SII-SWORD/CoKE huggingface dataset:
Carboxysome assembly protein CsoS2/2B (CSOS2/2B)
Type: Family

This family represents carboxysome assembly proteins, including CsoS2 and S2B (also known as carboxysome shell proteins), which are alpha-carboxysome scaffold proteins required for alpha-carboxysome (Cb) assembly. They mediate interaction between RuBisCO and shell proteins to organize and assemble Cb . The N-terminal repeats of this intrinsically disordered protein bind simultaneously to both subunits of RuBisCO and minimally 2 N-terminal repeats are necessary for RuBisCO assembly into the Cb in vivo .
Head-to-tail connector protein, podovirus-type (Connector_podovirus)
Type: Family

The tail of bacteriophage T7, a member of the Podoviridae family, is composed of at least four proteins; one of them is gene product 8 (gp8), known as the connector . DNA enters the viral head during DNA packaging through a channel formed by the connector. The connector sits at a unique 5-fold vertex of the icosahedral capsid , which is also involved in the delivery of the genome during DNA ejection. Purified gp8 protein has been shown to assemble as a dodecamer .

This family includes connector proteins from Podoviridae and bacterial proteins.
Tail specific protease, C-terminal (Tail_Prtase_C)
Type: Domain

This entry represents the C-terminal domain of tail-specific protease Prc, involved in the cleavage of a C-terminal peptide of 11 residues from the precursor form of penicillin-binding protein 3 (PBP3) . This protease belongs to MEROPS serine peptidase family S41A (C-terminal processing peptidase-1, clan SK). This domain is typically between 88 to 187 amino acids in length.
Centromere protein Cenp-K (Centromere_CenpK)
Type: Family

Cenp-K is one of seven new Cenp-A-nucleosome distal (CAD) centromere components (the others being Cenp-L, Cenp-O, Cenp-P, Cenp-Q, Cenp-R and Cenp-S) that are identified as assembling on the Cenp-A nucleosome associated complex, NAC . The Cenp-A NAC is essential, as disruption of the complex causes errors of chromosome alignment and segregation that preclude cell survival despite continued centromere-derived mitotic checkpoint signalling. Cenp-K is centromere-associated through its interaction with one or more components of the Cenp-A NAC. It may be involved in incorporation of newly synthesized Cenp-A into centromeres via its interaction with the Cenp-A-NAC complex .

The homologue in Schizosaccharomyces pombe is known as inner kinetochore subunit sim4 .
Uncharacterised protein family, calcium binding protein, CcbP (Uncharacterised_Ca-bd_CcbP)
Type: Family

CcbP is a Ca(2+) binding protein found in bacteria which is thought to bind Ca(2+) by protein surface charge. When bound to Ca(2+), the protein becomes more compact and the level of free calcium decreases. Within the bacteria, Ca(2+) has a role in the early stages of heterocyst differentiation. The free Ca(2+) concentration which is regulated by CcbP is critical for the differentiation process . Calcium signalling is widespread in bacterial species, and prokaryotic cells like eukaryotes are equipped with all the elements to maintain Ca2+ homeostasis .
Chlorosome envelope protein C (Chlorosome_envelope_CsmC)
Type: Family

Chlorosomes are light-harvesting antennae found in green bacteria. This entry represents Chlorosome envelope protein C (CsmC) which is one of the proteins that exists in the chlorosome envelope and has been shown to exist as a homomultimer with CsmD in the chlorosome envelope . CsmC is thought to be important in chlorosome elongation and shape .
Type III secretion system, AvrPto (T3SS_AvrPto)
Type: Family

This entry represents the bacterial effector protein AvrPto, from Pseudomonas syringae and in particular the central core region of the protein that consists of a three-helix bundle motif. AvrPto is part of a type III secretion system from P.syringae which is involved in the bacterial speck disease of tomato. In resistant plants, AvrPto interacts with the host Pto kinase, which elicits an antibacterial defence response. In plants lacking resistance, the Pto kinase is not present and AvrPto acts as a virulence factor, promoting bacterial growth .
Ataxin-1, N-terminal (Ataxin-1_N)
Type: Domain

This entry represents the N-terminal domain of Ataxin-1, which directly binds Capicua and modulates Capicua repressor activity in Drosophila and mammalian cells. It is also thought to be involved in RNA metabolism and the expansion of the polyglutamine tract may alter this function.

Ataxin-1 is typically between 49 and 781 amino acids in length and have a conserved IQT sequence motif. The polyglutamine expanded mutant type of Ataxin-1 does not bind Capicua with as high affinity as wild-type Ataxin-1. It is associated with spinocerebellar ataxia type 1 (SCA1) .
Mediator of RNA polymerase II transcription subunit 3 (Med3)
Type: Family

Med3 is a subunit of the RNA polymerase II mediator complex. It is a direct target of Cyc8-Tup1 transcriptional corepressor .

The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins.

The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11.
Chitin synthesis regulation, Congo red resistance, RCR protein (Chitin_synth_reg_RCR)
Type: Family

RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls. Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall . RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5 .
Spidroin, C-terminal (Spidroin_C)
Type: Domain

Spidroin is spider dragline silk. It is composed of two proteins, major ampullate spidroin 1 (MaSp1) and major ampullate spidroin 2 (MaSp2) . MaSp1 contains five α-helices . Spidroins contain repetitive units capped between non-repetitive N-terminal and C-terminal domains, whose composition varies among species and thus determines the variety of mechanical properties of spider silks. The C-terminal domains are conserved among spider silk proteins .

This is the C-terminal domain of spidroin.
Replication protein 1a, necrotic phentoype-determining domain (1a_necrotic_phenotyp-det_dom)
Type: Domain

Replication protein 1a is a core component of the viral replicase complex in Cucumber mosaic virus and related plant viruses. 1a protein is the major virulence factor of the cucumber mosaic virus (CMV). The Ns strain of CMV causes necrotic lesions to Nicotiana spp. while other strains cause systemic mosaic .
Cytomegalovirus glycoprotein N, N-terminal (Cytomegalovirus_glycopN_N)
Type: Domain

This domain family is found in viruses, and is approximately 30 amino acids in length. The signature is found in association with

. This family is an envelope glycoprotein of (Human herpesvirus 5) .
Dispersed gene family protein 1, domain 4 (Dispersed_gene_fam_prot1_dom4)
Type: Domain

Dispersed gene family protein 1 of Trypanosoma cruzi is likely to be highly expressed, and is expressed from the sub-telomeric region . However, its function is not known. This entry represents domain 4 on this protein which is likely disordered.
Zinc finger, CGNR (Znf_CGNR)
Type: Domain

Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates . Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few . Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target.

This entry represents a C-terminal zinc finger domain. It seems likely to be DNA-binding given the conservation of many positively charged residues. The domain is named after a highly conserved motif found in many members of the family.
HDA1 complex subunit 2/3 (Hda2/3)
Type: Family

This entry contains the class II histone deacetylase complex subunits Hda2 and Hda3 from fungi.
Complementary sex determiner, C-terminal (Sex_determ_C)
Type: Domain

This entry represents the C-terminal end of the sex determination protein.

Sex determination proteins are found in eukaryotes. Proteins in this family are typically between 168 and 410 amino acids in length. It plays a role in the gender determination of around 20% of all animals.

In the honeybee, the mechanism of sex determination depends on the complementary sex determiner (csd) gene which produces an SR-type protein. Males are hemizygous (haploid) or homozygous for csd alleles while females are heterozygous (diploid). Heterozygosity generates an active protein which initiates female development .

When the csd gene is heterozygous, it activates the feminizer gene (fem) by directing the splicing to form female fem mRNAs, which encode the Fem protein . This leads to female development. In contrast, hemizygous or homozygous csd genes are non-active, resulting in male-specific splicing of fem mRNAs .
D-Ala-teichoic acid biosynthesis protein DltX (DltX)
Type: Family

This entry represents a family of DltX proteins of approximately 50 amino acids in length predominantly found in bacillota, including

from Bacillus thuringiensis. Members of this group are small, single-pass transmembrane proteins required for the D-alanylation of teichoic acids. DltX binds to the MBOAT protein DltB (

) and the SGNH hydrolase-like protein DltD (

) . This family was previously known as DUF3687.
Motility repressor MogR, DNA-binding domain (MogR_DNA-bd)
Type: Domain

This domain family is found in bacteria, and is approximately 150 amino acids in length. MogR is involved in the transcriptional repressor of flagellar motility genes, such as flaA, during extracellular growth at 37 degrees Celsius and during intracellular infection. It binds directly to gene promoter region and probably prevents RNA polymerase binding. At low temperatures, MogR repression activity is modulated by the DegU response regulator in an unknown mechanism. MogR is required for full virulence .

MogR binds AT rich flagellar gene promoter regions upstream of the flagellar gene. These regions follow the pattern 5'-TTTTNNNNNAAAA-3'. This domain is the DNA binding domain of MogR .
Cytosolic motility protein (Cytosolic_motility_protein)
Type: Family

This entry represents proteins found in nematodes. They complex with MSP (major sperm protein) to allow motility . Their action is quite similar to the action of bacterial actin molecules.
DNA replication regulator, HobA (HobA)
Type: Family

This family of proteins is found exclusively in epsilon-proteobacteria. Proteins in this family are approximately 180 amino acids in length. The crystal structure of HobA from Helicobacter pylori has been reported at 1.7A resolution; HobA represents a modified Rossmann fold consisting of a five-stranded parallel β-sheet (β1-5) flanked on one side by α2, α3 and α6 helices and α4 and α5 on the other. The α1 helix is extended away from and has minimal interaction with the globular part of the protein. Four monomers interact to form a tetrameric molecule. Four calcium atoms bind to the tetramer and these binding sites may have functional relevance. The closest structural homologue of HobA is a sugar isomerase (SIS) domain containing protein, the phosphoheptose isomerase from Pseudomonas aeruginosa. The SIS proteins share strong sequence homology with DiaA from Escherichia coli; yet, HobA and DiaA share no sequence homology .
Cell adhesion molecule Dscam1, C-terminal (Dscam1_C)
Type: Domain

This entry is specific to the insecta, predominantly Drosophila spp. This entry is found in association with

,

and

. The Cell adhesion molecule Dscam1 (also known as Down syndrome cell adhesion molecule) belongs to a family of cell membrane molecules involved in the differentiation of the nervous system. This is the C-terminal cytoplasmic tail region of Dscam1. In Drosophila melanogaster (Fruit fly) the gene has at least 59 different transcripts. Dscam1 may play a role in the nervous and immune systems .
ATPase, vacuolar ER assembly factor, Vma12 (ATPase_Vma12)
Type: Family

Transmembrane ATPases are membrane-bound enzyme complexes/ion transporters that use ATP hydrolysis to drive the transport of protons across a membrane. Some transmembrane ATPases also work in reverse, harnessing the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP.

V-ATPases (also known as V1V0-ATPase or vacuolar ATPase) are found in the eukaryotic endomembrane system, and in the plasma membrane of prokaryotes and certain specialised eukaryotic cells. V-ATPases hydrolyse ATP to drive a proton pump, and are involved in a variety of vital intra-and inter-cellular processes such as receptor mediated endocytosis, protein trafficking, active transport of metabolites, homeostasis and neurotransmitter release . V-ATPases are composed of two linked complexes: the V1 complex (subunits A-H) contains the catalytic core that hydrolyses ATP, while the V0 complex (subunits a, c, c', c'', d) forms the membrane-spanning pore. V-ATPases may have an additional role in membrane fusion through binding to t-SNARE proteins .

The yeast vacuolar proton-translocating ATPase (V-ATPase) is the best characterised member of the V-ATPase family. A total of thirteen genes are required for encoding the subunits of the enzyme complex itself and an additional three for providing factors necessary for the assembly of the whole. Vma12 is one of these latter, all three of which are localised to the endoplasmic reticulum .
SidE, PDE domain (SidE_PDE)
Type: Domain

This entry represents the phosphodiesterase (PDE) domain from the SidE family of proteins found in the Dot/Icm pathway of Legionella pneumophila bacteria. This domain catalyses the conjugation of ADP-ribosylated ubiquitin (ADPR-Ub), previously synthesised by the mono-ADP-ribosyltransferase (mART) domain, to a serine residue on substrates to generate a protein-phosphoribosyl-Ub (PR-Ub) product . These pathogen proteins are secreted bacterial effector proteins, which are translocated inside the host cell using the Dot/Icm secretion system . The SidE family of enzymes carry out ubiquitination of host cell proteins in an E1/E2-independent manner .

The SidE family includes four large proteins SidE, SdeA, SdeB, and SdeC, required for efficient intracellular bacterial replication and catalyses ubiquitination in an E1/E2-independent manner. These proteins contain four domains: a DUB domain, a phosphodiesterase (PDE) domain, a mono-ADP-ribosyltransferase (mART) domain, and a coiled-coil (CC) domain .

Ubiquitination is a post-translational modification that regulates many cellular processes, the conventional ubiquitination cascade culminates in a covalent linkage between the C terminus of ubiquitin (Ub) and a target protein . SidE family proteins can catalyse the non-canonical ubiquitination of several different substrate proteins, including Rab small GTPases, Reticulon-4 (Rtn4), and Rag small GTPases, as well as SidE proteins themselves . This specificity resides on the specific ubiquitin-binding surfaces of mART and the unique features of the PDE domain .

The DUB activity of SdeA is important for regulating the dynamics of ubiquitin association with the bacterial phagosome, but is not necessary for its role in intracellular bacterial replication .
Duffy-antigen binding, C-terminal (Duffy-antigen-binding_C)
Type: Domain

This domain is located at the C-terminal of the Duffy-antigen binding protein of Plasmodium spp. Duffy-antigen binding protein is an antigen on these parasites which enable them to invade erythrocytes . Proteins containing this domain are typically between 449 and 1061 amino acids in length. These proteins are found in association with

. There are two conserved sequence motifs: NKNGG and QKHDF.
Beta-1,3-xylanase (Beta-xylanase)
Type: Family

Many glycoside hydrolases are modular proteins composed of catalytic modules appended to one or more non-catalytic carbohydrate-binding modules (CBMs). CBMs bind to a range of polysaccharides that include crystalline cellulose and hemicelluloses such as glucan, xylan, mannan, and glucomannan. The main function of CBMs is to increase the catalytic efficiency of the enzymes against soluble and/or insoluble substrates by bringing the catalytic module into prolonged and intimate contact with its substrate.

This entry represents the family 31 carbohydrate-binding module (CBM31) of beta-1,3-xylanase .

Beta-1,3-xylan is a homopolymer of b-1,3-linked D-xylose and is a polysaccharide peculiar to marine algae. Beta-1,3-xylanase is a beta-1,3-xylan hydrolyzing enzyme .
Mediator complex, subunit Med2, fungi (Mediator_Med2_fun)
Type: Family

The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins.

The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11.

This family of mediator complex subunit 2 proteins is conserved in fungi. Cyclin-dependent kinase CDK8 or Srb10 interacts with and phosphorylates Med2. Post-translational modifications of Mediator subunits are important for regulation of gene expression .
Mediator complex, subunit Med29, metazoa (Mediator_Med29_met)
Type: Family

The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins.

The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11.

Med29, along with Med11 and Med28, in mammals, is part of the core head-region of the complex. Med29 is the apparent orthologue of the Drosophila melanogaster Intersex protein, which interacts directly with, and functions as a transcriptional coactivator for, the DNA-binding transcription factor Doublesex, so it is likely that mammalian Med29 serves as a target for one or more DNA-binding transcriptional activators .
Mediator complex, subunit Med30, metazoa (Mediator_Med30_met)
Type: Family

The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins.

The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11.

Med30 is a metazoan-specific subunit of Mediator , having no homologues in yeasts.