for lacking steroid dehydrogenase activity, which is typically associated with the SDR family. The exact biological function of these proteins remains unclear, but their conserved presence across different species suggests a potential role that is yet to be fully understood. The members of this family share a degree of sequence similarity indicative of a common evolutionary origin, and they may possess enzymatic activity that diverges from the canonical functions observed in other SDR family members.
Membrane-embedded heme-iron electron transfer protein (Heme-iron_electron_transfer)
Type: Family

This family of proteins includes components involved in electron transfer processes during anaerobic respiration. Members function as membrane-embedded heme-iron units that transfer electrons from quinones to other subunits of enzyme complexes. Some proteins in this family are associated with nitrate reductase enzyme complexes, enabling the use of nitrate as an electron acceptor. Others exhibit menaquinol-oxidizing activity, transferring electrons to unidentified acceptors on the cytoplasmic side of the membrane. A subset of these proteins, despite similarity to nitrate reductase subunits, do not display nitrate reductase activity.
R3H domain-containing (R3H_domain_containing)
Type: Family

The R3H domain-containing protein family is involved in various cellular processes. Members of this family are implicated in the regulation of germline mitosis, karyosome formation, and the establishment of dorsoventral polarity in eggs and embryos. They play a role in the localization and translation of grk mRNA in oocytes and may influence germline mitosis by promoting cyclin E proteolysis via the SCF-ubiquitin-proteasome complex. Additionally, certain isoforms within this family may function as competitive inhibitors of calmodulin-dependent enzymes, such as calcineurin, particularly in neuronal contexts.
Apoptosis and cytoskeleton modulation protein (Apopto_cytoskel_mod)
Type: Family

This family of proteins is involved in various cellular processes, including the modulation of apoptosis, tumor suppression, and the organization of the microtubule cytoskeleton. Members of this family are characterized by their ability to influence apoptotic pathways, with some isoforms promoting apoptosis in response to specific signals such as TNF or DNA damage, while other isoforms have an inhibitory effect on apoptosis. Additionally, certain members may have roles in transcriptional activity modulation and development, particularly at the neuromuscular junction. Some proteins within this family are implicated in tumor suppression in specific developmental contexts. Others contribute to cellular structure and dynamics, such as the disassembly of microtubule organizing centers during interphase. The presence of a J domain suggests a commonality in the mechanism of action across the family, potentially involving interactions with other molecular partners.
Glycosyltransferase 41/O-GlcNAc transferase (Glycosyltr_41/O-GlcNAc_trsf)
Type: Family

The glycosyltransferase 41 family is characterized by enzymes that modify proteins through the addition of sugar moieties, impacting various biological processes. Members of the O-GlcNAc transferase subfamily, such as SPINDLY, are involved in the gibberellin signaling pathway, affecting plant growth and development. These enzymes catalyze the transfer of N-acetylglucosamine to serine or threonine residues of proteins via O-glycosidic bonds. Some family members also exhibit O-fucosyltransferase activity, influencing protein interactions and stability. Additionally, the family includes enzymes like UDP-glucose:protein N-beta-glucosyltransferase, which transfers glucose to asparagine residues within specific protein motifs. This activity suggests a role in a general protein glycosylation system, with implications for protein function and signaling pathways.
Chitin-binding developmental regulator (Chitin_bind-dev_reg)
Type: Family

This family of proteins is involved in various developmental processes, including the regulation of shape and survival during different life stages. Members of this family are characterized by their ability to bind chitin, which is a key component in the structure of cuticles and extracellular matrices. They play critical roles in the morphological transformations that occur during metamorphosis, such as the pupal shape change in insects. Additionally, these proteins are essential for the proper segregation of chromosomes during meiosis and are involved in the formation of the peritrophic membrane, which is important for the maintenance of gut structure and function. Some family members are also implicated in the formation of a cohesive chitin layer in oocytes post-fertilization, indicating a role in early embryonic development.
Blood Group Antigen-Binding Lectin (BG_Antigen-Binding_Lectin)
Type: Family

This family of proteins acts as defensive agents by recognizing specific blood group fucosylated oligosaccharides, including antigens A, B, H, and Lewis B-type. They are involved in the immune response and cell-cell recognition processes. Members of this family do not interact with Lewis A antigen and exhibit low affinity for monovalent haptens.
DENN domain-containing protein 2 (DENN_domain_containing_2)
Type: Family

This family of proteins functions as guanine nucleotide exchange factors (GEFs) primarily activating RAB9A and RAB9B. They facilitate the conversion of these Rab proteins from an inactive GDP-bound state to an active GTP-bound form. Members of this family are involved in various cellular processes, including endosomal transport, particularly from late endosomes to the trans-Golgi network, and EGFR trafficking from recycling endosomes to the cell membrane. Some proteins in this family may also participate in cytoskeletal organization, influence cell morphology and growth, and may be implicated in tumorigenicity. Additionally, they might play a role in signaling pathways that lead to the activation of MAPK1/ERK2, although certain members could potentially inhibit ERK2 activation.
TRAFAC Dynamin-like GTPase (TRAFAC_Dynamin-like_GTPase)
Type: Family

This family of proteins includes members that are part of the TRAFAC class dynamin-like GTPase superfamily, specifically the Dynamin/Fzo/YdjA family. These proteins are involved in membrane remodeling processes. One member, a probable transmembrane GTPase, is implicated in determining thylakoid and chloroplast morphology and in regulating the organization of the thylakoid network within chloroplasts. Another member, a dynamin-like protein, is part of a heterotetrameric complex that may mediate liposome fusion and requires tetramerization for GTPase activity. This indicates a role in membrane dynamics and vesicle trafficking. The family is characterized by GTPase activity and the ability to bind and remodel membranes, which is essential for various cellular processes including organelle maintenance and intracellular transport.
BEACH domain-containing protein (BEACH_domain_protein)
Type: Family

This family of proteins is involved in various cellular processes including autophagy, protein sorting, cell morphogenesis, and membrane fusion. Members of this family play critical roles in the regulation of antigen presentation in dendritic cells, B-cell survival, cytokinesis, phagocytosis, osmoregulation, and brain development. They are implicated in the formation of axonal tracts and the response of neural cells to guidance cues. Some proteins in this family function as adapter proteins linking ubiquitinated proteins to the autophagic machinery for selective degradation. They are also involved in Wnt signaling regulation and may influence osteoclastogenesis. Domains present in these proteins, such as the FYVE domain, are important for binding to specific phospholipids, and the LC3-interacting region (LIR) motif mediates interactions with components of the autophagy pathway.
RRM MRD1 RNA Processing and Ribosome Biogenesis (RRM_MRD1_RNA_proc_ribogen)
Type: Family

The RRM MRD1 family is involved in various aspects of RNA processing and ribosome biogenesis. Members of the family play a role in embryo pre-implantation development and are implicated in pre-rRNA processing, which is essential for the production of mature ribosomal RNA and the subsequent assembly of ribosomal subunits. Some proteins within the family are nucleolar components of the spliceosomal ribonucleoprotein complexes, suggesting a role in RNA splicing. Others are required for the synthesis of the 60S ribosomal subunit, likely participating in the processing of 27S rRNA to produce mature 25S rRNA. The family's functions are critical for the proper functioning of the cell's protein synthesis machinery.
Intracellular Trafficking Regulator (Intracell_Traff-Reg)
Type: Family

This family of proteins is involved in intracellular trafficking and the regulation of endosome-to-lysosome pathways. They are essential for the axonal transport of various cargos, including mitochondria, growth factors, and neurotransmitter receptors, to their respective destinations within the cell. Members of this family are known to interact with motor proteins, such as kinesin, to facilitate the anterograde and retrograde movement of vesicles and organelles along microtubules. They play a role in neuronal outgrowth, synaptic function, and the recycling and degradation of membrane receptors. Some members are implicated in the regulation of autophagy and exocytosis, as well as in the formation of cytoplasmic inclusion bodies that may have a protective role against neurodegeneration.
Sentrin-specific protease (Sentrin-specific_protease)
Type: Family

This family of proteins includes sentrin-specific proteases that are involved in the post-translational modification of proteins through the process of SUMOylation, where small ubiquitin-like modifier (SUMO) proteins are attached to target proteins. Members of this family are responsible for the cleavage of SUMO2 and SUMO3 from substrates, a process known as desumoylation. They play a crucial role in regulating various cellular processes, including DNA repair, transcriptional activation, and cell cycle progression. Specifically, they act as regulators of the cGAS-STING pathway by desumoylating CGAS, which enhances its DNA-binding activity and subsequent activation. Additionally, they are involved in chromosome alignment and spindle assembly by modulating the kinetochore complex and protecting certain proteins from ubiquitin-mediated degradation.
Hsp70 co-chaperone J-domain-containing protein (Hsp70_co-chaperone_J-domain)
Type: Family

This family of proteins includes co-chaperones that interact with Hsp70 proteins, particularly HSPA5/BiP, to modulate the unfolded protein response (UPR) and endoplasmic reticulum-associated degradation (ERAD) pathways. Members of this family contain a J domain that stimulates the ATPase activity of HSPA5/BiP and a divergent targeting domain that recognizes aggregation-prone sequences, facilitating the recognition of misfolded proteins. These proteins are involved in the regulation of ERN1/IRE1 activity in the endoplasmic reticulum by disrupting its dimerization and inactivation under unstressed conditions. They are essential for the survival of B-cell progenitors and normal antibody production, indicating a significant role in immune response. Additionally, some members may participate in pre-mRNA splicing and are required for cellular growth under various temperature conditions.
Cation Transport P-type ATPase (Cation_Transport_ATPase)
Type: Family

This family of proteins includes P-type ATPases that are involved in the transport of various metal ions across cellular membranes. Members of this family are primarily responsible for the homeostasis of heavy metals, such as zinc, cobalt, nickel, and cadmium, by either importing or exporting these ions to maintain cellular function and protect against oxidative stress. Some proteins in this family are also implicated in the regulation of gene expression related to competence development in bacteria.
Developmental regulator and protease inhibitor (Dev_reg/Prot_inhib)
Type: Family

This family of proteins includes members that are involved in developmental processes, such as eye and limb formation, and osteoblast differentiation. Some family members are known to interact with signaling pathways, for instance, by binding and stabilizing Wnt signaling proteins to facilitate gradient formation during development. Others exhibit inhibitory activity against cysteine and aspartic proteinases, which suggests a role in protease regulation. Additionally, certain proteins in this family can promote endothelial cell proliferation, migration, and angiogenesis, as well as contribute to matrix assembly and cell adhesiveness.
UNC-93 regulatory protein (UNC-93_regulatory)
Type: Family

This family of proteins is involved in the regulation of potassium channel complexes, which may affect muscle contraction coordination. Members of this family play a role in the formation of muscle connections, specifically in the development of muscle arm extensions that link the body wall to motor axons in the nervous system. The function suggests a regulatory role in neuromuscular systems, potentially influencing muscle function and coordination.
Golgi-associated and autophagy-related protein (Golgi-autophagy_related)
Type: Family

This family of proteins is involved in various aspects of intracellular vesicular transport, particularly associated with the Golgi apparatus and autophagy processes. Members of this family play roles in maintaining the structure of the Golgi, mediating vesicle formation and trafficking between endosomes and the Golgi, and facilitating the autophagy pathway. Some proteins in this family are characterized by the presence of coiled-coil domains and GRIP domains, which may be involved in Golgi targeting and interaction with other Golgi-associated proteins.
Plant secondary wall-associated transcription factors (Plant_SW-associated_TFs)
Type: Family

This family of proteins includes transcription factors that play crucial roles in plant development and response to environmental stimuli. Members of this family are involved in the regulation of secondary wall biosynthesis, particularly in fibers and vessels, by binding to specific DNA consensus sequences and activating downstream genes. They function in transcriptional networks that control cellulose, xylan, and lignin synthesis, and are essential for the proper expression of genes associated with secondary wall formation. Some family members are also implicated in photomorphogenesis, xylem formation and differentiation, lateral root formation, stomatal closure, seed coat mucilage deposition, trichome initiation, and metal ion homeostasis. Additionally, they may participate in the regulation of flavonoid biosynthesis and anther development. Collectively, these transcription factors are key regulators of plant structure, growth, and adaptation to environmental challenges.
tRNA (32-2'-O)-methyltransferase regulator THADA (tRNA_methyltransferase_THADA)
Type: Family

The THADA family proteins are involved in the post-transcriptional modification of tRNAs and energy homeostasis. Members of this family function in conjunction with specific methyltransferases to methylate the 2'-O-ribose of nucleotides at position 32 in the anticodon loop of tRNAs, a modification important for the stability and function of the tRNA molecule. Additionally, THADA proteins play a crucial role in regulating metabolic processes. They are implicated in the control of calcium signaling pathways that influence energy storage and thermogenesis. By modulating the activity of calcium-transporting ATPases, THADA proteins can affect lipid storage and heat production, and may also influence feeding behavior through actions in the nervous system.
Pectinesterase Inhibitor (PME_Inhibitor)
Type: Family

This family of proteins includes inhibitors of pectin methylesterase (PME), which are involved in the modulation of PME activity and pectin methylesterification. These proteins play a crucial role in maintaining cell wall integrity, particularly in response to pathogenic attacks such as those from necrotrophic pathogens. They are also implicated in the regulation of plant development processes, including seed germination, root growth, and phyllotactic patterning, by controlling the degree of pectin methylesterification in various plant tissues. The activity of these inhibitors is pH-dependent, with a higher affinity in slightly acidic conditions.