SII-SWORD/CoKE huggingface dataset:
Baseplate tail-tube protein gp48, T4-like virus (Gp48_T4-like)
Type: Family

This viral tail tube protein is also referred to as Gp48. It is required for the assembly and length regulation of the tail tube of bacteriophage T4 .
RNA polymerase, 132kDa subunit, poxvirus-type (RNA_pol_132_poxvirus)
Type: Family

All three classes of poxvirus genes -early, intermediate and late -are transcribed by the viral RNA polymerase compex . This complex is composed of nine distinct subunits which total more than 500kDa in mass. The two largest subunits (147 and 136kDa) are homologous to the largest subunits of eukaryotic and prokaryotic RNA polymerases and, like them, are thought to form a claw-shaped structure whose cleft is the site of template interaction and phosphodiester bond formation. While the smaller subunits of poxvirus RNA polymerase show much less similarity, if any, to the smaller subunits of the eukaryotic and prokaryotic enzymes, it is thought that they may play a similar role in interacting with transcription factors.

The 132kDa subunit is the second largest subunit of the poxvirus DNA dependent RNA polymerase and shows structural similarity to the second-largest RNA polymerase subunits of eubacteria, archaebacteria, and eukaryotes.
LDB19, N-terminal (LDB19_N)
Type: Domain

This entry represents a predicted Ig-like β sandwich domain found towards the N terminus of protein LDB19 . It is also found in other sequences and is related to the arrestin N-terminal fold .
Protein of unknown function DUF2688 (DUF2688)
Type: Family

Members of this protein family are annotated as KleB, and may play a role in the regulation of transcription in plasmids.
Mechanosensitive ion channel MscS, porin domain (MscS_porin)
Type: Domain

The small mechanosensitive channel, MscS, is a part of the turgor-driven solute efflux system that protects bacteria from lysis in the event of osmotic shock . The MscS protein alone is sufficient to form a functional mechanosensitive channel gated directly by tension in the lipid bilayer. The MscS proteins are heptamers of three transmembrane subunits with seven converging M3 domains, and this MscS_porin is towards the N-terminal of the molecules. The high concentration of negative charges at the extracellular entrance of the pore helps select the cations for efflux .

This entry represents the porin domain of MscS proteins.
RNA polymerase, 30kDa subunit, chordopox-type, N-terminal (RNA_pol_30_chordopoxvir-type_N)
Type: Domain

All three classes of poxvirus genes -early, intermediate and late -are transcribed by the viral RNA polymerase compex . This complex is composed of nine distinct subunits which total more than 500kDa in mass. The two largest subunits (147 and 136kDa) are homologous to the largest subunits of eukaryotic and prokaryotic RNA polymerases and, like them, are thought to form a claw-shaped structure whose cleft is the site of template interaction and phosphodiester bond formation. While the smaller subunits of poxvirus RNA polymerase show much less similarity, if any, to the smaller subunits of the eukaryotic and prokaryotic enzymes, it is thought that they may play a similar role in interacting with transcription factors.

This entry represents the N-terminal domain of the 30kDa subunit of RNA polymerase from the chordopox branch of poxviruses . This subunit may have a role in RNA chain elongation.
The function of this domain is not known, but it contains two conserved sequence motifs, GIEYSKD and LRY, and shows structural similarity to the eukaryotic transcriptional elongation factor SII.
CLASP N-terminal domain (CLASP_N_dom)
Type: Domain

This domain is found in the N-terminal region of CLIP-associated proteins (CLASPs), which are widely conserved microtubule plus-end-tracking proteins that regulate the stability of dynamic microtubules . The domain is also found in other proteins involved in microtubule binding, including STU1, MOR1 and spindle pole body component Alp14.
Conjugal transfer protein TrbD, putative (Conjug_TrbD_put)
Type: Family

Members of this protein family are annotated as conjugal transfer protein TrbD; however, currently no function is known.
Poxvirus poly(A) polymerase, catalytic subunit, C-terminal (Poxvirus_polyA_pol_cat_C)
Type: Domain

Poly(A) polymerase (

) catalyses template-independent extension of the 3'-end of a DNA or RNA strand by one nucleotide at a time. The Poxvirus enzyme creates the 3'(poly)A tail of mRNAs, and is a heterodimer of a catalytic and a regulatory subunit. The Poxvirus enzyme creates the 3'(poly)A tail of mRNAs, and is a heterodimer composed of a catalytic (VP55, also known as PAP-L) and a regulatory subunit (VP39). VP55 comprises three domains: the N-terminal or N domain, the central or catalytic domain, and the C-terminal or C domain, all three domains having distinct topologies. The core comprises a mixed nine-stranded twisted β sheet, with the first seven strands being folded from one long (118 residue) polypeptide segment that follows the N domain and the last two strands originating from the extreme C-terminal-most 15 residues of the entire polypeptide chain. Of the four α-helices in the catalytic domain, the two longest (J and L) near the surface pack against one side of the β-sheet in a nearly parallel orientation to the β-strands .

This domain is found at the C terminus of the pox virus PolyA polymerase protein VP55 .
Poxvirus poly(A) polymerase, catalytic subunit, N-terminal (Poxvirus_polyA_pol_cat_N)
Type: Domain

Poly(A) polymerase (

) catalyses template-independent extension of the 3'-end of a DNA or RNA strand by one nucleotide at a time. The Poxvirus enzyme creates the 3'(poly)A tail of mRNAs, and is a heterodimer of a catalytic and a regulatory subunit. The Poxvirus enzyme creates the 3'(poly)A tail of mRNAs, and is a heterodimer composed of a catalytic (VP55, also known as PAP-L) and a regulatory subunit (VP39). VP55 comprises three domains: the N-terminal or N domain, the central or catalytic domain, and the C-terminal or C domain, all three domains having distinct topologies. The core comprises a mixed nine-stranded twisted β sheet, with the first seven strands being folded from one long (118 residue) polypeptide segment that follows the N domain and the last two strands originating from the extreme C-terminal-most 15 residues of the entire polypeptide chain. Of the four α-helices in the catalytic domain, the two longest (J and L) near the surface pack against one side of the β-sheet in a nearly parallel orientation to the β-strands .

This domain is found at the N terminus of the pox virus Poly(A) polymerase protein VP55 .
Protein of unknown function DUF2628 (DUF2628)
Type: Family

Some members in this family of proteins have been annotated as YigF. Their function is currently unknown.
Protein of unknown function DUF2635 (DUF2635)
Type: Family

This family consists of uncharacterised proteins found in bacteria and bacteriophages. It includes protein Gp38 from Enterobacteria phage Mu.
WYL domain containing protein (WYL_prot)
Type: Family

This entry represents a group of WYL domain containing proteins. WYL is named for three conserved amino acids found in a subset of domains of this superfamily. These residues are not strongly conserved throughout the family. Rather, the conservation pattern includes four basic residues and a position often occupied by a cysteine , which are predicted to line a ligand-binding groove typical of the Sm-like SH3 β-barrels. It is predicted to be a ligand-sensing domain that could bind negatively charged ligands, such as nucleotides or nucleic acid fragments, to regulate CRISPR-Cas and other defense systems such as the abortive infection AbiG system .
Domain of unknown function DUF2726 (DUF2726)
Type: Domain

This domain found in bacterial proteins has no known function.
Dihydroorotase, bacterial (DHOase_bac)
Type: Domain

This entry represents the catalytic domain of a small family of bacterial dihydroorotases.
Lipid-binding, putative (Lipid-bd_put)
Type: Family

This entry represents a small family of uncharacterised proteins found in Bacteroidetes that may be involved in lipid binding.
Prophage protein BhlA/UviB (Phage_BhlA/UviB)
Type: Family

BhlA is a SP-beta prophage-derived protein found in Bacillus subtilis and other Bacilli. A related protein, UviB, has also been described in Clostridia, where it is believed to be involved in bacteriocin secretion or immunity .
Phage tail assembly chaperone TAC-10 (TAC-10)
Type: Family

This is a family of phage tail assembly chaperone proteins .
Protein 3a, betacoronavirus (Protein_3a_bCoV)
Type: Family

Coronavirus encodes two viroporins, E protein and protein 3a, which act as ion-conductive pores in planar lipid bilayers and are required for maximal SARS-CoV replication and virulence . In betacoronavirus, this protein plays a role in viral egress via lysosomal trafficking . Protein 3a from SARS-CoV-2 also blocks autolysosomes formation by binding and sequestering the host component VPS39 for homotypic fusion and protein sorting (HOPS) on late endosomes. This prevents fusion of autophagosomes with lysosomes, disrupting autophagy and facilitating virus egress .

This entry represents protein 3a encoded by Orf3/3a, also known as X1, which forms homotetrameric potassium, sodium or calcium sensitive ion channels (viroporin) and may modulate virus release. It has also been shown to up-regulate expression of fibrinogen subunits FGA, FGB and FGG in host lung epithelial cells .

3a protein is a pro-apoptosis-inducing protein. It localises to the endoplasmic reticulum (ER)-Golgi compartment. SARS-CoV causes apoptosis of infected cells through NLRP3 inflammasome activation, as ORF3a is a potent activator of the signals required for this activation, pro-IL-1beta gene transcription and protein maturation. This protein also promotes the ubiquitination of apoptosis-associated speck-like protein containing a caspase recruitment domain (ASC) mediated by its interaction with TNF receptor-associated factor 3 (TRAF3). The expression of ORF3a induces NF-kappa B activation and up-regulates fibrinogen secretion with the consequent high cytokine production . Another apoptosis mechanism described for this protein is the activation of the PERK pathway of unfolded protein response (UPR), which causes phosphorylation of eIF2alpha and leads to reduced translation of cellular proteins as well as the activation of pro-apoptotic downstream effectors (i.e ATF4, CHOP) .
N-acetylmuramidase (Muramidase)
Type: Domain

This domain is found in proteins from bacteria and viruses. It is found C-terminal in a novel Salmonella bacteriophage endolysin, where it has been shown to be responsible for its N-acetylmuramidase (lysozyme) activity .
Protein of unknown function DUF3833 (DUF3833)
Type: Family

This is a family of uncharacterised proteins found in Proteobacteria.
Phage tail assembly chaperone protein, TAC (Phage_TAC_12)
Type: Family

This is a family of phage tail assembly chaperone proteins from Siphoviridae phages. TACs are required for the morphogenesis of all long-tailed phages. The proposed function for the TAC is to coat the tape-measure protein to prevent it from forming unproductive complexes or precipitating before the tail tube protein has been incorporated .
Tail terminator, bacteriophage (Tail_terminator_phage)
Type: Family

This entry represents a family of likely phage tail termination proteins which form a hexameric ring that connects the phage neck to the tail.
Lsr2 dimerization domain (Lsr2_dim_dom)
Type: Domain

This entry represents the dimerization domain found at the N-terminal of Lsr2. Lsr2 dimers show a self-associative propensity allowing chromosome compaction and gene regulation in response to external stress .

Lsr2 is a small, basic DNA-binding protein present in Mycobacterium and related actinomycetes that regulates gene expression and influences the organization of bacterial chromatin. Lsr2 is a dimer that binds to AT-rich regions of chromosomal DNA and physically protects DNA from damage by reactive oxygen intermediates (ROI). It is a functional homologue of the H-NS-like proteins . H-NS proteins play a role in nucleoid organisation and also function as a pleiotropic regulator of gene expression .

The Lsr2 protein is composed of two domains. The N-terminal domain mediates the dimerization of Lsr2 . The C-terminal DNA-binding domain of Lsr2 interacts with the minor groove of DNA, and shares similarity to other bacterial nucleoid-associated DNA-binding domains . The C-terminal domain is found associated with a variety of other protein domains (such as Ku and Ribonuclease T) where it presumably provides a DNA-binding activity.
Bacteriophage phiKZ, Orf92, internal head (Phage_phiKZ_Orf92_int-head)
Type: Family

Phage internal head proteins (IP) are proteins that are encoded by a bacteriophage and assembled into the mature virion inside the capsid head. The most analogous characterised IP proteins are those of bacteriophage T4, which are known to be proteolytically processed during phage maturation, and then subsequently injected into the host cell during infection. The phiKZ_IP family consists of internal head proteins encoded by phiKZ-like phages. Each phage encodes three to six members of this family . Members of the family reside in the head and are cleaved during phage maturation to separate an N-terminal propeptide from a C-terminal domain. The C-terminal domain remains in the mature capsid. The N-terminal propeptide domain is either mostly or completely removed from the mature capsid. In one case, an unrelated polypeptide is embedded in the propeptide and also remains in the mature capsid. The phiKZ-like IP proteins are not discernibly homologous to the T4 IP proteins, and it is not known if the phiKZ-like IP proteins are injected into the host cell, or have some other function within the head.
Uncharacterised protein family PrgI (Uncharacterised_PrgI)
Type: Family

This family of bacterial proteins is functionally uncharacterised. Proteins in this family are typically between 116 and 146 amino acids in length. PrgI is found encoded on plasmids of Enterococcus faecalis, its function is not known.
Fungus-induced protein (Fungus-induced)
Type: Family

This entry represents fungus-induced proteins which may have role in hypoxia response .
Protein of unknown function DUF2738 (DUF2738)
Type: Family

This is a family of plant and viral proteins whose function is unknown.
Neuronal protein 3.1 (Neuronal_3.1)
Type: Family

Neuronal protein 3.1, also known as P311, is found in neurone and muscle cells . It contains a conserved PEST (Pro, Glu, Ser, and Thr) motif, which is involved in protein-protein interactions, as well as in targeting proteins for degradation by the ubiquitin/proteasome system.

In addition to a potential role in neural function, P311 may be involved in regulating glioma motility and could have some function in myo-fibroblast transformation and prevention of fibrosis . It has also been identified as a potential regulator of alveolar generation .
Protein of unknown function DUF3862 (DUF3862)
Type: Family

Proteins in this family show structural similarity to beta-lactamase inhibitory proteins.
Protein of unknown function YvrJ (YvrJ)
Type: Family

This entry is represents a family of uncharacterised protein. The function of the Bacillus subtilis YvrJ protein is not known, but its expression is regulated by the cell envelope stress-inducible sigma factor YvrI .
TRAPP III complex, Trs85 (TRAPP_III_complex_Trs85)
Type: Family

This entry represents Trs85, a subunit of the TRAPP III complex . Trs85 is a multimeric guanine nucleotide-exchange factor for Ypt1, required for membrane expansion during autophagy and the CVT pathway. It directs Ypt1 to the phagophore assembly site .
Bacteriophage P22, Mnt (Phage_P22_Mnt)
Type: Family

Mnt is a repressor which is involved in the genetic switch between lysogenic and lytic growth in bacteriophage P22. The C-terminal domain of the protein consists of a dimer of two antiparallel coiled coils with a right handed twist, which is both stronger and has closer inter-helical separation compared with those found in left-handed coiled coils .

This entry is represented by Bacteriophage P22, Mnt. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Protein of unknown function, OB-fold-containing (Protein_unknown_function_OB)
Type: Family

The function of the proteins in this entry is not known, but they contain a novel variant of the nucleic acid-binding OB fold .
Protein of unknown function DUF3050 (DUF3050)
Type: Family

This family of proteins has no known function.
Replicative helicase inhibitor G39P, N-terminal (G39P_N)
Type: Domain

G39P inhibits the initiation of DNA replication by blocking G40P replicative helicase. G39P has a bipartite structure consisting of a folded N-terminal domain and an unfolded C-terminal domain. The C-terminal domain is essential for helicase interaction .
Cell wall-active antibiotics response LiaF-like, C-terminal (LiaF-like_C)
Type: Domain

This domain is found in various prokaryotic proteins, including cell wall-active antibiotic response proteins. This entry includes protein product of the yvqF gene, LiaF, located immediately upstream of vraS. It is associated with glycopeptide resistance in Staphylococcus aureus . This domain has been described as Toast_rack from its structural resemblance.
Protein of unknown function DUF2694 (DUF2694)
Type: Family

This family of proteins with unknown function appears to be restricted to Mycobacterium spp.
Endosialidase, beta-barrel domain (B-barrel_Endosialidase)
Type: Domain

This entry represents the β-barrel domain of endosialidases which is nested in a β-propeller domain. This β-barrel domain is approximately 80 amino acids in length and represents one of the two sialic acid binding sites of the enzyme .
Endosialidase, beta-propeller domain (Endosialidase_beta_prop)
Type: Domain

This entry represents the β propeller domain of endosialidases, which consists of catalytically active part of the enzymes. This core domain forms stable SDS-resistant trimers. There is a nested β barrel domain in this domain. This domain is typically between 443 and 460 amino acids in length .
Endosialidase, N-terminal extension domain (Endosialidase_N-extension)
Type: Domain

This entry represents the N-terminal extension domain of endosialidases which is approximately 70 amino acids in length. The two N-terminal domains (this domain and the β propeller) assemble in the compact 'cap' whereas the C-terminal domain forms an extended tail-like structure. The very N-terminal part of the 'cap' region (residues 246 to 312) holds the only α-helix of the protein and is presumably the residual part of the deleted N-terminal head-binding domain .
Endosialidase, C-terminal domain (Endosialidase_C_dom)
Type: Domain

This entry represents the C-terminal domain of endosialidase, which is approximately 160 amino acids in length. There are two conserved sequence motifs: VSR and YGA. The endosialidase protein forms homotrimeric molecules and this domain complexes into a tail-spike stalk. The stalk region folds in a triple β-helix that is interrupted by a small triple β-prism domain. The tail-spike is a multifunctional protein device used by the phage to fulfil the following functions: (i) to adsorb to the bacterial polySia capsule (ii) to de-polymerise the capsule to gain access to the outer bacterial membrane, and finally (iii) to mediate tight adhesion to the membrane, a prerequisite for the initiation of the infection cycle .
Insertion element IS1 protein InsA, helix-turn-helix domain (InsA_HTH_dom)
Type: Domain

This entry represents the helix-turn-helix domain found at the C-terminal of InsA.
Putative exodeoxyribonuclease 8, PDDEXK-like domain (Put_RecE_PDDEXK-like_dom)
Type: Domain

This entry represents a PDDEXK-like domain of unknown function found in proteins from bacteria and viruses. Many of these proteins are annotated as exodeoxyribonuclease 8, which is involved in the RecE pathway of recombination. The PD-(D/E)XK domain is ubiquitously found in enzymes involved in metabolism of nucleic acids, mostly in nucleases .
TSCPD domain (TSCPD_dom)
Type: Domain

The domain is found in isolation in many proteins where it has a conserved C-terminal motif TSCPD, after which the domain is named. Most copies of the domain possess 4 conserved cysteines that may be part of an Iron-sulphur cluster. This domain is found at the C-terminal of some ribonucleoside-diphosphate reductase enzymes.
Histidyl tRNA synthetase-related domain (HisRS-related_dom)
Type: Domain

This entry represents the histidyl-tRNA synthetase-related (HisRS-related) domain, found largely in Gcn2 protein kinases . In yeast, Gcn2 phosphorylates the alpha subunit of eukaryotic initiation factor-2 (eIF-2) when the cells face the starvation for amino acids. The HisRS-related domain is required for activation of Gcn2 kinase function .
Domain of unknown function DUF3824 (DUF3824)
Type: Domain

This repeating domain is proline-rich but its function is unknown.
Domain of unknown function DUF3825 (DUF3825)
Type: Domain

This uncharacterised domain has conserved residues suggestive of an enzymatic role probably related to RNA metabolism.
Staygreen protein (Staygreen)
Type: Domain

This domain is found in a family of proteins have been implicated in chlorophyll degradation . Intriguingly members of this family are also found in non-photosynthetic bacteria.
RNHCP domain (RNHCP)
Type: Domain

This domain is found in uncharacterised bacterial proteins. It is typically between 94 and 143 amino acids in length and has a conserved RNHCP sequence motif.
Colicin D, C-terminal (ColicinD_C)
Type: Domain

Colicin D is a bacteriocin that kills target cells by cleaving tRNA(Arg). This entry represents a domain found in the C terminus of colicin D, which is responsible for its catalytic activity . The domain is also found in some S-type pyocins, which are also bacteriocins.
Mating-type protein, C-terminal domain (Homeodomain1_C)
Type: Domain

Mating in fungi is controlled by the loci that determine the mating type of an individual, and only individuals with differing mating types can mate. Basidiomycete fungi have evolved a unique mating system, termed tetrapolar or bifactorial incompatibility, in which mating type is determined by two unlinked loci; compatibility at both loci is required for mating to occur. The multi-allelic tetrapolar mating system is considered to be a novel innovation that could have only evolved once, and is thus unique to the mushroom fungi.

This domain is found in the C-terminal of some mating-type proteins.
Transposase, zinc-ribbon (Transposase_Zn_ribbon)
Type: Domain

This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding β-ribbon domain that could bind DNA.
Protein of unknown function DUF3197 (DUF3197)
Type: Family

This protein family, whose function is unknown, is found in bacterial proteins.
Protein of unknown function DUF2706 (DUF2706)
Type: Family

This family of proteins with unknown function appears to be restricted to Rickettsia spp.
ISXO2-like transposase domain (Tnp_ISXO2-like)
Type: Domain

This domain probably functions as an integrase that is found in a wide variety of transposases, including ISXO2.
PXPV repeat (PXPV)
Type: Repeat

This short repeat is found in multiple copies in a variety of proteins predominantly found in proteobacteria. The function of this region is unknown.
YXWGXW repeat (YXWGXW_rpt)
Type: Repeat

This short repeat contains the motif YXWXXGXW where X can be any amino acid. It is generally found in 2-5 copies in short secreted bacterial proteins. Its function is as yet unknown.
Xylosyltransferase, C-terminal (XylT_C)
Type: Domain

This domain is found in metazoan xylosyltransferases, which include xylosyltransferase 1 and xylosyltransferase 2. These enzymes initiate the biosynthesis of glycosaminoglycan chains in proteoglycans by transferring xylose from UDP-xylose to specific serine residues of the core protein .