SII-SWORD/CoKE huggingface dataset:
BKRF4 (BKRF4)
Type: Family

This entry represents the histone binding protein BKRF4 of the Epstein-Barr virus, which interacts with histone H2A-H2B dimers. BKRF4-HBD binds to H2A-H2B via a triple-anchor binding mode involving the N-terminal region (NTR), the DWP motif (containing D81, W84, P86), and the C-terminal region (CTR). This binding enables BKRF4 to associate with partially disassembled nucleosomes at DNA damage sites, thereby promoting nucleosome disassembly and suppressing host DNA damage response (DDR) signalling. BKRF4 thereby inhibits the recruitment of RNF168 and prevents 53BP1 foci formation, blocking the host antiviral response. This histone chaperone mimicry represents a viral strategy to manipulate host chromatin and attenuate antiviral signalling .
BNLF2a (BNLF2a)
Type: Family

This entry represents the BNLF2a protein family found in Epstein-Barr virus. BNLF2a is a membrane-associated protein that inhibits TAP-mediated peptide transport into the endoplasmic reticulum for binding to HLA class I molecules. By preventing peptide loading, BNLF2a helps the virus evade detection by cytotoxic T cells during the lytic phase of EBV infection. BNLF2a blocks the binding of both peptides and ATP to TAP, thereby inhibiting antigen presentation. The protein has a hydrophobic C-terminal domain that likely functions as a membrane anchor .
Late promoter-activating protein (Lpa)
Type: Family

This entry represents the Late promoter-activating protein (Lpa) from bacteriophage P1. Lpa is a trans-activating factor involved in the late regulation of the P1 lytic growth cycle. It may function as the transcriptional activator of all late P1 functions. The protein has DNA-binding activity .
AP-4 complex accessory subunit Tepsin, VHS/ENTH-like domain (Tepsin_VHS/ENTH-like)
Type: Domain

This entry describes the VHS/ENTH-like domain found in human AP-4 complex accessory subunit Tepsin and similar animal proteins. The Epsin N-Terminal Homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. ENTH is structurally similar to the VHS domain and is composed of a superhelix of eight α-helices. ENTH domains bind both, inositol phospholipids and proteins. They contribute to the nucleation and formation of clathrin coats on membranes . Tepsin associates with the Adapter-like complex 4 (AP-4) and may therefore play a role in vesicular trafficking of proteins at the trans-Golgi network .
CENPJ, tubulin-binding region (Tubulin-bd_CENPJ)
Type: Domain

This region, also known as PN2-3 domain, is found in the human Centrosomal P4.1-associated protein (CPAP, also known as CENPJ). The region represented by this entry binds and caps the longitudinal surface of the tubulin beta-subunit . This binding site also targeted by fungal and bacterial peptide-like inhibitors of the vinca domain, sharing a very similar binding mode with these compounds . Members of this group are mainly found in vertebrates and arthropods.

CENPJ is involved in centriole-length regulation. It allows persistent slow growth of the centriolar microtubule plus end and its overexpression leads to abnormally long microtubules . CENPJ not only inhibits microtubule nucleation from the centrosome, but acts as a microtubule plus-end tracking protein that stabilises centriolar microtubules and inhibits microtubule polymerisation and extension from the distal ends of centrioles .
TRIM8/14/16/25/29/45/65, coiled-coil region (TRIM8/14/16/25/29/45/65_CC)
Type: Domain

This entry represents a long helical region connecting domains in TRIM proteins such as TRIM16, TRIM29, TRIM25, TRIM 65, TRIM47, TRIM8 and TRIM14. Many members of this entry act as E3 ubiquitin-protein ligases . The TRIM Coiled-Coil (TRIM_CC) domain is a long helical region found in Tripartite Motif (TRIM) proteins, which are part of the RING finger E3 ubiquitin ligase family . This domain plays a crucial role in protein-protein interactions, particularly in the dimerisation and self-association of TRIM proteins .
NorR-like, AAA+ ATPase lid domain (AAA_lid_NorR)
Type: Domain

This entry represents the AAA+ ATPase lid domain, often found C-terminal to the RNA polymerase sigma factor 54 interaction domain

in bacterial transcription factors, including NorR and NtrC.

Some bacterial regulatory proteins activate the expression of genes from promoters recognised by core RNA polymerase associated with the alternative sigma-54 factor. These have a conserved domain of about 230 residues involved in the ATP-dependent interaction with sigma-54. About half of the proteins in which this domain is found (algB, dcdT, flbD, hoxA, hupR1, hydG, ntrC, pgtA and pilR) belong to signal transduction two-component systems and possess a domain that can be phosphorylated by a sensor-kinase protein in their N-terminal section. Almost all of these proteins possess a helix-turn-helix DNA-binding domain in their C-terminal section. The domain which interacts with the sigma-54 factor has an ATPase activity. This may be required to promote a conformational change necessary for the interaction . The domain contains an atypical ATP-binding motif A (P-loop) as well as a form of motif B. The two ATP-binding motifs are located in the N-terminal section of the domain.
Plastid division protein CDP1-like, 1st alpha solenoid domain (CDP1-like_a_solenoid_1)
Type: Domain

This entry represents the first α-helical solenoid domain at the N-terminal of Plastid division protein CDP1, chloroplastic and Protein ACCUMULATION AND REPLICATION OF CHLOROPLASTS 6, chloroplastic (ARC6) from Arabidopsis thaliana, and similar sequences mainly from plants and cyanobacteria. This domain is usually found next to

.

Armadillo/beta-catenin-like (ARM) repeat is a specific subclass of α-helical solenoid domains. ARM repeats are composed of tandem three-helix bundles that form a superhelical structure, primarily facilitating protein-protein interactions . ARM repeats are predominantly found in plastid division regulators (PDR), where they play a crucial role in the coordination and regulation of plastid division in plants .

This group of proteins function as key components of the plastid division machinery, which is responsible for the constriction and division of plastids, including chloroplasts and non-green plastids . It includes proteins such as FtsZ, ARC6, DRP5B, and MinE. ARC6 and PARC6 are essential for the chloroplast replication process , which implies the assembly and constriction of the tubulin-like FtsZ ring on the stromal surface of the inner envelope membrane (IEM) and the dynamin-like ARC5 ring on the cytosolic surface of the outer envelope membrane (OEM). They are also involved in stromule biogenesis and may contribute to plant gravitropism. ARC6 facilitates FtsZ ring assembly and promotes the recruitment of MCD1, which is essential for forming the chloroplast Z-ring. CDP1, on the other hand, is required for the localisation of PDV1 and the correct formation of the FtsZ ring in non-green plastids .
Tubulin-folding cofactor D, ARM repeats (ARM_TBCD_2nd)
Type: Domain

This is the second region of armadillo (ARM)-like repeats found in human Tubulin-specific chaperone D (TBCD) and its homologues in eukaryotes. It is found next to

.

Tubulin-folding cofactor D (TBCD) can interact with beta tubulin, which is regulated via its interaction with ARL2 (ADP ribosylation factor-like protein 2), a small monomeric G protein. ARL2 inhibits the beta-tubulin GTPase activating protein (GAP) activity of TBCD, and its interaction with native tubulin dimers . TBCD does not co-polymerise with microtubules either in vivo or in vitro, but instead modulates microtubule dynamics by sequestering beta-tubulin from GTP-bound alpha/beta-heterodimers in microtubules .

The tubulin heterodimer consists of one alpha- and one beta-tubulin polypeptide. In humans, five tubulin-specific chaperones termed TBCA/B/C/D/E are essential for bring the alpha- and beta-tubulin subunits together into a tightly associated heterodimer. Following the generation of quasi-native beta- and alpha-tubulin polypeptides (via multiple rounds of ATP-dependent interaction with the cytosolic chaperonin), TBCA and TBCB bind to and stabilise newly synthesised beta- and alpha-tubulin, respectively. The exchange of beta-tubulin between TBCA and TBCD, and of alpha-tubulin between TBCB and TBCE, resulting in the formation of TBCD/beta and TBCE/alpha. These two complexes then interact with each other and form a supercomplex (TBCE/alpha/TBCD/beta). Interaction of the supercomplex with TBCC causes the disassembly of the supercomplex and the release of E-site GDP-bound alpha/beta tubulin heterodimer, which becomes polymerization competent following spontaneous exchange with GTP .
Putative surface-exposed virulence protein BigA, beta-sandwich domain (BigA_beta)
Type: Domain

This entry represents a β-sandwich domain found in Putative surface-exposed virulence protein BigA from Salmonella typhimurium and similar proteins from proteobacteria. This domain is found adjacent to the C-terminal autotransporter domain (

) and is part of the passenger domain that is transported through the autotransporter barrel. While the autotransporter domain forms a β-barrel for translocation, the specific function of this β-sandwich domain remains to be determined.

BigA is an autotransporter protein characterised by a C-terminal outer membrane barrel (

) that facilitates the transport of its passenger domain across the membrane. The N-terminal region contains a variable passenger domain, which is translocated through the barrel. After export, the passenger domain may undergo auto-catalytic cleavage, cleavage by an external protease, or remain uncleaved, depending on the specific protein .
BigA/YdbA-like, N-terminal domain (BigA/YdbA-like_N)
Type: Domain

This entry represents the N-terminal 8-stranded β-barrel domain found in the BigA family of bacterial virulence proteins and related proteins such as YdbA from Escherichia coli. This domain is located N-terminal to the repetitive region in BigA proteins and is part of the passenger domain that is transported through the C-terminal autotransporter barrel. While the BigA protein has been implicated in bacterial virulence, the specific function of this N-terminal domain remains to be determined.

BigA is an autotransporter protein characterised by a C-terminal outer membrane barrel (

) that facilitates the transport of its passenger domain across the membrane. The N-terminal region contains a variable passenger domain, which is translocated through the barrel. After export, the passenger domain may undergo auto-catalytic cleavage, cleavage by an external protease, or remain uncleaved, depending on the specific protein .
Probable ATP-binding protein BrxC, 4th six-stranded beta-sheet domain (BREX_BrxC_4th)
Type: Domain

This entry represents the 4th domain of the BrxC protein from the BREX (bacteriophage exclusion) system. This α/β domain contains a distinctive six-stranded β-sheet with α-helices. It is predicted to be the 4th of 8 domains in the full-length BrxC protein.

BrxC is a P-loop-containing, probable ATPase associated with type 1 BREX (bacteriophage exclusion) systems, which provide immunity against bacteriophage infections by methylating specific DNA sites to distinguish self from non-self . Although phage adsorption is permitted, BREX systems block phage DNA replication. BrxC, a probable ATP-binding protein, operates within a six-protein complex (BrxA-BrxB-BrxC-PglX-PglZ-BrxL) that confers resistance to a range of bacteriophages.
Probable ATP-binding protein BrxC, alpha-helical domain (BREX_BrxC_helical)
Type: Domain

This entry represents the small α-helical domain of the BrxC protein from the BREX (bacteriophage exclusion) system. This domain is predicted to be the 6th of 8 domains in the full-length BrxC protein. This small α-helical domain may be involved in protein-protein interactions within the BREX complex or contribute to the structural stability of the BrxC protein.

BrxC is a P-loop-containing, probable ATPase associated with type 1 BREX (bacteriophage exclusion) systems, which provide immunity against bacteriophage infections by methylating specific DNA sites to distinguish self from non-self . Although phage adsorption is permitted, BREX systems block phage DNA replication. BrxC, a probable ATP-binding protein, operates within a six-protein complex (BrxA-BrxB-BrxC-PglX-PglZ-BrxL) that confers resistance to a range of bacteriophages.
Probable ATP-binding protein BrxC, winged helix-turn-helix domain (BREX_BrxC_wHTH)
Type: Domain

This entry represents the winged helix-turn-helix (wHTH) domain of the BrxC protein from the BREX (bacteriophage exclusion) system. This domain is predicted to be the 5th of 8 domains in the full-length BrxC protein. The winged helix-turn-helix domain likely plays a role in DNA binding.

BrxC is a P-loop-containing, probable ATPase associated with type 1 BREX (bacteriophage exclusion) systems, which provide immunity against bacteriophage infections by methylating specific DNA sites to distinguish self from non-self . Although phage adsorption is permitted, BREX systems block phage DNA replication. BrxC, a probable ATP-binding protein, operates within a six-protein complex (BrxA-BrxB-BrxC-PglX-PglZ-BrxL) that confers resistance to a range of bacteriophages.
At3g05675-like, ankyrin-like domain (At3g05675-like_ankyrin)
Type: Domain

This entry describes a region of ankyrin-like repeats found at the C-terminal of BTB/POZ containing proteins mostly from plants, including At3g05675, At2g13690, At1g63850, At5g60050 and At3g50780 from Arabidopsis thaliana.

At3g05675 and related proteins may act as a substrate-specific adapter of an E3 ubiquitin-protein ligase complex (CUL3-RBX1-BTB) which mediates the ubiquitination and subsequent proteasomal degradation of target proteins .
Baseplate wedge 3 tail fiber network component (BW3TFN)
Type: Family

This entry represents the Baseplate Wedge 3 Tail Fibre Network (BW3TFN) component found in bacteriophage A511 and related phages. The protein forms dimers that constitute an essential part of the bacteriophage tail fibre structure. The BW3TFN protein (gp105 in phage A511,

) is located in the proximal part of the tail fibre and interacts with the Baseplate Wedge 3 (BW3) protein, which crosses the surface of BW3TFN dimers. The protein retains the structure and functionality of T4 BW3TFN gp8 but has a more streamlined architecture, making it about half the size. BW3TFN proteins are found in many contractile tail bacteriophages and related injection systems. Multiple BW3TFN dimers arranged in series form a rigid scaffold that constitutes the proximal part of the phage tail fibre and is involved in the transmission of the conformational signal from the baseplate to the receptor binding proteins during host cell attachment .
Filamentous dsRNA virus capsid protein (CcFV1_CP)
Type: Family

This entry represents the capsid protein (CP, P4) of Colletotrichum camelliae filamentous virus 1 (CcFV-1), a unique dsRNA virus that forms filamentous particles rather than the typical isometric particles found in other dsRNA viruses. The CcFV-1 CP is encoded by ORF4 on dsRNA4 and has a molecular mass of approximately 31 kDa. This protein encapsidates the viral dsRNA genome (consisting of 8 segments) into elongated and flexuous particles that can reach over 4600 nm in length. The protein contains a high proportion of proline, alanine, and serine residues, resembling the PAS-rich proteins found in related mycovirus species. CcFV-1 represents a possible evolutionary link between dsRNA and (+)ssRNA viruses, with the CP potentially employing a novel genome packaging mechanism . Structure prediction suggests that this protein is composed of three domains, with the N-terminal domain forming a helix swapped dimer interface.
CASAMP, N-terminal domain (CAMSAP_N)
Type: Domain

This entry represents the N-terminal of human Calmodulin-regulated spectrin-associated protein 1-3 (CASAMP1-3, ) and similar animal proteins, including the homologues from Caenorhabditis elegans and Drosophila melanogaster Patronin. This domain is a presumed calponin-homology (CH) domain.

The calmodulin-regulated spectrin-associated (CAMSAP) proteins are defined by a CKK domain that binds microtubules . It includes CAMSAPs from vertebrates and Patronin from invertebrates . CAMSAP1 is the representative member. It contains a conserved region, CC1, that binds to both spectrin and Ca2+/calmodulin in vitro and links spectrin-binding to neurite outgrowth . Patronin binds to and protects the MT minus-end against depolymerization . CAMSAP2 is a key microtubule-organising protein that specifically binds the minus end of non-centrosomal microtubules and regulates their dynamics and organisation. CAMSAP proteins carry an N-terminal region that includes two CH domains represented by

and

, a central region including a predicted coiled-coil, and a C-terminal CKK domain

, which is involved in binding CAMSAP proteins to microtubules .
Chimallin (Chimallin)
Type: Family

The Phikzvirus chimallin family consists of proteins that self-assemble to form a protective proteinaceous shell around viral DNA. This shell compartmentalises proteins and DNA during viral infection, creating a micrometre-scale compartment with narrow pores. It serves as the site of viral replication, where proteins involved in DNA replication are localised. Additionally, the shell provides a docking surface for capsids during the packaging process. The structure likely plays a crucial role in protecting the viral genome against host defences, ensuring successful viral replication and packaging . This group also contain some uncharacterised sequences from other tailed bacteriophages.
Metallo-beta-lactamase VIM-1/2/7 (VIM-1/2/7)
Type: Family

This protein family includes the metallo-beta-lactamases VIM-1/7 from Pseudomonas aeruginosa, VIM-2 from Escherichia coli, and similar VIM (Verona integron-encoded metallo-beta-lactamase)-type proteins from gammaproteobacteria. These proteins are class B1 beta-lactamases that confer resistance to the beta-lactam antibiotics, including penicillins, cephalosporins and carbapenems via hydrolysis of the beta-lactam ring .

VIM-type metallo-beta-lactamases (MBLs) are integron-associated and are widely distributed acquired MBLs. MBLs (class B of the Ambler beta-lactamase classification) have been divided into three subclasses B1, B2 and B3, based on their sequence and structural relationships, and on their substrates, with the B1 and B2 MBLs being most closely related to each other . This subgroup of VIM-type MBLs belongs to the B1 subclass. B1 enzymes are most active with two zinc ions bound in the active site, and have a broad-spectrum substrate profile .
UL148C (UL148C)
Type: Family

This entry represents a family of viral membrane proteins UL148C found in Human cytomegalovirus (HCMV). UL148C is predicted to contain two transmembrane helices and is located in the host cell membrane. The specific function of this protein remains to be determined.
Transcriptional regulator UL34 (UL34)
Type: Family

This entry represents the UL34 protein family found in herpesvirales. UL34 acts as a transcriptional repressor of the US3 gene expression through a specific DNA sequence named the transcriptional repressive element (tre). The protein is localised to the host nucleus during viral infection . Structure prediction suggests that this entry forms a compact α-helical domain.
Carbamoyl phosphate synthase, preATP-grasp domain (CPSase_preATP-grasp)
Type: Domain

This entry represents the preATP-grasp domain found twice in Carbamoyl phosphate synthase proteins. This domain is found associated with

.

Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (

) or ammonia (

), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates . CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate . The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (

) (ACC), propionyl-CoA carboxylase (

) (PCCase), pyruvate carboxylase (

) (PC) and urea carboxylase (

).

Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain . CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites . The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain.

Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein . The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP . There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia . CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains .
Auxiliary capsid protein, crAss001 (AuxCP)
Type: Family

This entry represents the auxiliary capsid protein found in Bacteroides phage crAss001. This protein forms an outer layer on the major capsid protein protrusions and is present in 535 copies in the virion. The central region (amino acids 75-237) is structurally similar to Helicobacter pylori flagellar cap protein FliD and is involved in interactions with the major capsid protein.