SII-SWORD/CoKE huggingface dataset:
LSM-interacting domain (LSM_interact)
Type: Domain

This short motif is found at the C terminus of Prp24 protein, Spliceosome associated factor 3, U4/U6 recycling protein (SART3) and their Drosophila orthologue, the RNA-binding protein 4F. It probably interacts with the Lsm proteins to promote U4/U6 formation .

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 .

SART3 (also known as Tip110) is an RNA-binding protein expressed in the nucleus of the majority of proliferating cells, including normal cells and malignant cells, but not in normal tissues except for the testes and fetal liver . It is involved in the regulation of mRNA splicing probably via its complex formation with RNPS1 (an RNA-binding protein with a serine-rich domain), a pre-mRNA-splicing factor . SART3 has also been identified as a nuclear Tat-interacting protein that regulates Tat transactivation activity through direct interaction and functions as an important cellular factor for HIV-1 gene expression and viral replication . In addition, SART3 is required for U6 snRNP targeting to Cajal bodies . It binds specifically and directly to the U6 snRNA, interacts transiently with the U6 and U4/U6 snRNPs, and promotes the reassembly of U4/U6 snRNPs after splicing in vitro .

SART3 contains an N-terminal HAT (half-a-tetratricopeptide repeat)-rich domain, a nuclearlocalization signal (NLS) domain, and two C-terminal RNA recognition motifs (RRMs).
Long-chain-fatty-acyl-CoA reductase, LuxC (CoA_reduct_LuxC)
Type: Family

This family consists of several bacterial Acyl-CoA reductase (also known as long-chain-fatty-acyl-CoA reductase) LuxC proteins. The channelling of fatty acids into the fatty aldehyde substrate for the bacterial bioluminescence reaction is catalysed by a fatty acid reductase multienzyme complex, which channels fatty acids through the thioesterase (LuxD), synthetase (LuxE) and reductase (LuxC) components .
Spindle assembly checkpoint component Mad1 (Mad1)
Type: Family

This family consists of pindle assembly checkpoint protein Mad1. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in Saccharomyces cerevisiae and higher eukaryotes. In Saccharomyces cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated .
Microfibril-associated glycoprotein (MAGP)
Type: Family

This family consists of several mammalian microfibril-associated glycoprotein (MAGP) 1 and 2 proteins. MAGP1 and 2 are components of elastic fibres. MAGP-1 has been proposed to bind a C-terminal region of tropoelastin, the soluble precursor of elastin. MAGP-2 was found to interact with fibrillin-1 and -2, as well as fibulin-1, another component of elastic fibres. This suggests that MAGP-2 may be important in the assembly of microfibrils .
Chromosomal protein MC1 (MC1)
Type: Family

This entry represents the chromosomal protein MC1, which protects DNA against thermal denaturation and shapes DNA by binding to it . Its global fold consists of a pseudo barrel with an extension of the β-sheet (beta4-beta5) forming an arm (LP5) . Some uncharacterised virus proteins are also included in this entry.
Mating factor alpha precursor, N-terminal (Mating_factor_alpha_N)
Type: Domain

This entry contains the N-terminal regions of the Saccharomyces mating factor alpha precursor protein. All proteins in this family contain one or more copies of

further toward their C terminus.
MRG (MRG)
Type: Family

This entry represents MRG protein family, whose members include MORF4L1/2 (MRG15/MRGX) and MSL3L1/2 from humans, ESA1-associated factor 3 (Eaf3) from yeasts and male-specific lethal 3 (MSL3) from flies. They contain an N-terminal chromodomain that binds H3K36me3, a histone mark associated with transcription elongation .

Saccharomyces cerevisiae Eaf3 is a component of both NuA4 histone acetyltransferase and Rpd3S histone deacetylase complexes . It was found that Eaf3 mediates preferential deacetylation of coding regions through an interaction between the Eaf3 chromodomain and methylated H3-K36 that presumably results in preferential association of the Rpd3 complex .

The Drosophila MSL proteins (MSL1, MSL2, MSL3, MLE, and MOF) are essential for elevating transcription of the single X chromosome in the male (X chromosome dosage compensation) . Together with two partly redundant non-coding RNAs, roX1 and roX2, they form the MSL complex, also known as dosage compensation complex or DCC. MSL complex upregulates transcription by spreading the histone H4 Lys16 (H4K16) acetyl mark and allows compensation for the loss of one X-chromosomal allele by increasing the transcription from the retained allele . The MSL3 chromodomain has been shown to bind DNA and methylated H4K20 in vitro .

Human MORF4L1, also known as MRG15, is a component of the NuA4 histone acetyltransferase complex that transcriptional activates genes by acetylation of nucleosomal histones H4 and H2A. This modification may both alter nucleosome - DNA interactions and promote interaction of the modified histones with other proteins which positively regulate transcription. NuA4 complex may also play a direct role in DNA repair when directly recruited to sites of DNA damage. MRG15 is also a component of the mSin3A/Pf1/HDAC complex which acts to repress transcription by deacetylation of nucleosomal histones. MRG15 was found to interact with PALB2, a tumour suppressor protein that plays a crucial role in DNA damage repair by homologous recombination . Furthermore, MRG15 play a role in the response to double strand breaks (DSBs) by recruiting the BRCA complex (BRCA1, PALB2, BRCA2 and RAD51) to sites of damaged DNA .
MRVI1 (MRVI1)
Type: Family

This family consists of mammalian MRVI1 proteins which are related to the lymphoid-restricted membrane protein (JAW1) and the IP3 receptor associated cGMP kinase substrates A and B (IRAGA and IRAGB). The function of MRVI1 is unknown although mutations in the Mrvi1 gene induces myeloid leukaemia by altering the expression of a gene important for myeloid cell growth and/or differentiation so it has been speculated that Mrvi1 is a tumour suppressor gene . IRAG is very similar in sequence to MRVI1 and is an essential NO/cGKI-dependent regulator of IP3-induced calcium release. Activation of cGKI decreases IP3-stimulated elevations in intracellular calcium, induces smooth muscle relaxation and contributes to the antiproliferative and pro-apoptotic effects of NO/cGMP [

, . Jaw1 is a member of a class of proteins with COOH-terminal hydrophobic membrane anchors and is structurally similar to proteins involved in vesicle targeting and fusion. This suggests that the function and/or the structure of the ER in lymphocytes may be modified by lymphoid-restricted resident ER proteins .
Mastadenovirus early E4 13kDa (M_adenovirusE4)
Type: Family

This family consists of Homo sapiens and simian mastadenovirus early E4 13kDa proteins. Human adenovirus 9 (HAdV-9) is unique in eliciting exclusively estrogen-dependent mammary tumours in Rattus spp. and in not requiring viral E1 region transforming genes for tumorigenicity. E4 codes for an oncoprotein essential for tumourigenesis by Ad9 .
Negative regulator of genetic competence, MecA (Neg-reg_MecA)
Type: Family

Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions .

This family contains several bacterial MecA proteins. In complex media competence development is poor, and there is little or no expression of late competence genes. Overexpression of MecA inhibits comG transcription .

MecA enables the recognition and targeting of unfolded and aggregated proteins to the ClpC protease or to other proteins involved in proteolysis. It acts negatively in the development of competence by binding ComK and recruiting it to the ClpCP protease. When overexpressed, it inhibits sporulation. It is also involved in Spx degradation by ClpC .
Centromere protein Mis12 (Centromere_Mis12)
Type: Family

Kinetochores are the chromosomal sites for spindle interaction and play a vital role for chromosome segregation. Fission Saccharomyces cerevisiae kinetochore protein Mis12, is required for correct spindle morphogenesis, determining metaphase spindle length . Thirty-five to sixty percent extension of metaphase spindle length takes place in Mis12 mutants . It has been shown that Mis12 might genetically interact with Mal2p .
RNA-dependent RNA polymerase, mitoviral (RNA_pol_mitovir)
Type: Family

This family consists of several Mitovirus RNA-dependent RNA polymerase proteins. The family also contains fragment matches in the mitochondria of Arabidopsis thaliana .
Bacterial mobilisation (MobC)
Type: Domain

This family consists of several bacterial MobC-like, mobilisation proteins. MobC proteins belong to the group of relaxases. Together with MobA and MobB they bind to a single cis-active site of a mobilising plasmid, the origin of transfer (oriT) region . The absence of MobC has several different effects on oriT DNA. Site- and strand-specific nicking by MobA protein is severely reduced, accounting for the lower frequency of mobilisation. The localised DNA strand separation required for this nicking is less affected, but becomes more sensitive to the level of active DNA gyrase in the cell. In addition, strand separation is not efficiently extended through the region containing the nick site. These effects suggest a model in which MobC acts as a molecular wedge for the relaxosome-induced melting of oriT DNA. The effect of MobC on strand separation may be partially complemented by the helical distortion induced by supercoiling. However, MobC extends the melted region through the nick site, thus providing the single-stranded substrate required for cleavage by MobA .
ATP synthase, F0 complex, subunit B/MI25 (ATP_synth_Bsub_B/MI25)
Type: Family

Transmembrane ATPases are membrane-bound enzyme complexes/ion transporters that use ATP hydrolysis to drive the transport of protons across a membrane. Some transmembrane ATPases also work in reverse, harnessing the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP.

F-ATPases (also known as ATP synthases, F1F0-ATPase, or H(+)-transporting two-sector ATPase) (

) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), with additional subunits in mitochondria. Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the α(3)β(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis . These ATPases can also work in reverse in bacteria, hydrolysing ATP to create a proton gradient.

This entry represents subunit B from the F0 complex in F-ATPases found in mitochondria of eukaryotes (known as ATP4 in yeast and MI25/ORF25 in plants ). The B subunits are part of the peripheral stalk that links the F1 and F0 complexes together, and which acts as a stator to prevent certain subunits from rotating with the central rotary element. The peripheral stalk differs in subunit composition between mitochondrial, chloroplast and bacterial F-ATPases. In mitochondria, the peripheral stalk is composed of one copy each of subunits OSCP (oligomycin sensitivity conferral protein), F6, B and D .
ATP synthase, F0 complex, subunit D, mitochondrial (ATP_synth_F0_dsu_mt)
Type: Family

Transmembrane ATPases are membrane-bound enzyme complexes/ion transporters that use ATP hydrolysis to drive the transport of protons across a membrane. Some transmembrane ATPases also work in reverse, harnessing the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP.

F-ATPases (also known as ATP synthases, F1F0-ATPase, or H(+)-transporting two-sector ATPase) (

) are composed of two linked complexes: the F1 ATPase complex is the catalytic core and is composed of 5 subunits (alpha, beta, gamma, delta, epsilon), while the F0 ATPase complex is the membrane-embedded proton channel that is composed of at least 3 subunits (A-C), with additional subunits in mitochondria. Both the F1 and F0 complexes are rotary motors that are coupled back-to-back. In the F1 complex, the central gamma subunit forms the rotor inside the cylinder made of the α(3)β(3) subunits, while in the F0 complex, the ring-shaped C subunits forms the rotor. The two rotors rotate in opposite directions, but the F0 rotor is usually stronger, using the force from the proton gradient to push the F1 rotor in reverse in order to drive ATP synthesis . These ATPases can also work in reverse in bacteria, hydrolysing ATP to create a proton gradient.

This entry represents subunit D from the F0 complex in F-ATPases found in mitochondria. The D subunit is part of the peripheral stalk that links the F1 and F0 complexes together, and which acts as a stator to prevent certain subunits from rotating with the central rotary element. The peripheral stalk differs in subunit composition between mitochondrial, chloroplast and bacterial F-ATPases. In mitochondria, the peripheral stalk is composed of one copy each of subunits OSCP (oligomycin sensitivity conferral protein), F6, B and D . There is no homologue of subunit D in bacterial or chloroplast F-ATPase, whose peripheral stalks are composed of one copy of the delta subunit (homologous to OSCP), and two copies of subunit B in bacteria, or one copy each of subunits B and B' in chloroplasts and photosynthetic bacteria.
Tetrahydromethanopterin S-methyltransferase subunit B (MtrB_MeTrfase)
Type: Family

Members of this protein family are the MtrB protein of the tetrahydromethanopterin S-methyltransferase complex. This system is universal in archaeal methanogens .

The N5-methyltetrahydromethanopterin: coenzyme M (

) of Methanosarcina mazei Go1 is a membrane-associated, corrinoid-containing protein that uses a transmethylation reaction to drive an energy-conserving sodium ion pump .
19kDa lipoprotein antigen (LpqH)
Type: Family

Most of the antigens of Mycobacterium leprae and Mycobacterium tuberculosis that have been identified are members of stress protein families, which are highly conserved throughout many diverse species. Of the M. leprae and M. tuberculosis antigens identified by monoclonal antibodies, all except the 18kDa M. leprae antigen and the 19kDa M. tuberculosis antigen are strongly cross-reactive between these two species and are coded within very similar genes .
Haemagglutinin, Mycoplasma (Hemogglutn_Mycoplasma)
Type: Domain

This family consists of several haemagglutinin sequences from Mycoplasma gallisepticum. The major plasma membrane proteins, pMGAs, of Mycoplasma gallisepticum are cell adhesin (hemagglutinin) molecules. It has been shown that the genetic determinants that code for the haemagglutinins are organised into a large family of genes and that only one of these genes is predominately expressed in any given strain .
Transport accessory protein MmpS (MmpS)
Type: Family

This entry represents a group of putative transport accessory proteins, including MmpS1-5 from Mycobacterium tuberculosis . They are part of an export system required for biosynthesis and secretion of siderophores, and are essential for virulence of Mycobacterium tuberculosis . MmpS4 possesses an N-terminal transmembrane (TM) helix and a C-terminal soluble domain .
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7, NDUB7 (NDUB7)
Type: Family

This family consists of the accessory subunit of complex I NADH-ubiquinone oxidoreductase NDUB7 (or NDUFB7, also known as B18), which is not involved in catalysis .
NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8 (NDUFB8)
Type: Family

This family consists of several eukaryotic NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 8 proteins. NADH:ubiquinone oxidoreductase (complex I) is an extremely complicated multiprotein complex located in the inner mitochondrial membrane. Its main function is the transport of electrons from NADH to ubiquinone, which is accompanied by translocation of protons from the mitochondrial matrix to the intermembrane space. Human complex I appears to consist of 41 subunits . This is an accessory subunit, not involved in catalysis.
RIN4, pathogenic type III effector avirulence factor Avr cleavage site (TypeIII_avirulence_cleave)
Type: Domain

This domain is conserved in small families of otherwise unrelated proteins in both mono-cots and di-cots, suggesting that it has a conserved, plant-specific function. It is found in the plant RIN4 (RPM1-interacting protein 4) where it appears to contribute to the binding of the protein to RCS (AvrRpt2 auto-cleavage site) and AvrB, the virulence factors from the infecting bacterium . The cleavage site for the AvrRpt2 avirulence protein would appear to be the sequence motifs VPQFGDW and LPKFGEW, both of which are highly conserved within the domain .
Necrosis inducing protein (NPP1)
Type: Family

This family consists of several NPP1-like necrosis inducing proteins from oomycetes, fungi and bacteria. Infiltration of NPP1 into leaves of Arabidopsis thaliana plants result in transcript accumulation of pathogenesis-related (PR) genes, production of ROS and ethylene, callose apposition, and HR-like cell death . Members of this entry are secreted effectors that acts as a pathogen-associated molecular pattern (PAMP) recognised by the plant immune system .
Nucleopolyhedrovirus P10 (NPV_P10)
Type: Family

This family consists of several nucleopolyhedrovirus P10 proteins which play a role in the proper virion occlusion of the polyhedra and is involved in the liberation of polyhedra from infected insect cells .
Na(+)-translocating NADH-quinone reductase subunit A (NqrA)
Type: Family

This family consists of several bacterial Na
+
-translocating NADH-quinone reductase subunit A (NQRA) proteins. The Na
+
-translocating NADH: ubiquinone oxidoreductase (Na
+
-NQR) generates an electrochemical Na
+
potential driven by aerobic respiration .
Zinc-binding loop region of homing endonuclease (Endonuclease_Zinc-binding_loop)
Type: Domain

This domain is the short zinc-binding loops region of a number of much longer chain homing endonucleases. Such loops are probably stabilised by the zinc and may be viewed as small but separate domains. The common structural feature of these domains is that at least three zinc ligands lie very close to each other in the sequence and are not incorporated into regular secondary structural elements. The biological roles played by these small zinc-binding domains are presently unknown .
Nanos/Xcat2 (Nanos/Xcar2)
Type: Family

In Drosophila melanogaster, Nanos functions as a localised determinant of posterior pattern. Nanos RNA is localised to the posterior pole of the maturing egg cell and encodes a protein that emanates from this localised source. Nanos acts as a translational repressor and thereby establishes a gradient of the morphogen Hunchback . Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function . Xcat-2 from Xenopus encodes a protein with a nanos-like zinc finger domain. It is found in the vegetal cortical region and is inherited by the vegetal blasomeres during development, and is degraded very early in development. The localised and maternally restricted expression of Xcat-2 RNA suggests a role for its protein in setting up regional differences in gene expression that occur early in development .

This entry consists of the Nanos protein and homologues, including Xcat-2.
Nanovirus component 8 (Nanovirus_C8)
Type: Family

This family consists of a group of 17.4kDa nanovirus proteins which are highly related to the Faba bean necrotic yellows virus component 8 protein whose function is unknown .
PilY1, beta-propeller domain (B-propeller_PilY1)
Type: Domain

This domain is found in homologues of Type IV pilus biogenesis factor PilY1. PilY1 is involved in pilus assembly, twitching motility and adhesion to host cells. It regulates surface-activated virulence possibly by acting as a surface-attachment mechanosensor . This domain has been shown to adopt a β-propeller structure .
TspB virulence factor (Neisseria_TspB)
Type: Family

This family consists mainly of Neisseria meningitidis TspB virulence factor proteins. Proteins in this family also include attachment protein G3P from Pseudomonas phage Pf3. G3P plays essential roles both in the penetration of the viral genome into the bacterial host via pilus retraction and in the extrusion process .
Neurochondrin (Neurochondrin)
Type: Family

This family contains several eukaryotic neurochondrin proteins. Neurochondrin induces hydroxyapatite resorptive activity in bone marrow cells resistant to bafilomycin A1, an inhibitor of macrophage- and osteoclast-mediated resorption. Expression of the gene is localised to chondrocyte, osteoblast, and osteocyte in the bone and to the hippocampus and Purkinje cell layer of cerebellum in the brain .
Nicastrin (Nicastrin)
Type: Family

Nicastrin and presenilin are two major components of the gamma-secretase complex, which executes the intramembrane proteolysis of type I integral membrane proteins such as the amyloid precursor protein (APP) and Notch. Nicastrin is synthesised in fibroblasts and neurons as an endoglycosidase-H-sensitive glycosylated precursor protein (immature nicastrin) and is then modified by complex glycosylation in the Golgi apparatus and by sialylation in the trans-Golgi network (mature nicastrin) .
Recombinase NinB (Recombinase_NinB)
Type: Family

The ninR region of Bacteriophage lambda contains two recombination genes, ninB and ninG (rap), that have roles when the RecF and RecBCD recombination pathways of Escherichia coli, respectively, operate on phage lambda . Genetic recombination in phage lambda relies on DNA end processing by Exo to expose 3'-tailed strands for annealing and exchange by beta protein. Phage lambda encodes an additional recombinase, NinB, which participates in the early stages of recombination by supplying a function equivalent to the E. coli RecFOR complex. These host enzymes assist loading of the RecA strand exchange protein onto ssDNA coated with ssDNA-binding protein. NinB has two structural domains with unusual folds, and exists as an intertwined dimer .
NinF (NinF)
Type: Family

This family consists of several bacteriophage NinF proteins as well as related sequences from prophages mainly found in enterobacterales.
Bacteriophage lambda NinG (Phage_lambda_NinG)
Type: Family

The ninR region of phage lambda contains two recombination genes, ninB (also known as orf) and ninG (also known as rap). These genes are involved in the RecF and RecBCD recombination pathways of Escherichia coli that operate on phage lambda . NinB and NinG participate in Red recombination, the primary pathway operating when wild-type lambda grows lytically in rec+ cells .