SII-SWORD/CoKE huggingface dataset:
B-cell lymphoma 9, beta-catenin binding domain (BCL9_beta-catenin-bd_dom)
Type: Domain

The Wnt pathway plays a role in embryonic development, stem cell growth and tumorigenesis.
B-cell lymphoma 9 (BCL9) associates with beta-catenin and Tcf in the nucleus when the Wnt pathway is stimulated leading to the transactivation of Wnt target genes .

This entry represents a beta-catenin binding domain found in BCL9 and BCL9 homologues.
Autophagy-related protein 22-like (Atg22-like)
Type: Family

Autophagy is a major survival mechanism in which eukaryotes recycle cellular nutrients during stress conditions. Atg22, Avt3 and Avt4 are partially redundant vacuolar effluxers, which mediate the efflux of leucine and other amino acids resulting from autophagy . This family also includes other transporter proteins.
Agglutinin-like protein, N-terminal (Agglutinin-like_N)
Type: Domain

This entry represents the N-terminal domain of yeast alpha-agglutinin and agglutinin-like (ALS) proteins. The ALS glycoproteins have been associated with binding of host-cell surface proteins and small peptides of random sequence, the formation of biofilms and amyloid fibers. The N-terminal domains of Candida albicans ALS3 and ALS9 were shown to be involved in peptide binding . The ligand recognition of these domains relies on a motif capable of binding the flexible C terminus of peptides in extended conformation. In baker's yeast alpha-agglutinin, this domain was implicated in high affinity binding to a-agglutinin that mediates cell-cell contact during mating .
Octaheme c-type cytochrome (Octahem_Cyt_c)
Type: Family

Members of this protein family bind heme covalently and contain eight (at least) CXXCH heme-binding motifs. A characterised member is the respiratory enzyme octaheme tetrathionate reductase from Shewanella .
HpaB/PvcC/4-BUDH N-terminal (HpaB/PvcC/4-BUDH_N)
Type: Domain

This domain is found in the N terminus of HpaB, which encodes part of the 4-hydroxyphenylacetate 3-hydroxylase from Escherichia coli . The enzyme is NADH-dependent and uses FAD as the redox chromophore. The domain is also found in pyoverdin chromophore biosynthetic protein (PvcC), which may play a role in one of the proposed hydroxylation steps of pyoverdine chromophore biosynthesis and in 4-hydroxybutyryl-CoA dehydratase (4-BUDH), a key enzyme in the metabolism of gamma-aminobutyrate .
Eukaryotic translation initiation factor 3 subunit G, N-terminal (eIF3g_N)
Type: Domain

eIF-3G (also termed eIF-3 subunit 4, eIF-3-delta, eIF3-p42, or eIF3-p44) is the RNA-binding subunit of eIF3. Subunit eIF-3G binds 18 S rRNA and beta-globin mRNA, and therefore appears to be a nonspecific RNA-binding protein. It is one of the cytosolic targets and interacts with mature apoptosis-inducing factor (AIF). The yeast orthologue is known as eIF3-p33; it plays an important role in the initiation phase of protein synthesis in yeast. It binds both mRNA and rRNA fragments due to an RNA recognition motif near its C terminus .

This entry represents a domain of approximately 130 amino acids in length found at the N terminus of eukaryotic translation initiation factor 3 subunit G. This domain is commonly found in association with the RNA recognition domain

.

At least eleven different protein factors are involved in initiation of protein synthesis in eukaryotes. Binding of initiator tRNA and mRNA to the 40S subunit requires the presence of the translation initiation factors eIF-2 and eIF-3, with eIF-3 being particularly important for 80S ribosome dissociation and mRNA binding . eIF-3 is the most complex translation inititation factor, consisting of about 13 putative subunits and having a molecular weight of between 550 - 700kDa in mammalian cells. Subunits are designated eIF-3a - eIF-3m; the large number of subunits means that the interactions between the individual subunits that make up the eIF-3 complex are complex and varied.
4-HPA 3-monooxygenase large component/Pyoverdin chromophore biosynthetic protein (HpaB/PvcC)
Type: Family

4-hydroxyphenylacetate (4HPA) 3-monooxygenase consists of two components, a large component, HpaB, which is an oxygenase, and a small component, HpaC, which is a reductase. 4-HPA 3-monooxygenase is NADH-dependent and uses FAD as the redox chromophore. HpaB utilises FADH2 supplied by HpaC to catalyse the hydroxylation of 4-hydroxyphenylacetic acid, leading to the production of 3,4-dihydroxyphenylacetic acid (DHPA) .

This entry represents the 4-HPA 3-monooxygenase large component, HpaB. It also represents the related enzyme pyoverdin chromophore biosynthetic protein (pvcC), which may play a role in one of the proposed hydroxylation steps of pyoverdine chromophore biosynthesis .
Serine/threonine-protein kinase OSR1/WNK, CCT domain (Kinase_OSR1/WNK_CCT)
Type: Domain

Oxidative-stress-responsive kinase 1 (OSR1) is involved in the signalling cascade which activates Na/K/2Cl co-transporter during osmotic stress. This entry represents the CCT domain found in OSR1, STE20/SPS1-related kinase and in WNK activators . This domain is found in eukaryotes, and is approximately 40 amino acids in length. There is a single completely conserved residue F that may be functionally important.
Pre-rRNA-processing protein Ipi1, N-terminal (Ipi1_N)
Type: Domain

This entry represents a domain found in the N terminus of the pre-rRNA-processing protein Ipi1. This domain can also be found in testis-expressed sequence 10 protein (TEX10).

In Saccharomyces cerevisiae, Ipi1 is a component of the RIX1 complex required for processing of ITS2 sequences from 35S pre-rRNA .
Ribulose-1,5-bisphosphate carboxylase small subunit, N-terminal (RuBisCO_ssu_N)
Type: Domain

This domain is found in the N-terminal region of the small subunit of ribulose-1,5-bisphosphate in plants. It contains a conserved APF sequence motif. There are also two completely conserved residues (L and P) that may be functionally important .
Ribulose bisphosphate carboxylase, small subunit (RuBisCO_ssu)
Type: Family

RuBisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) is a bifunctional enzyme that catalyses both the carboxylation and oxygenation of ribulose-1,5-bisphosphate (RuBP), thus fixing carbon dioxide as the first step of the Calvin cycle. RuBisCO is the major protein in the stroma of chloroplasts, and in higher plants exists as a complex of 8 large and 8 small subunits. The small subunits induce conformational changes in the large subunits enhancing its catalytic rate. Studies in Oryza sativa demonstrate that the availability of the small subunit upregulates the transcript levels of the large subunit . While the large subunit is coded for by a single gene, the small subunit is coded for by several different genes, which are distributed in a tissue specific manner. They are transcriptionally regulated by light receptor phytochrome , which results in RuBisCO being more abundant during the day when it is required.
Nuclear pore localisation protein Npl4, ubiquitin-like domain (Npl4_Ub-like_dom)
Type: Domain

Npl4, along with Ufd1, forms the heterodimer adaptor complex UN, which is involved in the recruitment of p97, an AAA ATPase, for tasks involving the ubiquitin pathway.

Npl4 has a N-terminal ubiquitin-like domain which has within its structure a β-grasp fold with a helical insert . This entry represents the ubiquitin-like domain.
Transcriptional activator PerC/bacteriophage SfV Orf40 (Tscrpt_act_PerC/SfV_Orf40)
Type: Family

This family includes PerC, which is a transcriptional activator of EaeA/BfpA expression in enteropathogenic bacteria . It also includes a number of uncharacterised proteins, such as Orf40 from bacteriophage SfV.
Adenylate cyclase class-I, N-terminal domain (Adenylate_cyclase_1_N)
Type: Domain

Adenylate cyclase is the enzyme responsible for the synthesis of cAMP from ATP. On the basis of sequence similarity, it has been proposed that there are three different classes of adenylate cyclases . Class I cyclases are found in enterobacteria and related Gram-negative bacteria.

This entry represents the N-terminal domain of class-I adenylate cyclases.
Adenylate cyclase class-I, conserved site (Adenylate_cyclase_1_CS)
Type: Conserved_site

Adenylate cyclase is the enzyme responsible for the synthesis of cAMP from ATP. From sequence data, it has been proposed that there are three different classes of adenylate cyclases . Class I cyclases are found in enterobacteria and related Gram-negative bacteria. They are proteins of about 850 residues that consist of two functional domains: a N-terminal catalytic domain and a C-terminal regulatory domain. There are two highly conserved regions, the first one is located in the catalytic domain and the second one in the regulatory domain. The second signature includes a conserved histidine which could be phosphorylated by a PTS system IIA enzyme, thus leading to the activation of the cyclase.
MMS19, C-terminal (MMS19_C)
Type: Domain

This entry represents the C-terminal domain of MMS19. This domain shares homology with some HEAT repeat sequences. MMS19 is a key component of the cytosolic iron-sulfur protein assembly (CIA) complex, a multiprotein complex that mediates the incorporation of iron-sulfur cluster into apoproteins specifically involved in DNA metabolism and genomic integrity .

In humans, MMS19 acts as an adapter between early-acting CIA components and a subset of cellular target iron-sulfur proteins such as ERCC2/XPD, FANCJ and RTEL1, thereby playing a key role in nucleotide excision repair (NER) and RNA polymerase II (POL II) transcription . It is also part of the MMXD (MMS19-MIP18-XPD) complex, which plays a role in chromosome segregation, probably by facilitating iron-sulfur cluster assembly into ERCC2/XPD .

In budding yeasts, the mms19 mutants were originally isolated in a screening for mutants hypersensitive to the alkylating agent methyl methanesulfonate (MMS) . Different from human MMS19, Mms19 in budding yeasts (also known as Met18) does not participate directly in NER .

In fission yeast, Mms19 is part of a silencing complex named Rik1-Dos2 complex, which contains Dos2, Rik1, Mms19 and Cdc20. This complex regulates RNA Pol II activity in heterochromatin, and is required for DNA replication and heterochromatin assembly .
Maltose/galactoside acetyltransferase domain (Mac_dom)
Type: Domain

This entry represents a domain found in maltose acetyltransferase, which is an enzyme uses acetyl-CoA as acetyl donor to acetylate cytoplasmic maltose .
Proteasome beta subunit, C-terminal (Proteasome_bsu_C)
Type: Domain

This domain is found in the C terminus of beta-type subunits of the proteasome, a multimeric complex that degrades proteins into peptides as part of the MHC class I-mediated Ag-presenting pathway . This domain is approximately 40 amino acids in length. It is found in association with

. It contains a conserved GTT sequence motif and a single completely conserved residue Y that may be functionally important.
Nitrile hydratase beta subunit domain (CN_hydtase_beta_dom_C)
Type: Domain

This entry represents the C-terminal domain of nitrile hydratase (NHase) beta subunit. Beta subunit consists of an N-terminal helical domain and a C-terminal SH3-like domain

,

]. Thiocyanate hydrolase (SCNase) is a member of the NHase family, comprises alpha, beta and gamma subunits which share sequence similarities with NHase beta subunit C-terminal, beta subunit N-terminal and NHase alpha subunit, respectively .

Nitrile hydratases (

) are unusual metalloenzymes that catalyse the hydration of nitriles to their corresponding amides. They are used as biocatalysts in acrylamide production, one of the few commercial scale bioprocesses, as well as in environmental remediation for the removal of nitriles from waste streams. Nitrile hydratases are composed of two subunits, alpha and beta, and they contain one iron atom per alpha beta unit .
Micronemal protein 1, galectin-like domain (MIC1_galectin-like_dom)
Type: Domain

MIC1 is released as part of a complex by Toxoplasma gondii prior to invasion. The complex, which consists of MIC4-MIC1-MIC6, participates in host cell attachment and penetration, and is critical in invasion . MIC1 is a lactose-binding lectin required for the complex to leave the early compartments of the secretory pathway .

This entry represents the C-terminal domain of MIC1, which has a galectin-like fold that interacts with and stabilises MIC6, providing a mechanism for an exit from the early secretory compartments and trafficking of the complex to micronemes . Members of this group belong to apicomplexa.
Phosphotransferase system, enzyme I (PTS_EI)
Type: Family

This entry represents phosphoenolpyruvate-protein phosphotransferase, also known as PTS enzyme I, which is a component of the phosphoenolpyruvate-dependent sugar phosphotransferase system (sugar PTS).

PTS catalyses the phosphorylation of incoming sugar substrates concomitantly with their translocation across the cell membrane. PTS enzyme I transfers the phosphoryl group from phosphoenolpyruvate to the phosphoryl carrier protein HPr .
PurE, prokaryotic type (PurE_prokaryotes)
Type: Family

The novo purine biosynthesis proceeds by two divergent paths. In bacteria, yeasts, and plants, 5-aminoimidazole ribonucleotide (AIR) is converted to 4-carboxy-AIR (CAIR) by two enzymes: N5-carboxy-AIR (N5-CAIR) synthetase (PurK) and N5-CAIR mutase (class I PurE). In animals, the conversion of AIR to CAIR requires a single enzyme, AIR carboxylase (class II PurE) . Class I and class II PurEs are mechanistically related but bind different substrates.
Uncharacterised conserved protein, UCP038861 (UCP038861)
Type: Family

This entry represents a group of uncharacterised conserved proteins that may function as AAA ATPases or DNA and RNA helicases.
Uncharacterised conserved protein, UCP038601 (UCP038601)
Type: Family

This entry represents a family of uncharacterised conserved proteins that may be related to the type VII secretion system ESAT-6-like proteins.
Uncharacterised conserved protein, UCP037923 (UCP037923)
Type: Family

This entry represents a family of uncharacterised conserved bacterial proteins that contain trypsin and autotransporter beta domains.
Capsular polysaccharide biosynthesis protein, Cps23fI-type, predicted (Caps_psacc_synth_Cps23fI-typ)
Type: Family

This entry represents a family of predicted Cps23fI-type capsular polysaccharide biosynthesis proteins.
Acetoin utilization protein AcuA (AcuA)
Type: Family

AcuA is part of the acuABC operon, which is possibly involved in the breakdown of acetoin and butanediol . It is also a acetyltransferase that controls the activity of the acetyl coenzyme a synthetase (AcsA) in Bacillus subtilis . It has a role in cell growth and sporulation on acetoin or butanediol , and may be involved in the breakdown of these compounds as a source of carbon.
Uncharacterised conserved protein, UCP020217 (UCP020217)
Type: Family

This entry represents an uncharacterised conserved protein with nucleotidyltransferase domain.
Voltage-dependent chloride channel 1/2 (VCCN1/2)
Type: Family

This entry represents a family plant proteins, including Voltage-dependent chloride channel 1 and 2 (VCCN1/2, also known as BESTROPHIN-like protein 1/2) from Arabidopsis thaliana, which are voltage-dependent chloride channels required for ion transport and homeostasis across the thylakoid membrane to adjust photosynthesis according to the light environment .
Uncharacterised conserved protein YmfJ (Uncharacterised_YmfJ)
Type: Family

This entry represents a group of uncharacterised proteins known as YmfJ.
Fascin, metazoans (Fascin_metazoans)
Type: Family

This family consists of several eukaryotic fascin proteins. Fascins are actin cross-linking proteins that function in the organisation of two major forms of actin-based structures: dynamic, cortical cell protrusions and cytoplasmic microfilament bundles . In humans there are three fascin isoforms identified: fascin1-3. Fruit flies only have one fascin, also known as protein singed, which links Btl/FGFR signalling to the actin cytoskeleton during Drosophila tracheal morphogenesis .
Structural maintenance of chromosomes protein (SMC)
Type: Family

The SMC (structural maintenance of chromosomes) family of proteins, exist in virtually all organisms, including bacteria and archaea. The SMC proteins are essential for successful chromosome transmission during replication and segregation of the genome in all organisms. They function together with other proteins in a range of chromosomal transactions, including chromosome condensation, sister-chromatid cohesion, recombination, DNA repair and epigenetic silencing of gene expression .

SMCs are generally present as single proteins in bacteria, and as at least six distinct proteins in eukaryotes. The proteins range in size from approximately 110 to 170kDa, and share a five-domain structure, with globular N- and C-terminal domains separated by a long (circa 100 nm or 900 residues) coiled coil segment in the centre of which is a globular ''hinge'' domain, characterised by a set of four highly conserved glycine residues that are typical of flexible regions in a protein. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T), which has been shown by mutational studies to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif (XXXXD, where X is any hydrophobic residue), and a LSGG motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases .

All SMC proteins appear to form dimers, either forming homodimers, as in the case of prokaryotic SMC proteins, or heterodimers between different but related SMC proteins. The dimers form core components of large multiprotein complexes. The best known complexes are cohesin, which is responsible for sister-chromatid cohesion, and condensin, which is required for full chromosome condensation in mitosis.

SMC dimers are arranged in an antiparallel alignment. This orientation brings the N- and C-terminal globular domains (from either different or identical protamers) together, which unites an ATP binding site (Walker A motif) within the N-terminal domain with a Walker B motif (DA box) within the C-terminal domain, to form a potentially functional ATPase. Protein interaction and microscopy data suggest that SMC dimers form a ring-like structure which might embrace DNA molecules. Non-SMC subunits associate with the SMC amino- and carboxy-terminal domains.

Proteins in this entry include SMC1/2/3/4 from Saccharomyces cerevisiae. SMC1-SMC3 heterodimer is part of the cohesin complex, which is required for sister chromatid cohesion in mitosis and meiosis . SMC2-SMC4 heterodimer is part of the condensin complex, which is required for chromosome condensation during both mitosis and meiosis .
Spermatogenesis-associated protein 20 (Ssp411)
Type: Family

This entry represents spermatogenesis-associated protein 20 (also known as sperm-specific protein 411 (Ssp411)), which is a testis-specific protein that contains a thioredoxin-like domain, and may play a role in fertility regulation . Other family members include a number of uncharacterised proteins with thioredoxin domains.
Peroxiredoxin, AhpC-type (Peroxiredoxin_AhpC-typ)
Type: Family

Peroxiredoxins are a family of ubiquitous proteins found in all kingdoms of life. They are important for antioxidant defence and, in eukaryotes, participate in redox signalling .

This family includes alkyl hydroperoxide reductase subunit C (AphC) from bacteria , and peroxiredoxins 1 (PRDX1), 2 (PRDX2), 4 (PRDX4) and 6 (PRDX6).
Ferredoxin-thioredoxin reductase catalytic subunit, cyanobacteria-type (FTR_bsu_Cyanobacter)
Type: Family

Ferredoxin thioredoxin reductase is a [4FE-4S] protein present in organisms performing oxygenic photosynthesis, and plays an important role in the ferredoxin/thioredoxin regulatory chain. It converts an electron signal (photoreduced ferredoxin) to a thiol signal (reduced thioredoxin), regulating enzymes by reduction of specific disulphide groups. It catalyses the light-dependent activation of several photosynthetis enzymes. Ferredoxin thioredoxin reductase is a heterodimer of subunit alpha and subunit beta. Subunit alpha is the variable subunit, and beta is the catalytic chain .

This entry represents the catalytic beta subunit, mainly from Cyanobacteria and plants .
Catalase active site (Catalase_AS)
Type: Active_site

Catalases (

) are antioxidant enzymes that catalyse the conversion of hydrogen peroxide to water and molecular oxygen, serving to protect cells from its toxic effects . Hydrogen peroxide is produced as a consequence of oxidative cellular metabolism and can be converted to the highly reactive hydroxyl radical via transition metals, this radical being able to damage a wide variety of molecules within a cell, leading to oxidative stress and cell death. Catalases act to neutralise hydrogen peroxide toxicity, and are produced by all aerobic organisms ranging from bacteria to man. Most catalases are mono-functional, haem-containing enzymes, although there are also bifunctional haem-containing peroxidase/catalases (

) that are closely related to plant peroxidases, and non-haem, manganese-containing catalases (

) that are found in bacteria . Based on a phylogenetic analysis, catalases can be classified into clade 1, 2 and 3. Clade 1 contains small subunit catalases from plants and a subset of bacteria; clade 2 contains large subunit catalases from fungi and a second subset of bacteria; and clade 3 contains small subunit catalases from bacteria, fungi, protists, animals, and plants .

Mono-functional, haem-containing catalases have a core that includes a haem-containing active site deeply buried in a β-barrel structure with two or three channels providing access to the haem. This entry covers a conserved histidine that has been shown to be important for the catalytic mechanism of the enzyme .
Putative O-fucosyltransferase, plant (FucosylTrfase_pln)
Type: Family

This entry represents a group of plant-specific O-fucosyltransferases and their homologues . O-fucosyltransferase-like proteins are GDP-fucose dependent enzymes with similarities to the family 1 glycosyltransferases (GT1). They are soluble ER proteins that may be proteolytically cleaved from a membrane-associated preprotein, and are involved in the O-fucosylation of protein substrates, the core fucosylation of growth factor receptors, and other processes .
Tyramine--L-glutamate ligase (MfnD)
Type: Family

MfnD is a tyramine-glutamate ligase involved in methanofuran biosynthesis. Methanofuran is the first in a series of coenzymes involved in the reduction of carbon dioxide to methane. The crystal structure of the enzyme exhibits a classical ATP-grasp fold .
Catalase, mono-functional, haem-containing, clades 1 and 3 (Catalase_clade1/3)
Type: Family

Catalases (

) are antioxidant enzymes that catalyse the conversion of hydrogen peroxide to water and molecular oxygen, serving to protect cells from its toxic effects . Hydrogen peroxide is produced as a consequence of oxidative cellular metabolism and can be converted to the highly reactive hydroxyl radical via transition metals, this radical being able to damage a wide variety of molecules within a cell, leading to oxidative stress and cell death. Catalases act to neutralise hydrogen peroxide toxicity, and are produced by all aerobic organisms ranging from bacteria to man. Most catalases are mono-functional, haem-containing enzymes, although there are also bifunctional haem-containing peroxidase/catalases (

) that are closely related to plant peroxidases, and non-haem, manganese-containing catalases (

) that are found in bacteria . Based on a phylogenetic analysis, catalases can be classified into clade 1, 2 and 3. Clade 1 contains small subunit catalases from plants and a subset of bacteria; clade 2 contains large subunit catalases from fungi and a second subset of bacteria; and clade 3 contains small subunit catalases from bacteria, fungi, protists, animals, and plants .

This entry represents clades 1 and 3 of the mono-functional, haem-containing catalases.