SII-SWORD/CoKE huggingface dataset:
Spore protein YkvP/CgeB, glycosyl transferase-like domain (YkvP/CgeB_Glyco_trans-like)
Type: Domain

This entry represents a glycosyl transferase-like domain found in spore protein YkvP and protein CgeB from Bacillus subtilis .

CgeB is a putative glycosyltransferase involved in the glycosylation of the Bacillus subtilis endospore crust . It is co-expressed with CgeA and CgeD, which are also implicated in crust glycosylation. The crust polysaccharide layer, which CgeB likely contributes to, consists of rhamnose- and galactose-related variants and may contain rare sugars. This glycosylation could protect the crust against biological degradation and scavenging .

YkvP is a spore protein that contains a motif conserved among cell wall binding proteins. Its expression is dependent on both SigK and GerE transcription factors. YkvP is intrinsic to mature spores. The conserved motif in YkvP is thought to function as a kind of signal sequence involved in protein assembly to forespores during sporulation .
Kinetochore protein Ndc80, CH domain (Ndc80_CH)
Type: Domain

This entry represents the calponin homology (CH) domain found towards the N terminus of Ndc80 proteins, a component of the NMS (Ndc80-MIND-Spc7) super complex which has a role in kinetochore function during late meiotic prophase and throughout the mitotic cell cycle . This complex is required for chromosome segregation and spindle checkpoint activity . It has been shown that Ndc80 from yeast is part of a complex called the Ndc80p complex . The four Ndc80 complex subunits associate as two rod-like heterodimers (Ndc80:Nuf2 and Spc24:Spc25) . This protein is required for kinetochore integrity and the organisation of stable microtubule binding sites in the outer plate of the kinetochore . Moreover, the NDC80 complex synergistically enhances the affinity of the SKA1 complex for microtubules and may allow the NDC80 complex to track depolymerising microtubules . The CH domains of Ndc80 and Nuf2 pair at one end and form a microtubule-attachment module .
Phosphatidylinositol transfer protein, N-terminal (PI_transfer_N)
Type: Domain

This entry represents the N-terminal domain of phosphatidylinositol transfer proteins (PITPs) which catalyse the transfer of phosphatidylinositol (PI) or phosphatidylcholine (PC) between membranes . There are three sub-families - all share an N-terminal PITP-like domain, whose sequence is highly conserved. It is described as consisting of three regions. The N-terminal region is thought to bind the lipid and contains two helices and an eight-stranded, mostly antiparallel β-sheet. An intervening loop region, which is thought to play a role in protein-protein interactions, separates this from the C-terminal region, which exhibits the greatest sequence variation and may be involved in membrane binding. PITP alpha (PIPNA,

) has a 16-fold greater affinity for PI than PC. Together with PITP beta (PIPNB,

), it is expressed ubiquitously in all tissues .
Gamma-glutamyltranspeptidase, conserved site (GGT_CS)
Type: Conserved_site

This entry represents a conserved site of GGTs.

Gamma-glutamyltranspeptidase (

) (GGT) catalyses the transfer of the gamma-glutamyl moiety of glutathione to an acceptor that may be an amino acid, a peptide or water (forming glutamate). GGT plays a key role in the gamma-glutamyl cycle, a pathway for the synthesis and degradation of glutathione and drug and xenobiotic detoxification . In prokaryotes and eukaryotes, it is an enzyme that consists of two polypeptide chains, a heavy and a light subunit, processed from a single chain precursor by an autocatalytic cleavage. The active site of GGT is known to be located in the light subunit. The sequences of mammalian and bacterial GGT show a number of regions of high similarity . Pseudomonas cephalosporin acylases (

) that convert 7-beta-(4-carboxybutanamido)-cephalosporanic acid (GL-7ACA) into 7-aminocephalosporanic acid (7ACA) and glutaric acid are evolutionary related to GGT and also show some GGT activity . Like GGT, these GL-7ACA acylases, are also composed of two subunits. This entry also includes the highly similar Scoloptoxin SSD14 from Scolopendra dehaani. SSD14 (which is also cleaved into alpha and beta subunits) has been shown to induce human platelet aggregation .

As an autocatalytic peptidase GGT belongs to MEROPS peptidase family T3 (gamma-glutamyltransferase family, clan PB(T)). The active site residue for members of this family and family T1 is C-terminal to the autolytic cleavage site. The type example is gamma-glutamyltransferase 1 from Escherichia coli.
BOD1/SHG1 domain (BOD1/SHG1_dom)
Type: Domain

This domain is found at the N-terminal of Biorientation of chromosomes in cell division protein 1-like 1 (BODL1) from animals, and covers the whole length of the protein sequence in its paralogues BD1L2/BOD1 and the orthologues from yeast SHG1.

BOD1L1 is a component of the fork protection machinery required to protect stalled/damaged replication forks from uncontrolled DNA2-dependent resection . It acts by stabilising RAD51 at stalled replication forks and protecting RAD51 nucleofilaments from the antirecombinogenic activities of FBH1 and BLM . BOD1L2 and BOD1 that are required for proper chromosome biorientation through the detection or correction of syntelic attachments in mitotic spindles .

The Shg1 subunit is one of the eight subunits of the COMPASS complex, complex associated with SET1, conserved in yeasts and in other eukaryotes up to humans. It is associated with the region of the Set1 protein that is N-terminal to the C-terminal, ie Set1-560-900. The function of Shg1 seems to be to slightly inhibit histone 3 lysine 4 (H3K4) di- and tri-methylation, and it is a pioneer protein. The COMPASS complex functions to methylate the fourth lysine of Histone 3 and for silencing of genes close to the telomeres of chromosomes .
Photosynthetic reaction centre, L/M, conserved site (Photo_RC_L/M_CS)
Type: Conserved_site

This entry represents a conserved site found in this group of proteins which includes two conserved histidine residues. In L and M chains, the first histidine is a ligand of the magnesium ion of the special pair bacteriochlorophyll, the second is a ligand of a ferrous non-haem iron atom. In photosystem II these two histidines are thought to play a similar role.

This entry describes the photosynthetic reaction centre L and M subunits, and the homologous D1 (PsbA) and D2 (PsbD) photosystem II (PSII) reaction centre proteins from cyanobacteria, algae and plants. The D1 and D2 proteins only show approximately 15% sequence homology with the L and M subunits, however the conserved amino acids correspond to the binding sites of the phytochemically active cofactors. As a result, the reaction centres (RCs) of purple photosynthetic bacteria and PSII display considerable structural similarity in terms of cofactor organisation.

The D1 and D2 proteins occur as a heterodimer that form the reaction core of PSII, a multisubunit protein-pigment complex containing over forty different cofactors, which are anchored in the cell membrane in cyanobacteria, and in the thylakoid membrane in algae and plants. Upon absorption of light energy, the D1/D2 heterodimer undergoes charge separation, and the electrons are transferred from the primary donor (chlorophyll a) via pheophytin to the primary acceptor quinone Qa, then to the secondary acceptor Qb, which like the bacterial system, culminates in the production of ATP. However, PSII has an additional function over the bacterial system. At the oxidising side of PSII, a redox-active residue in the D1 protein reduces P680, the oxidised tyrosine then withdrawing electrons from a manganese cluster, which in turn withdraw electrons from water, leading to the splitting of water and the formation of molecular oxygen. PSII thus provides a source of electrons that can be used by photosystem I to produce the reducing power (NADPH) required to convert CO2 to glucose .

Also in this entry is the light-dependent chlorophyll f synthase (ChlF) from cyanobacteria such as Chlorogloeopsis fritschii. ChlF synthesizes chlorophyll f or chlorophyllide f, which is able to absorb far red light, probably by oxidation of chlorophyll a or chlorophyllide a and reduction of plastoquinone .
Photosystem II protein D1/D2 (D1/D2)
Type: Family

This entry includes D1 (PsbA) and D2 (PsbD) photosystem II (PSII) reaction centre proteins from cyanobacteria, algae and plants. The D1 and D2 proteins only show approximately 15% sequence homology with the L and M subunits, however the conserved amino acids correspond to the binding sites of the phytochemically active cofactors. As a result, the reaction centres (RCs) of purple photosynthetic bacteria and PSII display considerable structural similarity in terms of cofactor organisation.

The D1 and D2 proteins occur as a heterodimer that form the reaction core of PSII, a multisubunit protein-pigment complex containing over forty different cofactors, which are anchored in the cell membrane in cyanobacteria, and in the thylakoid membrane in algae and plants. Upon absorption of light energy, the D1/D2 heterodimer undergoes charge separation, and the electrons are transferred from the primary donor (chlorophyll a) via pheophytin to the primary acceptor quinone Qa, then to the secondary acceptor Qb, which like the bacterial system, culminates in the production of ATP. However, PSII has an additional function over the bacterial system. At the oxidising side of PSII, a redox-active residue in the D1 protein reduces P680, the oxidised tyrosine then withdrawing electrons from a manganese cluster, which in turn withdraw electrons from water, leading to the splitting of water and the formation of molecular oxygen. PSII thus provides a source of electrons that can be used by photosystem I to produce the reducing power (NADPH) required to convert CO2 to glucose .

Also in this entry is the light-dependent chlorophyll f synthase (ChlF) from cyanobacteria such as Chlorogloeopsis fritschii. ChlF synthesizes chlorophyll f or chlorophyllide f, which is able to absorb far red light, probably by oxidation of chlorophyll a or chlorophyllide a and reduction of plastoquinone .
Aerolysin-like, C-terminal (Aerolysin-like_C)
Type: Domain

This entry represents the C-terminal region of Aerolysin from Aeromonas sobria and similar sequences mainly from proteobacteria, animals and plants. This protein is a cytolytic toxin that forms pores in host membranes after proteolytic removal of a C-terminal propeptide, leading to destruction of the membrane permeability barrier and cell death. The pores are formed by transmembrane β-strands and are approximately 3 nm in diameter .
Pyruvate carboxylase-like (PCB-like)
Type: Family

This entry represents a group of enzymes involved in transfer of carboxyl group such as Pyruvate carboxylase, Oxaloacetate decarboxylase and Methylmalonyl-CoA carboxyltransferase. Pyruvate carboxylase (PCB) catalyses a 2-step reaction, involving the ATP-dependent carboxylation of the covalently attached biotin in the first step and the transfer of the carboxyl group to pyruvate in the second, leading to oxaloacetate production . In B.subtilis, this enzyme plays an anaplerotic function as it is necessary for growth on glucose, but is not required for sporulation . Oxaloacetate decarboxylase catalyses the decarboxylation of oxaloacetate coupled to Na+ translocation whereas Methylmalonyl-CoA carboxyltransferase 5S subunit specifically catalyses the transfer of the carboxyl group from biotin of the 1.3S subunit to pyruvate to form oxaloacetate and 1.3S biotin .
Alpha crystallin/Heat shock protein Hsp-16.1/Hsp-16.2 (Alpha-crystallin/HSP_16)
Type: Family

This entry represents a group of alpha-crystallin domain containing proteins from animals, including the A and B subunits of alpha-crystallin and related small heat shock proteins Hsp-16.1/Hsp-16.11/Hsp-16.2 elegans whose function is not yet clear.

This entry also includes the Drosophila melanogaster small heat-shock-related protein, lethal(2) essential for life, the orthologue of human alpha-crystallin B .

HSPs can be divided into HSP100, HSP90, HSP70, HSP60, HSP40 and small heat shock proteins (sHSPs) according to their molecular weight and homology. Small heat shock proteins contain an alpha-crystallin domain and variable N- and C-terminal extensions. sHsps are generally active as large oligomers consisting of multiple subunits, and are believed to be ATP-independent chaperones that prevent aggregation and are important in refolding in combination with other Hsps .

The crystallins are water-soluble structural proteins that occur in high concentration in the cytoplasm of eye lens fibre cells. Four major groups of crystallin have been distinguished on the basis of size, charge and immunological properties: alpha-, beta-and gamma-crystallins occur in all vertebrate classes (though gamma-crystallins are low or absent in avian lenses); and delta-crystallin is found exclusively in reptiles and birds .

Alpha-crystallin occurs as large aggregates, comprising two types of related subunits or chains (A and B) that are highly similar to the small (15-30kDa) heat shock proteins (HSPs), particularly in their C-terminal halves. The relationship between these families is one of classic gene duplication and divergence, from the small HSP family, allowing adaptation to novel functions. Divergence probably occurred prior to evolution of the eye lens, alpha-crystallin being found in small amounts in tissues outside the lens .

Alpha-crystallin has chaperone-like properties including the ability to prevent the precipitation of denatured proteins and to increase cellular tolerance to stress . It has been suggested that these functions are important for the maintenance of lens transparency and the prevention of cataracts. This is supported by the observation that alpha-crystallin mutations show an association with cataract formation.
Fucosyltransferase, C-terminal (Glyco_tran_10_C)
Type: Domain

This is the C-terminal domain of a family of fucosyltransferases, known as glycosyltransferase family 10 . This enzyme transfers fucose from GDP-Fucose to GlcNAc in an alpha(1,3) linkage . The C-terminal Rossman-like domain is presumed to be involved in acceptor interactions
Neuron-derived neurotrophic factor, first Fn(III) domain (NDNF_Fn(III)_1)
Type: Domain

This domain is found centrally located in animal Neuron-derived neurotrophic factor (NDNF), which contains a fibronectin type III domain and one of the predicted N-linked glycosylation sites . NDNF is a glycosylated and disulfide-bonded secreted protein expressed in brain and spinal cord that promotes migration and neurite growth. It also promotes endothelial cell survival, vessel formation and plays an important role in the process of revascularisation.
POPDC1-3 domain (POPDC1-3_dom)
Type: Domain

This entry represents a conserved domain found in the POPDC family of proteins, also known as the Popeye (POP) family, which includes POPDC1, 2 and 3 and is predominantly found in aminals. POPDC1 (also known as Blood vessel epicardial substance) 2 and 3 are preferentially expressed in developing and adult striated muscle . These proteins act as cAMP effectors and play a role in cardiac pacemaking and conduction. The POPDC proteins have been shown to regulate potassium and sodium channels .

POPDC1 has been associated with phenotypes including limb-girdle muscular dystrophy-25 (), cardiac arrhythmias and changes in POPDC protein expression have been linked to many cancers .

POPDC3 may play a role in the maintenance of heart function mediated, at least in part, through cAMP-binding and it is also important for skeletal muscle function. It may play a role in the regulation of KCNK2/TREK-1-mediated current amplitude. Pathogenic variants in POPDC3 are responsible for a novel type of autosomal recessive limb girdle muscular dystrophy .
CBG09102/CBG15751-like domain (CBG09102/CBG15751-like_dom)
Type: Domain

This entry represents a domain found in a group of uncharacterised sequences from nematodes, including CBG09102 and CBG15751 from Caenorhabditis briggsae. This domain may adopt a β-sandwich fold consisting of thirteen β-strands.
SWOLLEN 1 (SWO1)
Type: Family

This family represents a group of plant sequences, including SWOLLEN 1 (SWO1,

) from Arabidopsis thaliana. SWO1 is an Agenet domain-containing protein, required for the maintenance of cell wall integrity under salt stress, through the interaction with importin alpha .
Ferredoxin-NADP reductase-like (Ferredox_Rdtase)
Type: Family

This family represents a group of ferredoxin reductases, including human Fdxr (NADPH:adrenodoxin oxidoreductase, mitochondrial) , Mycobacterium FprA and FprB (Probable ferredoxin/ferredoxin--NADP reductase).
NHL41-like (NHL41-like)
Type: Family

This family represents a group of plant proteins, including NHL41 from Arabidopsis thaliana (also known as late embryogenesis abundant protein, AT3G24600,

) which may play a role in abscisic acid and stress response .
Fanconi anaemia group A protein, C-terminal (Fanconi_A_C)
Type: Domain

This domain is found towards the C-terminal of human Fanconi anaemia group A protein (FANCA) and related proteins. It contains ARM repeats.

Fanconi anemia (FA) is a human disorder characterised by cancer susceptibility and cellular sensitivity to DNA crosslinks and other damages. The FA complex repairs the interstrand cross-linking (ICL) lesions and coordinates activities of the downstream DNA repair pathway including nucleotide excision repair, translesion synthesis, and homologous recombination. It is required for the monoubiquitylation of FANCD2 and FANCI heterodimer. The FA core complex consists of FANCA, FANCB, FANCC, FANCE, FANCF, FANCG, FANCL, FANCM, FANCT (UBET2), FAAP100 and FAAP24 .
Cell division control protein 48 homolog C (CDC48c)
Type: Family

This entry represents Cell division control protein 48 homolog C from Arabidopsis thaliana (CDC48c) and similar proteins predominantly found in plants. CDC48c is thought to function in cell division and growth processes. Members of this group contain an ATPase domain (

).
Short-chain dehydrogenase TIC 32 (TIC32)
Type: Family

This entry represents Short-chain dehydrogenase TIC 32, chloroplastic from Pisum sativum (TIC32) and similar plant proteins. TIC32 is involved in protein precursor import into chloroplasts. It is part of the redox regulon that consists of TIC32, TIC 55 and TIC62 .
GIR1-2/SIED1 (GIR1-2/SIED1)
Type: Family

This family of proteins includes protein GL2-INTERACTING REPRESSOR 1/2 (GIR1/2) and their paralogue, protein salt-induced and EIN3/EIL1-dependent 1 (SIED1), which regulators of plant development and stress responses. GIR1/2 are involved in the modulation of root hair development and act as negative regulators in this process. They may function as adapter proteins, interacting with other proteins to control gene expression related to root hair formation . SIED1 is implicated in ethylene-dependent salt stress responses, where they play a role in reducing the accumulation of reactive oxygen species, thereby protecting the plant from oxidative damage .
Proton pump-interactor 1-4 (PPI1-4)
Type: Family

The Proton pump-interactor protein family (PPI, which includes PPI1-4 from Arabidopsis and BIP103/131 from rice) is implicated in the regulation of plasma membrane ATPase activity in plants. Members of this family may interact with the plasma membrane ATPases, such as AHA1, to modulate their activity . PPI2 is known to promote AHA1 activity by binding to a unique site, suggesting a role in the fine-tuning of ATPase function

]. These interactions are crucial for maintaining ion gradients across the plasma membrane, which is essential for various physiological processes including nutrient uptake, pH regulation, and cell volume control.
Signaling peptide TAXIMIN 1/2 (TAXIMIN_1/2)
Type: Family

This family of proteins includes signaling peptides TAXIMIN 1/2 that play a crucial role in the regulation of lateral organ separation in plants, including fruits and leaves . Members of this family are involved in the response to environmental cues, such as light stress, by controlling the accumulation of protective compounds . They are also subject to modulation by external factors, including certain antibiotics which can influence their activity during stress responses.
Galaxin-like (Galaxin-like)
Type: Family

This family of proteins includes galaxins and related proteins that share common structural features such as the presence of repetitive motifs containing dicysteine residues.

Galaxins are characterised by their role in biomineralization processes . These proteins are typically involved in the formation of calcium carbonate skeletons in marine organisms, such as corals. They may function by influencing the nucleation and growth of calcium carbonate crystals, contributing to the structural integrity and resilience of coral skeletons. Galaxins are also of interest for their potential applications in biomimetic materials science and understanding the impact of environmental changes on coral reef ecosystems.
Ankyrin repeat domain-containing protein 13, C-terminal (ANKRD13_C)
Type: Domain

This entry represents the C-terminal domain of ankyrin repeat domain-containing protein 13 (ANKRD13). At least 4 subtypes are known to exist, termed A-D. ANKRD13C has been experimentally characterised and acts as a chaperone for biogenesis and folding of the DP receptor for prostaglandin D2 . ANKRD13A/B/D are ubiquitin-binding proteins that specifically recognise and bind Lys-63-linked ubiquitin. They positively regulate the internalisation of ligand-activated EGFR by binding to the Ub moiety of ubiquitinated EGFR at the cell membrane . This domain belongs to the LolA/B superfamily of lipoprotein sorting proteins.
Ribitol-5-phosphate xylosyltransferase 1-like (RXYLT1-like)
Type: Family

This entry represents human Ribitol-5-phosphate xylosyltransferase 1 (RXYLT1) and similar proteins predominantly found in animals.

RXYLT1 acts as a UDP-D-xylose:ribitol-5-phosphate beta1,4-xylosyltransferase, which catalyses the transfer of UDP-D-xylose to ribitol 5-phosphate (Rbo5P) to form the Xylbeta1-4Rbo5P linkage on O-mannosyl glycan .
Interleukin-16-like (IL-16-like)
Type: Family

This entry represents human interleukin-16 (IL-16) and similar sequences from vertebrates and arthropods.

Interleukins (IL) are a group of cytokines that play an important role in the immune system. They modulate inflammation and immunity by regulating growth, mobility and differentiation of lymphoid and other cells.

Interleukin-16 (IL-16, also known as Pro-interleukin-16 or Lymphocyte chemoattractant factor) is a proinflammatory cytokine that signals via CD4, inducing chemotactic and immunomodulatory responses of CD4+ lymphocytes, monocytes and eosinophils . The cytokine has been implicated in the exacerbation of a number of infectious, immune-mediated and autoimmune inflammatory disorders, including atopic dermatitis, irritable bowel syndrome, systemic lupus erythematosus, neurodegenerative disorders, and viral infections .
NALCN channel auxiliary factor 1/2 (NALCN_aux_factor_1/2)
Type: Family

This family of proteins includes auxiliary components of the NALCN sodium channel complex, NALF1/2 . These proteins are involved in regulating the resting membrane potential and controlling neuronal excitability . They are likely to interact with the NALCN channel to modulate its function and play a crucial role in maintaining the electrical stability of neurons.