SII-SWORD/CoKE huggingface dataset:
PSF, NOPS domain (PSF_NOPS)
Type: Domain

This entry represents the NOPS domain and the C-terminal coiled-coil region of PSF (also known as SFPQ). The C-terminal coiled-coil region functions in mediating DBHS dimerization, while some surface-exposed basic residues within the NOPS domain may be involved in nucleic acid binding .

PSF is a member of the DBHS (Drosophila behavior human splicing) family. It participates in a wide range of gene regulatory processes and cellular response pathways. It has been shown to affect the alternative splicing of CD45 and Tau and regulate the 3' polyadenylation of mRNAs. It is often localised in the paraspeckles and may be involved in the nuclear retention of mRNAs. It is involved in translation and transcription. It can bind directly to DSBs and play a role in DNA repair. PSF can also be utilized as an essential host factor for viral RNA multiplication and replication . In addition to the common DHBS core, which encompasses RRM1 and RRM2, the protein-protein interaction NOPS domain and the coiled-coil domain, PSF features additional domains, such as a RGG motif and a proline-rich region in its N terminus .

DBHS (Drosophila behavior human splicing) family are characterised by a core domain arrangement consisting of tandem RNA recognition motifs (RRMs), a conserved intervening sequence referred to as a NONA/ParaSpeckle (NOPS) domain, and a ~100 amino acid coiled-coil domain. Its members include p54nrb (also known as NONO), PTB-associated splicing factor/splicing factor proline-glutamine rich (PSF or SFPQ) and PSPC1 (paraspeckle protein component 1). They are found in the nucleoplasm and can be triggered by binding to local high concentrations of various nucleic acids to form microscopically visible nuclear bodies, paraspeckles or large complexes such as DNA repair foci. They may also function cytoplasmically and on the cell surface in defined cell types. All three DBHS proteins are conserved throughout vertebrate species, while flies, worms, and yeast express a single DBHS protein .
Cytidylyl-2-hydroxyethylphosphonate methyltransferase fom3-like (Fom3-like)
Type: Family

This family contains Cytidylyl-2-hydroxyethylphosphonate methyltransferase Fom3 which catalyzes the C-methylation of cytidylyl-2-hydroxyethylphosphonate (HEP-CMP) to form cytidylyl-2-hydroxypropylphosphonate (HPP-CMP) . It is involved in fosfomycin biosynthesis .
Hopanoid C2-methyltransferase, HpnP-like (HpnP-like)
Type: Family

The enzyme in this family is involved in the C2 methylation of bacterial hopanoids. Although the reaction is shown with methylcobalamin acting as the methyl donor, it is possible that SAM might be the methyl donor for the reaction (because this is another function of the SAM cofactor) .
Methylation of yatakemycin, YtkT (Methylation_of_yatakemycin)
Type: Family

Yatakemycin (YTM) is an antitumour natural product. YtkT is a radical S-adenosylmethionine (SAM) protein that when mutated fails to produce YTM. YtkT is a novel C-methyltransferase that contributes to an advanced intermediate during formation of the cyclopropane ring through a radical mechanism in the YTM biosynthetic pathway .
OxsB-like (OxsB-like)
Type: Family

OxsB is involved in the biosynthesis of a unique four-membered oxetane ring found in the oxetanocin A, a nucleoside analog with antitumor, antiviral and antibacterial properties . The biosynthetic pathway is currently unknown . In addition, OxsB has methyltransferase activity in vitro and is able to catalyse the radical mediated, stereoselective C2'-methylation of dAMP to form methylated 2'-dAMP . It also catalyses the demethylation of S-adenosyl-L-methionine (SAM) to S-adenosyl-L-homocysteine (SAH) .
Paromamine deoxygenase (Paromamine_deoxygenase)
Type: Family

This entry represents AprD4 from Streptoalloteichus hindustanus (

) and similar sequences from actinomycetes. AprD4 is a radical SAM enzyme involved in C3-deoxygenation of the intermediate paromamine during biosynthesis of the aminoglycoside apramycin. It acts as a diol-dehydratase, and works with the partner protein, AprD3, a reductase . Members of this family have a non-canonical CX3CX3C motif for binding of a [4Fe-4S] cluster.
Bleomycin-like antibiotic biosynthesis, pyrimidine ring methyltransferase (Pyrimidine_methyltransferase)
Type: Family

This entry contains a radical SAM enzyme responsible for the methylation of the pyrimidine ring in bleomycin-like antibiotics, including bleomycin itself, zorbamycin and tallysomycin .
RBM15B, RNA recognition motif 2 (RBM15B_RRM2)
Type: Domain

This entry represents the RNA recognition motif 2 (RRM2) of RBM15B.

RNA binding motif protein 15B (RBM15B, also known as OTT3) is a paralogue of RBM15. Like RBM15, RBM15B has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF .

RBM15B belongs to the Spen (split end) protein family, which shares a domain architecture comprising three N-terminal RNA recognition motifs (RRMs) and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain.
RBM15B, RNA recognition motif 3 (RBM15B_RRM3)
Type: Domain

This entry represents the RNA recognition motif 3 (RRM3) of RBM15B.

RNA binding motif protein 15B (RBM15B, also known as OTT3) is a paralogue of RBM15. Like RBM15, RBM15B has post-transcriptional regulatory activity. It is a nuclear protein sharing with RBM15 the association with the splicing factor compartment and the nuclear envelope as well as the binding to mRNA export factors NXF1 and Aly/REF .

RBM15B belongs to the Spen (split end) protein family, which shares a domain architecture comprising three N-terminal RNA recognition motifs (RRMs) and a C-terminal SPOC (Spen paralog and ortholog C-terminal) domain.
ACF, RNA recognition motif 1 (ACF_RRM1)
Type: Domain

This entry represents the RNA recognition motif 1 (RRM1) of ACF.

ACF (APOBEC-1-stimulating protein, also known as ASP) is an RNA-binding subunit of a core complex that interacts with apoB mRNA to facilitate C to U RNA editing . It may also act as an apoB mRNA recognition factor and chaperone, and play a key role in cell growth and differentiation. ACF shuttles between the cytoplasm and nucleus .
Prp24, RNA recognition motif 3 (Prp24_RRM3)
Type: Domain

This entry represents the RNA recognition motif 3 (RRM3) of Prp24.

Prp24 is an RNA-binding protein with four well conserved RNA recognition motifs (RRMs). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly . Prp24 specifically binds free U6 RNA primarily with RRM 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases .
Long chronological lifespan protein 2 (LCL2)
Type: Family

This family of yeast proteins has no known function. Mutants have a long chronological lifespan and genetic interactions suggest that LCL2/ YLR104W is a novel component of ERAD (endoplasmic reticulum-associated degradation pathway) .
Heterogeneous nuclear ribonucleoprotein Q, RNA recognition motif 1 (hnRNPQ_RRM1)
Type: Domain

This entry represents the RNA recognition motif 1 (RRM1) of heterogeneous nuclear ribonucleoprotein Q (hnRNP Q).

hnRNP Q (also known as NSAP1 or GRY-RBP) is a RNA-binding protein found in the spliceosome complex and the apobec-1 editosome . It acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport . hnRNP Q has also been identified as SYNCRIP (synaptotagmin-binding, cytoplasmic RNA-interacting protein), a dual functional protein participating in both viral RNA replication and translation . As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton . Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli .

hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains .
Meiosis-specific kinetochore protein (Meikin)
Type: Family

The meiosis-specific kinetochore factor Meikin plays a crucial role in both mono-orientation and centromeric cohesion protection during meiosis I, partly by stabilizing the localization of the cohesin protector shugoshin, and also by recruiting Polo-like kinase PLK1 to the kinetochores. PLK1 is required for mono-orientation and the protection of centromeric cohesion .
Protein PAIR1 (PAIR1)
Type: Family

The representative of this plant family is PAIR1 (HOMOLOGOUS PAIRING ABERRATION IN RICE MEIOSIS1), a protein that plays an essential role in establishment of homologous chromosome pairing in meiosis. Mutations in the gene encoding this protein also affect spindle formation and sporulation . This family also contains the Putative recombination initiation defects 3 (AtPRD3) involved in the meiotic recombination initiation .

In flowering plants, gametophyte formation relies on meiosis. In meiosis I, the homologous chromosomes are separated into two daughter cells. In meiosis II, the sister chromosomes are then separated into newly formed daughter cells. During prophase I, several events occurs: sister chromatid cohesion, homologous chromosome synapsis, recombination, crossover formation and chromosome segregation. Homologous recombination is initiated from the formation of DNA double-strand breaks (DSBs). The formation of DSBs is catalyzed by Spo11 and its homologues. So far, six Arabidopsis proteins, AtSPO11-1, AtSPO11-2, AtPRD1, AtPRD2, AtPRD3 and AtDFO, have been shown to be involved in DSB formation .
Tte1186a maturase (Tte1186a_maturase)
Type: Family

Tte1186 catalyzes the formation of a thioether cross-link in the peptide Tte1186a, which is encoded by an orf located upstream of the maturase, under reducing conditions in the presence of SAM. Tte1186 contains three [4Fe-4S] clusters that are indispensable for thioether cross-link formation; however, only one cluster catalyzes the reductive cleavage of SAM .
Heterogeneous nuclear ribonucleoprotein Q, RNA recognition motif 2 (hnRNPQ_RRM2)
Type: Domain

This entry represents the RNA recognition motif 2 (RRM2) of heterogeneous nuclear ribonucleoprotein Q (hnRNP Q).

hnRNP Q (also known as NSAP1 or GRY-RBP) is a RNA-binding protein found in the spliceosome complex and the apobec-1 editosome . It acts as an interaction partner of a multifunctional protein required for viral replication, and is implicated in the regulation of specific mRNA transport . hnRNP Q has also been identified as SYNCRIP (synaptotagmin-binding, cytoplasmic RNA-interacting protein), a dual functional protein participating in both viral RNA replication and translation . As a synaptotagmin-binding protein, hnRNP Q plays a putative role in organelle-based mRNA transport along the cytoskeleton . Moreover, hnRNP Q has been found in protein complexes involved in translationally coupled mRNA turnover and mRNA splicing. It functions as a wild-type survival motor neuron (SMN)-binding protein that may participate in pre-mRNA splicing and modulate mRNA transport along microtubuli .

hnRNP Q contains an acidic auxiliary N-terminal region, followed by two well-defined and one degenerated RNA recognition motifs (RRMs), and a C-terminal RGG motif; hnRNP Q binds RNA through its RRM domains .
Sperm acrosome membrane-associated protein 6 (SPACA6)
Type: Family

Spaca6 is an immunoglobulin-like sperm protein required for sperm-oocyte fusion in mice .
Mucin-20 (MUC20)
Type: Family

Mucin-20 (MUC20) was identifiied as a gene that is up-regulated in the renal tissues of patients with immunoglobulin A nephropathy . It is a regulator of the Met signaling cascade. MUC20 associates with Met which is the hepatocyte growth factor (HGF) receptor, and has a role in suppressing the Grb2-Ras pathway. Production of MUC20 reduced HGF-induced matrix metalloproteinase expression and proliferation, which require the Grb2-Ras pathway .
p54nrb, RNA recognition motif 1 (p54nrb_RRM1)
Type: Domain

This entry represents the RNA recognition motif 1 (RRM1) of p54nrb.

p54nrb (also known as NONO) belongs to the DBHS (Drosophila behavior human splicing) family. p54nrb is a multifunctional protein involved in numerous nuclear processes including transcription, splicing, and RNA export . p54nrb binds both, single- and double-stranded RNA and DNA . It forms a heterodimer with paraspeckle component 1 (PSPC1 or PSP1), localizing to paraspeckles in an RNA-dependent manner as well as with polypyrimidine tract-binding protein-associated-splicing factor (PSF) . p54nrb contains two conserved RNA recognition motifs (RRMs) at the N terminus .

DBHS (Drosophila behavior human splicing) family are characterised by a core domain arrangement consisting of tandem RNA recognition motifs (RRMs), a conserved intervening sequence referred to as a NONA/ParaSpeckle (NOPS) domain, and a ~100 amino acid coiled-coil domain. Its members include p54nrb (also known as NONO), PTB-associated splicing factor/splicing factor proline-glutamine rich (PSF or SFPQ) and PSPC1 (paraspeckle protein component 1). They are found in the nucleoplasm and can be triggered by binding to local high concentrations of various nucleic acids to form microscopically visible nuclear bodies, paraspeckles or large complexes such as DNA repair foci. They may also function cytoplasmically and on the cell surface in defined cell types. All three DBHS proteins are conserved throughout vertebrate species, while flies, worms, and yeast express a single DBHS protein .
Mitochondrial import receptor subunit TOM5 homologue, viridiplantae (TOM5_viridi)
Type: Family

Protein import into the mitochondria involves several translocase complexes: the preprotein translocase of the outer mitochondrial membrane (TOM complex) and the two preprotein translocases of the inner mitochondrial membrane (called TIM complexes).

TOM5 is a component of the TOM complex. This entry represents TOM5 from the plant complex, which consist at least of six subunits .
Mitochondrial import receptor subunit TOM6 homologue, plants (TOM6_plants)
Type: Family

Protein import into the mitochondria involves several translocase complexes: the preprotein translocase of the outer mitochondrial membrane (TOM complex) and the two preprotein translocases of the inner mitochondrial membrane (called TIM complexes).

This entry represents TOM6 from the plant TOM complex, which consist at least of six subunits .
S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase (tRNA_wybutosine-synthase)
Type: Family

This entry respresents S-adenosyl-L-methionine-dependent tRNA 4-demethylwyosine synthase Tyw1 from eukaryotes and archaea. They are involved in the pathway wybutosine-tRNA(Phe) biosynthesis. It binds one [4Fe-4S] cluster and one [2Fe-2S] cluster. The [4Fe-4S] cluster is coordinated with three cysteines and an exchangeable S-adenosyl-L-methionine . The two carbon source required for this reaction has been identified as pyruvate. The exact role of the SAM molecule has yet to be determined. There appear to be two distinct sets of proteins with different multi-domain architectures, however they are sufficiently similar in the Radical SAM portion that they remain a single cluster .

Wybutosine is a hyper modified guanosine with a tricyclic base found at the 3'-position adjacent to the anticodon of eukaryotic phenylalanine tRNA. It is important for translational reading-frame maintenance .
Threonylcarbamoyladenosine tRNA methylthiotransferase (ThrcA_tRNA_MEthiotransferase)
Type: Family

The enzyme in this family catalyses the methylthiolation of N6-threonylcarbamoyladenosine (t6A), leading to the formation of 2-methylthio-N6-threonylcarbamoyladenosine (ms2t6A) at position 37 in tRNAs that read codons beginning with adenine. The enzyme binds two 4Fe-4S clusters. One cluster is coordinated with three cysteines and an exchangeable S-adenosyl-L-methionine .
p54nrb, RNA recognition motif 2 (p54nrb_RRM2)
Type: Domain

This entry represents the RNA recognition motif 2 (RRM2) of p54nrb.

p54nrb (also known as NONO) belongs to the DBHS (Drosophila behavior human splicing) family. p54nrb is a multifunctional protein involved in numerous nuclear processes including transcription, splicing, and RNA export . p54nrb binds both, single- and double-stranded RNA and DNA . It forms a heterodimer with paraspeckle component 1 (PSPC1 or PSP1), localizing to paraspeckles in an RNA-dependent manner as well as with polypyrimidine tract-binding protein-associated-splicing factor (PSF) . p54nrb contains two conserved RNA recognition motifs (RRMs) at the N terminus .

DBHS (Drosophila behavior human splicing) family are characterised by a core domain arrangement consisting of tandem RNA recognition motifs (RRMs), a conserved intervening sequence referred to as a NONA/ParaSpeckle (NOPS) domain, and a ~100 amino acid coiled-coil domain. Its members include p54nrb (also known as NONO), PTB-associated splicing factor/splicing factor proline-glutamine rich (PSF or SFPQ) and PSPC1 (paraspeckle protein component 1). They are found in the nucleoplasm and can be triggered by binding to local high concentrations of various nucleic acids to form microscopically visible nuclear bodies, paraspeckles or large complexes such as DNA repair foci. They may also function cytoplasmically and on the cell surface in defined cell types. All three DBHS proteins are conserved throughout vertebrate species, while flies, worms, and yeast express a single DBHS protein .
Spore photoproduct lyase, Clostridia type (SPL_Clostridia)
Type: Family

These enzymes are involved in the repair of UV radiation-induced DNA damage during spore germination. They can repair thymine dimer 5-thyminyl-5,6-dihydrothymine (known as spore photoproduct (SP)) by in situ monomerization of spore photoproduct to two thymines. This family of enzymes uses the SAM as a cofactor (rather than in a stoichiometric manner). This set of SPL enzymes is distinguished from the other SPL family because its fourth conserved Cys residue occurs before the CxxxCxxC motif, unlike in the other SPL family, in which is occurs after the CxxxCxxC motif .

This entry represents spore photoproduct lyases mostly from Clostridia.
Spore photoproduct lyase, Bacilli type (SPL_Bacilli)
Type: Family

These enzymes are involved in the repair of UV radiation-induced DNA damage during spore germination . They can repair thymine dimer 5-thyminyl-5,6-dihydrothymine (known as spore photoproduct (SP)) by in situ monomerization of spore photoproduct to two thymines . This family of enzymes uses the SAM as a cofactor (rather than in a stoichiometric manner) .

This entry represents spore photoproduct lyases from Bacilli.
Negative regulator of systemic acquired resistance SNI1 (SNI1)
Type: Family

SNI1 was isolated in a screen for negative regulators of NPR1, a transcriptional coactivator of plant pathogen defence gene PR1 . SNl1 has been shown to cooperate with the transcription repressor CBNAC, which binds to cis-elements on the PR1 promoter, to suppress PR1 expression . SNI1 also regulates DNA damage sensor proteins RAD17 and ATR, suggesting that DNA damage responses is an intrinsic component of the plant immune responses. SNI1 is a subunit of the Structural Maintenance of Chromosome (SMC) 5/6 complex involved in DNA damage responses .
U2 small nuclear ribonucleoprotein B'', RNA recognition motif 2 (U2B''_RRM2)
Type: Domain

This entry represents the RNA recognition motif 2 (RRM2) of U2B".

U2B" (also termed U2 snRNP B") is a unique protein that comprises the U2 snRNP. It was initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA . Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity . U2B" does not require an auxiliary protein for binding to RNA and its nuclear transport is independent of U2 snRNA binding. U2B" contains two RNA recognition motifs (RRMs). It also contains a nuclear localization signal (NLS) in the central domain. However, nuclear import of U2B'' does not depend on this NLS. The N-terminal RRM is sufficient to direct U2B" to the nucleus .
Protein PALE CRESS (PALE_CRESS)
Type: Family

The PAC (PALE CRESS) protein is required for leaf and chloroplast development . PAC mutation arrests chloroplast development at an early stage, affecting the abundance and maturation of specific chloroplast-encoded transcripts. The PAC protein may be a nucleus-encoded factor that functions in plastid mRNA maturation and accumulation .
U2 small nuclear ribonucleoprotein B'', RNA recognition motif 1 (U2B''_RRM1)
Type: Domain

This entry represents the RNA recognition motif 1 (RRM1) of U2B".

U2B" (also termed U2 snRNP B") is a unique protein that comprises the U2 snRNP. It was initially identified to bind to stem-loop IV (SLIV) at the 3' end of U2 snRNA . Additional research indicates U2B" binds to U1 snRNA stem-loop II (SLII) as well and shows no preference for SLIV or SLII on the basis of binding affinity . U2B" does not require an auxiliary protein for binding to RNA and its nuclear transport is independent of U2 snRNA binding. U2B" contains two RNA recognition motifs (RRMs). It also contains a nuclear localization signal (NLS) in the central domain. However, nuclear import of U2B'' does not depend on this NLS. The N-terminal RRM is sufficient to direct U2B" to the nucleus .
Putative cell wall protein (Put_cell_wall)
Type: Family

This family of plant proteins have not known function. It includes putative cell wall protein from Arabidopsis thaliana (At2g208700).
Type 2 DNA topoisomerase 6 subunit B-like, plants (MTOPVIB_plant)
Type: Family

MTOPVIB (meiotic topoisomerase VIB-like) is a structural homologue of the archaeal topo VIB subunit . MTOPVIB forms a complex with the two Arabidopsis thaliana SPO11 orthologues (SPO11-1 and SPO11-2) and is essential for meiotic DSB formation . The SPO11 protein catalyzes the formation of meiotic DNA double strand breaks (DSBs) and it is the eukaryotic homologue of the archaeal DNA topoisomerase VIA.
Mediator of RNA polymerase II transcription subunit 30 (MED30)
Type: Family

The large protein complex Mediator is a central coregulator of transcription in eukaryotes. It acts as a bridge to pass on the information from the transcription factors to the basal transcriptional unit at the core promoter, resulting in either transcriptional activation or repression. The plant Mediator subunits typically show very low homology to other species, plant Meds being closer to human than to yeast counterparts. The plant Mediator appears to be composed of one or more members of 34 subunits, as opposed to 25 and 30 members in yeast and metazoans, respectively . This entry represents subunit 30 of the plant complex.
Photosynthetic NDH subunit of subcomplex B 5, chloroplastic (PNSB5)
Type: Family

The chloroplast NADH dehydrogenase-like complex (NDH) was first discovered based on its similarity to complex I in respiratory electron transport. However, it seems to be a ferredoxin-dependent plastoquinone reductase rather than an NAD(P)H dehydrogenase. Furthermore, it also comprises a subcomplex on the stromal side of the thylakoid membrane and a lumenal subcomplex . The chloroplast NDH complex has been divided into four categories: membrane, lumen, A, and B subcomplexes. The subcomplex A and membrane subcomplex are conserved in cyanobacteria, but the subcomplex B and lumen subcomplex are specific to chloroplasts. PNSB5/ NDH18 is a subunit of subcomplex B .