SII-SWORD/CoKE huggingface dataset:
Nucleolar protein 9 (NOP9)
Type: Family

Nucleolar protein 9 (NOP9) is an RNA-binding nucleolar protein found in yeast and required for pre-rRNA processing. It is a component of both the 90S pre-ribosome and the pre-40S ribosome . This entry also includes APUM23 from Arabidopsis. APUM23 is a nucleolar PUF protein involved in pre-rRNA processing .
U6 snRNA-associated Sm-like protein Lsm3 (Sm-like_LSM3)
Type: Family

This entry represents Sm-like protein Lsm3. It can be found in the nuclear Lsm2-8 complex or in the cytoplasmic Lsm1-7 complex.

The Lsm2-8 complex associates with multiple snRNP complexes containing the U6 snRNA (U4/U6 snRNP, U4/U6.U5 snRNP, and free U6 snRNP). It binds and stabilizes the 3'-terminal poly(U) tract of U6 snRNA and facilitates the assembly of U4-U6 di-snRNP and U4-U6-U5 tri-snRNP . The Lsm1-7 complex associates with deadenylated mRNA and promotes decapping in the 5'-3' mRNA decay pathway .

The Sm and the Lsm proteins, characterised by the Sm-domain, have RNA-related functions. The Sm heptamer ring associates with four (U1, U2, U4, U5) snRNPs, while Lsm2-8 heptamer is part of the U6 snRNP. Another Lsm heptameric complex, Lsm1-7, which differs from Lsm2-8 by one Lsm protein, functions in mRNA decapping, a crucial step in the mRNA degradation pathway .
Plastoglobular protein 18-like (PG18-like)
Type: Family

This family of proteins can be found in plants and Cyanobacteria, including PG18 (At4g13200) from Arabidopsis and thylakoid protein sll1769 from Synechocystis sp. . PG18 is a plastoglobular protein involved in chloroplast function and thylakoid formation . Proteins in this family are typically between 108 and 202 amino acids in length.
Single-pass membrane and coiled-coil domain-containing protein 3 (SMCO3)
Type: Family

The function of this protein is not known. It is described as single-pass membrane and coiled-coil domain-containing protein 3.
RNA polymerase I subunit H (Polr1has)
Type: Family

RNA polymerase I subunit H is involved in male sterility in mice .
Tankyrase 1-binding protein-like (TNKS1BP1-like)
Type: Family

TNKS1BP1 (also known as TAB182) interacts with the telomeric poly(ADP-ribose) polymerase, tankyrase 1 . It is an integral component of the CNOT complex, which has transcriptional regulatory, deadenylation and E3 ligase activity .

This family also includes uncharacterised protein KIAA1671.
THO complex subunit 2 (Tho2)
Type: Family

THO/TREX, a nuclear protein complex conserved from yeast to humans, plays an important role in mRNP biogenesis connecting transcription elongation, mRNA export and preventing genetic instability. THO could be relevant to different mRNA processing steps, including the 3'-end formation, transcript release and export . This entry represents the Tho2 subunit of the THO/TREX complex.
Large ribosomal subunit protein mL46 (Ribosomal_mL46)
Type: Family

This entry includes the mitochondrial large ribosomal subunit protein mL46, also known as MRLP46 in mammals and MRLP17 in yeasts Saccharomyces cerevisiae and Schizosaccharomyces pombe .
Protein Mtf2/C5D6.12-like (Mtf2/C5D6.12-like)
Type: Family

This entry represents mitochondrial translation factor 2 (Mtf2) in fungi.

Unlike mammalian mitochondrial DNA, yeast mitochondrial genomes contain introns. Specifically, Schizosaccharomyces pombe mitochondrial DNA (mtDNA) contains only three introns: two in the cox1 gene and one in the cob1 gene. The cox1 gene encodes cytochrome c oxidase subunit 1, a crucial component of the mitochondrial electron transport chain. Mtf2 is a translation activation factor that is part of the MRH5C complex. It is essential to ensure proper cytochrome c oxidase expression, as it recruits cox1 mRNA to the mitochondrial ribosome for translation initiation. Interestingly, S. pombe Mtf2 (C5D6.12) shares weak amino acid sequence similarity with its counterpart in Saccharomyces cerevisiae. Additionally, Mtf2 from S. cerevisiae is required for overall mitochondrial protein synthesis, whereas the S. pombe counterpart has a more limited role, as it is required for cox1 gene expression .
Zinc finger protein 608/609 (ZN608/ZN609)
Type: Family

Zinc finger proteins 608 and 609 (ZNF608/ZNF609) are putative transcription factors. ZNF608 represses the expression of ZNF609, which in turn represses recombination-activating gene 1 (Rag1) and Rag2 expression in thymocytes . Interestingly, ZNF609 generates circular RNA (Cir-ZNF609), a novel kind of noncoding RNA that form loop structures without 5'-3' polarities and polyadenylated tails. Cir-ZNF609 has been found to regulate myoblast proliferation and AKT3 expression . Cir-ZNF609 has also been linked to vascular endothelial dysfunction .
Cell surface glycoprotein CD200 receptor (CD200R)
Type: Family

This entry includes cell surface glycoprotein CD200 receptor 1-5 (CD200R1-5) from mice and CD200R1/CD200R1L from humans. CD200R is a family of inhibitory receptors principally affecting myeloid cell function . Family members are receptors for the CD200/OX2 cell surface glycoprotein with potential activatory and inhibitory functions that may play important roles in immune regulation and balance .
Corepressor interacting with RBPJ 1 (CIR1)
Type: Family

Corepressor interacting with RBPJ 1 (CIR1, also known as recepin) interacts CBF1, which is a member of the CSL family of DNA binding factors, which mediate either transcriptional repression or transcriptional activation. CIR1 binds to histone deacetylase and to SAP30 and serves as a linker between CBF1 and the histone deacetylase complex . It interacts with a variety of proteins, including Epstein-Barr virus RPMS1 and the NKAP transcriptional repressor of notch signaling .
UBL3-like (UBL3-like)
Type: Family

Proteins in this entry possess a ubiquitin-2 like Rad60 SUMO-like domain. These ubiquitin-fold proteins are plasma membrane-anchored by prenylation . Proteins include mammalian ubiquitin-like protein 3, which has a ubiquitous distribution , and plant membrane-anchored ubiquitin-fold proteins 1 to 6, which, in Arabidopsis, recruit and dock specific E2 ubiquitin-conjugating enzymes to the plasma membrane. They appear to interact noncovalently with an E2 surface opposite the active site that forms a covalent linkage with Ub . This entry also includes uncharacterised proteins from fungi.
Exportin-6 (XPO6)
Type: Family

Exportin-6 is a nuclear export receptor that transfers profilin-actin complexes from nucleus to cytoplasm . Reduced interaction of Exp6 and RanGTP has been linked to cellular senescence .
Exportin-T (XPOT)
Type: Family

Exportin-T (Xpot) mediates the nuclear export of aminoacylated tRNAs . Its budding yeast homologue, known as Los1, is involved in nuclear export of pre-tRNA and in re-export of mature tRNAs . It binds to RanGTP and mature tRNAs cooperatively to form a nuclear export complex .
Uncharacterized protein C27D6.3-like (C27D6.3-like)
Type: Family

This uncharacterised family consists of proteins from nematodes.
Uncharacterized protein C13orf46-like (C13orf46-like)
Type: Family

This family of uncharacterised proteins includes human protein C13orf46.
Uncharacterized protein C9orf153-like (C9orf153-like)
Type: Family

This family of uncharacterised proteins from mammals includes human protein C9orf153.
WW domain-binding protein 4 (WBP4)
Type: Family

WW domain-binding protein 4 (WBP4; also known as formin-binding protein 21) is a component of the spliceosome, which is involved in pre-mRNA splicing . It contains a matrin-type zinc finger and two tandem WW domains. It interacts with the splicing factor SIPP1, and its binding and activation of pre-mRNA splicing depend on the WW domains . This entry also includes zinc finger protein ZOP1 from Arabidopsis thaliana, which is also a pre-mRNA splicing factor that associates with several typical components of the splicing machinery and promotes Pol IV-dependent siRNA accumulation, DNA methylation, and transcriptional silencing .
Protein phosphatase 1 regulatory subunit 21 (PPP1R21)
Type: Family

The function of PPP1R21 is not clear. It has been linked to human disease .
Zinc finger protein 622/Rei1/Reh1 (Znf622/Rei1/Reh1)
Type: Family

This entry represents a group of proteins that contain at least two copies of a C2H2-type zinc finger, including cytoplasmic 60S subunit biogenesis factor ZNF622 from animals , Reh1 and Rei1 from budding yeasts, and core trichothecene cluster protein 15 (TRI15) from Fusarium.

Cytoplasmic 60S subunit biogenesis factor ZNF622, Reh1 and Rei1 are involved in maturation of the large (60S) ribosomal subunit. Rei1 is required for re-importing the 60S subunit export factor Arx1 from the cytoplasm to the nucleus, and both Reh1 and Rei1 are required for cytoplasmic maturation of the 60S subunit, that the two proteins have redundant functions, but without both the 60S subunit is labile to salt .

TRI15 is a component in the biosynthesis of trichothecene mycotoxins, although its role is unknown .
Flagellar hook-associated protein 2 (FliD)
Type: Family

The flagellar hook-associated protein 2 (HAP2 or FliD) forms the distal end of the flagella, and plays a role in mucin specific adhesion of the bacteria .
Uncharacterized protein C11orf91-like (C11orf91-like)
Type: Family

This family of uncharacterised proteins includes human protein C11orf91.
Intraflagellar transport-associated protein (IFTAP)
Type: Family

IFTAP (C11ORF74) interacts with the IFT-A complex and is accumulated at the distal tip in the absence of an IFT-A subunit IFT139. In IFTAP-knockout (KO) cells, the BBSome components cannot enter cilia. However, IFTAP-KO mice demonstrated no obvious anatomical abnormalities associated with ciliary dysfunctions .
Dopamine receptor-interacting protein 1 (C14orf28-like)
Type: Family

This family includes Dopamine receptor-interacting protein 1 (DRIP1, also known as C14orf28 in human) and similar proteins from vertebrates. C14orf28 has been shown to inhibit apoptosis in colorectal cancer and contribute to oncogenicity . The mouse member is thought to be a regulator of the dopamine receptor signalling pathway .
Large ribosomal subunit protein mL57 (Ribosomal_mL57)
Type: Family

This family consists of yeast large ribosomal subunit protein mL57 (also known as 54S ribosomal L15/MRPL15) .
Codanin-1 (Codanin-1)
Type: Family

Codanin-1 may act as a negative regulator of histone chaperone anti-silencing function 1 (ASF1) in chromatin assembly . This family also includes the cytoplasmic codanin-1-like protein from Drosophila disks lost (dlt, also known as protein vanaso). Dlt regulates cell proliferation and cell survival of differentiated cells independent of cell division .

Mutations in the codanin-1 gene cause congenital dyserythropoietic anemia 1 (CDA1), which is an autosomal recessive blood disorder characterised by morphological abnormalities of erythroblasts, ineffective erythropoiesis, macrocytic anemia and secondary hemochromatosis .
DENN domain-containing protein 1A/1B/1C (DENND1A/B/C)
Type: Family

This entry includes proteins containing an N-terminal tripartite DENN domain, including DENND1A (also known as connecdenn 1), DENND1B (connecdenn 2) and DENND1C (connecdenn 3). These proteins act as guanine-nucleotide exchange factors for Rab35 through the DENN domain. Inactive GDP-bound RAB35 is converted into its active GTP-bound form by the exchange of GDP to GTP. The DENN domains of DENND1A and DENND1B, but not DENND1C, bind Rab35, indicating that binding and activation are separate. The C-termini of DENND1A, DENND1B and DENND1C differ significantly, but each binds to clathrin and to the clathrin adaptor AP-2. This is a means to regulate clathrin-mediated endocytosis of synaptic vesicles and exit from early endosomes .
Centromere protein H (CENP-H)
Type: Family

Chromosome segregation in eukaryotes requires the kinetochore, a multi-protein structure that assembles on centromeric DNA, and which acts to link chromosomes to spindle microtubules. Kinetochore structure and composition is highly conserved among vertebrates. The inner kinetochore is essential for kinetochore assembly, and is involved in chromosome segregation via regulation of the spindle. Inner kinetochore components include the multi-subunit CENP-H/I complex, which may function, in part, in directing centromere protein A (CENP-A) deposition to centromeres, where CENP-A is a centromere-specific histone H3 variant required for the organisation of centromeric chromatin during interphase. The CENP-H/I complex contains three functional classes of proteins :

CENP-H class (includes CENP-H, -I, -K, -L)

CENP-M class (includes CENP-M)

CENP-O class (includes CENP-O, -P, -Q, -R, -50)

CENP-H is required for the localisation of CENP-C, but not CENP-A, to the centromere. However, it may be involved in the incorporation of newly synthesised CENP-A into centromeres via its interaction with the CENP-A/CENP-HI complex. CENP-H contains a coiled-coil structure and a nuclear localisation signal. CENP-H is specifically and constitutively localised in kinetochores throughout the cell cycle, and may play a role in kinetochore organisation and function throughout the cell cycle .

Studies show that CENP-H may be associated with certain human cancers .
Transmembrane protein 180 (TMEM180)
Type: Family

The function of TMEM180 is not clear.
Protein CYCLOPS (CYCLOPS)
Type: Family

CYCLOPS (also known as IPD3) is required for root symbiosis with mycorrhizal fungi in plants . It forms a signal transduction complex with CCaMK that is specifically required for symbiotic infection . CYCLOPS binds to a motif within the ERN1 promoter and in combination with CCaMK positively regulates transcription of ERN1, a gene that encodes an AP2/ERF transcription factor .
Phosphatidylinositol-glycan biosynthesis class X protein (PIGX)
Type: Family

PIG-X is an essential component of glycosylphosphatidylinositol-mannosyltransferase I . It probably acts by stabilizing the mannosyltransferase PIG-M . It has also be shown to interact with reticulocalbin 1 (RCN1) and reticulocalbin 2 (RCN2), and may negatively regulate the expression of these two genes .
Autophagy-related protein 11 (ATG11)
Type: Family

Autophagy-related protein 11 (ATG11; also known as cytoplasm to vacuole targeting protein 9) is required for transport of proteins from the cytosol to the vacuole , including whole mitochondria for autophagic digestion (mitophagy) in the autophagosome during starvation . It also acts as the scaffold that recruit ATG proteins to the pre-autophagosome . The orthologue in mammals is known as RB1-inducible coiled-coil protein 1 (RB1CC1) ; the orthologue in Schizosaccharomyces pombe is Taz1-interacting factor 1 (taf1) .
Transmembrane protein 201 (TMEM201)
Type: Family

TMEM201, also known as SAMP1, is a RanGTP binding transmembrane protein found in the inner nuclear membrane . It is functionally associated with the LINC complex protein Sun1 and proteins of the A-type lamina network .

In Caenorhabditis elegans, it plays a role in nuclear migration .
1,4-alpha-glucan branching enzyme MT3115-like (Branching_enz_MT3115-like)
Type: Family

This entry consists of 1,4-alpha-glucan branching enzymes. Branching enzymes (BEs) generally belong to glycoside hydrolase family 13 (GH13); however this group belongs to the GH57 family. This enzyme catalyzes the formation of branch points in alpha-glucans by cleavage of an alpha-1,4 glycosidic bond and subsequent transfer of the cleaved-off oligosaccharide to a new alpha-1,6 position .
Actin maturation protease (ACTMAP)
Type: Family

This entry represents a group of animal proteins that includes the human protein ACTMAP (actin maturation protease, also known as C19orf54), its homologues from vertebrates, and the orthologue protein CG33108 from Drosophila melanogaster. ACTMAP is responsible for the non canonical excision of the acetylated methionine of actin molecules after translation. It seems to have a crucial effect in all cell types .
SRR1-like protein (SRR1L)
Type: Family

This entry includes the plant Sensitivity To Red Light Reduced proteins (SRR1), yeast SRR1-like protein Ber1 and mammalian homologue SRR1 domain containing (SRRD) protein.

SRR1 are signalling proteins thought to be involved in regulating the circadian clock input pathway, which is required for normal oscillator function. In Arabidopsis thaliana it regulates the expression of clock-regulated genes such as CCA1 and TOC1. It is also involved in both the phytochrome B (PHYB) and PHYB-independent signaling pathways . The mouse homologue of the plant circadian-regulating protein SRR1 plays roles in heme-regulated circadian rhythms and cell proliferation .

The yeast SRR1-like protein Ber1 is involved in microtubule stability .
Cytoplasmic dynein 2 light intermediate chain 1 (DYNC2LI1)
Type: Family

This entry includes cytoplasmic dynein 2 light intermediate chain 1 (DYNC2LI1), which is required for correct intraflagellar transport and the bi-directional movement of components required for the assembly, maintenance and functioning of primary cilia . DYNC2LI1 is a component of and stabilises the dynein-2 complex, which is important for left-right axis determination during embryonic development . Mutations in the DYNC2LI1 gene cause cause short rib polydactyly syndrome, an autosomal recessive, perinatal lethal skeletal disorder characterised by short, horizontal ribs, short limbs and polydactyly .
Protein FAM228 (FAM228)
Type: Family

This entry includes FAM228A and FAM228B. Their function is not known.
Syndetin (VPS50)
Type: Family

Syndetin (VPS50) is a component of the endosome-associated recycling protein (EARP) complex. This complex and the Golgi-associated retrograde protein (GARP) complex share four of the five subunits, but EARP contains syndetin in place of the Vps54 subunit of GARP, with the effect that the EARP complex is directed to endosomes rather than the Golgi. EARP in required for membrane-fusion during endocytic recycling of receptors and is described as a tethering complex .
Zinc finger protein 277 (ZNF277)
Type: Family

This entry includes the uncharacterised zinc finger proteins, including ZNF277 from human and C19B12.07c from the fission yeast Schizosaccharomyces pombe. ZNF277 contains a C2H2-type 1 and a C2H2-type 2 zinc finger whereas C19B12.07c contains a single C2H2-type zinc finger.
Ribosomal subunit protein mS25/mL61, mitochondrial (Ribosomal_mS25/mL61)
Type: Family

This entry includes subunits of the mitochondrial ribosome including the small ribosomal subunit protein mS25 (also known as MRPS25) from mammals , and its orthologues from yeast, the large ribosomal subunit protein mL61 (also known as Mrp49) .
Zinc finger protein 830-like (ZNF830-like)
Type: Family

Zinc finger protein 830 (ZNF830; also known as coiled-coil domain-containing protein 16 or CCDC16) contains a C2H2-type zinc finger and a coiled-coil region. It is a component of the XAB2 complex, which binds RNA , and a component of a pentameric intron-binding complex that is pre-assembled and then incorporated into the spliceosome .

This entry also includes protein ABA AND ROS SENSITIVE 1 (ARS1) from Arabidopsis. It is essential for seed germination and ROS homeostasis in response to ABA and oxidative stress .
Selenocysteine insertion sequence-binding protein 2 (SECISBP2)
Type: Family

Selenocysteine insertion sequence-binding protein 2 (SECISBP2) is required for the incorporation of the amino acid selenocysteine (Sec) into proteins during translation. The mRNA triplet UGA is usually a stop codon, but the presence of a Sec insertion sequence element (SECIS) in the 3'-untranslated region of an mRNA, and its binding to SECISBP2, leads to insertion of Sec into the protein instead. Mutations in the SECISBP2 gene that alter the amino acid sequence or cause splicing defects lead to abnormal thyroid hormone metabolism. A splice variant of SECISBP2 is localized to the mitochondrion rather than the nucleus .

This entry also includes selenocysteine insertion sequence-binding protein 2-like (SECISBP2L), which also binds SECIS, but in mammals does not lead to incorporation of Sec into proteins, because it lacks the SECIS dependent domain association that is found in SECISBP2. An invertebrate orthologue is fully competent for Sec incorporation, however .

Homologues are also known from bacteria.
Splicing factor 45 (RBM17)
Type: Family

This entry includes proteins with a G-patch domain and a RNA recognition motif domain, including mammalian splicing factor 45 (SPF45; also known as RNA-binding motif protein 17 or RBM17) and plant DNA-damage-repair/toleration protein DRT111 (also known as RSN2). SPF45 is an mRNA spliceosomal protein that is required for alternative splicing and the utilization of cryptic splice sites. The beta-110 mutation in the haemoglobin beta causes activation of a cryptic 3' splice site that is the cause of human beta-thalassemia (sickle-cell anemia) . DRT111 is also required for pre-mRNA splicing, particularly the mRNA for receptor-like kinase SNC4, which activates the defence response to microbial pathogens in plants .
Josephin-1/2 (JOSD1/2)
Type: Family

Josephin proteins 1 and 2 are deubiquitinating enzymes (DUBs; peptidase family C86) that contain the Josephin domain, characteristic of the MJD family of DUBs. Josephin-1 (JOSD1) releases 'Lys-63'-linked and 'Lys-48'-linked poly-ubiquitin chains, provided it is monoubiquitinated itself. Josephin-2 (JOSD2) releases 'Lys-63'-linked poly-ubiquitin chains, but does not require ubiquitination to be active. Ubiquitinated JOSD1 is localized to the plasma membrane, whereas JOSD2 is cytoplasmic . Josephin-like proteins are also found in Arabidopsis thaliana and Drosophila melanogaster.
Small ribosomal subunit protein mS40 (MRPS18B)
Type: Family

This entry represents the small ribosomal subunit protein mS40, previously known as 28S ribosomal protein S18b (MRPS18B) and similar sequences from metazoa .
Small ribosomal subunit protein uS10m (Ribosomal_uS10m)
Type: Family

This entry includes uS10m (also known as 28S ribosomal protein S10 (MRPS10)), a component of the mitochondrial small ribosomal subunit from metazoa .
Spermatogenesis-defective protein 39 (Spe-39)
Type: Family

Spermatogenesis-defective protein 39 (spe-39) from the nematode Caenorhabditis elegans is involved in endosomal maturation and intracellular membrane reorganization during spermatogenesis . Also included in this entry is vacuolar protein sorting-associated protein 16B (Vps16B; also known as protein full-of-bacteria) from the fruit fly Drosophila melanogaster. Vps16B is required for phagosome maturation and the innate immune response to bacteria .
Protein LZIC (LZIC)
Type: Family

Protein LZIC is closely related to ICAT. It contains a leucine zipper domain and an ICAT domain, with particular conservation of residues that are used by ICAT for beta-catenin-binding . However, LZIC does not interact with beta-catenin in vitro or in vivo .
WD repeat-containing protein 31 (WDR31)
Type: Family

The function of WD40-repeat (WDR)-containing proteins, one of the largest eukaryotic protein families, is largely unknown. This family represents WDR31.
WDR47 (WDR47)
Type: Family

WD40-repeat 47, also known as Nemitin, is a microtubule-associated protein that is essential for brain development. It is involved in microtubule dynamics and regulation of autophagic flux for axonal outgrowth and guidance .
Immunity-related GTPase family Q protein (IRGQ)
Type: Family

IRG proteins (immunity-related GTPases) contain a Ras-like G domain and were first described as genes strongly induced by infection. Despite its phylogenetic relationship to the IRG proteins, IRGQ (FKSG27) is not a GTPase . Its function is not known.
Methyltransferase (Class A) (Methyltransferase_A)
Type: Family

The enzymes in this subgroup represent the Class A Radical SAM Methyltransferases. These proteins all have a single canonical Radical SAM core domain and utilise a methylene radical generated on a unique methylated cysteine residues. They use two moles of SAM per turnover, the first being a methyl donor, methylating the conserved Cys residue and the other being reductively cleaved to form the 5'-deoxyadenosyl radical and Methionine .