SII-SWORD/CoKE huggingface dataset:
Transcription initiation factor TFIID subunit 2, TPR repeats (TPR_TAF2_C)
Type: Domain

This is a region of tetratricopeptide (TPR)-like repeats found towards the C-terminal end of human Transcription initiation factor TFIID subunit 2 (TAF2) and similar eukaryotic sequences.

In yeast, TAF2 functions as a component of the DNA-binding general transcription factor complex TFIID. Its binding to a promoter, whether or not it contains a TATA element, represents the initial step in pre-initiation complex (PIC) formation. TAF2 plays a crucial role in regulating gene expression by RNA polymerase II through various mechanisms, including interaction with transcription activators, recognition and selectivity of core promoters, interactions with TFIIA and TFIIB, chromatin modification via histone acetylation by TAF1, facilitation of DNA unwinding, and initiation of transcription. In mammals, the TAF2 basal transcription factor complex plays a major role in the initiation of RNA polymerase II (Pol II)-dependent transcription . It recognises and binds to promoters with or without a TATA box via its TBP subunit (TATA-box-binding protein), promoting the assembly of the PIC . The complex comprises TBP and TBP-associated factors (TAFs), including TAF1, TAF2, TAF3, TAF4, TAF5, TAF6, TAF7, TAF8, TAF9, TAF10, TAF11, TAF12, and TAF13 . TAF2, in particular, forms a promoter DNA-binding subcomplex with TAF7 and TAF1 .
E3 ubiquitin-protein ligase synoviolin-like, TPR repeats (TPR_SYVN1_N)
Type: Domain

This region of tetratricopeptide (TPR)-like repeats is found at the N-terminal end of human E3 ubiquitin-protein ligase synoviolin (SYVN1), ERAD-associated E3 ubiquitin-protein ligase HRD1 from Saccharomyces cerevisiae, and E3 ubiquitin-protein ligase AMFR, and similar proteins mainly found in animals. SYVN1 accepts ubiquitin specifically from endoplasmic reticulum-associated UBC7 E2 ligase and transfers it to substrates, promoting their degradation. It is a component of the endoplasmic reticulum quality control system . AMFR mediates the polyubiquitination of lysine and cysteine residues on target proteins, such as CD3D, CYP3A4, CFTR, INSIG1, SOAT2/ACAT2 and APOB for proteasomal degradation .
HD-Zip IV, C-terminal domain (HD-Zip_IV_C)
Type: Domain

This entry represents the C-terminal domain in transcription factors of the class IV homeodomain-leucine zipper (HD-Zip IV) including GLABRA2, ANTHOCYANINLESS2 (ANL2), ARABIDOPSIS THALIANA MERISTEM LAYER1 (ATML1), PROTODERMAL FACTOR2 (PDF2), ROC1-9 and HDG1-12, found in plants. This domain is predicted to fold into a central β-sheet with α-helices on both sides.

GLABRA2 regulates the frequency of trichome initiation and determines trichome spacing . ANL2 is involved in anthocyanin distribution and root development . PDF2 and ATML1 are involved in shoot epidermal cell differentiation. ATML1 and PDF2 function redundantly as positive regulators of shoot epidermal cell differentiation, and at least one copy of these genes is essential for embryo development . HDG5 is involved, together with PDF2, in the regulation of flower organ development by promoting the expression of APETALA 3 (AP3) in the epidermis and internal cell layers of developing flowers . ROC1 may be involved in protoderm differentiation and radial pattern formation during early embryogenesis .
Major capsid protein 1, PFV (PFV_capsid)
Type: Family

The Pyrobaculum filamentous virus Major capsid protein is involved in the formation of a helical, filamentous nucleocapsid that measures approximately 400 nm in length and 20 nm in width. This family of proteins works in conjunction with capsid protein 2 to wrap around viral DNA, maintaining it in an A-form. This structural conformation is likely achieved through non-specific desolvation and specific coordination of DNA phosphate groups by positively charged residues. Such a configuration is crucial for protecting viral DNA, particularly under extreme conditions such as the desiccation experienced by the host organism .
Gp11, Phage 80a (Phage_80a_gp11)
Type: Family

This entry represents a small family of phage proteins that include gp11 from Staphylococcus phage 80alpha. This protein is composed of three α-helices and appears to adopt a confident homotrimeric arrangement in structure prediction. The function of this protein is unknown.
Depolymerase 2 capsule K5-specific, C-terminal domain (K52_C)
Type: Domain

This entry represents the C-terminal β-sandwich domain found in bacteriophage-encoded depolymerase 2, capsule K5-specific (K52). This domain is found in phages with dual host specificity, where each phage encodes two different capsule depolymerases with specificity for different capsular types. This domain is C-terminal to a pectin lyase-like fold (

) with enzymatic activity that cleaves bacterial capsular polysaccharides into oligosaccharides.

Depolymerase 2 and related proteins target bacterial capsular polysaccharides. They may function as receptor binding proteins (RBP) and could mediate the attachment to the host capsular exopolysaccharides. They display a depolymerase activity that specifically degrades the K5-type polysaccharides of the Klebsiella pneumoniae capsule, which allows the phage to reach the host cell membrane and bind the entry receptor . These enzymes are often components of phage tail spikes or tail fibres and enable phages to attach to and degrade bacterial capsules, particularly in Klebsiella species.
Gp33 protein (Gp33)
Type: Family

This entry represents the Gene 33 protein (Gp33) found in Bacillus phage SP01 and related bacteriophages. Gp33 from Bacillus phage SP01 is thought to act as a regulatory subunit of the Bacillus subtilis RNA polymerase during viral infection . Some homologs in other bacteriophages are annotated as sigma factor accessory proteins, suggesting a role in modulating host transcription.
Gp168 (Gp168)
Type: Family

This entry represents a bacteriophage protein family that includes Gp168 from phage Twort, which inhibits bacterial DNA replication. The protein exists as a hexamer in solution but binds as a dimer to the bacterial β-clamp, a protein essential for DNA replication. Unlike other β-clamp binding proteins that interact with the hydrophobic binding pocket, Gp168 occupies the central DNA sliding channel of the β-clamp, preventing DNA loading. This represents a novel mechanism for bacteriophage-mediated inhibition of host DNA synthesis. Key residues include Y14, which forms hydrogen bonds with the β-clamp and is essential for the interaction. Gp168 can bind β-clamps from both Staphylococcus aureus and Bacillus subtilis, suggesting cross-species activity. A related protein, Gp240 from phage G1, shares 46% sequence identity with Gp168 and likely functions through a similar mechanism. According to structural and sequence analysis, Gp168 represents a new class of proteins with no significant similarity to other known protein structures .
Gp49 (Gp49)
Type: Family

This entry represents the Gene 49 protein (Gp49) found in Mycobacteriophage D29 and L5. The protein contains disordered regions at both the N-terminal (residues 1-49) and internally (residues 114-157). The C-terminal region contains several conserved cysteine residues that may be functionally important. The specific function of this protein within the phage life cycle has not yet been determined.
Gp58, bacteriophage (Gp58_bacteriophage)
Type: Family

This entry represents a small, highly conserved family of bacteriophage proteins including Gp58 protein from Bacillus phage SP01. The function of this protein remains unknown. The family is characterised by a conserved CxxC motif (CNGCGK) followed by another conserved cysteine, suggesting a potential metal-binding role or zinc-finger-like structure. Members of this family are approximately 35 amino acids in length and are found in various Bacillus phages.
Head completion protein 1 (HCP1)
Type: Family

This entry represents the phage Head completion protein 1 (HCP1) that forms part of the connector complex between the phage capsid and tail in lactococcal phages. This protein has been characterised in Lactococcus phage p2, a member of the Skunavirus genus (formerly 936 group of lactococcal phages), which infects Lactococcus lactis. This protein exhibits an open central channel for viral DNA ejection and plays a crucial role in the morphogenesis of the virion after genome packaging. In lactococcal phage p2, this protein (ORF-8) is located at a position normally occupied by the first head completion protein, binding to both the portal protein and the stopper (head completion protein 2). The connector complex is essential for the packaging of phage DNA inside the capsid and subsequent DNA release during host infection. Similar head completion proteins are likely present in other members of the Skunavirus genus that infect dairy-relevant Lactococcus strains .
Gp82 (Gp82)
Type: Family

This entry represents a family of proteins related to Gene 82 protein (Gp82) from Mycobacterium phage L5. The function of this protein is currently unknown. It is found in mycobacteriophages, which are viruses that infect Mycobacterium species. Structure prediction suggests this protein may form a homodimer.
Tail tubular protein gp12 (Phage_gp12)
Type: Family

This entry represents the tail tubular protein gp12 protein family found in phages. Gp12 exists as a monomer in solution, but assembles into a hexameric nozzle structure when incorporated into the tail complex. In phage T7, six copies of gp12 assemble into a hexameric tube attached to the adaptor protein ring (gp11) at the portal vertex. The nozzle forms part of the tail complex that completes phage assembly after DNA packaging . During phage infection, the nozzle serves as a tunnel for DNA delivery into the host cytoplasm. The tail assembly begins after the terminase complex cleaves the mature DNA genome and dissociates from the portal, allowing the tail proteins to assemble on the exposed portal clip domain .
ORF43.1 (ORF43.1)
Type: Family

This entry represents an uncharacterised protein found in the 3' region of the regA gene (ORF43.1) in Enterobacteria phage RB18 and related proteins. Their function remains unknown.
Repressor protein C (Repressor_C)
Type: Family

This entry represents the repressor protein (c) of the Streptomyces temperate phage phi-c31. This protein is involved in the establishment and maintenance of lysogeny. This protein contains a DNA-binding helix-turn-helix motif near the C-terminal. Lysogens of phi-c31 are not inducible by UV irradiation or by mitomycin C, but can be induced by high multiplicity of infection with c-defective or virulent phages or, in the case of those possessing temperature-sensitive repressors, by heat .
1.05 protein (1.05)
Type: Family

This entry represents an uncharacterised gene 1.05 protein found in Enterobacteria phage T3. The function of this small phage protein is currently unknown. Structure prediction suggests that this region forms a compact domain composed of 6 β-strands that form a small β-sandwich.
Gp5.9 (Gp5.9)
Type: Family

This entry represents a group of phage proteins that act as a DNA mimic to inhibit the bacterial RecBCD complex, encoded by gene 5.9 (Gp5.9). The T7 gp5.9 protein adopts a parallel coiled-coil architecture with an N-terminal β-sheet. The protein's highly acidic surface mimics DNA structure, allowing it to compete with DNA for the binding site on RecBCD. By binding predominantly to the RecB arm domain, gp5.9 prevents RecBCD from binding to DNA, thereby protecting the phage genome from degradation. This inhibitory mechanism is functionally similar to lambda phage Gam protein, though structurally distinct. Low nanomolar concentrations of gp5.9 are sufficient to inhibit RecBCD helicase activity in vitro .

In long proteins, this entry is only found at the C-terminal, while in shorter proteins it covers the full length.
Phage tail protein, C-terminal domain (Gp26_C)
Type: Domain

This entry represents a C-terminal domain that is found in a range of probable phage tail proteins (Gene product 26). The domain forms an elaborated β-sandwich domain.
Tail tube protein, phage 16 (TTP_Phage_16)
Type: Family

This entry represents a family of bacteriophage tail tube proteins. The tail tube forms the inner channel of the contractile tail, which is used for DNA transfer from the capsid to the host during infection.
Y01A (Y01A)
Type: Family

This entry represents a family of small proteins found in T4-like bacteriophages, including Y01A proteins. The function of these proteins is currently unknown. The proteins are approximately 12 kDa in size and are highly conserved across a wide range of phages that infect different bacterial hosts, including Enterobacteria, Acinetobacter, Shewanella, Klebsiella, and other Gram-negative bacteria. Structure prediction suggests that these proteins are composed of a small β-sheet of three strands packed with two α-helices, with an additional β-hairpin between the two helices. Structure prediction also suggests these proteins are likely to form homodimers.
Major outer capsid P8 (MOCP_P8)
Type: Family

This entry represents the major outer capsid protein P8 from dsRNA bacteriophage phi6, which forms the T=13 shell of the nucleocapsid. The protein consists of two α-helical domains: an N-terminal peripheral domain and a C-terminal core domain, joined by a ~10-residue linker that allows the trimer to adopt either a closed or an open conformation. In the open conformation, the trimers swap domains with each other, allowing assembly of the outer shell. This domain-swapping is regulated by calcium concentration, which induces the transition of P8 from the closed to open conformation. The structure includes a proline residue (Pro93) that breaks a helix in the C-terminal domain and may play a role in modulating the equilibrium between open and closed states .
Gp119 (Gp119)
Type: Family

This entry represents the vertex-binding protein gp119 from the jumbo bacteriophage PhiKZ that infects Pseudomonas aeruginosa. This α-helical protein forms part of the vertex-binding complex attached to the inner surface of the viral capsid. Gp119, along with gp28 and the gp85 dimer, forms a sandwich structure at the centre of the vertex-binding complex. It interacts with one major capsid protein (MCP) subunit in hexameric capsomer 1 and with gp91 (which binds to the pentameric capsomer), thereby bridging the pentameric capsomer and hexameric capsomer 1. Neighbouring vertex-binding complexes are connected via interactions between gp28 from one complex and gp119 from an adjacent complex. This protein plays a critical role in stabilising the capsid vertex by facilitating the connection between the pentameric capsomer and surrounding hexameric capsomers. Similar proteins are found in other jumbo phages, suggesting a conserved mechanism for capsid assembly and stabilisation in large viruses .
Gp244 (Gp244)
Type: Family

This entry represents the capsid decoration protein gp244 from jumbo bacteriophage PhiKZ that infects Pseudomonas aeruginosa. This protein is located in the outer surface of the viral capsid, specifically positioned on the top of each pentameric capsomer. The structure consists of a core domain and an N-terminal arm. The core domain mainly consists of three α-helices, a four-stranded β-sheet and a long loop. Five copies of gp244 molecules form a ring-like structure that caps and enhances the stability of a pentameric capsomer. Each gp244 subunit makes contact with two of the five major capsid protein (MCP) subunits within the pentameric capsomer. The N-terminal arm of each gp244 subunit extends towards an adjacent gp244 subunit, engaging in favourable hydrophobic interactions. The long loop in the core domain is positioned near the boundary between two MCP subunits, establishing extensive interactions with both. Additionally, the C-terminal arm of each MCP subunit extends to the junction between two gp244 molecules, interacting with both. This protein plays a critical role in stabilising the pentameric vertices of the capsid. Similar proteins are found in other jumbo phages, suggesting a conserved mechanism for capsid assembly and stabilisation in large viruses .
Gp35 (Gp35)
Type: Family

This entry represents the capsid decoration protein gp35 from jumbo bacteriophage PhiKZ that infects Pseudomonas aeruginosa. This protein decorates the outer surface of the viral capsid near the vertices. Only the C-terminal portion of gp35 (residues 160-266) was resolved in the cryo-EM structure, as the N-terminal portion showed no clear density. Structure predictions suggest the unresolved N-terminal region forms a lengthy loop that could exhibit significant flexibility. Gp35 is positioned at the quasi-three-fold axis formed by each pentameric capsomer and its two adjacent hexameric capsomers 1. This strategic positioning allows gp35 to interact with these three capsomers simultaneously, thereby reinforcing the stability of the viral capsid near the vertices. While trimeric decoration proteins at quasi-three-fold axes are common in other phages (e.g., P74-26, TW1), gp35 is unusual in adopting a monomeric structure. This protein plays a critical role in stabilising the capsid vertex. Similar proteins are found in other jumbo phages, suggesting a conserved mechanism for capsid assembly and stabilisation in large viruses .
Gp85 (Gp85)
Type: Family

This entry represents the vertex-binding protein gp85 from jumbo bacteriophage PhiKZ that infects Pseudomonas aeruginosa. This protein forms a homodimer and functions as a key component of the vertex-binding complex attached to the inner surface of the viral capsid. The gp85 dimer, along with gp28 and gp119, forms a sandwich structure at the centre of the vertex-binding complex. The two subunits within the gp85 dimer share nearly identical structures. This dimer interacts with almost all other members in the vertex-binding complex (except for gp91 and gp184) and also interacts with two major capsid protein (MCP) subunits in hexameric capsomer 1. The gp85 dimer plays a critical role in maintaining the stability of the capsid vertex by bridging multiple components of the vertex structure. Similar proteins are found in other jumbo phages, suggesting a conserved mechanism for capsid assembly and stabilisation in large viruses .
AAA+ ATPase At3g28540-like, C-terminal domain (At3g28540-like_C)
Type: Domain

This domain is found at the C-terminal end of AAA-ATPase At3g28540 from Arabidopsis thaliana and similar plant proteins. This domain is predicted to have a helical bundle and is found associated with

.

The AAA ATPase BCS1 subfamily is a group of proteins that belong to the larger AAA ATPase family. These proteins are characterised by their ATPase activity, which is essential for various cellular processes, including protein unfolding, disassembly of protein complexes, and membrane fusion. The BCS1 subfamily is specifically involved in mitochondrial functions, as indicated by the presence of mitochondrial AAA-ATPases within the group. One member, the AAA-ATPase ASD, is known to play a role in regulating morphology and anatomy during seed maturation. Another member, Protein HYPER-SENSITIVITY-RELATED 4, has a unique function of binding to the Yariv phenylglycoside .
TANC1/2-like, AAA+ ATPase lid domain (AAA_lid_TANC1/2)
Type: Domain

This domain is found in Protein TANC1, TANC2 and similar proteins mainly found in animals. This domain is often found associated with a long region of ankyrin repeats (

).

TANC proteins function as scaffolding components in the postsynaptic density and dendritic spines. These proteins are involved in the organisation and stabilisation of synaptic structures. TANC1 proteins are likely involved in the postsynaptic density, interacting with various synaptic proteins such as DLG1, DLG4, and HOMER1, and may play a role in synaptic signalling and plasticity. TANC2 proteins act as immobile postsynaptic posts in dendritic spines, recruiting KIF1A-driven dense core vesicles, which are crucial for synaptic function and vesicle trafficking. The interaction of TANC2 with KIF1A is modulated by calcium levels, indicating a role in calcium-dependent synaptic processes .
Capsid protein, anulavirus (Anulav_capsid)
Type: Family

The Anulavirus capsid protein family is involved in the formation of a quasi-spherical capsid structure, typically ranging from 25 to 35 nanometers in diameter. This structural protein self-assembles to create the protective shell of a virus, which encases the viral genome. The capsid plays a crucial role in the viral life cycle by protecting the genetic material from degradation and aiding in the delivery of the viral genome into host cells during infection .
Minor capsid protein p17 (P17)
Type: Family

This entry represents the African swine fever virus minor capsid protein p17. This protein is a component of the viral inner capsid shell, where three copies of p17 encircle each p72 capsomer, anchoring them on the inner membrane and forming a rigid zipper structure that stabilises the capsomers. It is essential for the assembly of the capsid and icosahedral morphogenesis. Additionally, p17 inhibits the host cGAS-STING pathway through interaction with STING1 and subsequent interference with the recruitment of downstream components TBK1 and IKBKE. It contains a transmembrane region and is found in the inner envelope of the virus and host endoplasmic reticulum and Golgi membranes .
Minor capsid protein p49 (P49)
Type: Family

This entry represents the minor capsid protein p49 of African swine fever virus (ASFV). The p49 protein plays an essential role in the formation of infectious virus particles. It is particularly required for the formation of the capsid vertices, where it localises in close proximity. Together with the penton and other minor capsid proteins, p49 forms a network below the outer capsid shell that stabilises the whole capsid. During virion assembly, it associates with the viral membrane and likely mediates the docking of the penton complex to the inner membrane, where it recruits capsomers to form the penton core. This protein is expressed during the late phase of the viral replicative cycle .
P15 (P15)
Type: Family

This entry represents a putative 15 kDa capsid protein (P15) found in baculoviruses. The protein is encoded by the p15 gene (also annotated as ORF88) in the Orgyia pseudotsugata multicapsid polyhedrosis virus (OpMNPV) genome. This protein is predicted to be a structural component of the viral capsid. The specific function of this protein in the baculovirus life cycle remains to be fully characterised .
U91 (U91)
Type: Family

This entry represents the herpesvirus U91 protein, a membrane protein with two predicted transmembrane helices. U91 is found in HHV-6B, a betaherpesvirus that causes roseola in young children. The protein is localised to the host cell membrane as a multi-pass membrane protein, with transmembrane regions at positions 18-38 and 98-118. The specific function of U91 in viral infection and pathogenesis remains to be determined .
G-protein coupled receptor BILF1-like (BILF1-like)
Type: Family

This entry represents the gammaherpesvirus G-protein coupled receptor (GPCR) BILF1 and related virus GPCR. These receptors are constitutively active and signal through Gi type G-proteins. BILF1 is a lytic gene in Epstein-Barr virus (EBV) and inhibits cAMP response element-binding protein (CREB) activation via stimulation of endogenous G proteins. The alcelaphine herpesvirus 1 homologue (A5) was found to be non-essential for the induction of malignant catarrhal fever in rabbits. Members of this family are 7-transmembrane GPCRs containing conserved cysteines in the amino terminus and extracellular loops, amino-terminal glycosylation sites, and intracellular phosphorylation sites .