SII-SWORD/CoKE huggingface dataset:
Centriole and centriolar satellite OFD1 (OFD1)
Type: Family

This family of proteins, which includes centriole and centriolar satellite protein OFD1, is involved in the structural integrity and functional regulation of centrioles, which are critical for cell division and signaling. Members of this family play a key role in determining the length of mother and daughter centrioles and are essential for the biogenesis of cilia, cellular projections that play a significant role in signal transduction for development and tissue maintenance . These proteins are also implicated in the regulation of Wnt signalling pathways and the determination of the left-right axis during embryonic development . Additionally, they participate in the recruitment of important ciliary proteins such as IFT88 and CEP164 to the centrioles .
F-box protein At3g26010-like (At3g26010-like)
Type: Family

This entry represents F-box protein At3g26010 from Arabidopsis thaliana and similar plant proteins. At3g26010 is a galactose oxidase/kelch repeat superfamily protein. Members of this family contain an F-box domain or an F-box associated interaction domain.
Mitogen-activated protein kinase-binding protein 1 (MABP1)
Type: Family

This entry represents the Mitogen-activated protein kinase-binding protein 1 (MAPKBP1, also known as JNKBP1) and related proteins. Members of this family contain two WD40 domains at the N-terminal that mediate interaction with NOD2, leading to the down-regulation of NOD2-induced signalling pathways . These proteins inhibit the activation of NF-kappa-B, a key transcription factor in inflammatory responses, and reduce the secretion of IL8, a pro-inflammatory cytokine. These proteins are also involved in the JNK signaling pathway, which is associated with various cellular processes including stress responses, apoptosis, and immune responses .
F-box/LRR-repeat protein At3g58940-like (FBL60-like)
Type: Family

This entry represents F-box/LRR-repeat protein At3g58940 from Arabidopsis thaliana (FBL60) and similar plant proteins.
Uridine diphosphate glucose pyrophosphatase NUDT22/Nudix hydrolase 9-like (NUDT22/NUDT9-like)
Type: Family

This entry represents a family of eukaryotic proteins, including animal Uridine diphosphate glucose pyrophosphatase NUDT22 and plant Nudix hydrolase 9 (NUDT9). NUDT22 hydrolyses UDP-glucose to glucose 1-phosphate and UMP and UDP-galactose to galactose 1-phosphate and UMP. Preferred substrate is UDP-glucose .
SEMI-ROLLED LEAF 2-like (SRL2-like)
Type: Family

This entry represents the SEMI-ROLLED LEAF 2 protein (SRL2) from Oryza sativa and related plant proteins. SRL2 is involved in the regulation of leaf development, specifically in the modulation of leaf rolling . This protein is mainly expressed in the vascular bundles of leaf blades, leaf sheaths, and roots, especially in their sclerenchymatous cells. SRL2 was implicated in the cellular differentiation processes on the abaxial (lower) side of leaves, influencing the development of specific cell types that contribute to the leaf's structure. This protein may play a role in the transdifferentiation of mesophyll cells into sclerenchymatous cells, which are known for their supportive function in plants.
Nebulin/Nebulette (NEBU/NEBL)
Type: Family

This family of proteins is involved in the structural and functional organisation of sarcomeres, the basic contractile units of muscle fibres. Members of this family bind to actin, contributing to the assembly and stabilization of the Z-disk, which is critical for muscle contraction . This entry includes nebulin (NEBU) which is located in the thin filament of striated muscle in vertebrates and is thought to bind and stabilise F-actin . Nebulette (NEBL), is a nebulin homologue specific to cardiac muscle .
AtLOH3-like (AtLOH3-like)
Type: Family

This family includes sequences mainly from plants, such as LOH3 (At1g19260,

) from Arabidopsis thaliana, a ceramide synthase that uses very-long-chain fatty acyl-CoA and trihydroxy long chain base (LCB) substrates to form the sphingolipid ceramide backbone
Complex I assembly factor TIMMDC1 (TIMMDC1)
Type: Family

This family of proteins includes complex I assembly factor TIMMDC1 from human and its orthologues, which are mitochondrial chaperones that are involved in the assembly of the mitochondrial NADH:ubiquinone oxidoreductase complex, also known as complex I . Members of this family participate in constructing the membrane arm of complex I, which is essential for the proper function of the enzyme in the respiratory chain.
Cysteine-tryptophan domain-containing zinc finger protein 3/5/7 (CWZF3/5/7)
Type: Family

This family of proteins includes Cysteine-tryptophan domain-containing zinc finger protein 3/5/7 and related plant sequences.

Members of this entry contain a CW-type zinc finger domain (

), which is implicated in the recognition of methylated histones, particularly histone H3 lysine 4 (H3K4me). These proteins are involved in chromatin modification and gene expression regulation. They can bind to specific methylated forms of histone H3, facilitating the recruitment of various effectors to mediate gene expression . Some members act as transcriptional activators, directly binding to DNA sequences to regulate target gene transcription, thereby influencing cellular processes such as the regulation of grain size in plants . They are also capable of promoting active chromatin states by increasing levels of specific histone modifications at target loci.
Late embryogenesis abundant protein Lea14-like_2 (Lea14-like_2)
Type: Family

This family includes Lea14-like proteins from plants. Unlike members of

, most proteins in this family lack the Water Stress and Hypersensitive response (WHy) domain. Their function is not clear.

LEA (late embryogenesis abundant) proteins were first identified in land plants. Plant LEA proteins have been found to accumulate to high levels during the last stage of seed formation (when a natural desiccation of the seed tissues takes place) and during periods of water deficit in vegetative organs. Later, LEA homologues have also been found in various species . They have been classified into several subgroups in Pfam and according to Bray and Dure .
F-box domain-containing protein-like (F-box_dom-containing)
Type: Family

This entry represents a group of uncharacterised proteins mainly from clade Poaceae that contain an F-box-like domain.
ATM interactor (ATMIN)
Type: Family

This family includes human ATM interactor (ATMIN, also known as ATM/ATR-substrate CHK2-interacting zinc finger protein (ASCIZ)) and related proteins from animals. These proteins are transcription factors that are essential for cell survival and the formation of RAD51 foci, a response to methylating DNA damage . Members of this family are also involved in the regulation of ATM (ataxia telangiectasia mutated) kinase activity, particularly in the absence of DNA damage, potentially by stabilising ATM . Furthermore, these proteins are known to bind to and activate the transcription of the DYNLL1 promoter, which may have further implications in cellular response mechanisms to DNA damage .
Coiled-coil-helix-coiled-coil-helix domain-containing protein 2/10-like (CHCHD2/10-like)
Type: Family

This family includes Coiled-coil-helix-coiled-coil-helix domain-containing protein 2 and 10 (CHCHD2/10) from human and its orthologues. CHCHD2/10 are homologous proteins that form a complex in the mitochondrial intermembrane space and cooperate to regulate mitochondrial function, playing a role in mitochondrial dynamics and cristae organisation . CHCHD2 is a transcription factor that binds to specific DNA elements and activate transcription under varying oxygen conditions, including both hypoxia and normoxia . It has been reported to regulate oxidative phosphorylation (OXPHOS), promoting the expression of the COX4I2 subunit during stress, inhibiting apoptosis . CHCHD10 regulates mitochondrial COX activity and mitochondrial respiration at hypoxia . Mutations in CHCHD2 and CHCHD10 have been identified as causing Parkinson's disease and amyotrophic lateral sclerosis/frontotemporal dementia/myopathy, respectively .
Guanine nucleotide-binding protein subunit gamma 3-like (GG3-like)
Type: Family

This entry represents a group of proteins from plants, including Guanine nucleotide-binding protein subunit gamma 3 from Arabidopsis thaliana (GG3) . Guanine nucleotide-binding proteins (G proteins) are involved as a modulator or transducer in various transmembrane signalling systems. The beta and gamma chains are required for the GTPase activity, for replacement of GDP by GTP, and for G protein-effector interaction. Guanine nucleotide-binding protein subunit gamma 4 from Oryza sativa (DEP1, also known as GGC3), involved in the regulation of grain size , also belongs to this entry.
NBPF (NBPF)
Type: Family

This family represents the neuroblastoma breakpoint family (NBPF) of proteins which contains a highly conserved domain of unknown function, which is known as NBPF, also known as Olduvai or DUF1220 . The NBPF/DUF1220 domain is present in multiple copies in NBPF proteins. An association has been established between DUF1220 subtype CON1 copy number and autism severity , and between subtype CON2 copy number and cognitive function .
Kinetochore protein NDC80 homolog, plants (NDC80_plants)
Type: Family

This family includes plant homologues of Kinetochore protein NDC80, mainly found in clade Streptophyta. NDC80 is essential for accurate chromosome segregation during cell division . Members of this family are involved in the formation of the kinetochore, a critical structure that attaches chromosomes to the spindle microtubules. They play a key role in the spindle checkpoint, ensuring that chromosomes are properly aligned and segregated to prevent aneuploidy and maintain genomic stability.
Testis-expressed protein 47-like (TEX47-like)
Type: Family

This entry represents human Testis-expressed protein 47 (TEX47) and similar proteins predominantly found in animals. The function of these proteins is unknown.

This domain has a detectable similarity to domains that are members of Acylphosphatase/BLUF domain-like superfamily

and are predicted to adopt similar structure.
Zinc finger protein 318-like (Znf318-like)
Type: Family

This family of proteins includes zinc finger matrin-type and zinc finger protein 318. Members of this family are involved in transcriptional regulation, acting as both coactivators and corepressors for androgen receptor (AR)-mediated transactivation . They play a role in spermatogenesis, particularly during meiotic division, suggesting a function in the regulation of gene expression during the development of sperm cells.
Centrosomal protein of 112 kDa (CEP112)
Type: Family

This family of proteins includes Centrosomal protein of 112 kDa which is thought to be involved in the organisation and function of the centrosome, a cellular structure critical for the organisation of microtubules and the segregation of chromosomes during cell division . Members of this family are known to play a role in the stabilization of microtubules as well as in the maintenance of centrosome cohesion and positioning . They may also be implicated in the regulation of cell cycle progression, particularly during the G2/M transition. Mutations in these proteins have been associated with various types of cancer, underscoring their importance in maintaining genomic stability and proper cell division . In neurons, it localises to the cytoplasm of dendrites and is also enriched in the nucleus where it interacts with the RNA polymerase III transcriptional repressor Maf1 to regulate gamma-aminobutyric acid A receptor surface expression. In addition, the protein has been identified as a component of the human centrosome .
Phosphatidylcholine:diacylglycerol cholinephosphotransferase 1/2-like (PDCT1/2-like)
Type: Family

This entry represents a group of proteins predominantly found in plants, including phosphatidylcholine:diacylglycerol cholinephosphotransferase 1 (PDCT1 or ROD1) and 2 (PDCT2) from Arabidopsis thaliana. PDCT1 catalyses the transfer of the phosphocholine headgroup from phosphatidylcholine (PC) to diacylglycerol, a major reaction for the transfer of 18:1 into phosphatidylcholine for desaturation and also for the reverse transfer of 18:2 and 18:3 into the triacylglycerols synthesis pathway . This entry also includes some uncharacterised proteins from bacteria.
F-box/LRR-repeat protein 15-like (FBL15-like)
Type: Family

This entry represents F-box/LRR-repeat protein 15 from Arabidopsis thaliana (FBL15) and similar plant proteins. Members of this family contain an F-box-like domain and LRR repeats.
Temptin-like (Temptin-like)
Type: Family

This entry represents Temptin from Aplysia californica and similar proteins from eukaryotes and bacteria.

Temptin is a component of the complex of water-borne protein pheromones that stimulates attraction and mating behaviour. It modulates pheromone signalling by direct binding to attractin .
At2g29880-like (At2g29880-like)
Type: Family

This entry represents the uncharacterised protein At2g29880 from Arabidopsis thaliana and related plant proteins, found mainly in clade Magnoliopsida. Members of this family contain a Myb/SANT-like domain at the N terminus [

]. Their function is unknown.
Cramped-like (Cramped-like)
Type: Family

This family of proteins includes cramped protein from Drosophila melanogaster and its orthologues from animals, cramped-like proteins. Cramped is involved in the regulation of gene expression patterns, particularly those governing developmental processes and segmental determination. They are associated with the Polycomb group (Pc-G) genes, which play a crucial role in maintaining the expression of homeotic selector genes. These genes are essential for proper segmental identity during development. Additionally, proteins in this family can influence chromatin structure, as they have been implicated in modifying position effect variegation (PEV), a phenomenon that affects gene silencing in certain genomic contexts .

This entry also includes TSL-kinase interacting protein 1 from Arabidopsis, whose function is not yet clear.
Radial spoke head protein 9 homolog (RSP9)
Type: Family

The Radial spoke head protein 9 homolog (RSPH9) is involved in the assembly and function of axonemal radial spoke complexes, which are crucial for the motility of sperm and cilia . Members of this family are essential for radial spoke head assembly and central pair microtubule stability, impacting the motility of olfactory and neural cilia. They also play a role in maintaining the structural integrity of ciliary axonemes in both 9+0 and 9+2 motile cilia, which are important for the proper functioning of ependymal motile cilia .
CLAVATA3/ESR (CLE)-related protein 14-like (CLE14-like)
Type: Family

This entry represents CLAVATA3/ESR (CLE)-related protein 14 from Arabidopsis thaliana (CLE14) and similar proteins predominantly found in plants. CLE14 is an extracellular signal peptide that regulates cell fate. It represses root apical meristem maintenance and functions as an elicitor of the root meristem differentiation through the CLV2/CRN complex signalling pathway. This protein inhibits irreversibly root growth by reducing cell division rates in the root apical meristem .
At5g58720-like (At5g58720-like)
Type: Family

This family represents the SMR domain-containing protein At5g58720 from Arabidopsis thaliana and related plant proteins, mainly from clade Magnoliopsida. Members of this family contain SMR domain which is typically involved in DNA repair processes and is found in a variety of proteins that participate in mismatch repair and the maintenance of genomic stability.
Centrosomal protein of 72 kDa-like (CEP72-like)
Type: Family

This family of proteins includes centrosomal protein of 72 kDa (CEP72) which is involved in centrosomal and spindle assembly functions . CEP72 plays a crucial role in the recruitment of essential proteins to the centrosome, a key cellular structure involved in organising microtubules. They are responsible for providing microtubule-nucleation activity through interaction with gamma-tubulin ring complexes (gamma-TuRCs), which is essential for the formation of a focused bipolar spindle during cell division. This spindle formation is necessary for generating proper tension between sister chromatids . Additionally, these proteins are implicated in the process of centriole duplication, ensuring the correct replication and segregation of these organelles. They also promote the centrosomal localisation of various proteins including CDK2, KIZ, AKAP9, CDK5RAP22, CEP152, WDR62, and CEP63 . This entry also includes leucine rich repeat containing 36 which is probably a CEP72 paralogue.
C3orf49-like (C3orf49-like)
Type: Family

This entry represents a group of proteins from vertebrates, including human Putative uncharacterized protein C3orf49.
Uncharacterized protein C57A10.07/YOR238W (C57A10.07/YOR238W)
Type: Family

This entry includes the uncharacterised proteins C57A10.07/YOR238W from S.pombe and S.cerevisiae, respectively, which are orthologues. Their function is not yet known.
Cilia- and flagella-associated protein 161 (CF161)
Type: Family

This entry represents human Cilia- and flagella-associated protein 161 (CF161) and similar proteins mainly found in animals. CF161 consists of microtubule inner proteins (MIPs) that are integral components of the dynein-decorated doublet microtubules (DMTs) in the axoneme of cilia . These proteins are essential for the proper functioning of motile cilia, as they play a critical role in cilia beating. The coordinated beating of cilia is vital for various physiological processes, including fluid movement across epithelial surfaces, cell motility, and sensory reception.
Transcriptional elongation regulator MINIYO (MINIYO)
Type: Family

This family includes Transcriptional elongation regulator MINIYO from Arabidopsis thaliana and related plant proteins. MINIYO acts as a positive regulator of transcriptional elongation, a crucial process in gene expression. Members of this family are essential for initiating cell differentiation by interacting with RNA polymerase II and the Elongator complex . They play a significant role in maintaining the levels of transcriptional elongation activity, particularly in tissues undergoing differentiation.
TNF receptor-associated factor homolog 1a/b (TRAF1A/B)
Type: Family

This family represents TNF receptor-associated factor homolog 1a/b from Arabidopsis thaliana, which function redundantly and are involved in the regulation of plant immune responses and autophagy . Members of this family contribute to the turnover of specific nucleotide-binding domain and leucine-rich repeat-containing (NB-LRR) immune receptors, which are crucial for recognising pathogen-associated molecular patterns and initiating immune responses. They are thought to interact with E3 ubiquitin-protein ligase complexes to modulate the ubiquitination and degradation of these immune receptors, thereby maintaining their homeostasis. Additionally, these proteins function as molecular adapters in autophagy, influencing the stability of ATG6, an essential component of the autophagy machinery. Their role in autophagy also involves cooperation with SINAT1 and SINAT2 for the ubiquitination and destabilisation of ATG6, which is necessary for the proper formation of autophagosomes.
E3 ubiquitin-protein ligase CCNB1IP1 homolog (HEI10-like)
Type: Family

This family of proteins includes plant E3 ubiquitin-protein ligase CCNB1IP1 homologues (also known as RING-type E3 ubiquitin transferase HEI10) that play a crucial role in meiosis, specifically in the formation of class I crossovers . These crossovers are essential for the exchange of genetic material between homologous chromosomes, which is a key step in the genetic diversity produced through sexual reproduction.
Preprotein translocase subunit SECE1-like (SECE1-like)
Type: Family

This entry represents Preprotein translocase subunit SECE1 from Arabidopsis thaliana and similar plant proteins. SECE1 is involved in the import/insertion pathway in the thylakoids .
FMR1 neighbor protein-like (FMR1-like)
Type: Family

This entry represents human FMR1 neighbor protein (FMR1NB) and similar sequences mainly found in mammals. Members of this family are located in the vicinity of the FMR1 gene, which is associated with Fragile X syndrome, a condition related to intellectual disability and developmental delays. FMR1NB, also named NY-SAR-35, is aberrantly expressed in various cancer tissues and is involved in cell proliferation and invasion .
Histone H2B, conserved site (HISTONE_H2B_site)
Type: Conserved_site

This entry represents a conserved region in the C-terminal part of H2B .

Histone H2B is one of the five histones, along with H1/H5, H2A, H3 and H4. Two copies of each of the H2A, H2B, H3, and H4 histones ensemble to form the core of the nucleosome . The nucleosome forms octameric structure that wraps DNA in a left-handed manner. Histones can undergo several different types of post-translational modifications that affect transcription, DNA repair, DNA replication and chromosomal stability.
Peroxisomal biogenesis factor 8-like (PEX8-like)
Type: Family

This entry represents Peroxisomal biogenesis factor 8 from Komagataella pastoris (PEX8) and similar fungal proteins. PEX8 is an essential component of the machinery required for the import of both PTS1 and PTS2 (and perhaps all) peroxisomal matrix proteins . This family also includes the ortologue PEX17 from Yarrowia lipolytica.
UBA domain-containing protein 6/RUP1 (Ucp6/RUP1)
Type: Family

This entry represents the orthologues UBA domain-containing protein 6 from Schizosaccharomyces pombe (Ucp6), UBA domain-containing protein RUP1 from Saccharomyces cerevisiae and similar fungal proteins. Ucp6 modulates the activity of the RSP5 HECT ubiquitin-protein ligase through its mediation of the interaction between RSP5 and the deubiquitinase UBP2. It is involved in the regulation of cell wall homeostasis .
F-box protein At4g00755-like (At4g00755-like)
Type: Family

This entry represents F-box protein At4g00755 from Arabidopsis thaliana and similar proteins predominantly found in plants. Many members of this family contain the F-box domain.
YqfX-like (YqfX-like)
Type: Family

This entry represents a group of uncharacterised proteins, including YqfX from Bacillus subtilis (

). The function of these proteins is unknown but the presence of predicted transmembrane helices suggests that they are likely associated with membrane.
WD repeat and HMG-box DNA-binding protein 1, HMG-box (HMG-box_WDHD1)
Type: Domain

This entry represents the HMG-box found at the C-terminal of WDHD1, which binds DNA .

WDHD1, also called acidic nucleoplasmic DNA-binding protein 1 (AND-1), acts as a replication initiation factor that brings together the MCM2-7 helicase and the DNA polymerase alpha/primase complex in order to initiate DNA replication. .