SII-SWORD/CoKE huggingface dataset:
Cilia- and flagella-associated protein 47 domain (CFAP47_dom)
Type: Domain

This domain is found in human Cilia- and flagella-associated protein 47 (CFAP47) and similar proteins mainly from animals. CFAP47 plays a role in flagellar formation and sperm motility . This domain is usually found associated with

.
CFAP65-like, ninth Ig-like domain (Ig_CFAP65-like_9th)
Type: Domain

This entry represents the ninth Ig-like domain of CFAP65 and related sequences. This domain is also found in hydrocephalus-inducing protein, which is required for ciliary motility .

Cilia-Flagella-Associated Protein 65 (CFAP65) is involved in the structural and functional integrity of cilia and flagella. This protein is implicated in the process of flagellar formation and is essential for proper sperm motility, suggesting a role in reproductive biology. CFAP65's function in flagellar assembly indicates its importance in the motility and sensory functions of cilia and flagella across different species .
CIZ1, C2H2-type zinc finger (Znf-C2H2_CIZ1)
Type: Domain

This C2H2-type zinc finger domain is found in human Cip1-interacting zinc finger protein (CIZ1), its orthologue from Drosophila Zinc finger protein on ecdysone puffs and similar animal proteins. CIZ1 may regulate the subcellular localisation of CIP/WAF1 .
Cmi2, C-terminal (HTH_Cmi2_C)
Type: Domain

This domain is found at the C-terminal of the predicted ArsR family transcription regulator Cmi2 and similar archaeal sequences.
Microprotein, apicomplexa 8 (Microp_apicomplexa_8)
Type: Family

This protein family includes uncharacterised microproteins encoded by small open reading frames (smORFs) from apicomplexa, including

from the parasite Babesia bovis .
Microprotein, apicomplexa 9 (Microp_apicomplexa_9)
Type: Family

This protein family includes uncharacterised microproteins encoded by small open reading frames (smORFs) from apicomplexa, including

from the parasite Babesia bovis .
Microprotein, apicomplexa 10 (Microp_apicomplexa_10)
Type: Family

This protein family includes uncharacterised microproteins encoded by small open reading frames (smORFs) from apicomplexa, including

from the parasite Babesia bovis . Members of this family are predicted to fold into a four-stranded antiparallel curved β-sheet followed by a single long α-helix.
Pre-mRNA-splicing factor SYF1, central HAT repeats domain (HAT_Syf1_central)
Type: Domain

This entry represents HAT repeats forming the central region of Syf1.

This entry includes a group of pre-mRNA-processing factors that are components of the spliceosome, involved in pre-RNA splicing, including Syf1 from human and its homologues from S.pombe, cwf3. These proteins contain HAT (Half A TPR) repeats which have a repetitive pattern characterised by three aromatic residues with a conserved spacing. They are structurally and sequentially similar to TPRs . The HAT repeats in these proteins can be divided in three segments, N-terminal, central and C-terminal.
Microprotein domain, apicomplexa 3 (Microp_dom_apicomplexa_3)
Type: Domain

This domain covers the whole length of uncharacterised microproteins encoded by small open reading frames (smORFs) from apicomplexa, including

from the parasite Babesia bovis , and is found at the N-terminal end of longer uncharacterised proteins from related species.
Microprotein, apicomplexa 13 (Microp_apicomplexa_13)
Type: Family

This protein family includes uncharacterised microproteins encoded by small open reading frames (smORFs) from apicomplexa, including

from the parasite Babesia bovis .
Microprotein domain, apicomplexa 4 (Microp_dom_apicomplexa_4)
Type: Domain

This domain covers the whole length of uncharacterised microproteins encoded by small open reading frames (smORFs) from apicomplexa, including

from the parasite Babesia bovis , and is found at the C-terminal end of longer uncharacterised proteins from related species.
Microprotein domain, apicomplexa 5 (Microp_dom_apicomplexa_5)
Type: Domain

This domain covers the whole length of uncharacterised microproteins encoded by small open reading frames (smORFs) from apicomplexa, including

from the parasite Babesia bovis , and is found towards the C terminus of longer uncharacterised proteins from related species.
Microprotein, apicomplexa 16 (Microp_apicomplexa_16)
Type: Family

This protein family includes uncharacterised microproteins encoded by small open reading frames (smORFs) from apicomplexa, including

from the parasite Babesia bovis .
Microprotein, apicomplexa 17 (Microp_apicomplexa_17)
Type: Family

This protein family includes uncharacterised microproteins encoded by small open reading frames (smORFs) from apicomplexa, including

from the parasite Babesia bovis .
Apc4, C-terminal half WD40 domain, schizosaccharomycetes (Apc4_C_schizosaccharomycetes)
Type: Domain

Apc4 is a component of the anaphase promoting complex/cyclosome (APC/C), a cell cycle-regulated E3 ubiquitin ligase that controls progression through mitosis and the G1 phase of the cell cycle. This complex acts by ubiquitination and degradation of target proteins. Apc4 consists of a β-propeller that is split by a long α-helical domain which generate an L-shaped molecule . APC4 interacts with APC5; the N-terminal of APC1 serves to stabilise the union between APC4 and APC5, both of which lie towards the bottom-front of the APC . This entry represents the C-terminal half of the β-propeller of Apc4 from S. pombe. Members of this group are specific to schizosaccharomycetes.
Anaphase-promoting complex subunit 4, C-terminal half WD40 domain (APC4_C)
Type: Domain

Apc4 is a component of the anaphase promoting complex/cyclosome (APC/C), a cell cycle-regulated E3 ubiquitin ligase that controls progression through mitosis and the G1 phase of the cell cycle. This complex acts by ubiquitination and degradation of target proteins. Apc4 consists of a β-propeller that is split by a long α-helical domain which generate an L-shaped molecule . APC4 interacts with APC5; the N-terminal of APC1 serves to stabilise the union between APC4 and APC5, both of which lie towards the bottom-front of the APC . This entry represents the C-terminal half of the β-propeller of ACP4 from animals .
ApeC, platyhelminthes (ApeC_platyh)
Type: Domain

This entry represents a divergent ApeC domain found in a group of proteins mainly from flatworms that also contain

. Its specific function is unknown. This domain is predicted to show an α-β configuration.
ATPase MORC2, chromo domain-like (Chromo_MORC2_6th)
Type: Domain

This domain is found in human ATPase MORC2 and similar sequences predominantly found in vertebrates. MORC2 is essential for epigenetic silencing by the HUSH (human silencing hub) complex. This domain, which is predicted to adopt an α-β configuration, is often found associated with

,

and

.
AtPDCT1/2, transmembrane domain (AtPDCT1_2_TM_dom)
Type: Domain

This entry represents a domain found in PDCT1/2 from Arabidopsis thaliana, which has a detectable similarity to domains members of the Acid phosphatase/Vanadium-dependent haloperoxidase superfamily and it is predicted to adopt similar structure. This domain is composed of five transmembrane helices.

This entry represents a group of proteins predominantly found in plants, including phosphatidylcholine:diacylglycerol cholinephosphotransferase 1 (PDCT1 or ROD1) and 2 (PDCT2) from Arabidopsis thaliana. PDCT1 catalyses the transfer of the phosphocholine headgroup from phosphatidylcholine (PC) to diacylglycerol, a major reaction for the transfer of 18:1 into phosphatidylcholine for desaturation and also for the reverse transfer of 18:2 and 18:3 into the triacylglycerols synthesis pathway . This entry also includes some uncharacterised proteins from bacteria.
AtuA-like, ferredoxin-fold domain (AtuA-like_ferredoxin_dom)
Type: Domain

This domain, with a ferredoxin-like fold, is often found at the C-terminal of AtuA-like proteins, although it is sometimes found as a separate protein in the same operon as AtuA. The precise function of this domain is now known.
Leucine-rich repeat and WD repeat-containing protein 1, LRR domain (LRR_LRWD1_dom)
Type: Domain

This entry represents the Leucine-rich repeat domain found at the N terminus of Leucine-rich repeat and WD repeat-containing protein 1 (LRWD1) from animals and related sequences.

LRWD1 (also known as CENP-33 and ORCA) is required for for G1/S transition. It recruits and stabilises the origin recognition complex (ORC) onto chromatin during G1 to establish pre-replication complex (preRC) and to heterochromatic sites in pre-replicated cells . This proteins consist of a LRR domain at the N terminus and a WD domain at the C terminus.
MABP1/WRD62, coiled-coil domain (WDR62-MABP1_CC)
Type: Domain

This entry represents the coil-coiled domain of WDR62, which is required for its dimerization . This domain is also found in MABP1.

MABP1 (Mitogen-activated protein kinase-binding protein 1) is a negative regulator of NOD2 function, leading to the down-regulation of NOD2-induced processes such as activation of NF-kappa-B signalling, IL8 secretion and antibacterial response . WDR62 is a microcephaly-related, microtubule (MT)-associated protein (MAP) that localises to the spindle pole and regulates spindle organisation by recruiting katanin to the spindle pole by forming a complex with TPX2/Aurora A . The microtubule-binding (MT) affinity of WDR62 is autoinhibited through JNK phosphorylation-induced intramolecular interaction . Additionally, WRD62 is implicated in the development of the cerebral cortex influencing both the proliferation and migration of neurons . The WD40 domains of WDR62 mediate the interaction with Aurora A and (MT binding) .
NAD-specific glutamate dehydrogenase, second domain (NAD-GDH_2nd)
Type: Domain

This domain is found in yeast NAD-specific glutamate dehydrogenase (GDH2, also known as DHE2) and similar fungal proteins. GDH2 is involved in the degradation of glutamate to ammonia and alpha-ketoglutarate.

This domain is found after

that is predicted to adopt an α/β globular structure with some similarity to the ACT domains of the bacterial large glutamate dehydrogenase and it is probably distantly related to these and other ACT-like domains.
Large ribosomal subunit protein eL24 (Ribosomal_eL24)
Type: Family

This entry represents human Large ribosomal subunit protein eL24 and related proteins from eukaryotes and archaea .

Ribosomal protein eL24/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (eL24, distinct from archaeal L24). eL24/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor binding site. eL24/L24 appears to play a role in the kinetics of peptide synthesis, and may be involved in interactions between the large and small subunits, either directly or through other factors. In mouse, a deletion mutation in L24 has been identified as the cause for the belly spot and tail (Bst) mutation that results in disrupted pigmentation, somitogenesis and retinal cell fate determination . L24 may be an important protein in eukaryotic reproduction: in shrimp, L24 expression is elevated in the ovary, suggesting a role in oogenesis , and in Arabidopsis, L24 has been proposed to have a specific function in gynoecium development .

Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.

Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome .
ParM (ASKHA_NBD_ParM_R1-like)
Type: Family

Type II plasmid partition systems utilise ParM NTPases in coordination with a centromere-binding protein called ParR to mediate accurate DNA segregation, a process critical for plasmid retention. This entry includes ParM from Escherichia coli (also called ParA locus 36 kDa protein, or protein StbA) and related proteins. It is a plasmid-encoded protein involved in the control of plasmid partition and required for accurate segregation of low-copy-number plasmid R1 .
Kunitz trypsin inhibitor 1 (KTI1)
Type: Family

This entry includes Kunitz trypsin inhibitor 1 (KTI1) from Arabidopsis thaliana and similar proteins which have trypsin protease inhibitor activity.
Cytoplasmic tRNA 2-thiolation protein 1-like, ATP-binding domain (CTU1-like_ATP-bd)
Type: Domain

This entry includes human cytoplasmic tRNA 2-thiolation protein 1, also called cytosolic thiouridylase subunit 1 (CTU1) and ATP-binding domain-containing protein 3 (ATPBD3). CTU1 plays a central role in 2-thiolation of mcm(5)S(2)U at tRNA wobble positions of tRNA(Lys), tRNA(Glu) and tRNA(Gln). It directly binds tRNAs and probably acts by catalysing adenylation of tRNAs, an intermediate required for 2-thiolation. This group of proteins belongs to the nucleotide alpha hydrolase (AANH) superfamily that includes N-type ATP PPases and ATP sulfurylases. This entry represent the adenosine binding domain which forms an α/β/α fold .

This entry also includes tRNA 2-thiolation protein NcsA from Haloferax volcanii and probable sulfurtransferases from archaea. NcsA is required for thiolation of mcm5S2U at the wobble uridine position of tRNA specific for lysine (tRNA(Lys)). It may also act as a sulfurtransferase that transfers sulfur from thiocarboxylated SAMP2 onto the uridine of tRNA at wobble position. NcsA is required for cell growth at elevated temperatures .
DE-cadherin-like, Ig-like domain (Shg-like_Ig-like)
Type: Domain

This immunoglobulin-like (Ig-like) domain is found in DE-cadherin from Drosophila melanogaster (Shg) and similar animal sequences.

Cadherins are a group of transmembrane proteins that serve as the major adhesion molecules located within adherens junctions. They can regulate cell-cell adhesion through their extracellular domain and their cytosolic domains connect to the actin cytoskeleton by binding to catenins . These proteins preferentially interact with themselves in a homophilic manner in connecting cells; thus acting as both receptor and ligand. They may play an important role in the sorting of different cell types during morphogenesis, histogenesis and regeneration. They may also be involved in the regulation of tight and gap junctions, and in the control of intercellular spacing. Cadherins are evolutionary related to the desmogleins which are component of intercellular desmosome junctions involved in the interaction of plaque proteins.

Structurally, cadherins comprise a number of domains: classically, these include a signal sequence; a propeptide of around 130 residues; a single transmembrane domain and five tandemly repeated extracellular cadherin domains, 4 of which are cadherin repeats, and the fifth contains 4 conserved cysteines and a C-terminal cytoplasmic domain . However, proteins are designated as members of the broadly defined cadherin family if they have one or more cadherin repeats. A cadherin repeat is an independently folding sequence of approximately 110 amino acids that contains motifs with the conserved sequences DRE, DXNDNAPXF, and DXD. Crystal structures have revealed that multiple cadherin domains form Ca2+-dependent rod-like structures with a conserved Ca2+-binding pocket at the domain-domain interface. Cadherins depend on calcium for their function: calcium ions bind to specific residues in each cadherin repeat to ensure its proper folding, to confer rigidity upon the extracellular domain and is essential for cadherin adhesive function and for protection against protease digestion.
ATP-dependent RNA helicase DHX37-like, C-terminal domain (DHX37-like_C)
Type: Domain

This domain is found at the C-terminal in human ATP-dependent RNA helicase DHX37 and related proteins. DHX37 is a component of the human SSU processome and plays an important role in processome maturation. This domain folds into an array of α-helices and it is involved in protein-protein interactions with other components such as PWP2 and WDR36 . It is also involved in the recruitment of DHX37 to the processome .
Dedicator of cytokinesis, TPR repeats region (TPR_DOCK)
Type: Domain

This entry corresponds to a TPR-like α-solenoid region in Dedicator of cytokinesis (DOCK) proteins.

Dedicator of cytokinesis (DOCK) proteins function as guanine nucleotide exchange factors (GEFs) that activate small GTPases by exchanging bound GDP for free GTP, thus converting them into their active GTP-bound form. These proteins are involved in various cellular processes, including cytoskeletal rearrangements, cell migration, phagocytosis of apoptotic cells, and regulation of adherens junctions between cells. Some family members may also play a role in disease processes such as Alzheimer's disease by interacting with presenilin proteins and affecting Tau phosphorylation. DOCK proteins are characterised by the presence of a conserved DOCKER domain, which is necessary for their GEF activity and interaction with small GTPases like RAC1 and RAC2.
Defensin-like domain (Defensin-like_dom)
Type: Domain

This entry represents a domain found in defensin-like proteins from plants. It may adopt a scorpion toxin-like fold.
DesK/YvfT, N-terminal domain (DesK/YvfT_N)
Type: Domain

This domain is found at the N-terminal of sensor histidine kinases predominantly found in bacilli, including DesK and YvfT from Bacillus subtilis. DesK is responsible for detecting changes in membrane fluidity during cold stress and activating the response regulator DesR by phosphorylation, which leads to the induction of the des gene for Delta5 acyl-lipid desaturase . YvfT is part of the YvfT/YvfU regulatory system and likely activates the response regulator YvfU by phosphorylation . This domain is composed of 5 transmembrane helices.

Sensor histidine kinases function as part of two-component regulatory systems. These kinases are involved in sensing environmental stimuli and initiating appropriate cellular responses. They play a critical role in adapting to environmental changes by modulating the activity of their respective response regulators.
Isopentenyl-diphosphate delta-isomerase, bacteria (Idi_bact)
Type: Family

This entry includes isopentenyl-diphosphate delta-isomerases from bacteria.

This entry represents type 1 of two non-homologous families of the enzyme isopentenyl-diphosphate delta-isomerase (IPP isomerase;

). IPP isomerase is a member of the Nudix hydrolase superfamily, and is a key enzyme in the isoprenoid biosynthetic pathway. It catalyses the interconversion of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate. Dimethylallyl phosphate is the initial substrate for the biosynthesis of carotenoids and other long chain isoprenoids . IPP is an essential building block for many compounds, including enzyme cofactors, sterols, and prenyl groups. This enzyme interconverts isopentenyl diphosphate and dimethylallyl diphosphate. The enzyme requires one Mn2+ or Mg2+ ion in its active site to fold into an active conformation and also contains the Nudix motif, a highly conserved 23-residue block (GX5EX7REUXEEXGU, where U = I, L or V), that functions as a metal binding and catalytic site. The metal binding site is present within the active site and plays structural and catalytical roles. IPP isomerase is well represented in several bacteria, archaebacteria and eukaryotes, including fungi, mammals and plants. Despite sequence variations (mainly at the N terminus), the core structure is highly conserved .
DEX1, C-terminal domain (DEX1_C)
Type: Domain

Protein defective in exine formation DEX1 is a factor required for proper pollen wall formation in Arabidopsis thaliana and other plant sequences. This entry represents the β-sandwich domain found towards the C-terminal of DEX1 in plants. Mutations in DEX1 are associated with changes in the microspore membrane and primexine formation, which disrupt normal deposition of sporopollenin. DEX1 is suggested to be either a component of the primexine matrix or of the ER and participates in the assembly of primexine precursors . This protein has been identified as a Ca2+ binding protein involved in regulating rice tapetal cell degradation and pollen formation .
DExH18, N-terminal (DExH18_N)
Type: Domain

This domain is found at the N-terminal end of DExH-box ATP-dependent RNA helicase DExH18, mitochondrial (also known as SUV3L) from Arabidopsis thaliana, Oryza sativa and similar sequences from plants. DExH18 is a major helicase players in mitochondrial RNA metabolism. It plays a role in the RNA surveillance system in mitochondria; regulates the stability of mature mRNAs, the removal of aberrantly formed mRNAs and the rapid degradation of non coding processing intermediates. This domain is predicted to adopt an all α-helical configuration.
Let-756-like, FGF domain (Let-756-like_FGF)
Type: Domain

This entry represents the FGF domain of Protein let-756 from Caenorhabditis elegans and similar sequences from invertebrates. Let-756 negatively regulates membrane protrusion from body wall muscles during larval development . This domain is predicted to adopt a β-trefoil fold.
DExH14, plug domain (DExH14_plug)
Type: Domain

This entry represents the plug domain of DExH-box ATP-dependent RNA helicase DExH14 from Arabidopsis, an RNA helicase that plays an essential role in pre-mRNA splicing as component of the U5 snRNP and U4/U6-U5 tri-snRNP complexes. This is a small α-helical bundle domain related to the plug domain of BRR2 proteins (

). Members of this group are specific to plants.