SII-SWORD/CoKE huggingface dataset:
Major core protein 4b (P4B)
Type: Family

This family includes the major core protein 4b from Vaccinia virus, also known as Major core protein OPG129. It is a major component of the virion core that undergoes proteolytic processing during the immature virion (IV) to mature virion (MV) transition. It is essential for the formation of a structurally normal core .
DNA-directed RNA polymerase, 18kDa subunit, poxviral (DNA-dir_RNA_pol_18kDa_poxviral)
Type: Family

DNA-directed RNA polymerases

(also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel.

RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3' direction, is known as the primary transcript.

Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise:

RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs.

RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors.

RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs.

Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700kDa, contain two non-identical large (>100kDa) subunits and an array of up to 12 different small (less than 50kDa) subunits.

The Poxvirus DNA-directed RNA polymerase (

) catalyses DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. The enzyme consists of at least eight subunits, this is the 18kDa subunit.
RNA polymerase-associated transcription specificity factor Rap94 (Pox_Rap94)
Type: Family

The Poxvirus RNA polymerase-associated transcription specificity factor Rap94 associates with RNA polymerase and may mediate binding of the core polymerase to VetF. It is required for transcription of early genes.
Poxvirus VLTF2, trans-activator (Poxvirus_VLTF2)
Type: Family

Late transcription factor VLTF-2, acts with RNA polymerase to initiate transcription from late gene promoters .
Poly(A) polymerase catalytic subunit, Poxvirus (PolyA_pol_cat_Poxvir)
Type: Family

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. This is the catalytic subunit.
Small ribosomal subunit protein eS25 (Ribosomal_eS25)
Type: Family

This entry represents eS25 ribosomal protein, found in eukaryotes and archaea, that is a component of the 40S ribosomal subunit.

Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.

Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome .
Stanniocalcin (Stanniocalcin)
Type: Family

Stanniocalcin (STC) is a calcium-and phosphate-regulating hormone produced in bony fish by the corpuscles of Stannius, which are located close to the kidney. It is a major antihypercalcemic hormone in fish. Recent results suggest that the biological repertoires of STCs in mammals will be considerably larger than in fish and may not be limited to mineral metabolism .
Transcription factor AP-2 (TF_AP2)
Type: Family

Activator protein-2 (AP-2) transcription factors constitute a family of closely related and evolutionarily conserved proteins that bind to the DNA
consensus sequence 5'-GCCNNNGGC-3' and stimulate target gene transcription . Five different isoforms of AP-2 have been identified in mammals, termed AP-2 alpha, beta, gamma, delta and epsilon. Each family member shares a common structure, possessing a proline/glutamine-rich domain in the N-terminal region, which is responsible for transcriptional activation , and a helix-span-helix domain in the C-terminal region, which mediates dimerisation and site-specific DNA binding .

The AP-2 family have been shown to be critical regulators of gene expression during embryogenesis. They regulate the development of facial prominence and limb buds, and are essential for cranial closure and development of the lens ; they have also been implicated in tumorigenesis. AP-2 protein expression levels have been found to affect cell transformation, tumour growth and metastasis, and may predict survival in some types of cancer . Mutations in human AP-2 have been linked with bronchio-occular-facial syndrome and Char Syndrome, congenital birth defects characterised by craniofacial deformities and patent ductus arteriosus, respectively .
Tenuivirus movement protein, NS4 (Tenui_NS4)
Type: Family

NS4 (also known as pc4) transports viral genome to neighbouring plant cells directly through plasmosdesmata, without any budding. It allows efficient cell to cell propagation, by bypassing the host cell wall barrier .
Tryptophan 2,3-dioxygenase (Trp_2_3_dOase)
Type: Family

This is a family of tryptophan 2,3-dioxygenase (

) enzymes involved in tryptophan metabolism, which catalyses the oxidative cleavage of the L-tryptophan (L-Trp) pyrrole ring .
WTF family (WTF)
Type: Family

This Schizosaccharomyces family consists of post-meiotic segregation distorting elements (meiotic drivers). Meiotic drivers are selfish genes that break Mendel's law by skewing transmission rates to their own advantage, thereby contributing to reproductive isolation . WTF family includes diverse meiotic drivers and drive suppressors but they generally drive into >85% of gametes when heterozygous . Wtf4, a member of the large Wtf family, encodes two different proteins: one that acts as a poison and one that acts as an antidote. The antidote remains inside the gametes that contain the wtf4 gene, while the poison is released in the surrounding environment and kills all the gametes that do not posses the antidote .
Mlp lipoprotein (Mlp)
Type: Family

The Mlp (for Multicopy Lipoprotein) family of lipoproteins is found in Borrelia species . These proteins were previously known as 2.9 lipoprotein genes . These surface expressed genes may represent new candidate vaccinogens for Lyme disease . Members of this family generally are downstream of four ORFs called A,B,C and D that are involved in hemolytic activity.
Mycoplasma lipoprotein, central domain (Mycoplasma_lipoprotein_cen_dom)
Type: Domain

This domain is found along with a C-terminal domain (

) in a group of Mycoplasma lipoproteins of unknown function.
Adenovirus E3-15 (Adeno_E3-15)
Type: Family

Adenoviruses have evolved multiple mechanisms to evade the host immune response. Several of the immunomodulatory proteins are encoded in early transcription unit 3 (E3) of human adenoviruses (Ads). These proteins appear to control viral interactions with the host . This entry represents the E3_15 family, including proteins from the E3 region which may protect virus-infected cells from TNF-induced cytolysis .
Caulimovirus virion-associated protein (Caulimo_virion-assoc)
Type: Family

The gene III product of cauliflower mosaic virus (CaMV) is known as virion-associated protein or P3 , which is tightly associated with the virus particles and has a regulatory function in the virus infection cycle. P3 decorate the virions; its N-terminal domain forms an antiparallel α-helical coiled-coil network at the surface and the C-terminal domain interacts with the C-terminal half of the viral coat protein . It is a DNA binding protein in which the DNA binding activity is located on its C-terminal part . A family of related proteins is expressed by other members of the Caulimoviridae.
Protein of unknown function DUF272 (DUF272)
Type: Family

This is a family of proteins of unknown function.
Protein of unknown function DUF273 (DUF273)
Type: Family

This is a family of proteins of unknown function.
ELF protein (ELF)
Type: Family

This is a family of hypothetical proteins from cereal crops.
Aerolysin-like toxin (Aerolysin-like)
Type: Family

This family appears to be distantly related to

. It includes toxins from bacteria, such as Clostridium epsilon toxin ETX , and from eukaryotes, such as the hydralysin-1 from Hydra viridissima .
Ethanolamine utilization protein EutN/carboxysome shell vertex protein CcmL (EutN_CcmL)
Type: Family

The ethanolamine utilization protein EutN is involved in the cobalamin-dependent degradation of ethanolamine . The crystal structure of EutN contains a central five-stranded β-barrel, with an α-helix at the open end of this barrel (

). The structure also contains three additional β-strands, which help the formation of a tight hexamer, with a hole in the centre. This suggests that EutN forms a pore, with an opening of 26 Amstrong in diameter on one face and 14 Amstrong on the other face .

Beside the Escherichia coli ethanolamine utilization protein EutN and the Synechocystis sp. carboxysome (beta-type) structural protein CcmL, this family also includes alpha-type carboxysome structural proteins CsoS4A and CsoS4B (previously known as OrfA and OrfB), propanediol utilization protein PduN, and some hypothetical homologous of various bacterial microcompartments. The carboxysome, a polyhedral organelle, participates in carbon fixation by sequestering enzymes. It is the prototypical bacterial microcompartment. Its enzymatic components, ribulose bisphosphate carboxylase/oxygenase(RuBisCO) and carbonic anhydrase (CA), are surrounded by a polyhedral protein shell. Similarly, the ethanolamine utilization (eut) microcompartment, and the 1,2-propanediol utilization (pdu) microcompartment encapsulate the enzymes necessary for the process of cobalamin-dependent ethanolamine degradation, and coenzyme B12-dependent degradation of 1,2-propanediol, respectively, within its polyhedral protein shells. It is interesting that both carboxysome structural proteins CcmL and CsoS4A assemble as pentamers in the crystal structures, which might constitute the twelve pentameric vertices of a regular icosahedral carboxysome. However, the reported EutN structure is hexameric rather than pentameric. The absence of pentamers in Eut microcompartments might lead to less-regular icosahedral shell shapes. Due to the lack of structure evidence, the functional roles of the CsoS4A adjacent paralog, CsoS4B, and propanediol utilization protein PduN are not yet clear .

This entry represents a family of related bacterial proteins with roles in ethanolamine and carbon dioxide metabolism.
GH3 family (GH3)
Type: Family

GH3 protein was first isolated from Glycine max (soybean) as an early auxin-responsive gene . Later, several plant GH3 family proteins have been identified and classified into three groups: group I proteins synthesise JA-amino acid conjugates , group II proteins produce indole-3-acetic acid (IAA) conjugates , group III protein are involved in the conjugation of amino acids to 4-substituted benzoate . This entry also includes proteins from bacteria, fungi and animals.
Bacillus/Clostridium Ger spore germination protein (Spore_Ger)
Type: Family

Dormant Bacillus subtilis spores germinate in the presence of particular nutrients called germinants. The spores are thought to recognise germinants through receptor proteins encoded by the gerA family of operons, which includes gerA, gerB, and gerK . The GerA proteins are predicted to be membrane associated.
DNA helicase/primase complex-associated protein (HSV_HEPA)
Type: Family

Proteins in this family are a component of the helicase/primase complex. The helicase generates single stranded DNA by unwinding the double helix at the replication forks, and the primase synthesizes short RNA primers that the polymerase then elongates . The function of the proteins, which have no known catalytic activity, is unknown, but they have been shown to be distantly related to B-family polymerases with a substantial reduction in nucleotide binding sites and loss of the active site .
Herpesvirus polymerase accessory protein (Herpes_PAP)
Type: Family

This is an accessory subunit of Herpesvirus DNA polymerase that acts to increase the processivity of polymerisation.
Herpesvirus transcription activation factor (Herpes_TAF50)
Type: Family

This is a family of early or early-intermediate transcription factors. This family includes EBV BRLF1 and similar ORF 50 proteins from other herpesviruses.
Herpesvirus capsid shell protein 1 (Herpes_1)
Type: Family

The family includes the triplex capsid protein 1 (TRX1, UL38 or VP19C) from herpesviruses, which is a structural component of the icosahedral capsid. The capsid is composed of pentamers and hexamers of the major capsid protein, which are linked together by heterotrimers called triplexes. These triplexes are formed by a single molecule of TRX1 and two copies of triplex protein 2 (TRX2) . Additionally, TRX1 is required for efficient transport of TRX2 to the nucleus, which is the site of capsid assembly .
HpcH/HpaI aldolase/citrate lyase domain (Aldolase/citrate-lyase_domain)
Type: Domain

This domain is found in a number of proteins, including 2-keto-3-deoxy-L-rhamnonate aldolase (

), 5-keto-4-deoxy-D-glucarate aldolase (

) and citrate lyase subunit beta (

). This domain has a TIM-barrel fold .
RNA-binding protein Hfq (Hfq)
Type: Family

This entry represents the RNA-binding pleiotropic regulator Hfq, a small, Sm-like protein of bacteria . It helps pair regulatory non-coding RNAs with complementary mRNA target regions. It enhances the elongation of poly(A) tails on mRNA . It appears also to protect RNase E recognition sites (A/U-rich sequences with adjacent stem-loop structures) from cleavage . Being pleiotropic, it differs in some of its activities in different species. Hfq binds the non-coding regulatory RNA DsrA (see Rfam:RF00014) in the few species known to have it: Escherichia coli, Shigella flexneri, Salmonella spp. In Azorhizobium caulinodans, an hfq mutant is unable to express nifA, and Hfq is called NrfA, for nif regulatory factor . The name Hfq reflects phenomenology as a host factor for phage Q-beta RNA replication.

The Hfq protein is conserved in a wide range of bacteria and varies in length from 70 to 100 amino acids. In all cases, a conserved Sm motif is located in the N-terminal halves of the molecules. The Hfq protein of E. coli is an 11kDa polypeptide that forms a hexameric ring-shaped structure. Structural studies have suggested that the β4 strand in one molecule dimerises with the β5 strand of a neighbouring subunit to form the hexamer. These two strands move with a concerted mobility which may explain the stability of the entire structure .

The architecture of the Hfq-RNA complex suggests two, not mutually exclusive, mechanisms by which Hfq might exert its function as modulator of RNA-RNA interactions. First, when Hfq binds single-stranded RNA, the target site is unwound in a circular manner. This would greatly destabilise surrounding RNA structures that are located several nucleotides on either side of the binding site, thereby permitting new RNA-RNA interactions. Secondly, the repetition of identical BPs on the Hfq hexamer implies that the binding surface can accommodate more than just a single RNA target. This would allow simultaneous binding of two RNA strands and could greatly enhance interaction between the strands .
Phosphomannomutase (PMM)
Type: Family

This enzyme (

) is involved in the synthesis of the GDP-mannose and dolichol-phosphate-mannose required for a number of critical mannosyl transfer reactions .
Bacteriophage lambda, Tail fiber protein, repeat-1 (Phage_lambda_Stf-r1)
Type: Repeat

This entry represents repeat 1 of Tail fibre protein from Bacteriophage lambda (Stf or Gp27) and similar proteins from the tailed bacteriophages Caudovirales, such as Long-tail fibre protein gp37 from Bacteriophage T4 (Gp37), and prophages mainly found in Gammaproteobacteria such as Prophage side tail fibre protein homologue StfQ from Escherichia coli (strain K12).

The strain of the Bacteriophage lambda used in most laboratories in the early 1990's carried some mutations respect to the wild type. Stf is the gene product of one of these mutations, which allow the virus to bind to an additional outer membrane receptor and accelerate the rate of adsorption onto the host cell surface but a higher failed infection frequency .
Poxvirus C4/C10 (Poxvirus_C4/C10)
Type: Family

This family represents proteins found in Poxvirus, including Protein C10 and Protein C4. Vaccinia virus protein C4 plays a role in the inhibition of host NF-kappa-B activation. It blocks the subunit p65/RELA translocation into the host nucleus .
Poxvirus F12L (Poxvirus_F12L)
Type: Family

The vaccinia virus F12L gene encodes a 65kDa protein called Protein OPG056 that is expressed late during infection and is important for plaque formation, EEV production and virulence. The F12L protein is located on intracellular enveloped virus (IEV) particles, but is absent from immature virions, intracellular mature virus and cell-associated enveloped virus. F12L shows co-localization with endosomal compartments and microtubules and appears to play a role in the the transport of IEV particles to the cell surface on microtubules. Together with protein OPG064/E2, forms a complex that interacts with host KLC2 (kinesin light chain isoform 2) to engage the kinesin-1 complex and thereby promote IEV trafficking .
Poxvirus J1 (Poxvirus_J1)
Type: Family

This family includes proteins from Poxvirus, such as Protein J1 (also known as Virion assembly protein OPG100), a late protein which is a part of a large complex required for early virion morphogenesis. This complex participates in the formation of virosomes and the incorporation of virosomal contents into nascent immature virions. J1 protein is important for DNA packaging during immature virions (IV) formation .
Poxvirus L3/FP4 (Poxvirus_L3/FP4)
Type: Family

This is a family of proteins expressed by members of the Poxviridae. Protein L3, also known as Protein OPG097, is required for transcription of early genes .
Poxvirus rifampicin-resistance (Poxvirus_Rif-R)
Type: Family

This family represents the Poxvirus rifampicin resistance protein (Scaffold protein OPG125), a scaffold protein which forms a transitory spherical honeycomb lattice providing curvature and rigidity to the convex membrane of crescent and immature virions (IV). This association occurs concomitantly with viral membrane formation. It is targeted by the drug rifampicin, which prevents the formation of this lattice, and hence virus morphogenesis. In the presence of rifampicin, irregularly shaped membranes that lack the honeycomb layer accumulate around areas of electron-dense viroplasm. This layer is lost from virions during maturation from IV to mature virion (MV), through the proteolysis of OPG158 N terminus .
Poxvirus mRNA capping enzyme, small subunit (Poxvirus_mRNA-cap_ssu)
Type: Family

This protein family includes mRNA-capping enzyme regulatory subunit OPG124, also known as mRNA-capping enzyme small subunit, from Vaccinia virus. This protein stabilizes the catalytic subunit and enhances its methyltransferase activity through an allosteric mechanism .

Vaccinia virus, the prototypic poxvirus, possesses a double-stranded DNA genome of 191,686 base pairs capable of encoding approximately 200 proteins. Virion enzymes produce mature viral mRNA with eukaryotic features, including a 5' cap and a 3' poly(A) tail. V. virus mRNA capping enzyme is a multifunctional protein with RNA triphosphatase, RNA guanylyltransferase, RNA (guanine-7) methyltransferase, and transcription termination factor activities. The protein is a heterodimer of 95kDa and 33kDa subunits encoded by the v.virus D1 and D12 genes, respectively. The capping reaction entails transfer of GMP from GTP to the 5'-diphosphate end of mRNA via a covalent enzyme-(lysyl-GMP) intermediate.
Rhabdovirus M1 matrix protein (Rhabdo_M1)
Type: Family

This is a family of phosphoproteins of unknown function expressed by Rhadovirus.
SNU66/SART1 family (SNU66/SART1)
Type: Family

This entry represents U4/U6.U5 tri-snRNP-associated proteins, including SART1 from animals, Snu66 from yeasts and DOT2 from Arabidopsis.
Dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48kDa subunit (DDOST_48_kDa_subunit)
Type: Family

Members of this family are involved in asparagine-linked protein glycosylation. In particular, dolichyl-diphosphooligosaccharide-protein glycosyltransferase (DDOST), also known as oligosaccharyltransferase (

), transfers the high-mannose sugar GlcNAc(2)-Man(9)-Glc(3) from a dolichol-linked donor to an asparagine acceptor in a consensus Asn-X-Ser/Thr motif. In most eukaryotes, the DDOST complex is composed of three subunits, which in humans are described as a 48kDa subunit, ribophorin I, and ribophorin II . However, the yeast DDOST appears to consist of six subunits (alpha, beta, gamma, delta, epsilon, zeta). The yeast beta subunit is a 45kDa polypeptide, previously discovered as the Wbp1 protein, with known sequence similarity to the human 48kDa subunit and the other orthologues. This family includes the 48kDa-like subunits from several eukaryotes; it also includes the yeast DDOST beta subunit Wbp1.

Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit Wbp1 is the beta subunit of the OST complex, one of the original six subunits purified . Wbp1 is essential , but conditional mutants have decreased transferase activity .