SII-SWORD/CoKE huggingface dataset:
TFIIH p62 subunit, N-terminal (TFIIH_BTF_p62_N)
Type: Domain

The N-terminal region of the TFIIH basal transcription factor complex p62 subunit (BTF2-p62) forms an interaction with the 3' endonuclease XPG, which is essential for activity. The 3' endonuclease XPG is a major component of the nucleotide excision repair machinery. The structure of the N-terminal region reveals that it adopts a pleckstrin homology (PH) fold .
YAP-binding/ALF4/Glomulin (YAP-bd/ALF4/Glomulin)
Type: Family

This entry contains a number of protein families with apparently unrelated functions. The yeast YAP binding proteins are stress response and redox homeostasis proteins, induced by hydrogen peroxide or induced in response to alkylating agent methyl methanesulphonate (MMS) . Aberrant root formation protein 4 (ALF4) of Arabidopsis thaliana (Mouse-ear cress),is required for the initiation of lateral roots independent from auxin signalling. It may also function in maintaining the pericycle in the mitotically competent state needed for lateral root formation . Glomulin (FAP68) is essential for normal development of the vasculature and may represent a naturally occurring ligand of the immunophilins FKBP59 and FKBP12 .
Mo25-like (Mo25)
Type: Family

Mo25-like proteins are involved in both polarised growth and cytokinesis. In fission yeast Mo25 is localised alternately to the spindle pole body and to the site of cell division in a cell cycle dependent manner .
Protein of unknown function DUF1761 (DUF1761)
Type: Family

This entry represents a family of conserved proteins with unknown function.
Yos1-like (Yos1)
Type: Family

In yeast, Yos1 is a subunit of the Yip1p-Yif1p complex and is required for transport between the endoplasmic reticulum and the Golgi complex .
Pre-mRNA-splicing factor 3 domain (Pre-mRNA_splic_Prp3_dom)
Type: Domain

This entry represents a domain that is located centrally in mammal U4/U6 small nuclear ribonucleoprotein Prp3 and Protein RDM16 from Arabidopsis thaliana and towards the N-terminal end in Prp3 from yeast.

Pre-mRNA processing factor 3 (PRP3) is a U4/U6-associated splicing factor. It plays a key role in the recognition of the snRNA duplex. Defects in PRPF3 are the cause of retinitis pigmentosa type 18 (RP18). RP leads to degeneration of retinal photoreceptor cells . In Arabidposis thaliana, protein RDM16 acts as a pre-mRNA splicing factor and functions in RNA-directed DNA methylation by influencing Pol V transcript levels .

This domain shows an α-helical structure .
DNA endonuclease activator Ctp1, C-terminal (Ctp1_C)
Type: Domain

This entry represents the C-terminal domain of the fission yeast Ctip (Ctp1) protein. Proteins containing this domain include DNA endonuclease RBBP8 (also known as CtBP-interacting protein, CtIP) from animals, protein gamma response 1 (GR1) from Arabidopsis and SAE2 from S. cerevisiae . SAE2 is a protein involved in repairing meiotic and mitotic double-strand breaks in DNA .

Although proteins containing this domain were described as endonucleases, it is now known that they actually function as endonuclease activators that cooperates with the MRE11-RAD50-NBN (MRN) complex in processing meiotic and mitotic double-strand breaks (DSBs) by ensuring both resection and intrachromosomal association of the broken ends . This domain contains highly conserved residues at its 15-residue extreme that are indispensable for MRN (Mre11-Rad50-Nbs1) complex activation, through the stimulation of Mre11 endonuclease activity .
Transcription factor Iwr1 domain (TF_Iwr1_dom)
Type: Domain

Iwr1 is involved in transcription from polymerase II promoters; it interacts with with most of the polymerase II subunits . Deletion of this protein results in hypersensitivity to the K1 killer toxin .
Protein of unknown function DUF1764, eukaryotic (DUF1764_euk)
Type: Family

This entry consists of eukaryotic proteins of unknown function, including many hypothetical proteins.
PI31 proteasome regulator, C-terminal (PI31_Prot_C)
Type: Domain

This entry represents the C-terminal of the PI31 protein. PI31 is a cellular regulator of proteasome formation and of proteasome-mediated antigen processing .
Uncharacterised protein family UPF0592 (UPF0592)
Type: Family

This entry represents a conserved region found in hypothetical proteins from fungi, mycetozoa and entamoebidae.
Ribonuclease P, Rpm2, mitochondrial (RNase_P_Rpm2_mt)
Type: Family

Ribonuclease P (RNase P) generates mature tRNA molecules by cleaving their 5' ends. Rpm2 is a protein subunit of the yeast mitochondrial RNase P. It has the ability to act as a transcriptional activator in the nucleus, where it plays a role in defining the steady-state levels of mRNAs for some nucleus-encoded mitochondrial components. Rpm2p is also involved in maturation of Rpm1 and in translation of mitochondrial mRNAs .
Karyogamy protein, KAR9 (Karyogamy_KAR9)
Type: Family

The KAR9 protein in Saccharomyces cerevisiae (Baker's yeast) is a cytoskeletal protein required for karyogamy, correct positioning of the mitotic spindle and for orientation of cytoplasmic microtubules . KAR9 localises at the shmoo tip in mating cells and at the tip of the growing bud in anaphase .
Transcriptional repressor Tup1, N-terminal (Tscrpt_rep_Tup1_N)
Type: Domain

The N-terminal region of the Tup protein has been shown to interact with the Ssn6 transcriptional co-repressor .
Cytochrome c oxidase biogenesis protein Cmc1-like (Cyt_c_biogenesis_Cmc1-like)
Type: Family

Cmc1 is a metallo-chaperone like protein which is known to localise to the inner mitochondrial membrane in Saccharomyces cerevisiae. It is essential for full expression of cytochrome c oxidase and respiration . Cmc1 contains two Cx9C motifs and is able to bind copper(I). Cmc1 is thought to play a role in mitochondrial copper trafficking and transfer to cytochrome c oxidase.
Ribonuclease P protein subunit Rpp40 (RNase_P_Rpp40)
Type: Family

Ribonuclease P (Rnp) is a ubiquitous ribozyme that catalyzes a Mg2 -dependent hydrolysis to remove the 5'-leader sequence of precursor tRNA (pre-tRNA) in all three domains of life . In bacteria, the catalytic RNA (typically ~120kDa) is aided by a small protein cofactor (~14kDa) . Archaeal and eukaryote RNase P consist of a single RNA and archaeal RNase P has four or five proteins, while eukaryotic RNase P consists of 9 or 10 proteins. Eukaryotic and archaeal RNase P RNAs cooperatively function with protein subunits in catalysis .

This entry represents Rpp40 from eukaryotes. Human RNase P is composed of a singular protein Pop1 and three subcomplexes, the Rpp20-Rpp25 heterodimer, Pop5-Rpp14-(Rpp30)2-Rpp40 heteropentamer, and Rpp21-Rpp29-Rpp38 heterotrimer .
RecQ mediated genome instability protein 1, OB-fold domain (RMI1_OB)
Type: Domain

This entry represents the the OB-fold domain of RMI1 (RecQ-mediated genome instability protein 1) and similar proteins . This domain forms a stable complex with Bloom syndrome protein BLM and DNA topoisomerase 3-alpha .
Chromatin structure-remodeling complex protein Rsc14 (Rsc14)
Type: Family

RSC is an ATP-dependent chromatin remodelling complex found in yeast. The RSC components Rsc7/Npl6 and Rsc14/Ldb7 interact physically and/or functionally with Rsc3, Rsc30, and Htl1 to form a module important for a broad range of RSC functions .
Carbon catabolite-derepressing protein kinase, ubiquitin-associated domain (SNF1_UBA)
Type: Domain

This ubiquitin-associated (UBA) domain is found in yeast carbon catabolite-derepressing protein kinases (Snf1) and similar proteins from fungi. Mutations in this domain significantly alter SNF1 kinase activation and biological activity .

Snf1, also called yeast adenosine monophosphate (AMP)-activated protein kinase (AMPK), is a global regulator of carbon metabolism in the yeast Saccharomyces cerevisiae . Snf1 is involved in the cellular responses to nutrient stress, as well as other environmental stresses .
Domain of unknown function at the cortex 1 (Duc1)
Type: Domain

This entry includes the Duc1 (Domain of Unknown Function at the Cortex 1) protein, which is involved in maintaining proper plasma membrane lipid composition and cytokinetic ring anchoring in Schizosaccharomyces pombe . Duc1 localises to the plasma membrane, except at the cell division site, and its localization is controlled by interactions with the ER-PM contact site proteins Scs2 and Scs22 through a FFAT-like motif. Duc1 promotes proper localization of the PI-5 kinase Its3, thereby maintaining appropriate levels of PI(4,5)P2 at the plasma membrane. This function is important for proper anchoring of the cytokinetic ring during cell division. Duc1 contains a conserved domain previously known as the DUF1769 domain of unknown function, which is represented in this entry.
Mitophagy receptor Atg43 (Atg43)
Type: Family

Mitophagy is a selective type of autophagy in which damaged or unnecessary mitochondria are sequestered by double-membranous structures called phagophores and delivered to vacuoles/lysosomes for degradation. This family represents Atg43 from fungi, a mitochondrial outer membrane protein that serves as a mitophagy receptor that tethers Atg8 to the mitochondrial outer membrane to promote selective autophagy .
Domain of unknown function DUF1771 (DUF1771)
Type: Domain

This domain is highly charged and may represent a small helical extension of the Smr domain

, known as N-ext, whose function is not yet clear .
Ribonucleotide reductase inhibitor (RNR_inhibitor)
Type: Family

This entry includes Schizosaccharomyces pombe (Fission yeast) Spd1. Spd1p inhibits fission yeast RNR activity by interacting with the Cdc22p .
Anthrone oxygenase (Anthrone_oxy)
Type: Family

This family consists of anthrone oxygenases found in bacteria and fungi, and similar proteins involved in the synthesis of different products. GedH from Aspergillus terreus is part of the gene cluster that mediates the biosynthesis of geodin , EncC from Neosartorya fumigata is involved in the biosynthesis of endocrocin , and MdpH from Aspergillus nidulans in the biosynthesis of monodictyphenone .
Mug135-like, C-terminal domain (Mug135-like_C)
Type: Domain

This entry represents a conserved domain found at the C-terminal end of certain meiotically up-regulated gene products (MUG) from fungi , including Meiotically up-regulated gene 135 protein from Schizosaccharomyces pombe (Mug135, also known as Tdk1,

). Mug135 is a killer meiotic driver (KMD), a selfish genetic element that by selectively kills meiotic products lacking its gene, thereby promoting its own propagation. This protein exists in a nontoxic tetrameric form during vegetative growth and meiosis but transforms into a distinct toxic form in spores .
Meiotic expression up-regulated protein (Meiotic_expression)
Type: Family

This family of proteins appear to be specific to Schizosaccharomyces (Fission yeast). Their exact function is unknown, but they are up-regulated in meiosis and some of them have been shown to be required for critical meiotic events .
Transcriptional regulatory protein RXT2, N-terminal (RXT2_N)
Type: Domain

The entry represents the N-terminal region of RXT2. RXT2, also known as RAF60, is a component of the Rpd3 histone deacetylase complex (HDAC). Histone deacetylation plays an important role in transcriptional regulation, cell cycle progression and developmental events .
Lethal giant larvae (Lgl)-like, C-terminal domain (Lgl_C_dom)
Type: Domain

The Lethal giant larvae (Lgl) tumour suppressor protein is conserved from yeast to mammals. The Lgl protein functions in cell polarity, at least in part, by regulating SNARE-mediated membrane delivery events at the cell surface . The N-terminal half of Lgl members contains WD40 repeats (see

), while the C-terminal half appears specific to the protein .
Eukaryotic translation initiation factor 3 subunit J (eIF3j)
Type: Family

This shows protein subunits of the eukaryotic translation initiation factor 3 J (eIF3j). It is a component of the eukaryotic translation initiation factor 3 (eIF-3) complex, which is involved in protein synthesis and, together with other initiation factors, stimulates binding of mRNA and methionyl-tRNAi to the 40S ribosome . In Saccharomyces cerevisiae, eIF3j has been shown to be required for processing of 20S pre-rRNA and binds to 18S rRNA and eIF3 subunits Rpg1p and Prt1p .
Sds3-like (Sds3)
Type: Family

Repression of gene transcription is mediated by histone deacetylases containing repressor-co-repressor complexes, which are recruited to promoters of target genes via interactions with sequence-specific transcription factors. The co-repressor complex contains a core of at least seven proteins . This entry represents the conserved region found in Sds3, Dep1 and BRMS1-homologue p40 proteins.
Nibrin, C-terminal (Nibrin_C)
Type: Domain

This is the C-terminal region of Nibrin (also known as DNA damage repair protein Nbs1) that has been identified to be necessary for the binding of Mre11 and Tel1 .

Nibrin (also known as Nbs1 or p95) plays an important role in the DNA damage response (DDR) and DNA repair. It is part of the nuclear MRN complex, which consists of Mre11, Rad50, and Nbs1, and is involved in double-strand break (DSB) repair, DNA recombination, maintenance of telomere integrity, cell cycle checkpoint control and meiosis . Mutations in the NBN gene coding for nibrin cause the Nijmegen Breakage Syndrome (NBS), a rare autosomal recessive disorder characterised by genomic instability and increased risk of haematopoietic malignancies .
Transcription factor PAP1 (TF_PAP1)
Type: Domain

The transcription factor Pap1 regulates antioxidant-gene transcription in response to H2O2 . This region is cysteine rich. Alkylation of cysteine residues following treatment with a cysteine alkylating agent can mask the accessibility of the nuclear exporter Crm1, triggering nuclear accumulation and Pap1 dependent transcriptional expression .
Mitochondrial inner membrane i-AAA protease complex subunit Mgr1 (i-AAA_Mgr1)
Type: Family

This entry represents Mitochondrial inner membrane i-AAA protease complex subunit MGR1 and similar proteins from Saccharomycetes. Mgr1 has been shown to be required for mitochondrial viability in yeast lacking mitochondrial DNA. It is a mitochondrial inner membrane protein, which interacts with Yme1 and is a subunit of the i-AAA protease complex .
Adenylate cyclase-associated CAP, C-terminal (Adenylate_cyclase-assoc_CAP_C)
Type: Domain

Cyclase-associated proteins (CAPs) are highly conserved actin-binding proteins present in a wide range of organisms including yeast, fly, plants, and mammals. CAPs are multifunctional proteins that contain several structural domains. CAP is involved in species-specific signalling pathways . In Drosophila, CAP functions in Hedgehog-mediated eye development and in establishing oocyte polarity. In Dictyostelium (slim mold), CAP is involved in microfilament reorganisation near the plasma membrane in a PIP2-regulated manner and is required to perpetuate the cAMP relay signal to organise fruitbody formation. In plants, CAP is involved in plant signalling pathways required for co-ordinated organ expansion. In yeast, CAP is involved in adenylate cyclase activation, as well as in vesicle trafficking and endocytosis. In both yeast and mammals, CAPs appear to be involved in recycling G-actin monomers from ADF/cofilins for subsequent rounds of filament assembly . In mammals, there are two different CAPs (CAP1 and CAP2) that share 64% amino acid identity.

This entry represents the C-terminal domain of CAP proteins, which is responsible for G-actin-binding. This domain has a superhelical structure, where the superhelix turns are made of two β-strands each .
Nucleoporin Nup153, N-terminal (Nup153_N)
Type: Domain

Nuclear pore complex protein Nup153 is a component of the nuclear pore complex (NPC), a complex required for the trafficking across the nuclear envelope. The N-terminal domain of Nup153 has NPC targeting activity and is found before the middle domain, which contains four zinc finger motifs of the C2C2-type .
Rad9-like Rad53-binding domain, fungi (Rad9_Rad53-bd_dom_fun)
Type: Domain

This entry represents a Rad53 binding domain (tudor domain) from yeast Rad9. In Saccharomyces cerevisiae (Baker s yeast), Rad9 is a key adaptor protein in DNA damage checkpoint pathways. DNA damage induces Rad9 phosphorylation and promotes the interaction between Rad9 and phosphorylated Rad53 . This interaction is achieved through the Rad53 binding domain from Rad9 and the FHA domains from Rad53 (

) . Confusingly, there is another Rad9 protein found in fission yeast and other eukaryotes (which is known as Ddc1 in budding yeast) that is also involved in DNA repair. However, these proteins are not related to the Rad9 proteins covered by this entry.
Prp19, coiled-coil region (Prp19_cc)
Type: Domain

This entry represents the coiled-coil region of Prp19.

Prp19, also known as DNA repair protein Pso4 (psoralen-sensitive mutant 4), is a ubiquitously expressed multifunctional E3 ubiquitin ligase with pleiotropic activities in DNA damage signalling, repair, and replicative senescence. It functions as a critical component of DNA repair and DNA damage checkpoint complexes. It senses DNA damage, binds double-stranded DNA in a sequence-independent manner, facilitates processing of damaged DNA, promotes DNA end joining, regulates replication protein A (RPA2) phosphorylation and ubiquitination at damaged DNA, and regulates RNA splicing and mitotic spindle formation in its integral capacity as a scaffold for a multimeric core complex .

Prp19 is essential for spliceosome assembly and stability. It is a core component of the PRP19C/Prp19 complex/NTC/Nineteen complex which is part of the spliceosome and participates in its assembly, its remodelling and is required for its activity. During assembly of the spliceosome, it mediates Lys-63-linked polyubiquitination of the U4 spliceosomal protein PRPF3. Ubiquitination of PRPF3 allows its recognition by the U5 component PRPF8 and stabilises the U4/U5/U6 tri-snRNP spliceosomal complex .

Prp19 contains an N-terminal E3 ubiquitin ligase U-box domain with E2 recruitment function that facilitates dimerisation and is essential for its auto-ubiquitination activity in vitro or when overexpressed , a coiled-coil Prp19 homology region that mediates its tetramerisation and interaction with CDC5L and SPF27 and a C-terminal seven-bladed WD40 β-propeller that forms an asymmetrical barrel-shaped structure important for substrate recognition and recruitment .
tRNA wybutosine-synthesis (tRNA_wybutosine-synth)
Type: Domain

The proteins in this entry appear to be important in wyosine base formation in a subset of phenylalanine specific tRNAs. It has been proposed that it participates in converting tRNA(Phe)-m(1)G(37) to tRNA(Phe)-yW .
Nucleotide exchange factor Fes1 (Nucleotide_exch_fac_Fes1)
Type: Domain

This entry represents a domain found in the Fes1 protein. Fes1 is a cytosolic homologue of Sls1, an ER protein which has nucleotide exchange factor activity. Fes1 in yeast has been shown to bind to the molecular chaperone Hsp70 and has adenyl-nucleotide exchange factor activity .
Peroxisome membrane protein, Pex16 (Pex16)
Type: Family

Pex16 is a peripheral protein located at the matrix face of the peroxisomal membrane .
Protein of unknown function DUF1774, fungi (DUF1774_fun)
Type: Family

This is a fungal protein of unknown function.
Mediator complex, subunit Med20 (Mediator_Med20)
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.

Proteins in this entry are subunit Med20 of the Mediator complex, and is found in the non-essential part of the head . and related to the TATA-binding protein (TBP). TBP is a highly conserved RNA polymerase II general transcription factor that binds to the core promoter and initiates assembly of the pre-initiation complex. Human TRF has been shown to associate with an RNA polymerase II-SRB complex .
Cyclin PHO80-like (Cyclin_PHO80-like)
Type: Family

Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles , and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E.

Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus .

This entry includes cyclin PHO80 and other cyclins that partner with the cyclin-dependent kinase (CDK) PHO85. The PHO80/PHO85 cyclin-cdk complex is used for a regulatory process other than cell-cycle control . This entry also includes other PHO80-like cyclins that are involved in the cell-cycle control. They belong to the P/U family and interact preferentially with CDKA1 .
Autophagy-related protein 16 domain (Autophagy-rel_prot_16_dom)
Type: Domain

Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells. In yeast, 15 Atg proteins coordinate the formation of autophagosomes. The pre-autophagosomal structure contains at least five Atg proteins: Atg1p, Atg2p, Atg5p, Aut7p/Atg8p and Atg16p, found in the vacuole . The C-terminal glycine of Atg12p is conjugated to a lysine residue of Atg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Autophagy protein 16 (Atg16) has been shown to bind to Atg5 and is required for the function of the Atg12p-Atg5p conjugate . Autophagy protein 5 (Atg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway .

This entry represents the coiled-coil domain (CC) of autophagy protein 16 (Apg16), which is required for self-assembly. Atg16 is required for the function of the Apg12p-Apg5p conjugate.
Ribonuclease H2, subunit C (RNase_H2_suC)
Type: Family

Whereas bacterial and archaeal RNases H2 are active as single polypeptides, eukaryotic RNase H2 is a heterotrimeric complex of the RNase H2A, RNase H2B, and RNase H2C proteins that are all required for proper function and activity

,

]. RNase H2 is an endonuclease that specifically degrades the RNA of RNA:DNA hybrids. It participates in DNA replication, possibly by mediating the removal of lagging-strand Okazaki fragment RNA primers during DNA replication.

This entry represents the non-catalytic C subunit of RNase H2.