SII-SWORD/CoKE huggingface dataset:
Domain X (Domain_X)
Type: Domain

Group II introns are widespread in plant cell organelles . In vivo, most plant group II introns do not self-splice, but require the assistance of proteinaceous splicing factors, known as maturases. In higher plants, maturases are encoded for in the nuclear genes , but are otherwise encoded by organellar introns.

This entry represents a sequence region known as domain X, which is conserved in group II introns and is required for maturase function .
Transcription factor TCF/LEF (TCF/LEF)
Type: Family

Members of this family of HMG box containing factors play an essential role in the Wnt/Wingless signalling cascade. They are known to associate with beta-catenin in the nucleus to mediate Wnt signaling . This family exist in vertebrates, Drosophila melanogaster and Caenorhabditis elegans, and includes transcription factor 7, transcription factor 7-like 1 and 2, lymphoid enhancer-binding factor 1 and proteins pangolin and pop-1 .
Maturase MatK, N-terminal domain (Maturase_MatK_N)
Type: Domain

Group II introns are widespread in plant cell organelles . In vivo, most plant group II introns do not self-splice, but require the assistance of proteinaceous splicing factors, known as maturases. In higher plants, maturases are encoded for in the nuclear genes , but are otherwise encoded by organellar introns.

Maturase MatK is usually encoded in the trnK tRNA gene intron, and probably assists in splicing its own and other chloroplast group II introns.

The N-terminal domain of MatK appears to be a divergent reverse transcriptase domain that has lost most of the conserved sequence motifs typical of functional reverse transcriptases . The function of this domain is not known, but it may be important in RNA splicing.
Enhancer of polycomb protein (Enhancer_polycomb)
Type: Family

The enhancer of polycomb gene of Drosophila encodes a chromatin protein conserved in yeast and mammals . The homologous yeast protein, known as enhancer of polycomb-like protein 1 (Epl1), is a subunit of the NuA4 histone acetyltransferase (HAT) complex, which is involved in transcriptional activation of selected genes principally by acetylation of nucleosomal histone H4 and H2A . Epl1 also found in a novel highly active smaller complex named Piccolo NuA4 (picNuA4), which strongly prefers chromatin over free histones as substrate . The NuA4 HAT complex is highly conserved in eukaryotes, and it plays primary roles in transcription, cellular response to DNA damage, and cell cycle control .

This entry represents all eukaryotic enhancer of polycomb proteins, including enhancer of polycomb-like proteins.
Spt5 C-terminal domain (Spt5_C_dom)
Type: Domain

The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe . The repeat has a characteristic TPA motif.
Bet v I type allergen (Bet_v_I_allergen)
Type: Family

This family consists of a number of plant proteins that are structurally related and seem to be involved in pathogen defence response. These proteins include:

Bet v I, the major pollen allergen from white birch. Bet v I is the main cause of type I allergic reactions observed in early spring.

Aln g I, the major pollen allergen from alder.

Api G I, the major allergen from celery.

Car b I, the major pollen allergen from hornbeam.

Cor a I, the major pollen allergen from hazel.

Mal d I, the major pollen allergen from apple.

Asparagus wound-induced protein AoPR1.

Kidney bean pathogenesis-related proteins 1 and 2.

Parsley pathogenesis-related proteins PR1-1 and PR1-3.

Pea disease resistance response proteins pI49, pI176 and DRRG49-C.

Pea abscisic acid-responsive proteins ABR17 and ABR18.

Potato pathogenesis-related proteins STH-2 and STH-21.

Soybean stress-induced protein SAM22.

Major strawberry allergen proteins Fra a 1-2, 1-3 and 1.04 to 1.08
Sulphate adenylyltransferase catalytic domain (Sulfurylase_cat_dom)
Type: Domain

This domain is the catalytic domain of ATP-sulfurylase or sulphate adenylyltransferase (

). ATP-sulfurylase catalyses the synthesis of adenosine-phosphosulphate (APS) from ATP and inorganic sulphate . Sometimes is found as part of a bifunctional polypeptide chain associated with adenylylsulphate kinase (

). Both enzymes are required for PAPS (phosphoadenosine-phosphosulphate) synthesis from inorganic sulphate .
Lipoprotein LPP20-like domain (LPP20-like_dom)
Type: Domain

This entry represents a domain covering almost the full length of LPP20, which belongs to the non-essential class of lipoproteins . It is also found in close homologues, and associated to other domains in a related group of sequences that have not yet been experimentally characterised.
Polyphosphate kinase middle domain (PP_kinase_middle)
Type: Domain

Polyphosphate kinase (Ppk) catalyses the formation of polyphosphate from ATP, with chain lengths of up to a thousand or more orthophosphate molecules . This entry represents the Ppk middle domain.
SSRP1, dimerization domain (SSRP1_DD)
Type: Domain

This is the dimerization domain found in structure-specific recognition protein SSRP1 (POB3 in yeast) and related proteins, which are components of the FACT complex - a general chromatin factor that acts to reorganise nucleosomes. The FACT complex is involved in multiple processes that require DNA as a template such as mRNA elongation, DNA replication and DNA repair . During transcription elongation the FACT complex acts as a histone chaperone that both destabilises and restores nucleosomal structure .

This domain has a Pleckstrin homology fold, made of 6 β-strands.
tRNAHis guanylyltransferase catalytic domain (tRNAHis_GuaTrfase_cat)
Type: Domain

The Thg1 protein from Saccharomyces cerevisiae is responsible for adding a GMP residue to the 5' end of tRNA His . The catalytic domain of Thg1 contains a RRM (ferredoxin) fold palm domain, just like the viral RNA-dependent RNA polymerases, reverse transcriptases, family A and B DNA polymerases, adenylyl cyclases, diguanylate cyclases (GGDEF domain) and the predicted polymerase of the CRISPR system . Thg1 possesses an active site with three acidic residues that chelate Mg++ cations . Thg1 likely catalyses polymerisation using a similar mechanism to the 5'-3' polymerases .
Cep57 centrosome microtubule-binding domain (Cep57_MT-bd_dom)
Type: Domain

This C-terminal domain of Cep57 binds, nucleates and bundles microtubules. The N-terminal part of the protein is the centrosome localisation domain .
GRASP-type PDZ domain (GRASP_PDZ)
Type: Domain

The Golgi apparatus is a highly dynamic organelle responsible for sorting out proteins and other biomolecules to the cell surface and to the extracellular milieu. The Golgi apparatus is comprised of flattened membrane-bound compartments called cisternae, which are apposed to one another to form a Golgi stack. The structural organization of the cisternae into stacks and their lateral connection, building the Golgi ribbon, requires a family of proteins called Golgi ReAssembly and Stacking Proteins (GRASP). Two homologues (GRASP55 and GRASP65) have been described in vertebrates and their functions have been associated to Golgi phosphorylation-regulated assembly/disassembly, protein secretion , Golgi remodeling in migrating cells, among others. There is only one gene for GRASP in lower eukaryotes. Essentially all GRASPs contain a conserved N-terminal GRASP region, which comprises two tandem PDZ domains (PDZ1 and PDZ2), a classical protein-peptide interaction domain, and is responsible for GRASP homo-oligomerization and for the attachment to the Golgi membrane. The C-terminal half which is not conserved between species but is rich in proline and serines residues, as well as glutamine and asparagine residues .
Phosphatidyl-N-methylethanolamine/Phosphatidylethanolamine N-methyltransferase (PEMT/MFAP)
Type: Family

This family includes yeast phosphatidyl-N-methylethanolamine N-methyltransferase CHO1/OPI3 and vertebrates phosphatidylethanolamine N-methyltransferases . In yeast, this enzyme catalyzes the second two steps of the methylation pathway of phosphatidylcholine (PC) biosynthesis, the SAM-dependent methylation of phosphatidylmonomethylethanolamine (PMME) to phosphatidyldimethylethanolamine (PDME) and of PDME to PC. In vertebrates, it catalyzes the three sequential steps of the methylation pathway of phosphatidylcholine biosynthesis, the SAM-dependent methylation of phosphatidylethanolamine (PE) to phosphatidylmonomethylethanolamine (PMME), PMME to phosphatidyldimethylethanolamine (PDME), and PDME to PC.
Type II secretion system protein GspC, N-terminal (T2SS_GspC_N)
Type: Domain

This is the N-terminal region of GspC proteins, which is part of the Type II secretion system. The region is made up of a short N-terminal cytoplasmic domain that is followed by the single transmembrane helix, a Pro-rich linker, and the so-called homology region domain in the periplasm. This inner membrane GspC interacts with the outer membrane secretin GspD via periplasmic domains, an interaction which is critical for the effectiveness of type II secretion . This domain can also be found in GspN from Pseudomonas aeruginosa.

The type II secretion system (T2SS) is one of several extracellular secretion systems in gram-negative bacteria. It delivers toxins and a range of hydrolytic enzymes including proteases, lipases and carbohydrate-active enzymes to the cell surface or extracellular space . T2SS systems are composed of 11 to 15 different proteins, which are generally called GspA to GspO and GspS. The T2SS spans the two bacterial membranes and ensures secretion of folded proteins across the outer membrane pore formed by GspD. The inner membrane complex contains GspC, GspL, GspM, and GspF. The cytoplasmic domains of GspL and GspF interact with an ATPase, GspE. GspE is thought to energize the formation of a short pseudopilus by several pilin-like proteins, GspG to GspK . GspD has been shown to interact with the inner membrane component GspC .
YukD-like (YukD-like)
Type: Family

YukD adopts a ubiquitin-like fold . Usually, ubiquitin covalently binds to protein and flags them for protein degradation; however conjugation assays have indicated that the classical YukD lacks the capacity for covalent bond formation with other proteins . In firmicutes (Gram-positive bacteria), the YukD-like proteins are standalone versions and the YukD-like family is associated in conserved gene neighbourhoods with members of the ESAT-6 export pathway
(also called Type VII secretion system or ESX), suggesting a role for YukD in regulating this export system . In actinobacteria, YukD-like proteins are often fused to a transporter involved in the ESAT-6/ESX secretion pathway . Members of the YukD family are also associated in gene neighbourhoods with other enzymatic members of the ubiquitin signaling and degradation pathway such as the E1, E2 and E3 trienzyme complex that catalyse ubiquitin transfer to substrates, and the JAB family metallopeptidases that are involved in its release . This suggests that a subset of the YukD family in bacteria are conjugated to target proteins and released from proteins as in the eukaryotic ubiquitin-mediated signaling and degradation pathway .
CTLH/CRA C-terminal to LisH motif domain (CTLH/CRA)
Type: Domain

RanBPM is a scaffolding protein and is important in regulating cellular function in both the immune system and the nervous system. The RanBPM protein contains multiple conserved domains that provide potential protein-protein interaction sites . This entry represents a domain at the C terminus of RanBPM containing the CT11-RanBPM (CRA) motif. The CRA motif was found to be important for the interaction of RanBPM with fragile X messenger ribonucleoprotein 1 (FMRP), but its functional significance has yet to be determined . The region comprising this domain contains the CTLH and CRA domains annotated by SMART; however, these may be a single domain, and is referred to as a C-terminal to LisH motif .
Putative integrase (Putative_integrase)
Type: Family

This entry represents a family of putative integrases found in association with IS elements.
Primase helical domain (Primase_helical_domain)
Type: Domain

This α helical domain is found in a set of archaeal plasmid replication proteins . The domain is found to the C terminus of the primase/polymerase domain and is necessary for primase activity. Mutations in this domain can result in defective template binding, dinucleotide formation and conformation change prior to DNA extension.
DNA-binding domain, IS481-type (DNA-bd_IS481-type)
Type: Domain

This entry represents a DNA-binding domain found in a number of putative transposases. This domain can be found in the upstream region of the conjoined ORF AB of insertion element 481 from Bordetella pertusis .
S-layer protein, C-terminal domain, lactobacillus (SlpA_C_lactobacillus)
Type: Domain

This short domain is found at the C-terminal end of Lactobacillus S-layer proteins and in a variety of bacterial cell surface proteins. The domain is about 60 residues in length (although previously defined as 2 copies of this domain). It usually occurs in tandem pairs. It may be distantly related to the SH3 domain. It is involved in the binding to TAs (teichoic acid binding domain), one of the components of the bacterial cell wall .
EIF3F/CSN6-like, C-terminal (EIF3F/CSN6-like_C)
Type: Domain

This domain is found at the C terminus of many regulatory proteins, including the eukaryotic initiation factor 3 subunit F (eIF3f) and COP9 signalosome complex subunit 6. The eIF3f C-terminal domain is critical for proper eIF3f activity in skeletal muscle through its interaction with mTOR (also known as FRAP, RAFT1 or RAPT) .
Maelstrom domain (Maelstrom)
Type: Domain

Maelstrom is a germ-plasm component protein that is involved in the piRNA pathway, though its precise function is not known. This protein contains a novel domain, known as the Maelstrom domain, which adopts the RNaseH fold. Maelstrom is essential for Piwi-mediated silencing and acts downstream of or in parallel to H3K9me3 in Drosophila .
HNS-dependent expression A (HdeA)
Type: Family

HNS (histone-like nucleoid structuring)-dependent expression A (HdeA) protein is a stress response protein found in highly acid resistant bacteria such as Shigella flexneri and Escherichia coli, but which is lacking in mildly acid tolerant bacteria such as Salmonella . HdeA is one of the most abundant proteins found in the periplasmic space of E. coli, where it is one of a network of proteins that confer an acid resistance phenotype essential for the pathogenesis of enteric bacteria . HdeA is thought to act as a chaperone, functioning to prevent the aggregation of periplasmic proteins denatured under acidic conditions. The HNS protein, a chromatin-associated protein that influences the gene expression of several environmentally-induced target genes, represses the expression of HdeA. HdeB, which is encoded within the same operon, may form heterodimers with HdeA. HdeA is a single domain α-helical protein with an overall fold that is similar to the fold of the N-terminal subdomain of the GluRS anticodon-binding domain.

This entry represents acid stress chaperone HdeA.
ESPR domain (ESPR)
Type: Domain

This conserved domain is called ESPR for Extended Signal Peptide Region. It is present at the N terminus of the signal peptides of proteins belonging to the Type V secretion systems, including the autotransporters (T5aSS), TpsA exoproteins of the two-partner system (T5bSS) and trimeric autotransporters (TAAs). ESPR severely impairs inner membrane translocation, suggesting that it adopts a particular conformation or it interacts with a cytoplasmic or inner membrane co-factor, prior to exportation. Deletion of ESPR causes mis-folding of the TAAs passenger domain in the periplasm , substantially impairing its translocation across the outer membrane .
Sde2, ubiquitin domain (Sde2_N)
Type: Domain

Sde2 (silencing defective 2) is a ubiquitin-fold-containing splicing regulator that supports splicing of selected pre-mRNAs in an intron-specific manner in Schizosaccharomyces pombe. Sde2 is translated as inactive precursor proteins harbouring the ubiquitin-fold domain linked through an invariant GGKGG motif to a C-terminal domain. The Sde2 protein has a ubiquitin-fold at its N-terminal, represented in this entry, which must be cleaved by the ubiquitin-specific proteases (USPs) Ubp5 and Ubp15. After cleavage, the C-terminal domain of Sde2, which starts with a lysine, gets incorporated into the spliceosome .
Protein NO VEIN, C-terminal (NOV_C)
Type: Domain

This domain of unknown function is found at the C-terminal of Protein NO VEIN from Arabidopsis, a protein essential for cell fate determination during embryogenesis . It mediates this process through an auxin-dependent pathway . It is also found in some restriction endonucleases.
Domain of unknown function DUF3885 (DUF3885)
Type: Domain

This short domain of unknown function is approximately 40 amino acids in length. There is a conserved YDDRG sequence motif and a single completely conserved aspartate residue that may be functionally important.
Anaphase-promoting complex subunit 4-like, WD40 domain (Apc4-like_WD40_dom)
Type: Domain

This entry represents the N-terminal propeller-shaped WD40 domain of the anaphase-promoting complex subunit 4 (Apc4) and similar proteins.

WD-40 repeats (also known as WD or beta-transducin repeats) are short ~40 amino acid motifs, often terminating in a Trp-Asp (W-D) dipeptide. WD40 repeats usually assume a 7-8 bladed β-propeller fold, but proteins have been found with 4 to 16 repeated units, which also form a circularised β-propeller structure. WD-repeat proteins are a large family found in all eukaryotes and are implicated in a variety of functions ranging from signal transduction and transcription regulation to cell cycle control and apoptosis. Repeated WD40 motifs act as a site for protein-protein or protein-DNA interaction, and proteins containing WD40 repeats are known to serve as platforms for the assembly of protein complexes or mediators of transient interplay among other proteins . The specificity of the proteins is determined by the sequences outside the repeats themselves. Examples of such complexes are G proteins (beta subunit is a β-propeller), TAFII transcription factor, and E3 ubiquitin ligase . In Arabidopsis spp., several WD40-containing proteins act as key regulators of plant-specific developmental events.
Homeodomain, phBC6A51-type (Homeodomain_phBC6A51-type)
Type: Domain

This domain, found in phage or prophage proteins, adopts a homeodomain fold with additional N and C-terminal helices and a C-terminal β-strand that forms an intersubunit β-barrel with a channel.
Protein of unknown function DUF3884 (DUF3884)
Type: Family

This family of proteins is functionally uncharacterised. Several of them are annotated as Tagatose 1,6-diphosphate aldolase, but there appears to be no direct evidence to support this. Proteins in this family are typically between 61 and 106 amino acids in length and have two completely conserved residues (Y and F) that may be functionally important.
Protein of unknown function DUF3886 (DUF3886)
Type: Family

This family of proteins is functionally uncharacterised. Proteins in this family are approximately 90 amino acids in length and contain two completely conserved L residues that may be functionally important.
Domain of unknown function DUF3887 (DUF3887)
Type: Domain

This domain is found in bacteria and archaea, and is approximately 90 amino acids in length. This domain can be found in N-terminal of the EstD protein from Thermotoga maritima. EstD exhibits significant esterase activity with a preference for short acyl chain esters (C4-C8) .
Rax2-like, C-terminal domain (Rax2-like_C)
Type: Domain

Diploid yeast cells repeatedly polarise and bud from their poles, due probably to the presence of highly stable membrane markers, and Rax2 is one such marker. It is inherited immutably at the cell cortex for multiple generations, and has a half-life exceeding several generations. The persistent inheritance of cortical protein markers would provide a means of coupling a cell's history with the future development of a precise morphogenetic form . Both Rax1 and Rax2 localise to the distal pole as well as to the division site and they interact both with each other and with Bud8p and Bud9p in the establishment and/or maintenance of the cortical markers for bipolar budding . Thus Rax2 is likely to control cell polarity during vegetative growth, and in fission yeast this is done by regulating the localisation of for3p . Rax2 is not involved in responses that require a reorientation of the direction of already established hyphal growth (tropisms) .

This entry represents the β-propeller domain found at the C-terminal of Rax2 and Polarized growth protein L1 which are structurally similar.
CHAT domain (CHAT_dom)
Type: Domain

Some proteins containing this domain appear to be related to peptidases in peptidase clan CD that includes the caspases. This domain has been termed the CHAT domain for Caspase HetF Associated with Tprs.
Protein of unknown function DUF3888 (DUF3888)
Type: Family

This family of proteins is functionally uncharacterised
Sister chromatid cohesion C-terminal domain (Nipped-B_C)
Type: Domain

This domain lies towards the C terminus of nipped-B or sister chromatid cohesion proteins.
Protein of unknown function DUF3889 (DUF3889)
Type: Family

This family of proteins is functionally uncharacterised. Proteins in this family are approximately 110 amino acids in length and contain two completely conserved residues (A and Y) that may be functionally important.
Domain of unknown function DUF3890 (DUF3890)
Type: Domain

This presumed domain, approximately 70 amino acids in length, is functionally uncharacterised.
Major facilitator superfamily associated domain (MFS_assoc_dom)
Type: Domain

This domain is found in a number of major facilitator superfamily proteins.
Anaphase-promoting complex subunit 1 (Apc1)
Type: Family

Apc1 is the largest of the subunits of the anaphase-promoting complex or cyclosome. The anaphase-promoting complex is a multiprotein subunit E3 ubiquitin ligase complex that controls segregation of chromosomes and exit from mitosis in eukaryotes . Infection of human fibroblasts with human cytomegalovirus (HCMV) leads to cell cycle dysregulation, which is associated with the inactivation of the anaphase-promoting complex .
Anaphase-promoting complex subunit 11, RING-H2 finger (RING-H2_APC11)
Type: Domain

Apc11 is one of the subunits of the anaphase-promoting complex or cyclosome (APC) . The APC subunits are cullin family proteins with ubiquitin ligase activity . Polyubiquitination marks proteins for degradation by the 26S proteasome and is carried out by a cascade of enzymes that includes ubiquitin-activating enzymes (E1s), ubiquitin-conjugating enzymes (E2s), and ubiquitin ligases (E3s). Apc11 acts as an E3 enzyme and is responsible for recruiting E2s to the APC and for mediating the subsequent transfer of ubiquitin to APC substrates in vivo. Apc11 contains a canonical RING-H2-finger domain, which includes one histidine and seven cysteine residues that coordinate two Zn2+ ions. In addition, it contains a third Zn2+-binding site and the third Zn2+ ion is not essential for its ligase activity . In Saccharomyces cerevisiae this RING-H2 finger protein defines the minimal ubiquitin ligase activity of the APC, and the integrity of the RING-H2 finger is essential for budding yeast cell viability .

This entry represents the RING-H2 finger found in Apc11.
Protein of unknown function DUF3891 (DUF3891)
Type: Family

This family consists of proteins that have not yet been functionally uncharacterised.
Protein of unknown function DUF3894 (DUF3894)
Type: Family

This family of bacterial proteins is functionally uncharacterised. They contain two conserved sequence motifs: FNIC and MALLNLT.