SII-SWORD/CoKE huggingface dataset:
CGI121/TPRKB (CGI121/TPRKB)
Type: Family

This entry represents the EKC/KEOPS complex subunit Cgi121 from fungi and its homologue, TPRKB from mammals. This entry also includes archaeal homologues .
Transcription factor Opi1/Ccg-8 (TF_Opi1_Ccg-8)
Type: Family

This entry represents a family of fungal transcription factors, including Transcriptional repressor OPI1 from Saccharomyces cerevisiae and Transcription factor ccg-8 from Neurospora crassa.

Opi1 is a leucine zipper containing yeast transcription factor that negatively regulates phospholipid biosynthesis . It represses the expression of several UAS(INO) cis acting element containing genes and its activity is mediated by phosphorylations catalysed by protein kinase A, protein kinase C and casein kinase II .

Ccg-8, also known as Clock-controlled protein 8, plays a pivotal role in azole adaptive responses by regulating the drug accumulation in the cells and regulates also phospholipid synthesis that is not involved in azole resistance .
Alkali metal cation/H+ antiporter Nha1, C-terminal (Cation/H_antiporter_C)
Type: Domain

The C terminus of the plasma membrane Nha1 antiporter plays an important role in the immediate cell response to hypo-osmotic shock which prevents an excessive loss of ions and water . This protein is found C-terminal to

.
RPAP1, C-terminal (RPAP1_C)
Type: Domain

This entry represents the C-terminal region that contains the motif GLHHH. This region is conserved from yeast to humans.

In Saccharomyces cerevisiae (Bakers yeast), inhibition of RNA polymerase II-associated protein 1 (RPAP1) synthesis leads to global changes in gene expression that closely resemble those observed upon loss of the RNAPII subunit Rpb11 . RPAP1 forms an interface between the RNA polymerase II enzyme and chaperone or scaffolding proteins, suggesting its essential role in linking RNA polymerase II to regulators involved in protein complex formation. Furthermore, it is required for the interaction of the RNA polymerase II complex with acetylated histone H3, indicating a function in the coordination between transcription and chromatin modification.
RPAP1, N-terminal (RPAP1_N)
Type: Domain

This entry represents the N-terminal region of RPAP-1 that is conserved from yeast to humans.

In Saccharomyces cerevisiae (Bakers yeast), inhibition of RNA polymerase II-associated protein 1 (RPAP1) synthesis leads to global changes in gene expression that closely resemble those observed upon loss of the RNAPII subunit Rpb11 . RPAP1 forms an interface between the RNA polymerase II enzyme and chaperone or scaffolding proteins, suggesting its essential role in linking RNA polymerase II to regulators involved in protein complex formation. Furthermore, it is required for the interaction of the RNA polymerase II complex with acetylated histone H3, indicating a function in the coordination between transcription and chromatin modification.
Svf1-like, N-terminal (Svf1-like_N)
Type: Domain

This entry represents the N-terminal domain of the stress survival proteins, such as survival factor 1 (Svf1). The protein Svf1 is required for yeast survival under conditions of oxidative stress, including cold stress . Cells deficient in Svf1 have increased levels of reactive oxygen species (ROS) under certain conditions. Svf1 affects cellular survival in part via modulation of the sphingolipid metabolic pathway . Two Svf1 family proteins have been identified in the genome of Schizosaccharomyces pombe (Svf1 and Svf2).

Svf1 is a ceramide binding protein that contributes to sphingolipid metabolism at Golgi compartments and its membrane-targeting is important to maintain flux of ceramides into complex sphingolipids. Svf1 consists of two lipocalin-like domains and binds ceramide via a hydrophobic pocket that is located at the interface between these two domains . Two histidine residues located in a small predicted α-helical cap covering the hydrophobic pocket, are essential for the ceramide binding. Their mutation results in loss of ceramide binding as well as cis-Golgi targeting of the protein. The arrangement of two tandem lipocalin-like domains is reminiscent to AttH-like proteins (

).
TATA-binding protein interacting (TIP20) (TATA-bd_TIP120)
Type: Domain

TIP120 (also known as cullin-associated and neddylation-dissociated protein 1) is a TATA binding protein interacting protein that enhances transcription .
Chromatin-remodelling complex, RSC SWI/SNF subunit Rsc7/Swp82 (CRC_Rsc7/Swp82)
Type: Family

This entry contains subunits of the chromatin remodelling complexes. Saccharomyces cerevisiae (Baker's yeast)

and its paralogue

have been identified as subunits of the RSC chromatin remodelling complex, and SWI/SNF chromatin remodelling complex respectively .
U3 small nucleolar RNA-associated protein 13, C-terminal (Utp13_C)
Type: Domain

A large ribonuclear protein complex is required for the processing of the small-ribosomal-subunit rRNA -the small-subunit (SSU) processome . This preribosomal complex contains the U3 snoRNA and at least 40 proteins, which have the following properties:

They are nucleolar.

They are able to coimmunoprecipitate with the U3 snoRNA and Mpp10 (a protein specific to the SSU processome).

They are required for 18S rRNA biogenesis.

There appears to be a linkage between polymerase I transcription and the formation of the SSU processome; as some, but not all, of the SSU processome components are required for pre-rRNA transcription initiation. These SSU processome components have been termed t-Utps. They form a pre-complex with pre-18S rRNA in the absence of snoRNA U3 and other SSU processome components. It has been proposed that the t-Utp complex proteins are both rDNA and rRNA binding proteins that are involved in the initiation of pre18S rRNA transcription. Initially binding to rDNA then associating with the 5' end of the nascent pre18S rRNA. The t-Utpcomplex forms the nucleus around which the rest of the SSU processome components, including snoRNA U3, assemble . From electron microscopy the SSU processome may correspond to the terminal knobs visualised at the 5' ends of nascent 18S rRNA.

Utp13 is a nucleolar protein and component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA .

Upt13 is also a component of the Pwp2 complex that forms part of a stable particle subunit independent of the U3 small nucleolar ribonucleoprotein that is essential for the initial assembly steps of the 90S pre-ribosome . Components of the Pwp2 complex are: Utp1 (Pwp2), Utp6, Utp12 (Dip2), Utp13, Utp18, and Utp21. The relationship between the Pwp2 complex and the t-Utps complex that also associates with the 5' end of nascent re-18S rRNA is unclear.

This is the C-terminal helical domain of yeast Utp13 and its orthologue from human, Transducin beta-like protein 3, whose function is not clear. This domain is also found in protein TORMOZ EMBRYO DEFECTIVE from plants, which is an essential protein involved in the regulation of cell division planes during embryogenesis and defines cell patterning .
TRAPP II complex, Trs120 (TRAPP_II_complex_Trs120)
Type: Family

The trafficking protein particle complex TRAPP is a multi-protein complex needed in the early stages of the secretory pathway. To date, two kinds of TRAPP complexes have been studied, TRAPPI and TRAPP II. These complexes differ in subunit composition . TRAPP I binds vesicles derived from the endoplasmic reticulum bringing them closer to the acceptor membrane. Trs120 is a subunit specific to the TRAPP II complex along with Trs65p and Trs130p(TRAPPC10). It is suggested that Trs120p is required for the stability of the Trs130p subunit, suggesting that these two proteins might interact in some way . It is likely that there is a complex function for TRAPP II in multiple pathways .
Chloroquine-resistance transporter-like (CRT-like)
Type: Family

This family represents the Plasmodium falciparum chloroquine resistance transporter (CRT) and homologous proteins. CRT regulates other transporters, like Na-H antiporter or nonselective cation transporters . The Arabidopsis homologues are involved in thiol transport from the plastid to the cytosol, playing a significant role in regulating GSH levels and the redox potential of the cytosol . Homologues from Dictyostelium discoideum are also included in this entry .
Sorting nexin, C-terminal (Sorting_nexin_C)
Type: Domain

This region is found at the C terminus of proteins belonging to the nexin family. It is found on proteins which also contain

.
3'5'-cyclic nucleotide phosphodiesterase PDE8 (PDEase_PDE8)
Type: Domain

This region is found at the N terminus of members of PDE8 phosphodiesterase family . Phosphodiesterase 8 (PDE8) regulates chemotaxis of activated lymphocytes .

The cyclic nucleotide phosphodiesterases (PDE) comprise a group of enzymes that degrade the phosphodiester bond in the second messenger molecules cAMP and cGMP. They are divided into 11 families. They regulate the localisation, duration and amplitude of cyclic nucleotide signalling within subcellular domains. PDEs are therefore important for signal transduction.

PDE enzymes are often targets for pharmacological inhibition due to their unique tissue distribution, structural properties, and functional properties. Inhibitors include: Roflumilast for chronic obstructive pulmonary disease and asthma , Sildenafil for erectile dysfunction and Cilostazol for peripheral arterial occlusive disease , amongst others.

Retinal 3',5'-cGMP phosphodiesterase is located in photoreceptor outer segments: it is light activated, playing a pivotal role in signal transduction . In rod cells, PDE is oligomeric, comprising an alpha-, a beta-and 2 gamma-subunits, while in cones, PDE is a homodimer of alpha chains, which are associated with several smaller subunits. Both rod and cone PDEs catalyse the hydrolysis of cAMP or cGMP to the corresponding nucleoside 5' monophosphates, both enzymes also binding cGMP with high affinity. The cGMP-binding sites are located in the N-terminal half of the protein sequence, while the catalytic core resides in the C-terminal portion.
Regulatory subunit Dfp1/Him1, central region (Regulatory_Dfp1/Him1)
Type: Domain

This region, together with the C-terminal zinc finger (

) is essential for the mitotic and kinase activation functions of Dfp1/Him1 .
Meiosis specific protein Spo22/ZIP4/TEX11 (Spo22/ZIP4/TEX11)
Type: Family

This entry includes a group of meiosis specific proteins, including Spo22 from budding yeasts, ZIP4 from plants and TEX11 from mammals. They play an important role in normal crossover formation and meiotic chromosome segregation . Impairment of these functions results in meiosis I (MI) segregation defect .
Protein Zds1, C-terminal (ZDS1_C)
Type: Domain

This region of the Zds1 protein is critical for sporulation and has also been shown to suppress the calcium sensitivity of Zds1 deletions . The C-terminal motif is common to both Zds1 and Zds2 proteins, both of which are putative interactors of Cdc55 and are required for the completion of mitotic exit and cytokinesis. They both contribute to timely Cdc14 activation during mitotic exit and are required downstream of separase to facilitate nucleolar Cdc14 release.
Mediator complex, subunit Med19, fungi (Mediator_Med19_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 entry represents the Med19 subunit of the Mediator complex in fungi.
Mitochondrial protein Pet127 (Pet127)
Type: Family

This entry represents a group of fungal mitochondria proteins, known as Pet127, that stimulate mitochondrial RNA degradation . Pet127 has been classified as part of the PD-(D/E)XK nuclease superfamily including a full set of active site residues .
Oxidoreductase putative, C-terminal (OxRdtase_put_C)
Type: Domain

This is the C terminus of putative oxidoreductases.
V-type ATPase assembly factor Pkr1 (Pkr1)
Type: Family

Pkr1 functions together with the other V-type ATPase assembly factors in the endoplasmic reticulum to efficiently assemble the V-type ATPase membrane sector V0 .
Nuclear control of ATP synthase 2 (NCA2)
Type: Family

NCA2 (Nuclear Control of ATPase), is one of the two nuclear genes involved in the control of mitochondrial expression of subunits 6 and 8 of the Fo-F1 ATP synthase in Saccharomyces cerevisiae. Mutations in either NCA2 or NCA3 (

) dramatically lower the level of the co-transcript encoding subunits 6 and 8 .

This entry also includes DGS1 from Arabidopsis. DGS1 is a mitochondrial outer membrane protein involved in galactoglycerolipid biosynthesis .
Mediator complex, subunit Med14 (Mediator_Med14)
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.

Saccharomyces cerevisiae (Baker's yeast) RGR1 mediator complex subunit affects chromatin structure, transcriptional regulation of diverse genes, and sporulation. It is required for glucose repression, HO repression, RME1 repression and sporulation . This subunit is also found in higher eukaryotes and MED14 is the agreed unified nomenclature for this subunit .
DNA replication regulator Sld3, C-terminal (DNA_replication_reg_Sld3_C)
Type: Domain

The Sld3 DNA replication regulator is required for loading and maintenance of Cdc45 on chromatin during DNA replication . This entry represents the C-terminal domain of Sld3 which includes the Sld3-Treslin domain (STD), essential for replication origin firing . This domain consists of two segments with 12 helices, sufficient to bind to Cdc45 . Treslin is the metazoan functional homologue of yeast Sld3, which differ in molecular size and amino acid sequence., which also contains a STD . Based on their similarities, it has been suggested that helicase activation in mammals has diverged in complexity during evolution from that in yeasts and may involve additional partners that interact with TopBP1 .
U3 small nucleolar RNA-associated protein 6 (Utp6)
Type: Family

Utp6 is a component of the small subunit (SSU) processome containing the U3 snoRNA that is involved in processing of pre-18S rRNA .
Kinetochore Mis14/Nsl1 (Mis14/Nsl1)
Type: Family

This entry includes Mis14 from S. pombe, Nsl1 from S. cerevisiae and Nsl1 homologues from animals. MIs14 is 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 . Nsl1 is an essential component of the kinetochore MIND complex, which is required for the spindle checkpoint and kinetochore integrity .
Histone deacetylation protein Rxt3 (Rxt3)
Type: Family

Rxt3 is a component of the Rpd3L histone deacetylase complex that is responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4) .
Protein of unknown function DUF1776, fungi (DUF1776_fun)
Type: Family

This is a fungal protein of unknown function. One of the proteins

has been localised to the mitochondria .
FACT complex subunit SPT16, middle domain (FACT_SPT16_M)
Type: Domain

This entry represents a domain found in the central region of Spt16 from diverse eukaryotes . This entry covers the dimerization domain (DD), which straddles nucleosomal DNA at the H2A-H2B dyad .

SPT16 is a component of the FACT (facilitator of chromatin transcription) complex, a general chromatin factor that acts to reorganise nucleosomes . In budding yeasts, the N-terminal domain (NTD) of SPT16 includes a smaller N-terminal lobe (residues 1-175) and a larger C-terminal lobe (residues 176-447).
Polynucleotide kinase 3 phosphatase (PNK3P)
Type: Family

Polynucleotide kinase 3 phosphatases play a role in the repair of single breaks in DNA induced by DNA-damaging agents such as gamma radiation and camptothecin .
Replication factor A, C-terminal (Rep_factor-A_C)
Type: Domain

Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA . Replication factor-A protein is also known as Replication protein A 70kDa DNA-binding subunit.

This entry is found at the C terminus of Replication factor A and similar proteins found and eukaryotes and archaea.
E3 ubiquitin ligase Bre1 (E3_ubiquit_lig_Bre1)
Type: Family

Bre1 is an E3 ubiquitin ligase that mediates monoubiquitination of histone H2B to form H2BK123ub1 in association with the E2 enzyme Rad6/Ubc2 .

This entry also includes Bre1 homologues from fission yeasts, Brl1 and Brl2. They are E3 ubiquitin-protein ligase components of the multisubunit protein complex (termed HULC) which mediates monoubiquitination of histone H2B to form H2BK123ub1 .
U4/U6.U5 small nuclear ribonucleoprotein 27kDa protein (SNRNP27)
Type: Domain

U4/U6.U5 small nuclear ribonucleoprotein 27kDa protein may play a role in mRNA splicing .
DASH complex subunit Dad1 (DASH_Dad1)
Type: Family

The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis . In Saccharomyces cerevisiae (Baker's yeast) DASH forms both rings and spiral structures on microtubules in vitro . Components of the DASH complex, including Dam1, Duo1, Spc34, Dad1 and Ask1, are essential and connect the centromere to the plus end of spindle microtubules . Throughout the cell cycle Dad1 remains bound to kinetochores and its association is dependent on the Mis6 and Mal2 .
DASH complex subunit Dad4 (DASH_Dad4)
Type: Family

The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis . In Saccharomyces cerevisiae (Baker's yeast) DASH forms both rings and spiral structures on microtubules in vitro .
DASH complex subunit Duo1 (DASH_Duo1)
Type: Family

The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis . In Saccharomyces cerevisiae (Baker's yeast) DASH forms both rings and spiral structures on microtubules in vitro .
RAI1-like (RAI1)
Type: Domain

Yeast RAI1 is homologous to Caenorhabditis elegans DOM-3 and human DOM3Z (DXO). They have both decapping and 5'-3' exoribonuclease activity and are a component of the mRNA 5'-end capping quality control mechanism . RAI1 is a single-copy gene in most organisms; however S. cerevisiae contains a second homologue, DXO1, which also possesses decapping and 5'-3' exoribonuclease activity, whereas RAI1 has decapping and pyrophosphohydrolase activities . This domain is also found in DXO1 homologue from Arabidopsis .
DASH complex subunit Dam1 (DASH_Dam1)
Type: Family

The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis . In Saccharomyces cerevisiae (Baker's yeast) DASH forms both rings and spiral structures on microtubules in vitro . Components of the DASH complex, including Dam1, Duo1, Spc34, Dad1 and Ask1, are essential and connect the centromere to the plus end of spindle microtubules .
DASH complex subunit Dad2 (DASH_Dad2)
Type: Family

The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis . In Saccharomyces cerevisiae (Baker's yeast) DASH forms both rings and spiral structures on microtubules in vitro .
DASH complex subunit Ask1 (DASH_Ask1)
Type: Family

The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis . In Saccharomyces cerevisiae (Baker's yeast) DASH forms both rings and spiral structures on microtubules in vitro . Components of the DASH complex, including Dam1, Duo1, Spc34, Dad1 and Ask1, are essential and connect the centromere to the plus end of spindle microtubules .
DASH complex subunit Dad3 (DASH_Dad3)
Type: Family

The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis . In Saccharomyces cerevisiae (Baker's yeast) DASH forms both rings and spiral structures on microtubules in vitro .
DASH complex subunit Spc34 (Spc34)
Type: Family

The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis . In Saccharomyces cerevisiae (Baker's yeast) DASH forms both rings and spiral structures on microtubules in vitro . Components of the DASH complex, including Dam1, Duo1, Spc34, Dad1 and Ask1, are essential and connect the centromere to the plus end of spindle microtubules .
Rad54, N-terminal (Rad54_N)
Type: Domain

This is the N-terminal of the DNA repair protein Rad54 . Rad54 functions in the recombinational DNA repair (RAD52) pathway. It dissociates RAD51 from nucleoprotein filaments formed on dsDNA and could be involved in the turnover of RAD51 protein-dsDNA filaments. Deficient mice also show significantly shorter telomeres than wild-type controls, indicating that the protein activity plays an essential role in telomere length maintenance in mammals. Non-homologous end joining (NHEJ) and homologous recombination (HR) represent the two major pathways of DNA double-strand break (DSB) repair in eukaryotic cells. LIG4 and RAD54L cooperate to support cellular proliferation, repair spontaneous DSBs, and prevent chromosome and single chromatid aberrations .