SII-SWORD/CoKE huggingface dataset:
Domain of unknown function DUF1722 (DUF1722)
Type: Domain

This domain of unknown function is found in bacteria and archaea and is homologous to the hypothetical protein ybgA from Escherichia coli.
Methanogenesis regulatory protein FilR1, middle domain (FilR1_middle_dom)
Type: Domain

This archaeal domain of unknown function has been found at the middle of Methanogenesis regulatory protein FilR1 and at the C-terminal of several transcriptional regulators of the ArsR family (see

). FilR1 is a member of the two-component regulatory system FilI/FilRs which is involved in the regulation of methanogenesis.
TmcA/NAT10, N-terminal (TmcA/NAT10_N)
Type: Domain

This entry represents a domain found at the N-terminal of TmcA from bacteria and NAT10 from eukaryotes.

The bacterial tRNA(Met) cytidine acetyltransferase (TmcA) catalyses the formation of N(4)-acetylcytidine (ac4C) at the wobble position of tRNA(Met), by using acetyl-CoA as an acetyl donor and either ATP or GTP . This modification is thought to ensure precise recognition of the AUG codon by strengthening C-G base-pair interaction and also prevent misrecognition of the near cognate AUA codon . RNA cytidine acetyltransferas (NAT10) are RNA cytosine acetyltransferases with specificity toward both 18S rRNA and tRNAs and contain additional putative nuclear and nucleolar localisation signals (NLS and NoLS respectively) .
Oligopeptide/dipeptide ABC transporter, C-terminal (Oligopep_ABC_C)
Type: Domain

This entry features a region found towards the C terminus of oligopeptide ABC transporter ATP binding proteins, immediately following the ATP-binding domain (

). All characterised members appear able to be involved in the transport of oligopeptides or dipeptides. Some are important for sporulation or antibiotic resistance. Some dipeptide transporters also act on the haem precursor delta-aminolevulinic acid.
Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT, C-terminal (MurT_C)
Type: Domain

This entry represents the C-terminal domain of MurT ligase mostly from bacteria. MurT is part of the bi-enzymatic complex MurT-GatD involved in the amidation of the α-carboxyl group of the D-isoglutamate residue in Lipid II in the peptidoglycan layer to produce D-isoglutamine. This domain contains an aspartate at position 349, the third residue in the catalytic triad GatD-C94, GatD-H189, MurT-D349. This C-terminal domain is built around a central six-stranded, predominantly parallel β-sheet between four α-helices on one side and two α-helices on the other. The MurT-GatD heterodimer adopts a boomerang-shaped conformation, with GatD packing against the C-terminal domain of MurT .
Fatty acid synthase beta subunit AflB /Fas1-like, central domain (Fas1/AflB-like_central)
Type: Domain

The domain has been identified in fungi and bacteria. This domain can be found in fatty acid synthase beta subunit from fungi, including Fas1 from yeasts and aflB from Aspergillus parasiticus. The beta subunit contains domains for: [acyl-carrier-protein] acetyltransferase and malonyltransferase, S-acyl fatty acid synthase thioesterase, enoyl-[acyl-carrier-protein] reductase, and 3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase.

Fas1 is a fatty acid synthetase catalyzes the formation of long-chain fatty acids from acetyl-CoA, malonyl-CoA and NADPH .
Mitochondrial Rho GTPase 1/3, EF hand associated, type-1 (EF_hand_assoc_1)
Type: Domain

This entry represents a region that typically appears on the C terminus of EF hands in eukaryotic GTP-binding proteins such as Mitochondrial Rho GTPase 1 from Bos taurus (MIRO-1), the product of the gene Arht, which may be involved in mitochondrial homeostasis and apoptosis. The EF hand domains of these proteins may have a regulatory role related to Ca(2+) binding .
EF hand associated, type-2 (EF_hand_assoc_2)
Type: Domain

This region predominantly appears near EF-hands (

) in GTP-binding proteins. It is found in all three eukaryotic kingdoms.
SEFIR domain (SEFIR_dom)
Type: Domain

The SEFIR domain (after SEFs and IL17Rs) is a conserved sequence segment
identified in transmembrane receptors (including SEFs, IL17Rs) and soluble
factors (including CIKS/ACT1) in eukaryotes and bacteria. In addition to the
SEFIR sequence homology, SEFs and IL17Rs share the same architecture. Their
extracellular regions are sequentially divergent but appear structurally
similar to a tandem fibronectin 3 (FN3)-like domain arrangement. A single
transmembrane region is followed by a high-complexity sequence region
involving the SEFIR domain and a C-terminal tail that is enriched with polar
residues and, sometimes, with low complexity regions .

The SEFIR domain is related to the TIR domain. The SEFIR
domain is similar to the TIR domain in length and secondary structure. The
similarity between the SEFIR and TIR domains involves the conserved boxes 1
and 2 of the TIR domain that are implicated in homotypic dimerization, but
there is no sequence similarity between SEFIR domains and the TIR sequence box
3 .

Proteins containing this domain also includes TRAF3IP2 from humans. TRAF3IP2 is a U-box E3 ubiquitin ligase for IL-17 signaling . A mutation (T536I) located in the SEFIR domain, abolished the homotypic interaction of ACT1 with IL-17 receptors, with no effect on homodimerization .
Carlavirus coat (Carlavirus_coat_N)
Type: Domain

This domain is found together with the viral coat protein domain (

) in coat/capsid proteins of the plant infecting Carlavirus. It is required for genome encapsidation by forming ribonucleoprotein complexes along with TGB1 helicase and viral RNA. The N- and the C terminus of this coat protein can be exposed on the surface of the virus particle. The central core sequence may be important in maintaining correct tertiary structure of the coat protein and/or play a role in the interaction with the viral RNA. Coat proteins are often used to distinguish between Carlavirus isolates.
Transcription regulator YsiA, C-terminal (Tscrpt_reg_YsiA_C)
Type: Domain

The members of this family are thought to be TetR-type (tetracycline resistance) transcriptional regulators that bear particular similarity to YsiA (

). This entry represents the C-terminal domain.
Transcription regulator QacR, C-terminal (Tscrpt_reg_QacR_C)
Type: Domain

This entry represents the C-terminal domain found in the multidrug-binding transcription regulator QacR (

) from Staphylococcus aureus, which is a member of the TetR (tetracycline-resistance) transcriptional regulator family of proteins. QacR is able to bind various environmental agents, which include a number of cationic lipophilic compounds, and thus regulate the transcription of QacA (

), a multidrug efflux pump . The C-terminal region of QacR contains a multifaceted, expansive drug-binding pocket, which is composed of several separate, but linked, binding sites . The C-terminal domains of QacR and TetR share a multi-helical, interlocking structure.
Transcription regulator MAATS, C-terminal (Tscrpt_reg_MAATS_C)
Type: Domain

This entry is named after the various transcriptional regulatory proteins that it contains, including MtrR (

), AcrR (

), ArpR (

), TtgR (

) and SmeT (

). These are members of the TetR (tetracycline resistance) family of transcriptional repressors, that are involved in the control of expression of multidrug resistance proteins .
Transcription regulator YcdC, C-terminal (Tscrpt_reg_YcdC_C)
Type: Domain

This entry represents the C-terminal domain found in the hypothetical transcriptional regulators RutR and YcdC (

) from Escherichia coli. Both of these proteins are member of the TetR (tetracycline resistance) transcriptional regulator family of proteins. RutR negatively controls the transcription of the rut operon involved in pyrimidine utilization. The C-terminal domains of RutR, YsiA and TetR share a multi-helical, interlocking structure. These proteins also contain helix-turn-helix (HTH) DNA-binding domains.
Glucan-binding protein C/Surface antigen I/II, V-domain (Glucan-bd_C/Surface_Ag-I/II_V)
Type: Domain

This domain is found in glucan-binding protein C (GbpC) and in the V-region of surface protein antigen; both these proteins belong to the Spa family of Streptococcal proteins . This domain consists of a β-supersandwich of 18 β-strands in two sheets.
Initiation factor 2 associated domain, bacterial (IF2_assoc_dom_bac)
Type: Domain

This entry represents a small conserved domain found towards the N terminus of bacterial translation initiation factor IF-2 family proteins. The domain is also found in the eukaryotic translation initiation factor 4 gamma in yeast and in a hypothetical Euglenozoa protein of unknown function.
Lethal giant larvae homologue 2 (LLGL2)
Type: Domain

This domain is found in lethal giant larvae homologue 2 (LLGL2) proteins and syntaxin-binding proteins like tomosyn . It has been identified in eukaryotes and tends to be found together with WD repeats (

).
Peptidase M16C associated (Peptidase_M16C_assoc)
Type: Domain

This domain appears in eukaryotes as well as bacteria and tends to be found near the C terminus of metalloproteases and related sequences belonging to MEROPS peptidase family M16 (subfamily M16C, clan ME), PreP subfamily. PREP is an ATP-independent protease that degrades both mitochondrial and chloroplastic transit peptides after their cleavage. It also degrades other unstructured peptides .
FAST kinase-like protein, subdomain 2 (FAST_2)
Type: Domain

This domain represents a conserved region of eukaryotic Fas-activated serine/threonine (FAST) kinases (

) that contains several conserved leucine residues. FAST kinase is rapidly activated during Fas-mediated apoptosis, when it phosphorylates TIA-1, a nuclear RNA-binding protein that has been implicated as an effector of apoptosis . Note that many family members are hypothetical proteins. This subdomain is often found associated with the FAST kinase-like protein, subdomain 2.
Light-independent protochlorophyllide reductase subunit B-like, C-terminal (LI-POR_suB-like_C)
Type: Domain

This domain is found in Light-independent protochlorophyllide reductase subunit B (LI-POR subunit B, also known as DPOR subunit B) and similar bacterial and plant chloroplast proteins. It often appears at the C-terminal of nitrogenase component 1 type oxidoreductases (

) and sometimes independently in certain bacterial proteins such as the Protochlorophyllide reductase BchB subunit of the cyanobacterium Synechocystis.

LI-POR subunit B is a component of the dark-operative protochlorophyllide reductase (DPOR), a nitrogenase-like metalloenzyme that uses Mg-ATP and reduced ferredoxin to reduce ring D of protochlorophyllide (Pchlide) to form chlorophyllide a (Chlide), leading to the specific architecture of chlorophylls. The X-ray crystallographic structure of this complex from the marine cyanobacterium Prochlorococcus marinus showed that the C-terminal domain of subunit B closes the substrate-binding cavity at the interface with the other component of the complex, possibly preventing the organism from Pchlide-induced photodynamic damage .

This domain is also associated with chlorophyllide reductase subunit Z, which converts chlorophylls (Chl) into bacteriochlorophylls (BChl) by reducing ring B of the tetrapyrrole .
Multiple C2 domain and Transmembrane region Proteins, C-terminal (MCTP_C)
Type: Domain

This domain is found at the C terminus of a group of animal and plant proteins that belong to the family Multiple C2 domain and Transmembrane region Proteins (MCTPs), including Protein QUIRKY and FT-interacting protein 1/3/4 from Arabidopsis thaliana [

,

,

,

and Multiple C2 and transmembrane domain-containing protein 1/2 from humans . Members of this group are generally involved in Ca2 signalling at the membrane and show calcium-ion dependent C2 domains (

).
RAP domain (RAP)
Type: Domain

The ~60-residue RAP (an acronym for RNA-binding domain abundant in Apicomplexans) domain is found in various proteins in eukaryotes. It is particularly abundant in apicomplexans and might mediate a range of cellular functions through its potential interactions with RNA .

The RAP domain consists of multiple blocks of charged and aromatics residues and is predicted to be composed of α-helical and β-strand structures. Two predicted loop regions that are dominated by glycine and tryptophan residues are found before and after the central β-sheet .

Some proteins known to contain a RAP domain are listed below:

Human hypothetical protein MGC5297,

Mammalian FAST kinase domain-containing proteins (FASTKDs),

Chlamydomonas reinhardtii chloroplastic trans-splicing factor Raa3.
Protocadherin (Protocadherin)
Type: Domain

The structure of protocadherins is similar to that of classic cadherins (

), but they also have some unique features associated with the cytoplasmic domains. They are expressed in a variety of organisms and are found in high concentrations in the brain where they seem to be localised mainly at cell-cell contact sites. Their expression seems to be developmentally regulated .
26S proteasome non-ATPase regulatory subunit 3, C-terminal (PSMD3_C)
Type: Domain

This eukaryotic domain is found at the C-terminal of 26S proteasome regulatory subunits including the non-ATPase regulatory subunit 3 (PSMD3), which is essential for proteasomal function . It occurs together with the PCI/PINT domain (

).

Intracellular proteins, including short-lived proteins such as cyclin, Mos, Myc, p53, NF-kappaB, and IkappaB, are degraded by the ubiquitin-proteasome system. The 26S proteasome is a self-compartmentalising protease responsible for the regulated degradation of intracellular proteins in eukaryotes . This giant intracellular protease is formed by several subunits arranged into two 19S polar caps, where protein recognition and ATP-dependent unfolding occur, flanking a 20S central barrel-shaped structure with an inner proteolytic chamber. This overall structure is highly conserved among eukaryotes and is essential for cell viability. Proteins targeted to the 26S proteasome are conjugated with a polyubiquitin chain by an enzymatic cascade before delivery to the 26S proteasome for degradation into oligopeptides.

The 26S proteasome can be divided into two subcomplexes: the 19S regulatory particle (RP) and the 20S core particle (CP) . The 19S component is divided into a "base" subunit containing six ATPases (Rpt proteins) and two non-ATPases (Rpn1, Rpn2), and a "lid" subunit composed of eight stoichiometric proteins (Rpn3, Rpn5, Rpn6, Rpn7, Rpn8, Rpn9, Rpn11, Rpn12) . Additional non-essential and species specific proteins may also be present. The 19S unit performs several essential functions including binding the specific protein substrates, unfolding them, cleaving the attached ubiquitin chains, opening the 20S subunit, and driving the unfolded polypeptide into the proteolytic chamber for degradation. The 26s proteasome and 19S regulator are of medical interest due to their involvement in burn rehabilitation .
Nitrate/nitrite sensing protein (Nitrate/nitrite_sensing)
Type: Domain

The nitrate and nitrite-sensing (NIT) domain is a (~250 aa) sensor domain found in various receptor components of signal transduction pathways from different bacterial lineages . The NIT domain is predicted to be all α-helical in structure .
MAP2/Tau projection (MAP2_projctn)
Type: Domain

This domain is found in the microtubule-associated protein 2 (MAP2)/Tau family of proteins which includes MAP2, MAP4, Tau, and their homologues. All isoforms contain a conserved C-terminal domain containing tubulin-binding repeats (

), and a N-terminal projection domain of varying size. This domain has a net negative charge and exerts a long-range repulsive force. This provides a mechanism that can regulate microtubule spacing which might facilitate efficient organelle transport .
Bacterial transglutaminase-like, N-terminal (Bac_transglu_N)
Type: Domain

This region is found towards the N terminus of various archaeal and bacterial hypothetical proteins. Some of these are annotated as being transglutaminase-like proteins, and in fact contain a transglutaminase-like superfamily domain (

).
Brevis radix (BRX) domain (Brevis_radix_dom)
Type: Domain

This is a short domain, approximately 35 residues in length that is found near the C terminus in a number of plant proteins, being repeated in some members.

It is found in Brevis radix-like proteins. These may act as a regulator of cell proliferation and elongation in the root . It is also found in proteins annotated as involved in disease resistance and in the regulation of chromosome condensation, which also contain other domains with varied functions, such as TIR (

) and FYVE (

) respectively.
Maf transcription factor, N-terminal (Maf_TF_N)
Type: Domain

This region is found in various leucine zipper transcription factors of the Maf family. These are implicated in the regulation of insulin gene expression , in erythroid differentiation , and in differentiation of the neuroretina .
Pro-opiomelanocortin N-terminal (Melanocortin_N)
Type: Domain

This domain represents the N-terminal peptide of pro-opiomelanocortin (NPP). It is thought to represent an important pituitary peptide, given its high yield from pituitary glands, and exhibits a potent in vitro aldosterone-stimulating activity .
Dynein heavy chain, tail (Dynein_heavy_tail)
Type: Domain

Dyneins are described as motor proteins of eukaryotic cells, as they can convert energy derived from the hydrolysis of ATP to force and movement along cytoskeletal polymers, such as microtubules. Dyneins generally contain one to three heavy chains, which belong to the AAA+ superfamily of mechanochemical enzymes . Each heavy chain consists of a flexible N-terminal tail known as the cargo-binding domain and a motor domain which consists of an ATP-hydrolysing AAA+ ring, a flexible microtubule-binding stalk, a linker and a C-sequence . The stalk has an ATP-sensitive microtubule-binding site (MTBD) at its tip , whereas the linker has been suggested to function as a mechanical element for generating dynein's power stroke .

The two categories of dyneins are the axonemal dyneins, which produce the bending motions that propagate along cilia and flagella, and the cytosolic dyneins, which drive a variety of fundamental cellular processes including nuclear migration, organisation of the mitotic spindle, chromosome separation during mitosis, and the positioning and function of many intracellular organelles. Cytoplasmic dyneins contain several accessory subunits ranging from light to intermediate chains.

Dynein heavy chains interact with other heavy chains to form dimers, and with intermediate chain-light chain complexes to form a basal cargo binding unit . The region featured in this family includes the sequences implicated in mediating these interactions . It is thought to be flexible and not to adopt a rigid conformation .
Peptidase S33 tripeptidyl aminopeptidase-like, C-terminal (Pept_S33_TAP-like_C)
Type: Domain

This entry represents a C-terminal domain associated with putative hydrolases and bacterial peptidases that belong to MEROPS peptidase family S33 (clan SC). They are related to a tripeptidyl aminopeptidase from Streptomyces lividans (

). A member of this family (

) is thought to be involved in the C-terminal processing of propionicin F, a bacteriocidin characterised from Propionibacterium freudenreichii .
Group II intron, maturase-specific (Mat_intron_G2)
Type: Domain

This region is found mainly in various bacterial and archaeal species, but a few members of this family are expressed by fungal and chlamydomonal species. It has been implicated in the binding of intron RNA during reverse transcription and splicing .
Exportin-1/Importin-beta-like (Exportin-1/Importin-b-like)
Type: Domain

The exchange of macromolecules between the nucleus and cytoplasm takes place through nuclear pore complexes within the nuclear membrane. Active transport of large molecules through these pore complexes require carrier proteins, called karyopherins (importins and exportins), which shuttle between the two compartments.

This domain is found close to the N terminus of yeast exportin 1 (Xpo1, Crm1,

), as well as adjacent to the N-terminal domain of importin-beta (

). Exportin 1 is a nuclear export receptor that translocates proteins out of the nucleus; it interacts with leucine-rich nuclear export signal (NES) sequences in proteins to be transported, as well as with RanGTP . Importin-beta is a nuclear import receptor that translocates proteins into the nucleus; it interacts with RanGTP and importin-alpha, the latter binding with the nuclear localisation signal (NLS) sequences in proteins to be transported .
Ly49-like, N-terminal (Ly49_N)
Type: Domain

The sequences making up this entry are annotated as, or are similar to, Ly49 receptors (e.g.

). These are type II transmembrane receptors expressed by mouse natural killer (NK) cells. They are classified as being activating (e.g.Ly49D and H) or inhibitory (e.g. Ly49A and G), depending on their effect on NK cell function . They are members of the C-type lectin receptor superfamily , and in fact in many family members this region is found immediately N-terminal to a lectin C-type domain (

).
FAE1/Type III polyketide synthase-like protein (FAE1_typ3_polyketide_synth)
Type: Domain

This domain is found in proteins that are described as 3-ketoacyl-CoA synthases, type III polyketide synthases, fatty acid elongases and fatty acid condensing enzymes, and are found in both prokaryotic and eukaryotic (mainly plant) species. The region contains the active site residues, as well as motifs involved in substrate binding .
Dynein heavy chain, linker (Dynein_heavy_linker)
Type: Domain

Dyneins are described as motor proteins of eukaryotic cells, as they can convert energy derived from the hydrolysis of ATP to force and movement along cytoskeletal polymers, such as microtubules. Dyneins generally contain one to three heavy chains, which belong to the AAA+ superfamily of mechanochemical enzymes . Each heavy chain consists of a flexible N-terminal tail known as the cargo-binding domain and a motor domain which consists of an ATP-hydrolysing AAA+ ring, a flexible microtubule-binding stalk, a linker and a C-sequence . The stalk has an ATP-sensitive microtubule-binding site (MTBD) at its tip , whereas the linker has been suggested to function as a mechanical element for generating dynein's power stroke .

The two categories of dyneins are the axonemal dyneins, which produce the bending motions that propagate along cilia and flagella, and the cytosolic dyneins, which drive a variety of fundamental cellular processes including nuclear migration, organisation of the mitotic spindle, chromosome separation during mitosis, and the positioning and function of many intracellular organelles. Cytoplasmic dyneins contain several accessory subunits ranging from light to intermediate chains.

This entry represents the linker of the dynein heavy chain motor domain.
TRASH transcription regulator C-terminal, prokaryotic (TRASH_TR_C_prok)
Type: Domain

This region is found in the C terminus of a number of prokaryotic transcriptional regulators. It is thought to function as a metal-sensing regulatory module .
7TM chemosensory receptor (7TM_chemorcpt)
Type: Family

This family includes a number of insect chemosensory receptors encoded by gustatory receptor (GR) and odorant receptor (OR) genes across the insect tree of life. They are seven-transmembrane ligand-gated ion channels, showing high sequence divergence, consistent with an ancient origin for the family .

This entry also includes some proteins from nematodes such as Egg laying defective protein egl-47 (Probable G-protein coupled receptor egl-47) from Caenorhabditis elegans .
Spider toxin omega agotoxin/Tx1 family (Toxin_34)
Type: Family

The Tx1 family lethal spider neurotoxin induces excitatory symptoms in mice . This family also includes type I, II and III omega-agatoxins .