SII-SWORD/CoKE huggingface dataset:
Nakanori-like (Nakanori)
Type: Family

This entry include the Nakanori, nontoxic mushroom protein that specifically binds to a complex of sphingomyelin, a major sphingolipid in mammalian cells, and cholesterol .
T6SS, immunity protein Tgi2PP (T6SS_Tgi2PP)
Type: Family

This protein family includes immunity protein Tgi2PP from Pseudomonas fluorescens (PFL_3036) (

), the immunity component of an effector immunity pair secreted by the type VI secretion system (T6SS) of this bacteria. Its structure consists of a short N-terminal 3-10 helix and a central five-stranded β-sheet flanked by three α-helices (

) .
Actin homologue MreB-like, C-terminal (MreB-like_C)
Type: Domain

Archaeal actin homologue Ta0583 is an active ATPase at physiological temperatures, which has a propensity to form filaments . It has the core actin structure and is highly homologous to MreB and ParM from bacteria . This entry represents the C-terminal actin-like domain .
Acanthaporin (Acanthaporin)
Type: Domain

This entry represents a domain found in acanthaporin, a pore-forming toxin from acanthamoebae, an opportunistic pathogen. This protein is cytotoxic for neuronal cells in humans and shows antimicrobial activity against diverse bacterial strains by permeabilising their membranes. It folds into a disulfide-bonded four-α-helix monomeric structure that dimerises at pH 8.0 due to the deprotonation of some histidine residues, which leads to a conformational change .
MRB1590-like, C-terminal domain (MRB1590-like_C)
Type: Domain

This entry represents the C-terminal helix-turn-helix like domain from the T. brucei kRNA editing factor MRB1590 .
T6SS, Immune protein Tsi2-like (T6SS_Tsi2-like)
Type: Family

This protein family includes immune protein Tsi2 (also known as Anti-toxin protein Tsi2) from Pseudomonas aeruginosa and similar sequences predominantly found in proteobacteria. Tsi2 is a immunity protein that plays a role in preventing early activation of toxin Tse2, which is transported via the type VI secretion system (T6SS). It binds to a large surface of Tse2 and thereby occludes the active site to specifically inhibit Tse2. Tsi2 forms a dimeric structure. Each monomer consists of two large α-helices arranged as an anti-parallel coiled-coil connected by a short turn (

) .
Mannose-6-phosphate isomerase, cupin domain (MPI_cupin_dom)
Type: Domain

This domain is found in Mannose-6-phosphate isomerase from bacteria, including Archaeoglobus fulgidus (MPI), Salmonella typhimurium, Escherichia coli among others. This enzyme catalyses the interconversion of mannose 6-phosphate and fructose 6-phosphate . This entry represents the C-terminal domain, which is found associated with

. This domain shows an all-β structure.
Maintenance of Photosystem II under High light 2, C-terminal domain (MPH2_C)
Type: Domain

This is a C-terminal helical domain found in chloroplast thylakoid lumenal proteins, including Maintenance of Photosystem II under High light 2 (also known as Thylakoid lumenal 16.5 kDa protein,

) from Arabidopsis thaliana. MPH2 is required for the adaptation of this organism to photo inhibitory light and fluctuating light environments .
Type VI secretion system spike protein VgrG3-like, C-terminal (T6SS_VgrG3-like_C)
Type: Domain

This domain is found in a group of proteins from tailed bacteriophages and prophages mainly found in proteobacteria and firmicutes, including Type VI secretion system spike protein VgrG3 from Vibrio cholerae (

). VgrG3 degrades the peptidoglycan cell wall of rival bacteria via its C-terminal region through its muramidase activity. This domain adopts a canonical T4-lysozyme-like fold showing eight α-helices and two 3-10 helices, which pack against a three-stranded antiparallel β-sheet (

) .
Acetyl-CoA carboxylase, BT domain (ACCA_BT)
Type: Domain

This is the BC-CT interaction domain (BT) which is between the BC (biotin carboxylase, which catalyses the MgATP-dependent carboxylation of N1' atom of biotin) and BCCP (biotin carboxyl carrier protein) domains of acetyl-CoA carboxylase. This domain helps to mediate interactions between the BC and CT (carboxyltransferase) domains .
Helicase MOV-10, N-terminal (MOV-10_N)
Type: Domain

Helicase MOV-10 is a 5'-3' RNA helicase required for RNA-mediated gene silencing by the RNA-induced silencing complex (RISC) [1-3]. It is involved in mRNA metabolism and translation, modulation of viral infectivity, inhibition of retrotransposition and regulation of synaptic transmission . It interacts with FMRP1 and regulates miRNA-mediated translational repression by AGO2 .

This entry represents the N-terminal domain of MOV-10, whose function is not known. According to structure predictions, it may consist in a helix-turn-helix domain which suggests a likely DNA-binding function.
Acetyl-CoA carboxylase (ACCA)
Type: Family

This family includes Acetyl-CoA carboxylases, such as acetyl-CoA carboxylase 1 (also known as acetyl-Coenzyme A carboxylase alpha, ACACA), which is cytosolic and acetyl-CoA carboxylase 2 (also known as ACC-beta), which is mitochondrial. These enzymes catalyse the carboxylation of acetyl-CoA to malonyl-CoA, the first and rate-limiting step of de novo fatty acid biosynthesis . This is a 2 steps reaction starting with the ATP-dependent carboxylation of the biotin carried by the biotin carboxyl carrier (BCC) domain, followed by the transfer of the carboxyl group from carboxylated biotin to acetyl-CoA .
Helicase MOV-10, Ig-like domain (MOV-10_Ig-like)
Type: Domain

Helicase MOV-10 is a 5'-3' RNA helicase required for RNA-mediated gene silencing by the RNA-induced silencing complex (RISC) [1-3]. It is involved in mRNA metabolism and translation, modulation of viral infectivity, inhibition of retrotransposition and regulation of synaptic transmission . It interacts with FMRP1 and regulates miRNA-mediated translational repression by AGO2 .

The function of this domain is unknown. According to structure predictions, it seems to adopt an Ig-like fold.
ESX-1 secretion system protein EccA1-like, N-terminal domain (T7SS_EccA1-like_N)
Type: Domain

This domain is found at the N-terminal end of ESX-1 secretion system protein EccA1 from Mycobacterium tuberculosis (

) and similar proteins predominantly from Actinobacteria. EccA1 is part of the ESX-1 specialised secretion system (a cluster of the type VII secretion system, T7SS). EccA1 contains a C-terminal ATPase domain (

and

) and a tetratricopeptide repeat (TPR) containing N-terminal domain, represented in this entry. The six tandem TPR motifs of this domain, packed in parallel, create a series of repeating antiparallel α-helices that give rise to an overall superhelix structure (

) .
Helicase MOV-10, helical domain (Mov-10_helical)
Type: Domain

Helicase MOV-10 is a 5'-3' RNA helicase required for RNA-mediated gene silencing by the RNA-induced silencing complex (RISC) [1-3]. It is involved in mRNA metabolism and translation, modulation of viral infectivity, inhibition of retrotransposition and regulation of synaptic transmission . It interacts with FMRP1 and regulates miRNA-mediated translational repression by AGO2 . This is a presumed helical domain found between

and

.
Helicase MOV-10-like, beta-barrel domain (MOV-10-like_beta-barrel)
Type: Domain

Helicase MOV-10 is a 5'-3' RNA helicase required for RNA-mediated gene silencing by the RNA-induced silencing complex (RISC) [1-3]. It is involved in mRNA metabolism and translation, modulation of viral infectivity, inhibition of retrotransposition and regulation of synaptic transmission . It interacts with FMRP1 and regulates miRNA-mediated translational repression by AGO2 .

This entry represents a presumed domain found in MOV-10 and similar sequences from animals, plants and fungi, which, according to structure predictions, it seems to form a β-barrel, closely related to the OB fold. This domain is found prior to the helicase domain.
Uncharacterized ATP-binding protein MJ1010-like, C-terminal domain (MJ1010-like_2nd)
Type: Domain

This domain is found at the C-terminal of a group of uncharacterised proteins that belong to the archaeal AAA+ ATPase superfamily, including MJ1010 from Methanocaldococcus jannaschii. This domain is usually found associated with

.
Putative T7SS secretion signal domain (T7SS_signal)
Type: Domain

This α-helical domain is likely to mediate secretion via a type VII secretion system due to similarity to

. Proteins containing this domain are found primarily in Actinomycetes.
TACO1/YebC-like, N-terminal domain (TACO1_YebC_N)
Type: Domain

This entry represents the N-terminal helical bundle domain from proteins in the TACO1/YebC family, which are thought to act as transcriptional regulators. In mammals, TACO1 protein activates the translation of mitochondriallye-ncoded COX1 . In bacteria, it negatively regulates the quorum-sensing response regulator by binding to its promoter region . This domain consists of three α-helices arranged in a bundle (

).
Excretory-secretory protein 2 (AceES-2)
Type: Family

This entry includes a group of proteins from nematodes, including Excretory-secretory protein 2 from Ancylostoma ceylanicum (AceES-2), a highly immunoreactive molecule secreted by adult worms at the site of intestinal attachment. AceES-2 folds into a five-stranded β-barrel flanked by short N- and C-terminal α-helices that lie parallel to each other on one side of the β-barrel, adopting a netrin-like (NTR) domain, similar to the C-terminal domain of netrins .
Cas3 inhibitor AcrF3-like (AcrF3-like)
Type: Family

AcrF3, a protein encoded by gene 35 from phage JBD5, has been reported to specifically inhibit the Cas3 protein of the P. aeruginosa PA14 strain (PaCas3) and to counteract the type I-F CRISPR-Cas system . AcrF3 eluted as a dimer in gel-filtration chromatography . In the complex structure, AcrF3 binds to PaCas3 at a ratio of 2:1, suggesting that AcrF3 functions as a homodimer that inhibits PaCas3 . A single AcrF3 molecule has a two-layer architecture with six α-helices .
TadZ-like, receiver domain (TadZ-like_ARD)
Type: Domain

This domain is found at the N-terminal of TadZ from Eubacterium rectale and similar bacterial proteins. TadZ is is an essential component of the Tad secretion system that probably functions as a localization factor. This protein is composed of two domains, both of which have lost its active sites. This entry represents the N-terminal atypical receiver domain (ARD), which is structurally similar to the RD of response regulators such as the chemotaxis protein CheY (

) .
TAF1C, beta-propeller domain (TAF1C_beta-prop)
Type: Domain

This is the β-propeller domain of TAF1C from mammals, the orthologue of yeast Rrn6 . TAF1C is a component of the transcription factor SL1/TIF-IB complex which is involved in the assembly of the PIC (preinitiation complex) during RNA polymerase I-dependent transcription .
Anti-CRISPR protein Acr30-35/AcrF1 (Acr30-35_AcrF1)
Type: Family

Pseudomonas phages have diverse anti-CRISPR (Acr) proteins that subvert the immune systems in their hosts. These systems depend on a CRISPR RNA (crRNA)-guided surveillance complex (Csy) for the degradation of foreign DNA. This family represents AcrF1, which inhibits DNA recognition of the Csy complex by interfering with base pairing between the DNA target strand and crRNA spacer. AcrF1 can use different mechanisms to block target DNA recognition .
TAF1C, C-terminal domain (TAF1C_C)
Type: Domain

This is the C-terminal domain of TAF1C (TATA box-binding protein-associated factor RNA polymerase I subunit C) from mammals, the orthologue of yeast Rrn6 . TAF1C is a component of the transcription factor SL1/TIF-IB complex, which is involved in the assembly of the PIC (preinitiation complex) during RNA polymerase I-dependent transcription .
TAF1C, helical bundle domain (TAF1C_HB)
Type: Domain

This is the helical bundle domain (HB, also referred to as the headlock domain) of TATA box-binding protein-associated factor RNA polymerase I subunit C (TAF1C) from animals, the orthologue of yeast Rrn6 . TAF1C is a component of the transcription factor SL1/TIF-IB complex, which is involved in the assembly of the PIC (preinitiation complex) during RNA polymerase I-dependent transcription .
MIOS-like, alpha-solenoid domain (MIOS_a-sol)
Type: Domain

GATOR complex protein MIOS, a component of the GATOR subcomplex GATOR2 which consists of MIOS, SEC13, SEH1L, WDR24 and WDR59, that activates mTORC1 and the TORC1 signaling pathway through the inhibition of the GATOR1 subcomplex . Sea4 is the counterpart from yeast, a component of the SEA complex which coats the vacuolar membrane and is involved in intracellular trafficking, autophagy, response to nitrogen starvation, and amino acid biogenesis . This entry represents a region between the WD40 and the zinc ribbon-like domains, which may have an α-solenoid structure.
Msx2-interacting protein, nuclear receptor-interacting domain (MINT_RID)
Type: Domain

This entry represents the nuclear receptor-interacting domain (RID) from Msx2-interacting protein (MINT), a widely expressed transcription repressor that regulates key transcription effectors in several signalling pathways , including MSX2, RBP-J, and nuclear receptors. This entry covers the C-terminal end of the RID domain described in .
Msx2-interacting protein, RAM7 domain (MINT_RAM7)
Type: Domain

This is the RBP-J binding domain (RAM7) found in the central region of Msx2-interacting protein (MINT), a widely expressed transcription repressor that regulates key transcription effectors in several signalling pathways , including MSX2, RBP-J, and nuclear receptors. Structure predictions from AlphaFold suggest that this domain adopts a β-solenoid structure which includes VNVLTGP/VNVLTTP repeats. RAM7 domain from MINT competes with the RAM domain of Notch for physical interaction with RBP-J . Through this domain, MINT sequesters and prevents RBP-J DNA binding thus, precluding trans-activation directed by the RBP-J coadapter, Notch1 intracellular domain .
Msx2-interacting protein, MID domain (MINT_MID)
Type: Domain

This is the Msx2-interacting domain (MID) found in Msx2-interacting protein (MINT), a widely expressed transcription repressor that regulates key transcription effectors in several signalling pathways , including MSX2, RBP-J, and nuclear receptors. This domain provides core activation functions to MINT; it confers OCFRE (osteocalcin (OC) FGF response element) activation .
Mimivirus sulfhydryl oxidase R596-like, C-terminal domain (MIMI_R596-like_C)
Type: Domain

This domain is found at the C-terminal of the FAD-linked sulfhydryl oxidase R596 from Acanthamoeba polyphaga mimivirus (APMV) and similar proteins predominantly found in giant viruses. This protein is a member of the Erv family of sulfhydryl oxidases. This domain folds into six α-helices forming a compact domain .
Mitochondrial dynamics protein MID51-like, C-terminal domain (MID51-like_C)
Type: Domain

This entry represents the cytosolic domain of mitochondrial dynamics protein MID51 and similar proteins predominantly found in vertebrates. MID51 promotes the recruitment and association of the fission mediator dynamin-related protein 1 (DNM1L) to the mitochondrial surface to drive mitochondrial fission. This entry represents the cytosolic domain, which adopts a nucleotidyltransferase fold with a mixed α/β topology configured into two lobes separated by a deep cleft .
Microneme protein MIC5-like domain (MIC5-like)
Type: Domain

Microneme protein MIC5 is found in Apicomplexa and expressed as a preproprotein which is proteolytically processed to a proprotein by the signal peptidase before being further processed in a post-Golgi compartment to the mature protein . The structure of MIC5 was determined in Toxoplasma gondii and it revealed that it is a subtilisin propeptide mimic and a potent inhibitor of TgSUB1 . This protein adopts a subtilisin-like prodomain structure, which consists of an open-sandwich antiparallel-α/antiparallel-β fold .
Gag polyprotein, C-terminal (Gag_C)
Type: Domain

This entry corresponds to the C-terminal region of Gag polyprotein from Spumaviruses, which contains a chromatin binding sequence (CBS) and GR boxes .

The Gag polyprotein is a core viral polyprotein that undergoes specific enzymatic cleavages in vivo to yield the mature protein. It is involved in capsid formation and genome binding. Shortly after infection, interaction between incoming particle-associated Gag proteins and host dynein allows centrosomal targeting of the viral genome (associated to Gag), prior to nucleus translocation and integration into host genome .
TET-Associated Glycosyltransferase (TAGT)
Type: Domain

This entry represents a Family 2/fringe-like glycosyltransferase domain that is found in DNA-modifying proteins of phages and eukaryotes . The name TAGT is derived from phage versions that are operonic with TET/JBP-dioxygenases . In kinetoplastids, the TAGT enzyme catalyses the second step in forming the hypermodified base J . The vertebrate GREB1 protein appears to catalyse the O-GlcNAcylation of ERalpha, protecting it from ubiquitination-based degradation .
Gp67, N-terminal domain (Gp67_N)
Type: Domain

Gp67 from Staphylococcus virus G1 (

, also known as ORF067) binds to the sigma(A)-subunit of the RNA polymerase (RNAP) of its host to block cell growth by inhibiting transcription. This protein is organized in two domains, an N-terminal β-sheet-rich domain (this entry) and a C-terminal α-helical domain, which are connected by a linker-α-helix on the surface of gp67 opposite the interaction surface .
Gp67, C-terminal domain (Gp67_C)
Type: Domain

Gp67 from Staphylococcus virus G1 (

, also known as ORF067) binds to the sigma(A)-subunit of the RNA polymerase (RNAP) of its host to block cell growth by inhibiting transcription. This protein is organized in two domains, an N-terminal β-sheet-rich domain (

) and a C-terminal α-helical domain, which are connected by an α-helical linker on the surface of gp67 opposite the interaction surface . This entry includes the C- terminal domain and the helical linker .
Tail spike protein-like, C-terminal domain (Tail_spike-like_C)
Type: Domain

This entry represents the C-terminal domain of Tail spike protein from Shigella phage Sf6 (

). This protein specifically mediates the attachment to their hosts. Its structure revealed a conserved architecture with a central, right-handed β-helix. The C-terminal domain adopts a β-sandwich fold and is reminiscent of viral capsid proteins (

) .
Emaravirus ABC_C protein (ABC_C)
Type: Family

This family corresponds to the ABC proteins of clade C of emaraviruses (plant-infecting bunyaviruses). They are involved in pathogenicity, and may act as silencing suppressors in some species [

, https://doi.org/10.3390/f13111868]. These proteins may adopt an all-α topology.
Influenza RNA polymerase PB2, N-terminal region (Flu_PB2_N)
Type: Domain

This entry represents the N-terminal extended region of RNA-directed RNA polymerase subunit PB2 (also known as Polymerase basic protein 2) from Influenza A virus and similar proteins from influenzavirus (orthomyxoviridae). This region is the N-terminal PB1 interaction domain.

Influenza virus encodes a large, multidomain RNA-dependent RNA polymerase that can both transcribe and replicate the viral RNA genome. In influenza virus, the polymerase is composed of three polypeptides: PB1, PB2 and PA/P3. PB1 houses the polymerase active site, whereas PB2 and PA/P3 contain, respectively, cap-binding and endonuclease domains required for transcription initiation by cap-snatching .
ABC_AB protein, Emaravirus (ABC_AB)
Type: Family

This family corresponds to the ABC proteins of clades A and B of emaraviruses (plant-infecting bunyaviruses). They are involved in pathogenicity, and may act as silencing suppressors in some species (Characterisation of a novel Emaravirus identified in mosaic-diseased Eurasian aspen (Populus tremula) [

, https://doi.org/10.3390/f13111868]. This family contains a hydrophobic region bordered by two highly conserved positions R/K and G. They may consist of three helices according to structure predictions.
Talin, R4 domain (Talin_R4)
Type: Domain

Talin is a cytoskeletal protein that plays a critical role in the formation of cell adhesions and regulation of integrin signalling. It activates integrins, couples them to F-actin, and recruits vinculin to focal adhesions . It is a long protein comprising an N-terminal globular head and a long C-terminal rod which has 13 helical bundles (R1-R13) organized into a compact cluster of four-helical bundles (R2-R4) within a linear chain of five-helical bundles. Nine of the helical bundles contain vinculin-binding sites (VBS), one of them is R4, represented in this entry .
Target of Nesh-SH3/FNDC1, C-terminal domain (TARSH/FNDC1_C)
Type: Domain

This domain is found at the C terminus of the Target of Nesh-SH3 (also known as ABI3BP protein

) and Fibronectin type III domain-containing protein 1 (FNDC1). Proteins containing this domain are found mainly in chordates.
Influenza RNA polymerase PB2, second domain (Flu_PB2_2nd)
Type: Domain

This entry represents the domain of the Flu PB protein that follows the N-terminal extended region.

Influenza virus encodes a large, multidomain RNA-dependent RNA polymerase that can both transcribe and replicate the viral RNA genome. In influenza virus, the polymerase is composed of three polypeptides: PB1, PB2 and PA/P3. PB1 houses the polymerase active site, whereas PB2 and PA/P3 contain, respectively, cap-binding and endonuclease domains required for transcription initiation by cap-snatching .
Influenza RNA polymerase PB2, middle domain (Flu_PB2_middle)
Type: Domain

This entry represents the middle domain of RNA-directed RNA polymerase subunit PB2 (also known as Polymerase basic protein 2) from Influenza A virus and similar proteins from influenzaviruses (orthomyxoviridae).

Influenza virus encodes a large, multidomain RNA-dependent RNA polymerase that can both transcribe and replicate the viral RNA genome. In influenza virus, the polymerase is composed of three polypeptides: PB1, PB2 and PA/P3. PB1 houses the polymerase active site, whereas PB2 and PA/P3 contain, respectively, cap-binding and endonuclease domains required for transcription initiation by cap-snatching .
Tas3, C-terminal helical domain (Tas3_C)
Type: Domain

RNA-induced transcriptional silencing complex protein tas3 (Tas3) (

) plays a role in the RNA interference (RNAi) pathway which is important for heterochromatin formation and accurate chromosome segregation. It is part of the RNA-induced transcriptional silencing (RITS) complex which provides a physical tether between the RNAi and heterochromatin assembly pathways .

This entry represents the C-terminal α-helical domain which self-associates into a helical polymer and is required for cis spreading of RITS in centromeric DNA regions

.
Polymerase basic protein 2, helical domain (PB2_helical)
Type: Domain

This entry represents the helical domain of RNA-directed RNA polymerase subunit PB2 (also known as Polymerase basic protein 2) from Influenza A virus and similar proteins from influenzaviruses (orthomyxoviridae).

Influenza virus encodes a large, multidomain RNA-dependent RNA polymerase that can both transcribe and replicate the viral RNA genome. In influenza virus, the polymerase is composed of three polypeptides: PB1, PB2 and PA/P3. PB1 houses the polymerase active site, whereas PB2 and PA/P3 contain, respectively, cap-binding and endonuclease domains required for transcription initiation by cap-snatching .
Influenza RNA polymerase PB2, sixth domain (Flu_PB2_6th)
Type: Domain

This entry represents the sixth domain of of RNA-directed RNA polymerase subunit PB2 (also known as Polymerase basic protein 2) from Influenza A virus and similar proteins from influenzaviruses (orthomyxoviridae).

Influenza virus encodes a large, multidomain RNA-dependent RNA polymerase that can both transcribe and replicate the viral RNA genome. In influenza virus, the polymerase is composed of three polypeptides: PB1, PB2 and PA/P3. PB1 houses the polymerase active site, whereas PB2 and PA/P3 contain, respectively, cap-binding and endonuclease domains required for transcription initiation by cap-snatching .