SII-SWORD/CoKE huggingface dataset:
Small aggregate formation protein (SmlA)
Type: Family

Dictyostelium is usually a unicellular soil organism. However, depletion of food triggers chemotactic aggregation resulting in the formation of a multicellular organism. SmlA is required for the proper function of a cell-counting mechanism that regulates organism size in Dictyostelium. SmlA affects secretion of the counting factor complex, whose concentration is indirectly proportional to aggregate size .
Maintenance of telomere capping protein 4 (MTC4)
Type: Family

This is a family of fungal proteins. Mutations in a member from Saccharomyces cerevisiae, YBR255W, affected growth rate . YBR255W has been identified among genes that affect telomere capping, and has been renamed maintenance of telomere capping protein 4 .
Sodium/solute symporter superfamily (Na+/solute_symporter_sf)
Type: Homologous_superfamily

Proteins in this entry contain a Na+/H+ antiporter like fold. Some members are annotated as sodium/solute symporters .
Sphingomyelinase C/Sphingomyelin phosphodiesterase 2-like (Sph/SMPD2-like)
Type: Family

This entry includes SMPD2/3 from animals, Isc1/Css1 from yeasts and sphingomyelinase C (also known as sph) from bacteria.

Neutral sphingomyelinase (nSMase) sphingomyelin phosphodiesterase SMPD2 hydrolyzes sphingomyelin to phosphocholine and ceramide. SMPD2, differently to nSMase SMPD3, which is prominent in brain, is ubiquitously expressed . Both are involved in vesicle budding from the plasma membrane .

Budding yeast Isc1 is inositol phosphosphingolipid phospholipase C that localizes to mitochondria in the post-diauxic phase of yeast growth . Fission yeast Isc1 homologue, Css1, localizes to the entire plasma membrane and secretory pathway .
Lymphocyte antigen 6 complex locus protein G5b (LY6G5B)
Type: Family

Lymphocyte Antigen 6 (Ly-6) superfamily members are cysteine-rich, generally GPI-anchored cell surface proteins with known or putative roles in immune function. Ly6G5b is a member of the family. It is a potentially secreted protein of unknown function .
Centrosomal protein CEP162-like (CEP162-like)
Type: Family

CEP162 (KIAA1009/QN1) is required for ciliogenesis. It is an axoneme-recognition protein that promotes and restricts transition zone formation at the cilia base. It has also been shown to interact with CEP290 and mediate its association with microtubules .
Sperm microtubule inner protein 11 (SPMIP11)
Type: Family

This entry includes Sperm microtubule inner protein 11 (SPMIP11 also known as TEX49). SPMIP11 is a microtubule inner protein (MIP) part of the axonemal dynein-decorated doublet microtubules (DMTs). It is likely involved in the stabilisation of the microtubule structure in the sperm flagella .
Uncharacterized protein C2orf80 (C2orf80)
Type: Family

This entry represents a cluster of uncharacterised, hypothetical proteins.
Uncharacterized protein At4g18490-like (At4g18490-like)
Type: Family

This is a family of uncharacterised proteins from plants.
Mitoregulin (Mtln)
Type: Family

Mitoregulin (Mtln), also known as LINC00116 in humans, is a lncRNA-encoded microprotein that binds cardiolipin and influences protein complex assembly in mitochondria . Mtln interacts directly with the beta subunit of the mitochondrial trifunctional protein, an enzyme critical in the beta-oxidation of long-chain fatty acids. It also increases mitochondrial membrane potential while decreasing mitochondrial reactive oxygen species . Members of this family are mainly found in vertebrates.
Coiled-coil domain-containing protein 107 (CCDC107)
Type: Family

Proteins in this family are found in mammals. Their function is not known.
Another-regulin (ALN)
Type: Family

This entry represents a family of short proteins from vertebrates, including another-regulin (ALN, also known as sarcoplasmic/endoplasmic reticulum calcium ATPase regulator ARLN). This protein is a SERCA regulator .
Uncharacterized membrane protein C365.16-ike (C365.16-ike)
Type: Family

This family is conserved in yeast and apicomplexa. The representative, SPBC365.16, is an uncharacterised mitochondrial membrane protein from fission yeast.
Uncharacterized protein C3orf22 (C3orf22)
Type: Family

This is a family of uncharacterised proteins from mammals of unknown function.
Mitogen-activated protein (MAP) kinase Sty1/HOG1 (MAPK_Sty1/HOG1)
Type: Family

This family is composed of the mitogen-activated protein kinases (MAPKs) Sty1 from Schizosaccharomyces pombe, Hog1 from Saccharomyces cerevisiae, and similar fungal proteins. Sty1 and Hog1 are stress-activated MAPKs that participate in transcriptional regulation in response to stress .

Hog1 is the key element in the high osmolarity glycerol (HOG) pathway and is activated upon hyperosmotic stress. Activated Hog1 accumulates in the nucleus and regulates stress-induced transcription . The HOG pathway is mediated by two transmembrane osmosensors, Sln1 and Sho1 .

Sty1 is activated in response to oxidative stress, osmotic stress, and UV radiation . It is regulated by the MAP2K Wis1, which is activated by the MAP3Ks Wis4 and Win1, which receive signals of the stress condition from membrane-spanning histidine kinases Mak1-3 . Activated Sty1 stabilizes the Atf1 transcription factor and induces transcription of Atf1-dependent genes of the core environmental stress response .

Mitogen-activated protein (MAP) kinases are integral components of kinase cascades, in which at least three protein kinases act sequentially to ultimately activate the MAP kinase itself . Activation occurs via dual phosphorylation on conserved threonine and tyrosine residues within a TXY motif. The MAP kinase family is involved in numerous cellular processes, including proliferation, differentiation, migration, transformation, and programmed cell death. These kinases are typically activated by a variety of extracellular stimuli, such as pro-inflammatory cytokines and physical stress. Once activated, MAP kinases phosphorylate a wide array of substrates, including transcription factors, cytoskeletal components, and regulators of apoptosis, translation, and other signalling pathways. They play a central role in signal transduction mechanisms, notably the MAPK/ERK cascade, influencing key cellular functions such as growth, adhesion, survival, and differentiation. In addition to their roles in transcriptional regulation, MAP kinases also participate in the modulation of endosomal dynamics, including lysosome processing, endosome cycling, and Golgi apparatus fragmentation during mitosis.
Mitogen-activated protein kinase 14 (MAPK14)
Type: Family

p38 kinases are mitogen-activated protein kinases (MAPKs), serving as important mediators of cellular responses to extracellular signals. They function in the regulation of the cell cycle, cell development, cell differentiation, senescence, tumorigenesis, apoptosis, pain development and pain progression, and immune responses. p38 kinases are activated by the MAPK kinases MKK3 and MKK6, which in turn are activated by upstream MAPK kinase kinases including TAK1, ASK1, and MLK3, in response to cellular stresses or inflammatory cytokines . p38 substrates include other protein kinases and factors that regulate transcription, nuclear export, mRNA stability and translation. p38 kinases are drug targets for the inflammatory diseases psoriasis, rheumatoid arthritis, and chronic pulmonary disease .

Vertebrates contain four p38 kinases, named alpha, beta, gamma, and delta, which show varying substrate specificity and expression patterns.

MAPK14/p38alpha is expressed in most tissues and is the major isoform involved in the immune and inflammatory response. It is the central p38 MAPK involved in myogenesis . It plays a role in regulating cell cycle check-point transition and promoting cell differentiation. p38alpha also regulates cell proliferation and death through crosstalk with the JNK pathway . Its substrates include MAPK activated protein kinase 2 (MK2), MK5, and the transcription factors ATF2 and Mitf .
Mitogen-activated protein kinase 13 (MAPK13)
Type: Family

p38 kinases are mitogen-activated protein kinases (MAPKs), which serve as important mediators of cellular responses to extracellular signals. They are activated by the MAPK kinases MKK3 and MKK6, which in turn are activated by upstream MAPK kinase kinases including TAK1, ASK1, and MLK3, in response to cellular stresses or inflammatory cytokines .

Vertebrates contain four p38 kinases, named alpha, beta, gamma, and delta, which show varying substrate specificity and expression patterns.

MAPK13/p38delta is found in skeletal muscle, heart, lung, testis, pancreas, and small intestine . It regulates microtubule function by phosphorylating Tau. It activates the c-jun promoter and plays a role in G2 cell cycle arrest . It also controls the degration of c-Myb, which is associated with myeloid leukemia and poor prognosis in colorectal cancer. p38delta is the main kinase involved in regulating the differentiation and apoptosis of keratinocytes .
Mitogen-activated protein kinase 12 (MAPK12)
Type: Family

p38 kinases are mitogen-activated protein kinases (MAPKs), which serve as important mediators of cellular responses to extracellular signals. They are activated by the MAPK kinases MKK3 and MKK6, which in turn are activated by upstream MAPK kinase kinases including TAK1, ASK1, and MLK3, in response to cellular stresses or inflammatory cytokines .

Vertebrates contain four p38 kinases, named alpha, beta, gamma, and delta, which show varying substrate specificity and expression patterns.

MAPK12/p38gamma is predominantly expressed in skeletal muscle. Unlike p38alpha and p38beta, p38gamma is insensitive to pyridinylimidazoles . It displays an antagonizing function compared to p38alpha. p38gamma inhibits, while p38alpha stimulates, c-Jun phosphorylation and AP-1 mediated transcription . p38gamma also plays a role in the signaling between Ras and the estrogen receptor and has been implicated to increase cell invasion and breast cancer progression . In Xenopus, p38gamma is critical in the meiotic maturation of oocytes .
Testis-expressed protein 46-like (TEX46-like)
Type: Family

This entry includes a group of animal proteins, including testis-expressed protein 46 from humans.
Protein LOW PSII ACCUMULATION 2 like (LPA2-like)
Type: Family

This entry represents a group of proteins from plants, including protein LOW PSII ACCUMULATION 2 (LPA2) from Arabidopsis whose function is not clear.
Mediator of RNA polymerase II transcription subunit 9, plant (Med9_plant)
Type: Family

This entry represents mediator of RNA polymerase II transcription subunit 9 (Med9) from plants . 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 .
Cilia- and flagella-associated protein 97 (Cfap97/Hemingway)
Type: Family

Drosophila Hemingway (Hmw) is required for motile cilia function and sperm flagella assembly . The human orthologue, known as cilia- and flagella-associated protein 97 (CFAP97) or KIAA1430, localizes to the primary cilium .
CFAP97 domain-containing protein 1/2 (CFAP97D1/2)
Type: Family

This family includes CFAP97D1 (CFAP97 domain-containing protein 1) and CFAP97D2. CFAP97D1 is required for sperm flagellum ultra-structure maintenance, thereby playing a critical role in sperm function and male fertility in mice .
Lysine-rich arabinogalactan protein 19 (AGP19)
Type: Family

This entry consists of AGP19 from Arabidopsis and related proteins. AGP19 is a member of the lysine-rich arabinogalactan protein (AGP) subfamily within the hydroxyproline-rich glycoprotein (HRGP) superfamily. AGPs are hyperglycosylated proteins implicated in different aspects of plant growth and development. Protein backbones of AGPs are rich in Pro/Hyp (hydroxyproline), Ser, Ala and Thr and are modified by the addition of type II arabinogalactan polysaccharides and arabinose oligosaccharides to Hyp residues . AGP19, as the other lysine-rich members AGP17 and AGP18, contains a C-terminal lysine-rich region and is thought to be related to sexual reproduction in flowering plants .
Protein LIAT1 (LIAT1)
Type: Family

This entry includes Liat1 (ligand of Ate1) from animals. Liat1 interacts with Ate1 and may be involved in Ate1-mediated N-terminal arginylation. Ate1 is a component of the N-end rule pathway, which recognizes and polyubiquitylates proteins containing N-terminal degradation signals, targeting them for degradation by the proteasome.

In primates, Liat1 genes are subtelomeric and Liat1 protein contains tandem repeats of a 10-residue sequence, whereas Liat1 proteins of other mammals contain a single copy of this motif .
Mediator of RNA polymerase II transcription subunit 8, plant (MED8_plant)
Type: Family

This entry represents mediator of RNA polymerase II transcription subunit 8 (Med8) from plants . It plays roles in plant immunity and in regulating organ size .

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 .
At1g76070-like (At1g76070-like)
Type: Family

This entry represents a group of plant proteins, including At1g76070 from Arabidopsis. Their function is not clear.
Protein Flattop (Fltp)
Type: Family

Flattop (Fltp, (also known as Cilia- and flagella-associated protein 126 CFAP126) regulates basal body docking and positioning in mono- and multiciliated cells . These are microtubule inner proteins (MIP) part of the doublet microtubules (DMTs) in cilia and sperm axoneme .
Coiled-coil domain-containing protein 138 (CCDC138)
Type: Family

The function of coiled-coil domain-containing protein 138 is not clear. However, it has been localised to basal bodies, suggesting to play a role in centrosomal and ciliary biology .
Protein LEKR1 (LEKR1)
Type: Family

The function of LEKR1 (leucine-, glutamate- and lysine-rich protein 1) is not clear.
Coiled-coil domain-containing protein 17 (CCDC17)
Type: Family

The function of CCDC17 (coiled-coil domain-containing protein 17) is not clear.
TATA box-binding protein-associated factor RNA polymerase I subunit C (TAF1C)
Type: Family

TAF1C is a component of the transcription factor SL1/TIF-IB complex, which is involved in the assembly of the PIC (preinitiation complex) during RNA polymerase I-dependent transcription .
Small integral membrane protein 33 (SMIM33)
Type: Family

This entry represents a group of animal proteins, including SMIM33. The function of SMIM33 is not clear.
Root meristem growth factor 3 (RGF3)
Type: Family

This entry includes the plant root meristem growth factor 3 (RGF3, also known as GOLVEN 7) from Arabidopsis, a signaling peptide that maintains the postembryonic root stem cell niche in a PIN2-traffic dependent manner .
Transmembrane protein 139 (TMEM139)
Type: Family

Transmembrane protein 139 (TMEM139) interacts with kAE1 (the human kidney isoform of anion exchanger 1) and promotes its intracellular trafficking .
Spermatogenesis-associated protein 45 (SPATA45)
Type: Family

The function of spermatogenesis-associated protein 45 is not clear.
Coiled-coil domain-containing protein 150 (CCDC150)
Type: Family

The function of CCDC150 is not clear.
Protein modifier of SNC1 1-like (MOS1-like)
Type: Family

This entry represents a group of plant proteins, including protein modifier of SNC1 1 (MOS1) from Arabidopsis. MOS1 regulates the expression of suppressor of npr1-1, constitutive1 (SNC1), which encodes a Toll/interleukin receptor-nucleotide binding site-leucine-rich repeat type of resistance protein. It may function in regulation of gene expression at chromatin level .
Centlein (CNTLN)
Type: Family

Centlein interacts with C-Nap1 and Cep68 and plays a role in centrosome cohesion . It has also been shown to bind to microtubules .
CUB domain-containing protein 1 (CDCP1)
Type: Family

CDCP1 is a cell surface glycoprotein that has been recognized both as a tumour marker and as a potential target to disrupt progression of cancer . CDCP1 has been shown to modulate cellsubstratum adhesion and motility in colon cancer cell lines .
Fertilization-influencing membrane protein (FIMP)
Type: Family

In mice, 4930451I11Rik encodes two isoforms: a transmembrane (TM) form and a secreted form. FIMP is the TM form. It is a sperm-specific transmembrane protein that is essential for the sperm-oocyte fusion process .
Altered inheritance of mitochondria protein 11 (AIM11)
Type: Family

This family consists of uncharacterised proteins from fungi. They have been named altered inheritance of mitochondria protein 11 (AIM11). Saccharomyces cerevisiae has a second paralogue: YBL059W/IAI11.
IgA-inducing protein (IGIP)
Type: Family

This entry includes IgA-inducing proteins (IGIPs) from animals . Monocyte-derived dendritic cells are the primary producers of human IGIP. IGIP induces expression of IgA in the presence of IL-10 .
Stationary phase protein 5 (Stationary_phase_5)
Type: Family

SPG5 (stationary phase protein 5) was identified as a protein required for survival at high temperature during stationary phase in Saccharomyces cerevisiae . SPG5 is a positive regulator of the proteasome that is strongly induced in the stationary phase. It is critical for survival of cells that have ceased to proliferate due to nutrient limitation .
Coiled-coil domain-containing protein 192 (CCDC192)
Type: Family

The function of CCDC192 is not clear.
Mast cell-expressed membrane protein 1 (MCEMP1)
Type: Family

MCEMP1 is a type II transmembrane protein found in human mast cells . It has been linked to stroke prognosis .
Coiled-coil domain-containing protein 171 (CCDC171)
Type: Family

The function of CCDC171 is not clear.
CLE-related protein 45-like (CLE45-like)
Type: Family

This entry includes a group of plant proteins, including CLAVATA3/ESR (CLE)-related protein 45 (CLE45) from Arabidopsis. CLE45 may be a suppressor of plant stem cell differentiation . CLE45 is part of the CLE peptide family.

The CLE peptide family members are small proteins that contain a signal peptide at their N-termini and conserved CLE domain(s) at their C-termini. The signal peptide is essential for secretion of the CLE peptide into the apoplastic space where it functions non-cell autonomously. They have a variety of functions, from embryo and endosperm development to meristem maintenance, from vascular development to autoregulation of nodulation (AON) .
Vertnin-like (Vertnin-like)
Type: Family

Vertnin is reported to be a maternal factor involved in dorsoventral patterning in zebrafish. It is rapidly transported to the animal pole region after fertilisation and binds to a bmp2b regulatory region to prevent its transcription . In mammals, it is associated with variations in vertebral number .
Mediator-associated protein 2, plant (MED2_plant)
Type: Family

This entry represents mediator of RNA polymerase II transcription subunit 2 (Med2) from plants.

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 .
Protein shortage in chiasmata 1-like (SHOC1-like)
Type: Family

This entry represents a group of plant proteins, including shortage in chiasmata 1 (SHOC1) from Arabidopsis. SHOC1 is essential for the formation of class I meiotic crossovers .
Apical junction component (Apical_junction)
Type: Family

This entry represents a family of proteins known variously as apical junction molecule, or apical junction component. In Caenorhabditis elegans, the coiled-coil protein Ajm-1 (apical junction molecule) controls epithelial junction integrity. Its localization to apical junctions is regulated by proteins LET-413 and DLG-1 .
Coiled-coil domain-containing protein 178 (CCDC178)
Type: Family

The function of CCDC178 is not clear.
Coiled-coil domain-containing protein 152 (CCDC152)
Type: Family

Coiled-coil domain-containing protein 152 (CCDC152) has been identified as a gene involved in cell cycle regulation, cellular proliferation and migration. Overexpression of CCDC152 reduced cell proliferation and migration through the JAK2/STAT signaling pathway .
Leukosialin (Leukosialin)
Type: Family

Leukosialin (CD43, sialophorin) is a large sialoglycoprotein expressed widely in various leukocytes (granulocytes, monocytes/macrophages and T-lymphocytes) . It is involved in leukocyte adhesion and migration . Leukosialin interacts with the T cell receptor (TcR) to initiate signaling events during T cell priming . The CD43 signaling pathway induces the expression of IFN-gamma by effector CD4+ T cells (Th, helper T cells) and to a lesser extent CD8+ T cells (Tc, cytotoxic T cells) . Besides its role in progression of the T cell differentiation program, CD43 plays a role in T cell homing from lymphoid organs to peripheral tissues .
Coiled-coil domain-containing protein 186 (CCDC186)
Type: Family

The function of CCDC186 is not clear.
Small integral membrane protein 26 (SMIM26)
Type: Family

The function of SMIM26 is not clear.
Cell division cycle-associated protein 3 (CDCA3)
Type: Family

This entry includes cell division cycle-associated protein 3 (CDCA3; also known as trigger of mitotic entry protein 1 or TOME-1), which is required for entry into mitosis. The protein is found at high levels during the G2 and M phases of mitosis, but declines rapidly during the G2 phase. Entry into mitosis requires the relocalization to the nucleus and activation of cyclin-dependent kinase 1 (cdk1) by association with cyclin B, and exit from mitosis occurs when cyclin B is degraded and the kinase activity decreases. Anaphase promoting complex (APC) is an E3 ligase active during anaphase and G1, and is required for the degradation of cyclin B. CDCA3 is a cytosolic protein and a substrate of APC. It associates with Skp-1 and is required for the degradation of the cdk1 inhibitor wee1, a tyrosine kinase. Degradation of CDCA3 leads to an accumulation of wee1 during interphase . The CDCA3 protein contains an F-box-like region and a KEN box; the latter is required for association with the APC complex.