SII-SWORD/CoKE huggingface dataset:
Testis-expressed protein 50 (TEX50)
Type: Family

The function of testis-expressed protein 50 (TEX50) is not clear.
Coiled-coil domain-containing protein 175 (CCDC175)
Type: Family

This function of this family of coiled-coil domain-containing proteins is not known.
Giardin subunit beta-like (Giardin_beta-like)
Type: Family

This entry includes giardin subunit beta and related proteins. Giardins are involved in parasite attachment to the intestinal mucosa and in the cytoskeletal disassembly and reassembly that marks the transition from infectious trophozoite to transmissible cyst. They may interact with other cytoskeletal proteins such as microtubules in the microribbons or crossbridges, to maintain the integrity of the ventral disk .
Mediator of RNA polymerase II transcription subunit 16 (MED16)
Type: Family

This entry includes mediator of RNA polymerase II transcription subunit 16 (MED16; also known as SENSITIVE TO FREEZING 6 or SFR6) which is known only from plants. It is a component of the Mediator complex, which is required for transcription of almost all RNA polymerase II-dependent genes. Mediator provides an interface for activator and repressor proteins to transmit information from regulatory DNA elements to core promoters . MED16 is a key component in acclimatization of plants to freezing temperatures .
tRNA ligase 1 (tRNA_ligase_1)
Type: Family

tRNA ligase 1 (RNL) is involved in the pre-tRNA splicing process in plants. Pre-tRNA splicing requires intron removal by an endonuclease, and a ligase for joining the resulting tRNA halves. In Arabidopsis, the endonuclease is encoded by two genes, SEN1 and SEN2 , and tRNA ligase is encoded by one gene, AtRNL . Like fungal tRNA ligases, a plant tRNA ligase is a multifunctional enzyme consisting of three domains each with a different activity in the order: ligase, kinase and cyclic phosphodiesterase (CPDase). The polynucleotide kinase domain heals the broken ends to generate the 3'-OH, 2'-PO4, and 5'-PO4 required for sealing by the ligase domain .
Telomerase RNA component interacting RNase (TRIR)
Type: Family

This entry includes telomerase RNA component interacting RNase (TRIR), an exoribonuclease that is a component of the telomerase RNA 3' end processing complex. It releases all four unpaired RNA nucleotides from either the 5' end or the 3' end but with a higher efficiency for purine bases .
AT hook-containing protein attf-4-like (Attf-4-like)
Type: Family

This entry represents a group of proteins from Nematoda, including Attf-4. Their function is not clear.
RWD domain-containing protein 3 (RWDD3)
Type: Family

RWDD3, also known as RSUME, is a RWD-containing protein that enhances SUMO conjugation by interacting with the SUMO conjugase Ubc9, increases Ubc9 thioester formation and therefore favours sumoylation of specific targets. It also increases IkappaB levels and stabilizes HIF-1alpha during hypoxia, leading to inhibition of NF-kappaB and increased HIF-1 transcriptional activity .
Uncharacterized protein PF07_0086 (PF07_0086)
Type: Family

This entry contains uncharacterised proteins mainly from eukaryotes. Protein PF07_0086 is from the malaria parasite Plasmodium falciparum.
Cell wall protein Sed1/Spi1 (Sed1/Spi1)
Type: Family

Sed1 is a major structural GPI-cell wall glycoprotein from Saccharomyces cerevisiae . It may have a possible role in mitochondrial genome maintenance . This family also includes Sed1 paralogue, Spi1, a cell wall protein that plays a role in resistance to cell wall stress , and related proteins from fungi.
Cilia- and flagella-associated protein 157 (CFAP157)
Type: Family

Cilia- and flagella-associated protein 157 (CFAP157) has been characterised as a component on the flagellum from the green alga Chlamydomonas reinhardtii by mass spectroscopy . Related proteins are found in animals. In mouse, CFAP157 is required for sperm motility and flagellum morphogenesis .
DNA-directed RNA polymerase III subunit RPC9 (RPC9)
Type: Family

RPC9, also known as Rpc17 in budding yeasts, is a subunit of DNA-directed RNA polymerase III that catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. It may be involved in the recruitment of pol III by the preinitiation complex .
Granulysin-like (Granulysin-like)
Type: Family

This entry represents a group of animal antimicrobial proteins, such as granulysin from humans and NK-lysin from horses . Granulysin is produced by human cytolytic T lymphocytes and natural killer cells that kills Mycobacterium tuberculosis .
Calcium-binding tyrosine phosphorylation-regulated protein (CABYR)
Type: Family

CABYR was originally isolated from spermatoza and was thought to be testis specific, but has been observed in lung and brain tumours . It is a polymorphic calcium binding protein that is phosphorylated during capacitation .
ADP-ribosylation factor-like protein 2-binding protein (ARL2BP)
Type: Family

Signal transducers and activators of transcription (STATs) mediate cell proliferation, differentiation and survival in immune responses. ADP-ribosylation factor-like protein 2-binding protein, also known as BART, plays an essential role in the nuclear retention of STAT3 through interaction with GTPase ARL2 (ARF-like 2) . BART is predominantly cytosolic but can also be found to be associated with mitochondria. BART is also involved in binding to the adenine nucleotide transporter ANT1 and may have a role in mitochondria transport and/or apoptosis .
Endothelial cell-specific molecule 1 (ESM1)
Type: Family

ESM1 (also known as endocan) is a proteoglycan expressed by the vascular endothelium. It may play an important role in regulating cell adhesion and raised plasma levels may reflect endothelial dysfunction .
Ras-related protein Rap1 (Rap1)
Type: Family

The Rap1 subgroup is part of the Rap subfamily of the Ras family. It can be further divided into the Rap1a and Rap1b isoforms. In humans, Rap1a and Rap1b share 95% sequence homology, but are products of two different genes located on chromosomes 1 and 12, respectively. Rap1a is sometimes called smg p21 or Krev1 in the older literature.

Rap1 proteins are believed to perform different cellular functions, depending on the isoform, its subcellular localization, and the effector proteins it binds. For example, in rat salivary gland, neutrophils, and platelets, Rap1 localizes to secretory granules and is believed to regulate exocytosis or the formation of secretory granules . High expression of Rap1 has been observed in the nucleus of human oropharyngeal squamous cell carcinomas (SCCs) and cell lines; interestingly, in the SCCs, the active GTP-bound form localized to the nucleus, while the inactive GDP-bound form localized to the cytoplasm . Rap1a, which is stimulated by T-cell receptor (TCR) activation, is a positive regulator of T cells by directing integrin activation and augmenting lymphocyte responses . In murine hippocampal neurons, Rap1b determines which neurite will become the axon and directs the recruitment of Cdc42, which is required for formation of dendrites and axons . In murine platelets, Rap1b is required for normal homeostasis in vivo and is involved in integrin activation .
Small integral membrane protein 9 (Smim9)
Type: Family

The small integral membrane protein 9 (Smim9) is an uncharacterised, membrane protein. It has a signal peptide, a small extracellular domain, a single transmembrane region, and a short cytoplasmic tail. It is known from mammals and birds.
Death effector domain-containing protein (DEDD/DEDD2)
Type: Family

This entry includes death effector domain-containing proteins, DEDD and DEDD2. DEDD is a scaffold protein that directs CASP3 to certain substrates and facilitates their ordered degradation during apoptosis . DEDD2 is involved in the regulation of nuclear events mediated by the extrinsic apoptosis pathway .
Coiled-coil domain-containing protein 196 (CCDC196)
Type: Family

This entry represents proteins from the coiled-coil domain-containing protein 196 family. They are derived from the CCDC196 gene. It is found only in mammals, and they contain a coiled coil. A human member of this protein has been recently reported .
Secretogranin-2 (ScgII)
Type: Family

Secretogranin-2 (ScgII), a neuroendocrine secretory granule protein, is almost exclusively found in large dense core vesicles of a wide variety of endocrine and neuronal tissues. It belongs to the chromogranin family, whose members are acidic proteins present in the secretory granules of a wide variety of endocrine and neuro-endocrine cells. ScgII has been linked to several neurological diseases, like Alzheimer's disease, Parkinson's disease, epilepsy, stroke or ischemia and and diabetic retinopathy. ScgII also plays a role in visual system plasticity by modulating a range of neurotransmitters and neuropeptides .

Secretoneurin (SN), a 33-amino acid neuropeptide derived from secretogranin II, acts as an angiogenic cytokine and chemoattractant for eosinophils . Manserin is another peptide derived from secretogranin II .
DNA-binding protein RHL1 (RHL1)
Type: Family

RHL1 is a component of the plant DNA topoisomerase VI complex. It is thought not to be involved in catalysis by topo VI, but in its regulation. RHL1 plays a role in the endoreduplication cycle, whereby cells amplify the genome without cell division. RHL1 has DNA-binding activity .
Uncharacterized protein ycf72 (YCF72)
Type: Family

This entry represents an uncharacterised protein from plant chloroplasts.
Activity-dependent neuroprotector homeobox protein (ADNP/ADNP2)
Type: Family

This entry includes a group of homeobox proteins, including ADNP and ADNP2 . ADNP regulates the expression of >400 genes during embryonic development, vital for mammalian brain formation . It has been linked to neurodegenerative diseases and has been shown to play an important roles in autophagy. ADNP has also been associated with the pathophysiology of schizophrenia . ADNP de novo mutations in humans result in a syndromic form of autism-like spectrum disorder (ASD), including cognitive and motor deficits, the ADNP syndrome (Helsmoortel-Van Der Aa) .
Chloroplast thylakoid lumenal protein MPH2 (MPH2)
Type: Family

MPH2 (encoded by At4g02530) is a chloroplast thylakoid lumenal protein required for growth acclimation of plants under fluctuating light environments. A role in disassembling monomeric complexes for regeneration of dimeric functional PSII supercomplexes has been suggested for MPH2 .
Putative NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8, mitochondrial (Put_Complex_I_su8)
Type: Family

Proteins in this family are believed (through sequence similarity) to be accessory subunits of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I) of plants.
Protein heading date repressor 1 (HDR1)
Type: Family

HDR1 regulates flowering time via a photoperiod-dependent pathway. It suppresses flowering under long-day conditions (LDs) by upregulating Hd1 and downregulating Ehd1. It is phosphorylated by OsK4, another suppressor of rice flowering under LDs .
WW domain-containing adapter protein with coiled-coil (WAC)
Type: Family

WAC interacts with RNF20/40 through its C-terminal coiled-coil region and promotes RNF20/40 s E3 ligase activity for H2B ubiquitination . Drosophila WAC, also known as Wacky, promotes the interaction between TTT and Pontin/Reptin, thereby promoting mTORC1 activity by facilitating mTORC1 dimerization and mTORC1-Rag interaction .
BRCA1-A complex subunit RAP80 (RAP80)
Type: Family

RAP80 is responsible for recruitment of the BRCA1-A complex (BRCA1, BARD1, BRCC36, Abraxas, and RAP80) to sites of DNA damage by binding Lys63-linked Ub chains through tandem α-helical Ub interacting motifs . RAP80 also contains an N-terminal SUMO interacting motif (SIM) that has been shown to specifically bind the SUMO-2 isoform .
Defect at low temperature protein 1 (DLT1)
Type: Family

This family of proteins from fungi includes Dlt1 from Saccharomyces cerevisiae. It is a protein of unknown function that is required for growth under high-pressure and low-temperature conditions .
Ubiquitin-associated protein 1 (UBAP1)
Type: Family

UBAP1 is a subunit of ESCRT-I, a complex facilitating endosomal sorting of ubiquitinated cargo . It interacts with ubiquitin via a SOUBA domain .
Putative glutathione transferase 3 (Put_GTT3)
Type: Family

This family is restricted to fungi. The function of proteins in this family is not known. Computational analysis of large-scale protein-protein interaction data suggests that proteins may be involved in glutathione metabolism .
Uncharacterized protein CXorf66 (CXorf66)
Type: Family

This family seems to be restricted to mammals. It includes uncharacterised protein CXorf66, also known as secreted glycoprotein in chromosome X (SGPX). This ORF is present in chromosome X and is up-regulated in some cancers .
Transmembrane protein 253 (TMEM253)
Type: Family

The function of proteins in this family is not known. The family consists of predicted transmembrane proteins from vertebrates.
Phospholipase A2, conodipine-like (PLA2_conodipine-like)
Type: Family

This entry includes phospholipase A2 from Conus purpurascens, known as Conodipine-P1/2/3 .
Ecto-NOX disulfide-thiol exchanger (ENOX)
Type: Family

ENOX proteins are growth-related cell surface proteins that catalyse both hydroquinone or NADH oxidation and protein disulfide-thiol interchange . The two enzymatic activities oscillate with a period length of 24 minutes and play a role in control of the ultradian cellular biological clock . ENOX proteins may play roles in cancer, cellular time-keeping, growth, aging and neurodegenerative diseases .
Thrombospondin type-1 domain-containing protein 1 (THSD1)
Type: Family

This entry represents human Thrombospondin type-1 domain-containing protein 1 and similar animal proteins. THSD1 is involved in endothelial cell to extracellular matrix adhesion . THSD1 forms a multimeric protein complex with FAK/talin/vinculin, wherein THSD1 promotes talin binding to FAK but not to vinculin, a key step in nascent adhesion assembly .
Golgi-associated PDZ and coiled-coil motif-containing protein (GOPC)
Type: Family

GOPC, also known as PIST or CAL, is primarily localized to the Golgi apparatus. It binds the G protein-coupled receptor beta1AR and modulates beta1AR intracellular trafficking . GOPC also interacts with cystic fibrosis transmembrane regulator (CFTR), retains CFTR in the cell and targets it for degradation .
Uncharacterized protein MJ0871-like (MJ0871-like)
Type: Family

This family of uncharacterised proteins is found mainly in methanogenic archaea and sulfate-reducing bacteria.
Yae1-like (Yae1-like)
Type: Family

This entry includes yeast Yae-1, human YAE1D1 (Yae1 domain-containing protein 1) and related proteins from eukaryotes. Yae1 depletion results in defective Fe-S maturation of the ribosome-associated ABC protein Rli1 .
Respiratory complex factor Rcf3 (Rcf3)
Type: Family

Rcf3 (YBR255c-A) associates with monomeric cytochrome c oxidase and respiratory chain supercomplexes. It is an homologue of the N-terminal Rcf2 peptide, and seems to have an overlapping role with Rcf2. A lack of Rcf2 and Rcf3 increases oxygen flux through the respiratory chain by up-regulation of the cytochrome c oxidase activity .

This family of proteins is found mainly in fungi.
Uncharacterized protein AN11006-like (AN11006-like)
Type: Family

This family of proteins mostly from fungi is uncharacterised.
Cilia- and flagella-associated protein 61 (CFAP61)
Type: Family

CFAP61/FAP61 is part of the calmodulin and spoke-associated complex (CSC) required for wild-type motility and for the stable assembly of a subset of radial spokes in motile cilia .
Phospholipase B1, membrane-associated (PLB1)
Type: Family

PLB1 is a membrane-associated phospholipase. It contains four tandem homologous domains (repeats 1 to 4) and a C-terminal membrane binding domain. Repeat 2 is the catalytic domain that catalyzes phospholipase A2, lysophospholipase, and lipase activities .
E3 ubiquitin-protein ligase complex, subunit SLX5/Rfp1 (E3_SLX5/Rfp1)
Type: Family

The STUbL pathway is alternative pathway for the elimination of sumoylated proteins. STUbLs (SUMO-targeted ubiquitin ligases), as represented by the Rfp1/Slx8 and Rfp2/Slx8 dimers in Schizosaccharomyces pombe, or the Slx5/Slx8 dimer in Saccharomyces cerevisiae, are conserved ubiquitin E3 enzymes that target sumoylated proteins for ubiquitylation and subsequent degradation or recycling . These complexes function as a two-component Ub ligase that controls genome stability and sumoylation via ubiquitination .

This family consists of Rfp1 and Slx5.
Dehydrodolichyl diphosphate synthase complex subunit Nus1 (Nus1/NgBR)
Type: Family

Nus1 (also known as Nogo-B receptor, NgBR) is a subunit of cis-prenyltransferase, a enzymatic activity critical for the synthesis of dolichol, an obligate carrier of oligosaccharides for protein glycosylation reactions . It plays an essential role in angiogenesis during wound healing and embryonic development. In mice, it is essential for endothelial cell glycosylation and vascular development . In zebrafish, it is bound by Nogo-B ligand that activates Akt pathway to stimulate endothelial cell chemotaxis . In humans, it is involved in breast cancer cell growth through modulating Ras signaling .
Cilia- and flagella-associated protein 36 (CFAP36)
Type: Family

The function of CFAP36 (also known as CCDC104) is not clear, although it has been shown to interact with ciliary protein Arl3 .
Shugoshin 1/2 (Shugoshin1/2)
Type: Family

Shugoshin (which is Japanese for guardian spirit) was first identified in Drosophila melanogaster (originally named Mei-S322) as a protein that is required for sister chromatid cohesion . Later, a few shugoshin orthologs from yeast to human were identified through similarities in their sequence architectures . Flies and budding yeast have only one known shugoshin (Mei-S322 and Sgo1, respectively), fission yeast, Xenopus laevis and mammals have two shugoshin-like proteins (Sgo1 and Sgo2 in yeast and SGOL1 and SGOL2 in vertebrates) .The functions of Sgo1 from different species can vary. For instance, in S. cevervisiae and D. melanogaster, Sgo1 protects cohesion at meiosis but not mitosis. In humans and X. laevis, SGOL1 protect centromeric cohesion during mitosis .

This family includes Shugoshin 1/2 from human and related sequences.
DBF4-type zinc finger-containing protein 2 (ZDBF2)
Type: Family

This entry represents DBF4-type zinc finger-containing protein 2 (ZDBF2, also known as KIAA1571) and homologues. The function of ZDBF2 is not clear.
Fibrous sheath-interacting protein 2 (FSIP2)
Type: Family

This entry represents the fibrous sheath-interacting protein 2 (FSIP2) family. Its function has been related to the acrosome development during spermiogenesis .
Structural maintenance of chromosomes flexible hinge domain-containing protein 1 (SMCHD1)
Type: Family

SMCHD1 plays roles in X-chromosome inactivation, imprinting and double-strand break repair. Mutations in the SMCHD1 gene have been linked to Facioscapulohumeral dystrophy. Its N-terminal half contains a GHKL (gyrase, Hsp90, histidine kinase, MutL) ATPase motif, whereas its C terminus contains an SMC (structural maintenance of chromosomes) domain homologous to that found in cohesins and condensins, which has DNA-binding activity and provides an interface for homodimerization .
E3 ubiquitin-protein ligase RNF170 (RNF170)
Type: Family

RNF170 is an endoplasmic reticulum membrane ubiquitin ligase that contributes to the ubiquitination of activated inositol 1,4,5-trisphosphate (IP3) receptors . When point mutated (arginine to cysteine at position 199), it causes autosomal dominant sensory ataxia (ADSA), a disease characterised by neurodegeneration in the posterior columns of the spinal cord .
BRO1 domain-containing protein BROX (BROX)
Type: Family

BROX has a Bro1 domain-like sequence and a C-terminal thioester-linkage site of isoprenoid lipid (CAAX motif). It interacts with CHMP4, a component of endosomal sorting complex required for transport III .
Methyltransferase-like protein 22 (METTL22)
Type: Family

METTL22 is a N-lysine methyltransferase that methylates Kin17, a DNA/RNA-binding protein with reported roles in DNA repair and replication and mRNA processing .
Transmembrane channel-like protein (TMC)
Type: Family

This entry represents the transmembrane channel-like (TMC) protein family. TMC proteins are thought to have important cellular roles, and may be modifiers of ion channels or transporters . Mutations in these genes are implicated in a number of human conditions, such as deafness and epidermodysplasia verruciformis . TMC4 is involved in a high-concentration salt taste sensation .
Hexosaminidase D-like (HEXDC-like)
Type: Family

HEXDC is a beta-hexosaminidase that hydrolyses the terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides .
Integrator complex subunit 1 (INTS1)
Type: Family

INTS1 is a component of the Integrator (INT) complex. INT consists of at least 14 subunits and associates with the C-terminal domain of the largest subunit of the RNA polymerase II (RNAPII) and has a role in the regulation of gene expression and RNA processing. Besides mediating the co-transcriptional 3'-end processing of the U-rich small nuclear RNAs (UsnRNAs), INT also functions in RNAPII promoter proximal pause-release and in the processing of enhancer RNAs. Mutations in the INTS1 gene cause a severe neurodevelopmental syndrome .
Allergen Asp f 4 (Allergen_Asp_f_4)
Type: Family

This entry represents a major allergen from Aspergillus fumigatus that is mainly found in filamentous ascomycete fungi and is strongly associated with allergic bronchopulmonary aspergillosis (ABPA) . The protein contains four conserved cysteine residues at positions 81, 198, 236, and 243 that are important for IgE antibody binding and protein structure. The C-terminal cysteines appear particularly important for immunoreactivity. Based on ECOD classification, this protein belongs to the Osmotin-like superfamily, suggesting it likely adopts a beta-rich immunoglobulin-like fold similar to other antifungal proteins in this group. This entry also includes an uncharacterised group of proteins from Myxococcales bacteria.
BRCA1-associated ATM activator 1 (BRAT1)
Type: Family

BRAT1 binds to ATM and BRCA1 and is involved in DNA damage-induced ATM activation . It is also involved in cell proliferation and mitochondrial functions . Mutations of the BRAT1 gene have been linked to epileptic encephalopathy .
Armadillo repeat-containing protein 2 (ARMC2)
Type: Family

ARMC2 is required for sperm flagellum axoneme organization and function. It is involved in axonemal central pair complex assembly and/or stability .
Tetratricopeptide repeat protein 36 (TTC36)
Type: Family

This family includes tetratricopeptide repeat protein 36 (TTC36) and homologues. The function of TTC36 is unknown. This entry also includes HmgX from Neosartorya fumigata, which is part of the L-tyrosine degradation gene cluster that mediates the biosynthesis of the brownish pigment pyomelanin as an alternative melanin .
Protein effector of transcription (Effector_transcript)
Type: Family

Effectors of transcription (ETs) are plant-specific regulatory proteins characterised by the presence of two to five C-terminal DNA- and Zn-binding repeats, and a highly conserved cysteine pattern. There are three ETs in Arabidopsis thaliana. AtET2 plays a role in the regulation of plant hormone GA (gibberellin) and cell-cycle-related protein GASA4 . Regulation of GA response has also been observed in Brassica napus ET, and could be a conserved feature of these proteins .
Proline-rich protein Hua1-like (Hua1-like)
Type: Family

This entry represents a group of proline-rich fungal proteins, including Hua1 from budding yeasts and SPAC17A5.10 from fission yeasts. Hua1 is predicted to be involved in assembly and disassembly of the actin cytoskeleton .