SII-SWORD/CoKE huggingface dataset:
Properdin, thrombospondin type 1 C-terminal (CFP_TSR_C)
Type: Repeat

This represents the C-terminal thrombospondin type I repeat (TSR_C) found in human Properdin (CFP) and similar proteins from vertebrates. Properdin is a glycoprotein constructed from a common pool of structure units or modules, which are homologous to the thrombospondin type 1 repeat, TSR. It is a positive regulator of the complement system that stabilises the alternative pathway C3-convertase C3bBb. Properdin also inhibits the factor H-mediated cleavage of C3b by factor I. In addition, this protein acts as a pattern recognition molecule capable of identifying and interacting with microbial surfaces, apoptotic cells, and necrotic cells . However this role of pattern recognition is controversial . Studies indicate that this domain is a TSR variants. CFP is a positive regulator of the alternate pathway (AP) of complement. It contains six thrombospondin repeat type I (TSP 1-6 domains and an N-terminal domain (

). This entry represents the last TSP type I domain, which binds to the first TSP type I domain (

), contributing to multimerisation .
F-93, winged-helix domain (F-93_WHD)
Type: Domain

This entry represents a WH-like domain (

) found in a putative transcription factor called F-93 from Sulfolobus spindle-shaped viruses (SSVs) (

) and related proteins. Members of this family appear to be related to MarR (

) and PadR (

) families of prokaryotic transcription factors.
MvcA insertion domain (MvcA_ins)
Type: Domain

This entry represents the insertion domain of MvcA, the MavC paralogue A of bacterial effector MavC from Legionella pneumophila. MvcA catalyses the reverse reaction of MavC, removing Ub from Ube2N through hydrolysis which regulates MavC activity. MvcA is similar at sequence and structural levels to MavC, and it exhibits deamidase activity toward ubiquitin . This domain is crucial for substrate recognition .
RickCE N-terminal domain (RickCE_N)
Type: Domain

This is a presumed domain found at the N-terminal end of rickCE ubiquitin-like proteases, such as

, which may have a Rossmann-like fold similar to that in glycosyltransferases.
Domain of unknown function DUF6946 (DUF6946)
Type: Domain

This domain is found in uncharacterised bacterial proteins either standalone or in combination with other domains. It is distantly related to the type II restriction endonucleases with predicted similar active site architecture. These proteins are most likely endonucleases based on the strict conservation of the putative active site residues.
Uncharacterized protein AF_0924 (AF_0924)
Type: Domain

This entry represents the AF_0924 protein from Archaeoglobus fulgidus. The structure of this protein (

) is composed of three α-helices and three β-strands.
Atadenovirus fibre, head domain (Fibre_HD)
Type: Domain

This entry represents the carboxy-terminal virus-distal fibre head domain present in Atadenovirus. This domain is putatively responsible for primary receptor recognition. Atadenovirus fibre head domains has a similar β-sandwich propeller topology found in other adenovirus fibre proteins (

) .
Domain of unknown function DUF6945 (DUF6945)
Type: Domain

This entry represents a WH-like domain found at the N-terminal end of an uncharacterised protein from Vibrio cholerae (

), whose function is unknown. This domain is also found in phage proteins.
TarS/TarP, linker domain (TarS/TarP_linker)
Type: Domain

TarS is an enzyme responsible for the glycosylation of wall teichoic acid polymers of the S. aureus cell wall, a process that has been shown to contribute for methicillin resistance in MRSA. TarS consist of three domains: catalytic, linker and trimerisation . This entry represents the linker domain that bridges the catalytic and trimerisation domains.

This domain is also found C-terminal in Poly(ribitol-phosphate) beta-N-acetylglucosaminyltransferase TarP which transfers GlcNAc to a different hydroxyl group of the target poly(RboP)-wall teichoic acid than TarS, with important consequences for immune recognition .
RH3 domain (RH3_dom)
Type: Domain

This entry represents the RH3 domain found in ORF E73 from Sulfolobus virus and related proteins. This domain shows significant similarity to domains found in proteins involved in transcriptional regulation, but with an additional third helix .
Gp5/Type VI secretion system Vgr, C-terminal trimerisation domain (Gp5_Vgr_C)
Type: Domain

This entry represents the C-terminal trimerisation domain found in Type VI secretion system spike protein VgrG(1-5, A,B) and Gp5. This domain associates to form a triple-stranded β-helix that forms an equilateral triangular prism, which acts as a membrane-puncturing needle . The interior of the β-helix has an increased hydrophobicity towards the C-terminal. The middle part of the helix has a pore, enriched with polar and charged side chains.
Xylose operon regulatory protein, N-terminal domain (XylR_PBP1)
Type: Domain

This entry represents the N-terminal domain of Xylose operon regulatory protein (XylR), an atypical AraC protein. This D-xylose-binding domain contains a periplasmic-binding protein (PBP) fold, similar to LacI/GalR transcription regulators, and mediates dimerisation .
AF_0587-like, pre-PUA domain (AF_0587-like_pre-PUA)
Type: Domain

This domain is found in AF_0587 from Archaeoglobus fulgidus and similar archaeal sequences. It is found N-terminal to the PUA domain (

).
Tail protein NMB1110-like, C-terminal domain (NMB1110-like_C)
Type: Domain

This domain is found at the C-terminal end of Tail protein, 43 kDa Neisseria meningitidis (NMB1110) and similar sequences found in tailed bacteriophages and prophages from proteobacteria. This domain is usually found associated with

.
Acylamino-acid-releasing enzyme-like, N-terminal domain (APH-like_N)
Type: Domain

This domain is found at the N-terminal of Acylamino-acid-releasing enzyme from Aeropyrum pernix (APH) and similar archaeal sequences. APH catalyses the removal of an N-acylated amino acid from peptides. This domain folds as a regular seven-bladed β-propeller .
Phosphocholine transferase AnkX, insertion domain (AnkX_ins)
Type: Domain

This entry represents the insertion domain of AnkX, a Legionella pneumophila PC transferase that mediates the recruitment of Rab1 to the cytosolic face of the Legionella-containing vacuole (LCVs). It is a virulence factor that modifies host RAB1 (RAB1A, RAB1B, or RAB1C) and RAB35 leading to the displacement of GDP dissociation inhibitors (GDI) and impairs accessibility to the GTPase effector LepB. It consists of two distinct structural units. The N-terminal contains a FIC domain, which encompasses the CDP-choline binding pocket and a C-terminal ankyrin repeats-containing domain . Unlike other FIC enzymes, AnkX comprises an additional insert domain located in the conserved β-hairpin which consists of α-helices and β-sheets that protrude from the enzyme and adapts a rigid, thorn-like structure .
AP205 coat protein (AP205_coat)
Type: Domain

AP205 is a single-stranded RNA bacteriophage that has a coat protein sequence that is not similar to any other known single-stranded RNA phage protein. The AP205 coat protein forms a dimer which adopts the conserved Leviviridae coat protein core fold with the exception of the N-terminal region. This coat protein has a similar structure that is circularly permuted compared to the other coat proteins .
PH0730-like, N-terminal domain (PH0730-like_N)
Type: Domain

This domain is found at the N-terminal end of PH0730 from Pyrococcus horikoshii and similar archaeal proteins that contain the domain

at the C-terminal. This domain adopts a winged helix fold.
ArnR1-like, winged-helix domain (ArnR1-like_WHD)
Type: Domain

This entry represents a WH-like domain present in ArnR1-like putative DNA binding protein. ArnR1-like transcription factors have been implicated in regulating the expression of components found in both the archaeal adhesive pilus and UV-inducible pili systems .
CRISPR system ring nuclease SSO1393-like, winged-helix domain (SSO1393-like_WHD)
Type: Domain

This entry represents a winged-helix (WH)-like domain found in CRISPR system ring nuclease SSO1393 from Sulfolobus solfataricus (

) and similar archaeal sequences. This protein has been described as a component of the CRISPR system .

SSO1393 has been described as a component of the CRISPR system . CRISPR (clustered regularly interspaced short palindromic repeat) is an adaptive immune system that provides protection against mobile genetic elements (viruses, transposable elements and conjugative plasmids) .
Dark, winged-helix domain (Dark_WHD)
Type: Domain

This entry represents the winged-helix (WH)-like found in Apaf-1/CED-4-related caspase activator Dapaf-1S from Drosophila melanogaster (Dark) and similar Dark (Drosophila Apaf-1-related killer) proteins from insects. Dark protein is part of the apoptosome complex and plays a key role in procaspases activation and apoptosis .
Cell invasion protein SipA, C-terminal actin binding domain (SipA_C)
Type: Domain

This domain is found at the C-terminal end of Cell invasion protein SipA (Salmonella Invasion protein A) from Salmonella typhimurium. SipA actin-binding protein that interferes with host cell actin cytoskeleton, and reduce the critical concentration for the formation of F-actin, contributing to bacterial invasion. This domain adopts a a compact, heart-shaped fold dominated by a helical secondary structure. It is responsible for the actin-binding and polymerisation activities of the protein .
Plasmid Fertility inhibition factor (PFIN)
Type: Family

FiwA-like proteins are fertility inhibition factors (FIN), which are employed by plasmids to block import of rival plasmids . FiwA is encoded by plasmid RP1 and blocks the transfer of plasmid R388 . A FiwA-like protein called Osa (oncogenic suppressive activity) inhibits the oncogenic properties of Agrobacterium tumefaciens . Osa is structurally similar to the ParB/Sulfiredoxin fold . Osa has been shown to have ATPase and DNAse activities, and can block T-DNA transfer into plants .
Mre11, C-terminal domain (Mre11_C)
Type: Domain

This entry represents the helix-turn-helix domain of Mre11 from Thermotoga maritima and similar proteins . Mre11, together with Rad50, form the MR protein complex involved in DNA double-strand break repair . This domain binds Rad50 and attaches flexibly to the nuclease domain which allows large conformational changes .
Maltose-forming alpha-amylase-like, C-terminal domain (PSMA-like_C)
Type: Domain

This domain is found in the maltose-forming alpha-amylase from the hyperthermophilic archaeon Pyrococcus sp. ST04 (PSMA,

). This enzyme is able to hydrolyse both alpha-1,4-glucosidic and alpha-1,6-glucosidic bonds. PSMA protein consists of two domains: an N-terminal domain with a typical glycoside hydrolase 57 family (β/α)7-barrel fold and a C-terminal domain composed of α-helical bundles. This entry represents the C-terminal domain .
Maltose-forming alpha-amylase-like, N-terminal domain (PSMA-like_N)
Type: Domain

This domain is found in the maltose-forming alpha-amylase from the hyperthermophilic archaeon Pyrococcus sp. ST04 (

). This enzyme is able to hydrolyse both alpha-1,4-glucosidic and alpha-1,6-glucosidic bonds. PSMA protein consists of two domains: an N-terminal domain with a typical glycoside hydrolase 57 family (β/α)7-barrel fold (this entry) and a C-terminal domain composed of α-helical bundles (

) .
M152, N-terminal domain (M152_N)
Type: Domain

This domain is found at the N-terminal of M152 from Murid herpesvirus 1 (

), a glycoprotein that shows structural similarity to m153 and m157 .
Sucrose hydrolase-like, C-terminal domain (SupH-like_C)
Type: Domain

This domain is found at the C-terminal end of Sucrose hydrolase from Xanthomonas campestris (SupH,

) and similar bacterial sequences. SupH shows a central domain that consists of an eight-stranded α/β barrel (

). This β-stranded domain is located on a side of the barrel fold .
Mucin-like protein 1 (MUCL1)
Type: Family

This entry represents the human mucin-like protein 1 and similar sequences from primates. Mucin-like 1 (MUCL1) is a small glycoprotein highly expressed mainly in breast cancer and salivary glands .
Mucin-20 repeat (MUC-20_rpt)
Type: Repeat

This entry represents a short repeat found in human Mucin-20 (MUC-20) and similar sequences from primates. MUC-20 may regulate the MET signalling cascade and seems to decrease the hepatocyte growth factor (HGF)-induced transient MAPK activation . This repeat is predicted to form a β-solenoid structure.
Y16Q-like (Y16Q-like)
Type: Family

This entry represents a family of proteins from tailed bacteriophages and bacterial prophages, including Uncharacterized 7.5 kDa protein in denB-rIIB intergenic region from Enterobacteria phage T4. This family includes sequences that are present in crAss phage. AlphaFold predicts these short proteins to adopt an α-helical hairpin structure. Its function is unknown.
Protein of unknown function DUF6887 (DUF6887)
Type: Family

This entry represents a family of uncharacterised cyanobacterial proteins.
New-glue 1-3-like (Ng_1-3-like)
Type: Family

This entry represents new glue proteins which are mucin-like proteins found mainly in arthropods.
YpzH protein family (YpzH)
Type: Family

This entry contains a family of small protein of unknown function. Proteins in this family are found in Firmicutes. These proteins adopt a β-sheet structure with four strands with an α-helix packed on one face between the second and third strands. Using AlphaFold we can identify a likely hexameric ring complex. Additionally these proteins likely form a cap on a goblet like hexameric complex of

. Analysis of genomic context suggests this larger complex is involved in spore germination and possibly phospholipid synthesis or regulation.
ESX-1 secretion-associated protein EspB, PPE domain (EspB_PPE)
Type: Domain

This entry represents the PPE domain of ESX-1 secretion-associated protein EspB, a member of the PE/PPE family and the only one described to date to form higher-order oligomers . It contains PE (Pro-Glu) and PPE (Pro-Pro-Glu) domains, and a C-terminal domain, which is processed by MycP1 protease during secretion. EspB oligomerises into a cylinder-like heptamer through its N-terminal domain, that form channel-like structures .
Campylobacter invasion antigen D, C-terminal (CiaD_C)
Type: Domain

This entry represents the C-terminal domain of Campylobacter invasion antigen D from Campylobacter jejuni (CiaD) and similar sequences mainly found in Campylobacterales. C. jejuni utilizes a cell binding and effector delivery mechanism to invade host cells. The Cia proteins (effectors) are exported from the bacterium's flagellar T3SS and are involved in enhancing C. jejuni cell invasion . This domain shows a pair of highly conserved C-terminal α-helices. Many members of the family also contain an N-terminal T3SS signal.
Helix-turn-helix family (HTH_67)
Type: Family

This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 270 and 293 amino acids in length. These proteins are composed of a large α-helical domain which appears to be related to MarR transcription factors.
MORF/ORRM1/DAG-like, MORF domain (MORF/ORRM1/DAG-like_MORF)
Type: Domain

This domain is found in Multiple organellar RNA editing factor 1 (MORF1) and ORRM1 from Arabidopsis thaliana, DAG protein from Antirrhinum majus, and similar proteins from plants involved in organellar RNA editing in mitochondria. This conserved domain, termed MORF domain, plays a role in the multimerization of MORF proteins. It adopts a globular fold with seven β-strands and three α-helices combined with four major loops .
Talin 1-like, rod-segment domain (TLN1-like_RS)
Type: Domain

This domain is found repeated in human Talin-1 (TLN1) and similar proteins mainly from animals. Talin is an essential component in focal adhesions (FAs), intracellular protein assemblies that serve as tension-sensing anchoring points to link cells to the extracellular environment . This protein plays a key regulatory role in FA dynamics, similar to the activation and inactivation of integrins. It consists of a globular head, a long rod made of 62 helices forming 13 helical bundle (rod segment, RS) domains, and a dimerisation (DD) motif at the C terminus. This entry represents four of these domains, RS 5, 6, 9 and 11 .
Domain of unknown function DUF6915 (DUF6915)
Type: Domain

This family of proteins is primarily found mainly in proteobacteria. Proteins in this family are typically between 124 and 153 amino acids in length. Proteins in this family have several conserved histidine residues that may form zinc-binding sites.
Virion DNA-directed RNA polymerase domain 2 (vRNAP_dom2)
Type: Domain

This domain is found in Virion DNA-directed RNA polymerase from Bacteriophage N4 (vRNAP), which is injected into the host upon infection and transcribes the phage early genes from promoters that have a 5-bp stem-3 nt loop hairpin structure. This entry represents a region located C-terminal to the mini-vRNAP, which possesses all RNAP functions .
GlcNAc-binding protein A, third domain (GbpA_D3)
Type: Domain

This entry represents the third domain D3 of GlcNAc-binding protein A from Vibrio cholerae (GbpA), which is thought to promote attachment to both epithelial cell surfaces and marine chitin. GbpA contains four domains. D3 binds to the surface of the bacteria. It shows distant structural similarity to bacterial surface proteins, adopting an immunoglobulin fold . Members of this group are found in proteobacteria.
Distal tail component, second carbohydrate binding domain (Dit-like_CBM2)
Type: Domain

This entry represents the second putative carbohydrate binding domain (CBM2) of the distal tail component from Lactobacillus phage J-1 (

, Dit), which is involved in host recognition. This domain folds into a β-sandwich with two β-sheets gathering 12 β-strands . It usually appears associated to

.
Baseplate wedge protein gp6, C-terminal domain III (Gp6_C-III)
Type: Domain

This entry represents a domain found in Baseplate wedge protein gp6 from Enterobacteria phage T4 (Gp6) and similar sequences from tailed bacteriophages and bacterial prophages. Gp6 is located next to the tail tube and is an intermediate (or inner) baseplate protein involved in tail assembly. Two molecules of Gp6 form a complex with Gp25 and Gp7, which is involved sheath contraction . This domain has been described as C-terminal domain III.
SAM domain-like (SAM_5)
Type: Domain

This entry corresponds to the most N-terminal SAM domain found in topoisomerase V proteins.
SSO1120-like, N-terminal thioredoxin-like domain (SSO1120-like_N)
Type: Domain

This entry represents a thioredoxin domain found at the N-terminal of a group of archaeal proteins, including the protein disulfide oxidoreductase (PDO) SSO1120 from the hyperthermophilic archaeon Sulfolobus solfataricus (

). This domain, a non-canonical thioredoxin fold, is composed of four β-strands and three α-helices, with a well-defined disulfide bond between Cys24 and Cys45. The domain does not contain any active site but is part of the larger structure that comprises the C-terminal unit with the CTKC active site motif. The N-terminal domain shows unexpected similarity with the N-terminal domain of the alkyl hydroperoxide reductase F component from Salmonella typhimurium, and a possible involvement of this atypical PDO in a new antioxidant system of S. solfataricus has been proposed .
CofJ (CofJ)
Type: Family

This entry represents CofJ from Escherichia coli (

) and similar sequences from Enterobacterales. CofJ is a soluble protein secreted via the CFA/III apparatus in Enterotoxigenic Escherichia coli (ETEC), which colonize the human gut causing severe diarrhoea. CofJ is a single-domain protein of 326 residues, comprised of an elongated β-sandwich core with three α-helices, four 3-10 helices and multiple loops on its surface. The protein has a cluster of exposed hydrophobic side-chains at one end and structural homology to the pore-forming proteins perfringolysin O and alpha-haemolysin. The crystal structure of CofJ was determined, revealing a large β-sandwich protein that bears no sequence or structural homology to TcpF, a protein encoded by the syntenic gene in the TCP operon of Vibrio cholerae. CofJ binds to lipid vesicles and epithelial cells, suggesting a role in membrane attachment during ETEC colonization .
Calpain-3/13-like, C-terminal EF-hand (CAPN3/13-like_C_EFh)
Type: Domain

This domain is found at the C-terminal end of human Calpain-13 (CAPN13) , Calpain-3 (CAPN3) and similar sequences from vertebrates. CAPN13 is thought to be a non-lysosomal thiol-protease. CAPN3 is a calcium-regulated non-lysosomal thiol-protease that cleaves proteolytically CTBP1 at 'His-409'. It mediates, with UTP25, the proteasome-independent degradation of p53/TP53 . This entry represents the last EF-hand domain of this protein .
C381 turret protein, middle domain (STIV_turret_M)
Type: Domain

This entry represents the middle jelly roll domain of the Sulfolobus turreted icosahedral virus (STIV) turret protein. The C381 turret protein is a component of the STIV virion vertex complex, which orchestrates virion assembly by coordinating interactions of the membrane and various protein components involved. The turret protein is apposed on the penton base C-terminal jelly-roll ring and forms a pentamer consisting of three consecutive layers of jelly-rolls, with each jelly-roll exhibiting different orientations. The interior of the C381 pentamer harbors two rather large cavities, which exhibit an overall positive electrostatic potential, suggesting that the turrets may act as STIV receptor-binding proteins carrying out recognition and attachment to the host receptors. The turret protein shares similarity with many carbohydrate-binding modules as well as domains involved in protein-protein interactions .
Neurofibromin, PH domain-like (PH_NF1)
Type: Domain

This entry represents the pleckstrin homology (PH)-like domain of neurofibromin (NF1) and similar sequences from animals and fungi. Neurofibromin is a Ras-specific GTPase-activating protein (RasGAP). Mutations in the gene encoding this protein cause neurofibromatosis type 1 (NF1). This domain forms a bipartite module with the Sec14p homologous segment, which together exhibit phospholipid binding activity. The domain interface architecture suggests a model of how the NF1 PH domain may regulate binding of a ligand by the Sec14 module .
C381 turret protein, N-terminal (C381_turret_N)
Type: Domain

This entry represents the N-terminal jelly roll domain of the Sulfolobus turreted icosahedral virus (STIV) turret protein. The C381 turret protein is a component of the STIV virion vertex complex, which orchestrates virion assembly by coordinating interactions of the membrane and various protein components involved. The turret protein is apposed on the penton base C-terminal jelly-roll ring and forms a pentamer consisting of three consecutive layers of jelly-rolls, with each jelly-roll exhibiting different orientations. The interior of the C381 pentamer harbours two rather large cavities, which exhibit an overall positive electrostatic potential, suggesting that the turrets may act as STIV receptor-binding proteins carrying out recognition and attachment to the host receptors. The turret protein shares similarity with many carbohydrate-binding modules as well as domains involved in protein-protein interactions .