SII-SWORD/CoKE huggingface dataset:
Crassvirus muzzle protein, N-terminal region (crAss_MUZ_N)
Type: Domain

This entry represents the N-terminal region of muzzle protein found at the distal end of the tail in bacteriophages of the Crassviridae family.

This large protein forms a hexameric assembly at the tip of the tail barrel and exhibits a novel fold designated as the 'crass fold'. The muzzle protein is composed of five domains: a ring-joining domain, a seven-bladed β-propeller domain, two immunoglobulin-like domains (IG1 and IG2), and the crass domain. The muzzle protein forms a gate-like structure that likely serves as a gatekeeper controlling the ejection of cargo proteins and viral DNA during infection. The gate is formed by a loop within blade 4 of the propeller domain. The crass domain, with its exposed surface loops, likely plays a role in contacting the host cell surface, initiating conformational changes that open the gate. The muzzle protein is highly conserved among crassviruses, though with length variations resulting from insertions in the crass and IG2 domains that affect surface properties. This protein has been structurally characterised in Bacteroides phage crAss001 .
KCTD7/14, C-terminal domain (KCTD7/14_C)
Type: Domain

This entry represents the C-terminal domain found in KCTD7 and KCTD14. The domain has a consistent structural motif with three antiparallel β-sheets packing against one α-helix. This domain adopts different interfaces in different KCTD subfamily members, resulting in distinct substrate binding mechanisms. The domain forms part of a pentameric assembly in native KCTD proteins. This domain is associated with

.

KCTD7 is a BTB/POZ domain-containing protein that has an impact on K+ fluxes, neurotransmitter synthesis, and neuronal function. It functions as a regulator of potassium conductance in neurones and is involved in the control of excitability of cortical neurones. KCTD7 may be involved in the control of the excitability of cortical neurones . Mutations in KCTD7 may cause progressive myoclonus epilepsy (PME) .
KCTD7, BTB domain (BTB_KCTD7)
Type: Domain

This entry represents the BTB domain in KCTD7 proteins.

KCTD7 is a BTB/POZ domain-containing protein that has an impact on K+ fluxes, neurotransmitter synthesis, and neuronal function. It functions as a regulator of potassium conductance in neurones and is involved in the control of excitability of cortical neurones. KCTD7 may be involved in the control of the excitability of cortical neurones . Mutations in KCTD7 may cause progressive myoclonus epilepsy (PME) .
Liprin-alpha, CC2 domain (LIP-1_CC2)
Type: Domain

This entry describes the dimeric coiled coil (CC2) found in liprin-alpha proteins mainly from animals. The CC2 domain is located after the coiled coil domain 1 (CC1). The long CC2 coiled coils are toward the outside of this CC1 oligomer, making them accessible for recognition by presynaptic binding partners of liprin-alpha, such as ELKS and RIM . This domain is usually found associated with

.

Liprin-alpha proteins contain three copies (repeats) of the SAM domain, which is a protein-protein interaction domain. They may form heterodimers with liprin-beta proteins through their SAM domains (

,

,

). They participate in mammary gland development and in axon guidance; in particular, liprin-alpha is involved in formation of the presynaptic active zone .

Liprin was originally identified as binding partners of the receptor protein tyrosine phosphatase LAR (leukocyte common antigen-related), which functions in axon guidance and mammary gland development . In vertebrates, there are two families of liprins, liprin-alpha and liprin-beta, which have four (alpha1-4) and two (beta1-2) members. In C. elegans and Drosophila, there are only one liprin-alpha (known as Syd-2 and Dliprin-alpha) and one liprin-beta. Another liprin family member, liprin-gamma, has also been identified in Drosophila . Liprins contain an N-terminal coiled-coil domain and a C-terminal liprin homology (LH) region comprised of three sterile alpha motif (SAM) domains . The N-terminal coiled coils of liprin-alpha mediate interactions with adapter proteins at the presynaptic active zone, while the SAM repeats bind proteins such as LAR receptor tyrosine phosphatase .
Leucine rich repeat variant domain (LRV_2)
Type: Domain

This entry represents a likely small cytoplasmic domain found in a small set of bacterial integral membrane proteins. This domain is composed of a couple of leucine-rich repeat variants. The function of this domain is unknown.
Major capsid protein 1 (MCP1_SIFV)
Type: Family

This entry represents the major capsid protein 1 (MCP1) found in filamentous viruses that infect hyperthermophilic archaea living in extreme environments (temperatures of 80-90 degrees C with pH values of 2-3). The MCP1 proteins form either homodimers or heterodimers with MCP2 and wrap around the viral DNA, maintaining it in an A-form, which helps protect the genome in extreme conditions. These proteins typically contain N-terminal α-helices that interact with the viral DNA and C-terminal four-helix bundles. In enveloped viruses, MCP1 can have a C-terminal extension that reaches out to make contacts with subunits in adjacent helical turns. Despite low sequence similarity between MCP1 proteins from different archaeal filamentous viruses, they share a relatively conserved fold, demonstrating common ancestry .
Mom (Mom)
Type: Family

The Mom protein family comprises iron-binding proteins that catalyse the methylcarbamoylation of adenine using acetyl-Coa. This modification, known as momylation, converts adenine into N6-methylcarbamoyl adenine, rendering viral DNA resistant to various host type I and type II restriction enzymes. Approximately 15% of DNA adenine residues are modified, targeting sequences 5'-(C or G)-A-(C or G)-N-(C or T)-3' . This process occurs just before viral DNA packaging and can also modify adenine residues in host cellular DNA, providing a protective mechanism against host defences. This family is related to the DruA family

.
Mitochondrial transcription rescue factor 1, C-terminal domain (MTRES1_C)
Type: Domain

This domain is found at the C-terminal end of MTRES1 and related proteins. This domain is predicted to fold as a β-sheet with two α-helices on one side.

Mitochondrial transcription rescue factor 1 (MTRES1) is a mitochondrial RNA-binding protein involved in the regulation of mitochondrial transcription. It functions as a protective factor that maintains appropriate mitochondrial RNA levels under stress conditions, with its protective role dependent on its RNA-binding capacity . In addition, MTRES1 is part of a mitoribosome-associated quality control pathway that safeguards against aberrant translation by responding to elongation interruptions during protein synthesis , . Acting as a heterodimer with MTRF, it facilitates the ejection of unfinished nascent polypeptide chains and peptidyl tRNAs from stalled ribosomes. The recruitment of mitoribosome biogenesis factors to these quality control intermediates suggests that MTRES1 and MTRF may also participate in mitoribosome rescue mechanisms .
Gp73 (Gp73)
Type: Family

This entry represents a family of small proteins found in mycobacteriophages, typified by the gene 73 protein (Gp73) from Mycobacteriophage L5. The function of this protein family is currently unknown. The protein is relatively small (85 amino acids) and appears to be phage-specific. Mycobacteriophage L5 is a temperate phage that infects Mycobacterium species and has been used as a genetic tool for mycobacterial genetics.
Gp3 (Gp3)
Type: Family

This entry represents a family of small proteins found in mycobacteriophages. Members of this family include the Gene 3 protein (Gp3) from mycobacteriophages L5 and D29, which belong to the Fromanvirus genus. The function of these proteins remains unknown. The proteins are approximately 83 amino acids in length and show conservation in the central region, particularly around potential binding sites.
Gp53 (Gp53)
Type: Family

This entry represents the mycobacteriophage Gene 53 protein (Gp53) found in phages such as L5 and D29 that infect Mycobacterium species. The specific function of this protein has not been experimentally determined.
Gp67, mycobacteriophage L5 (Gp67_L5)
Type: Family

This entry represents a small protein found in mycobacteriophage L5 and related phages Gp67. The protein is 43 amino acids in length. The specific function of this protein remains to be determined.
Gp42 (Gp42)
Type: Family

This entry represents the Gene 42 protein (Gp42) found in mycobacteriophages such as D29 and L5. These are small proteins of approximately 70 amino acids in length. The specific function of this protein family is currently unknown. The predicted structure contains a three-stranded β-sheet with an α-helix between strands 1 and 2. Proteins in this family are often annotated as minor tail proteins.
Transcriptional antitermination N peptide (N_peptide)
Type: Family

This entry represents the bacteriophage N protein (or Probable regulatory protein N), which plays an essential role in transcriptional antitermination. Upon interaction with the N-utilisation (nut) site on the nascent phage transcript, and together with host factors, the N protein converts the RNA polymerase to a termination-resistant form. The arginine-rich region (~18 amino acids) at the N-terminal of the N protein is specifically recognised by its boxB RNA hairpin target. Besides binding to boxB RNA, N protein also interacts with a host factor called NusA. The N peptide adopts a bent α-helical conformation that packs tightly through hydrophobic and electrostatic interactions against the major groove face of the boxB RNA hairpin. Multiple arginines in the peptide form hydrogen bonds with the RNA at specific positions . This family is likely related to

.
Bacteriophage N4, Gp8 (Phage_N4_Gp8)
Type: Family

This entry represents Gene product 8 (Gp8), a phage-encoded inhibitor of bacterial DNA replication. The protein is encoded by coliphage N4 and targets the host DNA sliding clamp by interacting with the delta subunit of the E. coli DNA polymerase III clamp loader. The protein inhibits replication elongation and is bacteriostatic. It specifically interferes with DNAP III processivity by interacting with the E. coli DNAP III delta subunit and inhibiting clamp loading. This represents a novel target in the bacterial replisome for inhibition of bacterial growth.
Nal1, C-terminal domain (Nal1_C)
Type: Domain

This entry represents the C-terminal in Nal1 found in rice and related plant proteins. The C-terminal of Nal1 has been determined to have serine protease activity. It consists of two perpendicular six-stranded β-barrel subdomains, and the putative catalytic triad is composed of H233, D291 and S385 . This entry also includes peptidases from bacterial proteins.

Narrow leaf 1 (Nal1) is a serine protease with pleiotropic roles in plant development, affecting several agronomic traits including leaf width, plant height, root architecture, and grain yield . Nal1 regulates lateral leaf growth by modulating basipetal polar auxin transport and vascular patterning, which are essential for proper leaf development. It also influences photosynthetic efficiency by regulating carboxylation activity, thereby impacting the rate of photosynthesis . In addition, Nal1 degrades the TOPLESS-related corepressor OsTPR2, thereby modulating the expression of downstream genes involved in hormone signalling pathways. Nal1 proteins also contribute to the determination of panicle and spikelet numbers, traits that are directly associated with grain productivity.
Nal1, N-terminal domain (Nal1_N)
Type: Domain

This entry represents the N-terminal domain in Nal1 found in rice and other plants. This domain contains an ATP-binding pocket that mediates the formation of a hexameric structure consisting of two stacked trimeric rings. ATP is embedded in a positively charged pocket stabilised by a network of residues, including R120, R122, K123, K139 and K142. This domain plays a critical role in the oligomerisation of Nal1, which is important for its protease activity . This entry also includes peptidases from bacterial proteins.

Narrow leaf 1 (Nal1) is a serine protease with pleiotropic roles in plant development, affecting several agronomic traits including leaf width, plant height, root architecture, and grain yield . Nal1 regulates lateral leaf growth by modulating basipetal polar auxin transport and vascular patterning, which are essential for proper leaf development. It also influences photosynthetic efficiency by regulating carboxylation activity, thereby impacting the rate of photosynthesis . In addition, Nal1 degrades the TOPLESS-related corepressor OsTPR2, thereby modulating the expression of downstream genes involved in hormone signalling pathways. Nal1 proteins also contribute to the determination of panicle and spikelet numbers, traits that are directly associated with grain productivity.
Narrow leaf 1 (Nal1)
Type: Family

Narrow leaf 1 (Nal1) is a serine protease with pleiotropic roles in plant development, affecting several agronomic traits including leaf width, plant height, root architecture, and grain yield . Nal1 regulates lateral leaf growth by modulating basipetal polar auxin transport and vascular patterning, which are essential for proper leaf development. It also influences photosynthetic efficiency by regulating carboxylation activity, thereby impacting the rate of photosynthesis . In addition, Nal1 degrades the TOPLESS-related corepressor OsTPR2, thereby modulating the expression of downstream genes involved in hormone signalling pathways. Nal1 proteins also contribute to the determination of panicle and spikelet numbers, traits that are directly associated with grain productivity.
Minor capsid protein P6 (NCLDV_P6)
Type: Family

This entry represents the minor capsid protein P6 found in nucleocytoplasmic large DNA viruses (NCLDVs). In Paramecium bursaria chlorella virus 1 (PBCV-1), P6 plays a role in stabilising the pentasymmetron structures of the viral capsid. The protein has a distinctive structural organisation with an N-terminal arm (residues 26-60), a central globular domain consisting of a five-stranded antiparallel β-sheet wrapped around a central α-helix and flanked by another α-helix, and a C-terminal arm (residues 177-214). The central globular domain is located at the conjunction of capsomers c, d, and f, with its C-terminal arm making contact with the central 3-fold cavity of capsomer d. P6 is likely membrane-associated, with transmembrane helix predictions suggesting the N-terminal may contain transmembrane regions. The short linker between the predicted transmembrane helix and the ordered portion of the protein suggests that the visible portion of P6 is close to the viral inner membrane .
Neuregulin 2, N-terminal domain (NRG2_N)
Type: Domain

This domain is found at the N-terminal in NRG2. This domain is predicted to fold into a β-barrel with an OB-fold topology. It is closely related to

. This domain is not present in other neuregulin proteins such as NRG1 and NRG3.

Neuregulin 2 (NRG2) belongs to the neuregulin family and plays important roles in cell communication. It serves as a direct ligand for ERBB3 and ERBB4 tyrosine kinase receptors . NRG2 recruits ERBB1 and ERBB2 coreceptors, leading to ligand-stimulated tyrosine phosphorylation and activation of the ERBB receptors.

Neuregulins (NRG) are a sub-family of EGF-like molecules that have been shown to play multiple essential roles in vertebrate embryogenesis including: cardiac development, Schwann cell and oligodendrocyte differentiation, some aspects of neuronal development, as well as the formation of neuromuscular synapses . Included in the family are heregulin; neu differentiation factor; acetylcholine receptor synthesis stimulator; glial growth factor; and sensory and motor-neuron derived factor . Multiple family members are generated by alternate splicing or by use of several cell type-specific transcription initiation sites. In general, they bind to and activate the erbB family of receptor tyrosine kinases (erbB2 (HER2), erbB3 (HER3), and erbB4 (HER4)), functioning both as heterodimers and homodimers.
Nanos, NED domain (NED_Nanos)
Type: Domain

This entry represents the effector domain (NED) of Nanos from Drosophila melanogaster and related proteins. This domain is necessary to repress mRNA targets. The NED domain recruits the CCR4-NOT complex through multiple and redundant binding sites, including a central region that interacts with the NOT module, which comprises the C-terminal domains of NOT1-3 . Nanos proteins use short linear motifs to directly recruit the CCR4-NOT complex.

Nanos is a maternal RNA-binding protein essential for the proliferation and self-renewal of germ cells. It functions by forming a translational regulatory complex with Pumilio (Pum) and Brain Tumour (Brat), which modulates mRNA stability and translation. This complex specifically binds to the Nanos Response Element (NRE), a 16-base pair sequence located in the 3'-UTR of hunchback (hb) mRNA, thereby repressing its translation. Nanos also plays a critical role in posterior development and serves as a rescuing factor for abdominal defects observed in posterior group mutants. While other posterior group proteins are not necessary for the functional activity of Nanos, they are involved in its localisation and distribution during embryogenesis .
Neuregulin 2, Ig-like domain (NRG2_Ig-like)
Type: Domain

This entry represents the Ig-like domain in NRG2 and related proteins, mainly found in mammals.

Neuregulin 2 (NRG2) belongs to the neuregulin family and plays important roles in cell communication. It serves as a direct ligand for ERBB3 and ERBB4 tyrosine kinase receptors . NRG2 recruits ERBB1 and ERBB2 coreceptors, leading to ligand-stimulated tyrosine phosphorylation and activation of the ERBB receptors.

Neuregulins (NRG) are a sub-family of EGF-like molecules that have been shown to play multiple essential roles in vertebrate embryogenesis including: cardiac development, Schwann cell and oligodendrocyte differentiation, some aspects of neuronal development, as well as the formation of neuromuscular synapses . Included in the family are heregulin; neu differentiation factor; acetylcholine receptor synthesis stimulator; glial growth factor; and sensory and motor-neuron derived factor . Multiple family members are generated by alternate splicing or by use of several cell type-specific transcription initiation sites. In general, they bind to and activate the erbB family of receptor tyrosine kinases (erbB2 (HER2), erbB3 (HER3), and erbB4 (HER4)), functioning both as heterodimers and homodimers.
Mitochondrial protein cyt-4, OB-fold C-terminal domain (OB_CYT4_C)
Type: Domain

This OB-fold domain is found at the C-terminal in CYT4 from Neurospora crassa and related proteins. This domain is usually found next to

.

CYT4 is a nuclear-encoded protein that plays a crucial role in RNA processing and splicing within mitochondria . CYT4 is required for mitochondrial RNA 5'- and 3'-end processing and splicing .
Capsid protein ORF3b (ORF3b)
Type: Family

This entry represents the coat (capsid) protein ORF3b family found in Oleavirus genus members of the Bromoviridae family, including Olive latent virus 2. The capsid protein self-assembles to form a quasi-spherical capsid of approximately 26 nm, or in a bacilliform shape. The protein is part of the virion and functions in viral RNA binding to form the viral nucleocapsid.
Ourmia capsid protein (Ourmia_CP)
Type: Family

This entry represents the capsid protein (CP) of Ourmia viruses. The protein self-assembles to form a baciliform capsid with a T=1 symmetry, approximately 18 nm in diameter. The capsid encapsulates three genomic RNAs.
Viral coat protein P2, C-terminal domain (P2_C)
Type: Domain

This entry represents the C-terminal jelly roll domain of P2.

P2 (30.2kDa) is the major outer-coat protein of the marine lipid-containing bacteriophage PM2. Each subunit of P2 is composed of two β-barrel jelly rolls, disposed normally to the surface of the capsid, which lend pseudo-6-fold symmetry to the molecules, facilitating their close packing within the capsid. There is a Ca2+ ion located between the two β barrels of P2 that helps PM2 molecular organisation .
DNA transfer protein Gp7 (P22_gp7)
Type: Family

This entry represents the bacteriophage P22 DNA ejection protein Gp7. This protein is one of three ejection proteins (along with Gp16 and Gp20) that are required to facilitate the transport of bacteriophage P22 double-stranded DNA safely through the membranes of Salmonella . These ejection proteins are lost from the virion and are presumed to be released with the DNA during ejection. Cryo-EM studies of empty P22 particles show a tube-like structure extending from the centre of the tail assembly that is likely composed of these ejection proteins . The specific functions of Gp7 in this process are not fully understood, but they appear to be involved in forming a conduit for the transport of DNA into the host cytoplasm, possibly through the outer membrane, peptidoglycan layer, periplasmic space, and inner membrane.
Minor capsid protein P4 (PBCV_P4)
Type: Family

This entry represents a small family of putative metallopeptidases found in the phycodnaviridae group. In Paramecium bursaria chlorella virus (PBCV), a member of this family has been identified as minor capsid protein P4. These proteins contain a HEXXH motif characteristic of metallopeptidases. The P4 protein plays a structural role in stabilising the viral capsid by glueing together neighbouring capsomers. The N-terminal part of P4 (residues 5-23) glues together two neighbouring capsomers. Its central domain (residues 24-54) is folded into a fist-like structure consisting of three short helices. The C-terminal part of P4 anchors in the central 3-fold cavity of a third capsomer. This protein is part of a network of minor capsid proteins that stabilise the viral capsid of nucleocytoplasmic large DNA viruses .
Bacteriophage PhiKZ vertex-binding protein gp86 (PhiKZ_Gp86)
Type: Family

This entry represents the vertex-binding protein gp86 from jumbo bacteriophage PhiKZ that infects Pseudomonas aeruginosa . This protein is a product of proteolytic cleavage by the head maturation protease Gp175, with the N terminus of the modelled part located near verified proteolytic sites. Gp86 has an elongated shape rich in α-helices and forms the peripheral edge of the vertex-binding complex attached to the inner surface of the viral capsid. It is further supported by two minor capsid proteins - Gp162I, which interacts with Gp86 by joining its α-helix with the α-helix bundle of Gp86, and Gp184, which inserts into the hollow between Gp86 and the centre of hexameric capsomer 1. Gp86 extensively interacts with almost all MCP subunits from hexameric capsomer 1 (except for subunit d, where Gp184 fills the gap). This protein plays a critical role in stabilising the capsid vertex by linking the vertex-binding complex to the hexameric capsomer. Similar proteins are found in other jumbo phages, suggesting a conserved mechanism for capsid assembly and stabilisation in large viruses.