SII-SWORD/CoKE huggingface dataset:
THSD1, second Ig-like domain (THSD1_D2)
Type: Domain

This domain is found in the human Thrombospondin type-1 domain-containing protein 1 (THSD1) and similar proteins mainly found in vertebrates. THSD1 is involved in endothelial cell to extracellular matrix adhesion . THSD1 forms a multimeric protein complex with FAK/talin/ vinculin, wherein THSD1 promotes talin binding to FAK but not to vinculin, a key step in nascent adhesion assembly . The domain represented by this entry is predicted to adopt Ig-like β-sandwich.

Thrombospondins are multimeric multidomain glycoproteins that function at cell surfaces and in the extracellular matrix milieu. They act as regulators of cell interactions in vertebrates. They are divided into two subfamilies, A and B, according to their overall molecular organisation. The subgroup A proteins TSP-1 and -2 contain an N-terminal domain, a VWFC domain, three TSP1 repeats, three EGF-like domains, TSP3 repeats and a C-terminal domain. They are assembled as trimer. The subgroup B thrombospondins, designated TSP-3, -4, and COMP (cartilage oligomeric matrix protein, also designated TSP-5) are distinct in that they contain unique N-terminal regions, lack the VWFC domain and TSP1 repeats, contain four copies of EGF-like domains, and are assembled as pentamers . EGF, TSP3 repeats and the C-terminal domain are thus the hallmark of a thrombospondin.
THSD1, third Ig-like domain (THSD1_D3)
Type: Domain

This domain is found in the human Thrombospondin type-1 domain-containing protein 1 (THSD1) and similar proteins mainly found in vertebrates. THSD1 is involved in endothelial cell to extracellular matrix adhesion . THSD1 forms a multimeric protein complex with FAK/talin/ vinculin, wherein THSD1 promotes talin binding to FAK but not to vinculin, a key step in nascent adhesion assembly . The domain represented by this entry is predicted to adopt Ig-like β-sandwich.

Thrombospondins are multimeric multidomain glycoproteins that function at cell surfaces and in the extracellular matrix milieu. They act as regulators of cell interactions in vertebrates. They are divided into two subfamilies, A and B, according to their overall molecular organisation. The subgroup A proteins TSP-1 and -2 contain an N-terminal domain, a VWFC domain, three TSP1 repeats, three EGF-like domains, TSP3 repeats and a C-terminal domain. They are assembled as trimer. The subgroup B thrombospondins, designated TSP-3, -4, and COMP (cartilage oligomeric matrix protein, also designated TSP-5) are distinct in that they contain unique N-terminal regions, lack the VWFC domain and TSP1 repeats, contain four copies of EGF-like domains, and are assembled as pentamers . EGF, TSP3 repeats and the C-terminal domain are thus the hallmark of a thrombospondin.
Paratox-like (Paratox-like)
Type: Family

This entry represents the conserved mosaic prophage protein Paratox (

) and related proteins from tailed bacteriophages and profagues from firmicutes. Paratox inhibits the natural competence regulator ComR and serves as a repressor of the competence regulon in vivo . This protein folds into an α/β structure consisting of a three-stranded β-sheet and two α-helices packed on one side of the sheet .
T6SS, Tle3 phospholipase effector, alpha/beta domain (Tle3_ab_dom)
Type: Domain

This entry represents a domain found at the N-terminal end of the type VI secretion system (T6SS) Tle3 phospholipase effector from adherent-invasive Escherichia coli and related proteobacterial proteins. Tle3 has a phospholipase A1 activity and its toxicity is neutralised by the cognate immunity protein Tli3. Tli3 and Tle3 form a stable complex in which a loop of Tli3 inserts deeply in the Tle3 substrate-binding pocket and thus inhibiting its function . This Tle3 domain folds into a globular α/β structure consisting of a central β-sheet and α-helices packed on both sides. It contains the typical nucleophile-elbow motif and structurally resembles classical α/β hydrolase fold but elaborated with a number of large loops.
PH domain (PH_23)
Type: Domain

This domain is found in uncharacterised fungal proteins. It shares significant sequence similarity to known Pleckstrin homology domains (PH-domains) and it is predicted to adopt similar structure. Proteins containing this domain also contain a DH-domain located N-terminal to the PH-domain and are likely members of the Dbl family of guanine nucleotide exchange factors.
PH domain, EVH1-like (PH_24)
Type: Domain

This domain is found in uncharacterised fungal proteins. It shares significant sequence similarity to known Pleckstrin homology domains (PH-domains), particularly to the EVH1 domain of the regulatory subunit 3 of Phosphoprotein phosphatase 4 PP4 (known as Falafel), and it is predicted to adopt a similar structure.
FIGL1, N-terminal domain (FIGL1_N)
Type: Domain

This domain is found N-terminal in the ATPase family AAA domain-containing protein FIGL1 from Arabidopsis thaliana and similar plant proteins. FIGL1 is involved in DNA double-strand break repair via homologous recombination (HR). This protein Limits class II meiotic crossover formation by regulating the invasion step of meiotic HR . This domain is predicted to fold into a three-helical bundle and precedes the AAA domain

and separated from it via a disordered linker.
Neuron-derived neurotrophic factor, N-terminal domain (NDNF_N)
Type: Domain

This domain is found N-terminal in human Neuron-derived neurotrophic factor (NDNF) and similar animal proteins. NDNF is a secretory protein that plays a role in various cellular processes . It acts as a chemorepellent on gonadotropin-releasing hormone expressing neurons regulating their migration to the hypothalamus . It also promotes neuron migration, growth and survival as well as neurite outgrowth and is involved in the development of the olfactory system . The domain represented by this entry is predicted to fold into a β-sandwich that has some similarity to Nucleoplasmin-like fold.
PARP12, winged helix domain (WH_PARP12)
Type: Domain

This domain is found at the N-terminal of human Protein mono-ADP-ribosyltransferase PARP12 and similar proteins from vertebrates. PARP12 is a mono-ADP-ribosyltransferase that mediates mono-ADP-ribosylation of target proteins . The domain represented by this entry has a detectable sequence similarity to HTH winged helix domains and it is predicted to adopt similar structure.
ABC transporter, TMD0 domain (TMD0_ABC)
Type: Domain

This transmembrane domain is found N-terminal in a number of ATP-binding cassette (ABC) transporters from animals and fungi. It is composed of four or five helices arranged in a bundle.
ABCC10-like, N-terminal domain (ABCC10-like_N)
Type: Domain

This domain is found N-terminal in the ABC transporter C family member 10 (ABCC10) from Arabidopsis thaliana and related proteins. ABCC10 is likely to pump for glutathione S-conjugates. This is a transmembrane domain whose function is unknown.
TMEM62, Ig-like domain (Ig_TMM62)
Type: Domain

This domain is found in the human Transmembrane protein 62 (TMEM62), uncharacterised At3g03305 protein from Arabidopsis thaliana and related eukaryotic proteins. TMEM62 has been identified as a potential therapeutic target to enhance survival from high-grade serous carcinomas . The domain represented by this entry is predicted to fold into a β-sandwich with an Ig-like topology. It is frequently found associated with

.
TMEM62, C-terminal domain (TMEM62_C)
Type: Domain

This domain is found C-terminal in the human Transmembrane protein 62 (TMEM62), the uncharacterised At3g03305 protein from Arabidopsis thaliana and related eukaryotic proteins. TMEM62 has been identified as a potential therapeutic target to enhance survival from high-grade serous carcinomas . The domain represented by this entry is likely transmembrane and composed of α-helices. It is frequently found associated with

and

. This domain is also found covering the whole length of the protein in the uncharacterised protein YKR040C from Saccharomyces cerevisiae.
VNG_1110C-like (VNG_1110C-like)
Type: Family

This entry represents a family of archaeal uncharacterised proteins, including VNG_1110C protein from Halobacterium salinarum. These proteins are predicted to adopt a globular structure consisting of three-stranded antiparallel β-sheet and two α-helices packed on one side of the sheet. They contain two semi-conserved RDSTQ and RIIGSP sequence motifs.
Nuclear pore complex protein GP210, Ig-like domain 15 (Ig_GP210_15th)
Type: Domain

This domain is found in the Nuclear pore complex protein GP210 from Arabidopsis thaliana and related plant proteins. GP210 is predicted to contain 16 Ig-like domains. This entry represents the 15th of these domains.
Nuclear pore complex protein GP210, C-terminal Ig-like domain (Ig_GP210_16th)
Type: Domain

This domain is found in the Nuclear pore complex protein GP210 from Arabidopsis thaliana and related plant proteins. GP210 is predicted to contain 16 Ig-like domains. This entry represents the 16th of these domains.
NFXL1, RRM-like domain (RRM_NFXL1)
Type: Domain

This domain is found in NF-X1-type zinc finger protein NFXL1 from Arabidopsis thaliana and related plant proteins. AtNFXL1, a homologue of the human transcription repressor NF-X1, plays an important role in the trichothecene response, as well as the general defence response in Arabidopsis . This domain has a detectable sequence similarity to known RRM domains and it is predicted to adopt similar structure.
INTS4, 8 helical bundle domain (INTS4_8HBD)
Type: Domain

This domain is found in human Integrator complex subunit 4 (INTS4) and its animal homologues. The domain represented by this entry makes extensive contacts with INTS7 and stabilise the beta-CASP domain of INTS9 in the cleavage module . It folds into an eight α-helical bundle.

INTS4 is a component of the Integrator complex which plays essential roles in snRNA 3' end processing and transcription termination . INTS4 along with INTS9 and INTS11 constitute the Integrator cleavage module, which contains endonuclease activity and resembles the cleavage module of the cleavage and polyadenylation specific factor required for 3' processing of mRNA transcripts.
PCA1, HMA heavy metal-associated domain (HMA_PCA1)
Type: Domain

This domain is found in the yeast P-type cation-transporting ATPase (PCA1) and similar fungal proteins. PCA1 is a cadmium transporting P-type ATPase which plays a critical role in cadmium resistance by extruding intracellular cadmium . This domain has a detectable similarity to heavy-metal-binding domains and it is predicted to adopt similar structure.
ANKLE2, third alpha/beta domain (ANKLE2_3rd)
Type: Domain

This domain is found in the human Ankyrin repeat and LEM domain-containing protein 2 (ANKLE2) and related proteins. Human ANKLE2 is involved in mitotic nuclear envelope reassembly by promoting dephosphorylation of BAF/BANF1 during mitotic exit . The domain represented by this entry is predicted to adopt a globular α/β structure consisting of a five-stranded antiparallel β-sheet and helices packed on one side of it.
YunG-like (YunG-like)
Type: Family

This entry represents the uncharacterised Bacillus subtilis YunG protein and its homologues. Members of this entry contain a potential catalytic triad composed of Cys, His and Asp residues.
Phage YunG-like (Phage_YunG-like)
Type: Family

This entry represents a small family of uncharacterised phage and prophage proteins. These proteins show structural similarity to the B. subtilis YunG protein and appear to conserve a putative catalytic triad of cys, his and asp. Structure predictions suggest that these proteins may form homodimers.
POF1B, helix-loop-helix domain (POF1B_HlH)
Type: Domain

This domain is found in human protein POF1B and its homologues. Human POF1B plays a key role in the organization of epithelial monolayers by regulating the actin cytoskeleton . This domain is predicted to adopt a structure consisting of two helices connected by a loop region. The function of this domain is unknown but mutation of a conserved arginine 329 in human is associated with premature ovarian failure. This point mutation reduces the capacity of the mutant protein to bind non-muscle actin filaments .
E3 ubiquitin-protein ligase listerin, HEAT-repeats region (LTN1_HEAT_5th)
Type: Domain

This entry represents a putative HEAT repeats region from the LTN1 family of proteins. The LTN1 family consists of E3 ubiquitin-protein ligases that are integral components of the ribosome quality control complex (RQC) . The RQC is a ribosome-associated complex responsible for the ubiquitination and subsequent extraction of incompletely synthesized nascent polypeptides for proteasomal degradation. Members of the LTN1 family are recruited to stalled 60S ribosomal subunits, often by NEMF, to mediate the ubiquitination of stalled nascent chains. This ubiquitination event is crucial for the recruitment of VCP/p97 or CDC48, which facilitates the extraction and degradation of the incomplete translation products. In some species, LTN1 proteins also ubiquitinate proteins derived from mRNAs lacking stop codons or translation arrest products induced by specific sequences. Additionally, they may play a role in chromatin function and transcription regulation indirectly.
TASOR, PIN domain (PIN_TASOR)
Type: Domain

This is a domain found in TASOR proteins, a key component of the HUSH complex, a vertebrate-specific multiprotein complex that mediates epigenetic repression of both exogenous and endogenous genetic elements . The HUSH complex regulates H3K9me3 deposition by promoting recruitment of SETDB1 and also recruits MORC2 to compact chromatin . TASOR is crucial in early embryonic development and contains a catalytically-inactive PARP domain, necessary for epigenetic regulation of target elements. This entry represents a PIN domain found towards the C terminus of TASOR and TASOR2 and shares detectable similarity to the PIN domain of SMG5.
TASOR, alpha/beta domain (TASOR_ab_dom)
Type: Domain

This is a domain found in TASOR proteins, a key component of the HUSH complex, a vertebrate-specific multiprotein complex that mediates epigenetic repression of both exogenous and endogenous genetic elements . The HUSH complex regulates H3K9me3 deposition by promoting recruitment of SETDB1 and also recruits MORC2 to compact chromatin . TASOR is crucial in early embryonic development and contains a catalytically-inactive PARP domain, necessary for epigenetic regulation of target elements.

This entry represents an α/β domain found towards the C terminus of TASOR and TASOR2 which consist of four β-sheets and short α-helices.
DEAH11/12, RRM domain (RRM_DEAH11/12)
Type: Domain

This RNA recognition motif (RRM) containing domain is found in the ATP-dependent RNA helicase DEAH11, DEAH12 from Arabidopsis thaliana and related plant proteins. This domain shares detectable similarity to RNA binding domains and is predicted to adopt an α/β structure with similar topology.
DEAH11/12, KH-domain (KH_DEAH11/12)
Type: Domain

This presumed KH domain is found in ATP-dependent RNA helicase DEAH11 and DEAH12 from Arabidopsis thaliana and similar sequences from plants and animals. Its specific function is unknown.
DEAH11/12, type I KH-domain (KH_DEAH11/12_1st)
Type: Domain

This domain is found in the ATP-dependent RNA helicase DEAH11 and DEAH12 from Arabidopsis thaliana and related plant proteins. This domain shares detectable similarity to type I KH domains and is predicted to adopt an α/β structure with similar topology.
DEAH11/12, second type I KH-domain (KH_DEAH11/12_2nd)
Type: Domain

This domain is found in the ATP-dependent RNA helicase DEAH11 and DEAH12 from Arabidopsis thaliana and related plant proteins. This domain shares detectable similarity to type I KH domains and is predicted to adopt an α/β structure with similar topology.
DEAH11/12, RNA-binding domain (RBD_DEAH11/12)
Type: Domain

This presumed RNA binding domain (RBD) is found in ATP-dependent RNA helicase DEAH11 and DEAH12 from Arabidopsis thaliana and similar sequences from plants. Its specific function is unknown.
Archaeo-eukaryotic primase 1D-like (AEP-like)
Type: Family

This entry represents a nucleotidyltransferase of the archaeo-eukaryotic primase superfamily predicted to produce an oligo/cyclic nucleotide signal that activates the associated effectors in the associated prokaryotic antiviral immunity system. These proteins feature a single aspartate in the DXD active site .
Arm-like repeat domain (Arm_rpt_dom)
Type: Domain

This entry represents a region of α-solenoid repeats found in a group of fungal proteins. This domain is sometimes found at the N-terminal end of the proteins followed by a NACHT domain

.
Alfy-like, armadillo-like repeat domain (Alfy-like_Arm-like)
Type: Domain

This entry represents a region of armadillo-like repeats found in human WD repeat and FYVE domain-containing protein 3 (WDFY3, also known as Alfy) and similar eukaryotic sequences. Alfy is required for selective macroautophagy (aggrephagy) . It is important for normal brain development .

This domain is also found in BEACH domain-containing protein lvsA involved in myosin-independent cytokinesis and early steps of phagocytosis . Another proteins containing this domain is SPIRRIG which is involved in cell morphogenesis .
At2g29880-like, C-terminal domain (At2g29880-like_C)
Type: Domain

This domain is found C-terminal in Uncharacterized protein At2g29880 from Arabidopsis thaliana and related plant proteins. Some proteins containing this domain have also a Myb/SANT-like domain (

) at the N terminus. The function of this domain is unknown.
At5g58720/SDE5-like, UBA-like domain (At5g58720/SDE5-like_UBA-like)
Type: Domain

This domain is found towards the N-terminal of SMR domain-containing protein At5g58720, Putative nuclear RNA export factor SDE5 from Arabidopsis thaliana and similar plant proteins. SDE5 is involved in sense transgene post-transcriptional gene silencing . This domain has detectable similarity to UBA domains, particularly to CUE domain. It is predicted to be composed of an α-helical bundle.
Cartilage intermediate layer protein 1/2 domain (CILP-1/2_dom)
Type: Domain

This domain is found in human human Cartilage intermediate layer protein 1/2 (CILP-1/2) and similar sequences mainly found in vertebrates. It is predicted to adopt an all-β structure and is often found immediately C-terminal to

.

CILP-1 is thought to play a role in cartilage scaffolding. CLIP-1 may act by antagonising TGF-beta1 (TGFB1) and IGF1 functions. It can suppress IGF1-induced proliferation and sulphated proteoglycan synthesis, and inhibits ligand-induced IGF1R autophosphorylation . It has been suggested to inhibit TGFB1-mediated induction of cartilage matrix genes through its interaction with TGFB1 . Overexpression may lead to impair chondrocyte growth and matrix repair and indirectly promote inorganic pyrophosphate (PPi) supersaturation in ageing and osteoarthritis cartilage. CLIP2 gene seems to be down-regulated osteoarthritic cartilage .
Cartilage intermediate layer protein 1/2, beta-sandwich domain 2 (CILP-1/2_b-sand_dom2)
Type: Domain

This domain is found in human human Cartilage intermediate layer protein 1/2 (CILP-1/2) and similar sequences mainly found in vertebrates. It is predicted to show a seven stranded β-sandwich fold.

CILP-1 is thought to play a role in cartilage scaffolding. CLIP-1 may act by antagonising TGF-beta1 (TGFB1) and IGF1 functions. It can suppress IGF1-induced proliferation and sulphated proteoglycan synthesis, and inhibits ligand-induced IGF1R autophosphorylation . It has been suggested to inhibit TGFB1-mediated induction of cartilage matrix genes through its interaction with TGFB1 . Overexpression may lead to impair chondrocyte growth and matrix repair and indirectly promote inorganic pyrophosphate (PPi) supersaturation in ageing and osteoarthritis cartilage. CLIP2 gene seems to be down-regulated osteoarthritic cartilage .
Cartilage intermediate layer protein 1/2, beta-sandwich domain (CILP-1/2_8th)
Type: Domain

This domain is found in human Cartilage intermediate layer protein 1/2 (CILP-1/2) and similar sequences mainly found in vertebrates. CILP-1 is thought to play a role in cartilage scaffolding. CLIP-1 may act by antagonising TGF-beta1 (TGFB1) and IGF1 functions. It can suppress IGF1-induced proliferation and sulfated proteoglycan synthesis, and inhibits ligand-induced IGF1R autophosphorylation . It has been suggested to inhibit TGFB1-mediated induction of cartilage matrix genes through its interaction with TGFB1 . Overexpression may lead to impair chondrocyte growth and matrix repair and indirectly promote inorganic pyrophosphate (PPi) supersaturation in ageing and osteoarthritis cartilage. CLIP2 gene seems to be down-regulated osteoarthritic cartilage . This domain, which is predicted to adopt a β-sandwich structure.
Cartilage intermediate layer protein 1/2, C-terminal (CILP-1/2_C)
Type: Domain

This domain is found at the C-terminal of human Cartilage intermediate layer protein 1/2 (CILP-1/2) and similar sequences mainly found in vertebrates. It may adopt a β-sandwich fold.

CILP-1 is thought to play a role in cartilage scaffolding. CLIP-1 may act by antagonising TGF-beta1 (TGFB1) and IGF1 functions. It can suppress IGF1-induced proliferation and sulphated proteoglycan synthesis, and inhibits ligand-induced IGF1R autophosphorylation . It has been suggested to inhibit TGFB1-mediated induction of cartilage matrix genes through its interaction with TGFB1 . Overexpression may lead to impair chondrocyte growth and matrix repair and indirectly promote inorganic pyrophosphate (PPi) supersaturation in ageing and osteoarthritis cartilage. CLIP2 gene seems to be down-regulated osteoarthritic cartilage .
Caspase-8, N-terminal domain (Dredd_N)
Type: Domain

This domain is found at the N-terminal of Caspase-8 from Drosophila melanogaster (Dredd) and similar proteins mainly found in insects. Dredd is an effector of the programmed cell death (PCD) activators rpr, grim and hid . It plays a role in the innate immune response and may be involved in apoptosis in the germline as well as soma . It plays a role in the innate immune response, it is required for resistance to Gram-negative bacterial infection . These proteins have a caspase domain (

) at the C-terminal. This domain is predicted to adopt an all-α configuration.
Caspase-8, second domain (Dredd_2nd)
Type: Domain

This domain is found adjacent the N-terminal domain of Caspase-8 from Drosophila melanogaster (Dredd) and similar proteins mainly found in insects. Dredd is an effector of the programmed cell death (PCD) activators rpr, grim and hid . It plays a role in the innate immune response and may be involved in apoptosis in the germline as well as soma . It plays a role in the innate immune response, it is required for resistance to Gram-negative bacterial infection . These proteins have a caspase domain (

) at the C-terminal. This domain is predicted to adopt an all-α configuration.
1,3-beta-glucan synthase component FKS1-like, domain-2 (FKS1-like_dom2)
Type: Domain

This domain is found in 1,3-beta-glucan synthase component FKS1 from Saccharomyces cerevisiae and similar fungal proteins. FKS1 is involved in cell wall synthesis, maintenance and remodelling. This domain is predicted to adopt an all-α structure . This domain is often found between

and

.
16S rRNA (adenine(1408)-N(1))-methyltransferase (NpmA)
Type: Family

This entry represents the 16S rRNA (adenine(1408)-N(1))-methyltransferase from Escherichia coli (NPMA) and similar bacterial proteins. NPMA specifically methylates the N1 position of adenine 1408 in 16S rRNA and confers resistance to various aminoglycosides, including kanamycin, neomycin, apramycin, ribostamycin and gentamicin .
26S proteasome regulatory subunit RPN11, C-terminal domain (RPN11_C)
Type: Domain

This entry represents the C-terminal helical domain of Ubiquitin carboxyl-terminal hydrolase RPN11 from Saccharomyces cerevisiae, its animal homologue 26S proteasome non-ATPase regulatory subunit 14 (also named RPN11) and similar eukaryotic 26S proteosomal subunits. This region is involved in forming a helical bundle with other RPN subunits to help with assembly of the proteosome lid .