SII-SWORD/CoKE huggingface dataset:
Pfam PF18495: Antitoxin VbhA (domain)
VbhT is a bacterial Fic protein of the mammalian pathogen B. schoenbuchensis7,8. It is composed of an N-terminal FIC domain and a C-terminal BID domain. FIC domains are known to catalyse adenylylation (also called AMPylation). This entry represents VbhA, an antitoxin that binds FIC domain (filamentation induced by cyclic AMP) of VbhT and inhibits its activity. It inhibits the adenylylation activity of VbhT by positioning close to the putative ATP-binding site, hence competing with ATP binding.
Pfam PF05713: Bacterial mobilisation protein (MobC) (family)
This family consists of several bacterial MobC-like, mobilisation proteins. MobC proteins belong to the group of relaxases. Together with MobA and MobB they bind to a single cis-active site of a mobilising plasmid, the origin of transfer (oriT) region. The absence of MobC has several different effects on oriT DNA. Site- and strand-specific nicking by MobA protein is severely reduced, accounting for the lower frequency of mobilisation. The localised DNA strand separation required for this nicking is less affected, but becomes more sensitive to the level of active DNA gyrase in the cell. In addition, strand separation is not efficiently extended through the region containing the nick site. These effects suggest a model in which MobC acts as a molecular wedge for the relaxosome-induced melting of oriT DNA. The effect of MobC on strand separation may be partially complemented by the helical distortion induced by supercoiling. However, MobC extends the melted region through the nick site, thus providing the single-stranded substrate required for cleavage by MobA.
Pfam PF04264: YceI-like domain (domain)
E. coli YceI is a base-induced periplasmic protein. The recent structure of a member of this family shows that it binds to poly-isoprenoid. The structure consists of an extended, eight-stranded, antiparallel beta-barrel that resembles the lipocalin fold.
Wikipedia: In molecular biology, Yce-I protein domain is a putative periplasmic protein. This entry represents the lipid-binding protein YceI from Escherichia coli and the polyisoprenoid-binding protein TTHA0802 from Thermus thermophilus. Its role is to help aid the biosynthesis of isoprenoid, an important molecule found in all living organisms.
Pfam PF00526: Dictyostelium (slime mold) repeat (repeat)
This entry represents a short repeat found in dictyostelium proteins. This repeat is composed of a beta hairpin. Structure predictions suggest that the conserved cysteines for disulphide bridges. With one pair forming between adjacent repeats (2 and 3) and one pair within a repeat 1 and 4.
Pfam PF18336: Fragile X messenger ribonucleoprotein 1, Tudor domain (domain)
This is the N-terminal Tudor domain (Tud1) found in Fragile X messenger ribonucleoprotein 1 (FMR1) and its paralogues, RNA-binding proteins FXR1/2. The Tud1 domain forms a canonical Tudor barrel. It is usually found in tandem with Agenet domain [pfam:PF05641].
Pfam PF19774: Family of unknown function (DUF6260) (family)
This family of proteins, functionally uncharacterised, is found in bacteria and viruses. Proteins in this family are typically between 341 and 365 amino acids in length. Some members are thought to be coat proteins.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF12903: Protein of unknown function (DUF3830) (family)
This is a family of bacterial and archaeal proteins, the structure for one of whose members has been characterised. PDB:3kop from [swissprot:A0JVT3] probably adopts a new hexameric form compared to previous structures. The putative active is near the domain interface. 3kop is most closely related, structurally to PDB:1zx8, where the potential active site is located near residues E51 and Y53 (conserved in 1zx8). Beyond the two residues above, the other residues are not conserved. Also the shape of the active site differs from that of 1zx8. PDB:1zx8 belongs to family DUF369. [pfam:PF04126], which is part of the cyclophilin-like clan.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF24578: Centrosome and spindle pole-associated protein 1, C-terminal (domain)
This domain is found at the C-terminal end of human Centrosome and spindle pole-associated protein 1 (CSPP1), which may play a role in cell-cycle-dependent microtubule organisation. This domain is predicted to show an alpha-helical configuration.
Pfam PF25001: Aegyptin, C-terminal domain (domain)
This domain is found at the C-terminal end of Aegyptin from Aedes aegypti and similar sequences from mosquitoes. Aegyptin modulates blood feeding of female mosquitoes on vertebrate hosts. This domain is predicted to adopt an all alpha configuration.
Pfam PF22371: Core protein P7, N-terminal core domain (domain)
This entry represents the N-terminal core region of Core protein P7 from Pseudomonas phage phi12, which adopts an alpha/beta -fold having structural similarities with BRCT domains involved in multiple protein-protein interactions in DNA repair proteins.
Pfam PF23243: HEATR1-like, HEAT repeats (repeat)
This entry represents HEAT repeats found in human HEAT repeat -containing protein 1 (HEATR1) and similar eukaryotic proteins. HEATR1 is a ribosome biogenesis factor involved in nucleolar processing of pre-18S ribosomal RNA.
Pfam PF20996: Family of unknown function (DUF5581) N-terminal domain (family)
This entry represents the N-terminal helical domain found in C20orf195 and its homologues found in chordates.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF14380: Wall-associated receptor kinase C-terminal (domain)
This WAK_assoc domain is cysteine-rich and lies C-terminal to the binding domain, GUB_WAK_bind, [pfam:PF13947].
Pfam PF23378: Family of unknown function (DUF7095) (family)
This family represents a group of proteins from halobacteria. They show several highly conserved motifs PVPV, LGL/MDP, AxWA, and PV/IHLEVC. Many members are annotated as nucleotidyltransferases.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF09318: Glycosyl transferase 1 domain A (family)
Glyco_trans_A_1 is family of found predominantly at the N-terminus of various prokaryotic alpha-glucosyltransferases. According to whether the domain exists as a whole molecule or as a half molecule determines the number of sugar residues that the molecule transfers. Two-domain proteins are processive in that they transfer more than one sugar residue, processively; single domain proteins transfer just one sugar moiety.
Pfam PF04321: RmlD substrate binding domain (domain)
L-rhamnose is a saccharide required for the virulence of some bacteria. Its precursor, dTDP-L-rhamnose, is synthesised by four different enzymes the final one of which is RmlD. The RmlD substrate binding domain is responsible for binding a sugar nucleotide.
Pfam PF22874: SBE2, middle domain (domain)
This entry represents a domain found central in Sbe2 and its paralogue, Sbe22 from budding yeast. These proteins are involved in bud growth and yeast cell wall formation. They may be also involved in the transport of cell wall components from the Golgi apparatus to the cell surface periphery.
Pfam PF04354: ZipA, C-terminal FtsZ-binding domain (domain)
This family represents the ZipA C-terminal domain. ZipA is involved in septum formation in bacterial cell division. Its C-terminal domain binds FtsZ, a major component of the bacterial septal ring. The structure of this domain is an alpha-beta fold with three alpha helices and a beta sheet of six antiparallel beta strands. The major loops protruding from the beta sheet surface are thought to form a binding site for FtsZ.
Pfam PF11997: Domain of unknown function (DUF3492) (family)
This presumed domain is functionally uncharacterised. This domain is found in bacteria, archaea and eukaryotes. This domain is typically between 259 to 282 amino acids in length. This domain is found associated with [pfam:PF00534]. This domain has two conserved sequence motifs: GGVS and EHGIY.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF05445: Poxvirus serine/threonine protein kinase (family)
This family of proteins contain poxvirus serine/threonine protein kinases, which are essential for phosphorylation of virion proteins during virion assembly .
Pfam PF12070: Protein SCAI (family)
SCAI is a transcriptional cofactor and tumour suppressor that suppresses MKL1-induced SRF transcriptional activity.  It may function in the RHOA-DIAPH1 signal transduction pathway and regulate cell migration through transcriptional  regulation of ITGB1.
Pfam PF14603: Helically-extended SH3 domain (domain)
This domain is the 70 C-terminal residues of ADAP - Adhesion and de-granulation promoting adapter protein. It shows homology to SH3 domains; however, conserved residues of the fold are absent. It thus represents an altered SH3 domain fold. An N-terminal, amphipathic, helix makes extensive contacts to residues of the regular SH3 domain fold thereby creating a composite surface with unusual surface properties. The domain can no longer bind conventional proline-rich peptides. There are key phosphorylation sites within the two hSH3 domains and it would appear that binding at these sites does not materially affect the folding of these regions although the equilibrium towards the unfolded state may be slightly altered. The binding partners of the hSH3 domains are still unknown.
Pfam PF00715: Interleukin 2 (domain)
T-Lymphocytes regulate the growth and differentiation of certain lymphopoietic and haemopoietic cells through the release of various secreted protein factors . These factors, which include interleukin-2 (IL2), are secreted by lectin- or antigen-stimulated T-cells, and have various physiological effects. IL2 is a lymphokine that induces the proliferation of responsive T-cells. In addition, it acts on some B-cells, via receptor-specific binding , as a growth factor and antibody production stimulant . The protein is secreted as a single glycosylated polypeptide, and cleavage of a signal sequence is required for its activity . Solution NMR suggests that the structure of IL2 comprises a bundle of 4 helices (termed A-D), flanked by 2 shorter helices and several poorly-defined loops. Residues in helix A, and in the loop region between helices A and B, are important for receptor binding. Secondary structure analysis has suggested similarity to IL4 and granulocyte-macrophage colony stimulating factor (GMCSF) .
Wikipedia: Interleukins (ILs) are a group of cytokines that are expressed and secreted by white blood cells (leukocytes) as well as some other body cells. The human genome encodes more than 50 interleukins and related proteins.
Pfam PF24163: Head completion protein (family)
This entry represents the Head completion protein (HCP) found in T5-like bacteriophages. HCP forms dodecameric ring assembly and is a component of the bacteriophage neck. It holds the portal protein PrtP dodecameric ring and connects with the trimeric layer of the tail tube via contacts with the tail completion (TCP) hexameric ring. HCP makes contacts with DNA. HCP consists of two domains. First domain folds into an alpha helical bundle composed of N- and C-terminal helices whereas the second domain adopts a beta-sandwich.
Pfam PF09755: Uncharacterized conserved protein H4 (DUF2046) (coiled_coil)
This is the conserved N-terminal 350 residues of a family of proteins of unknown function possibly containing a coiled-coil domain.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF02464: Competence-damaged protein (family)
CinA is the first gene in the competence-inducible (cin) operon, and is thought to be specifically required at some     stage in the process of transformation. This Pfam family  consists of putative competence-damaged proteins from the  cin operon. Some members of this family have nicotinamide mononucleotide (NMN) deamidase activity.
Pfam PF20876: Effector protein VipE (domain)
Legionella pneumophila use the Icm/Dot type IVB secretion system to deliver into the host cell effectors that inhibit phagosome maturation and modulate host vesicle trafficking pathways. VipE is one of those effectors. This entry represents the N-terminal domain that adopts an alpha-helical fold.
Pfam PF07924: Nuclease A inhibitor-like protein (domain)
This family represents the nuclease A inhibitor NuiA expressed by Anabaena sp ([swissprot:Q44296]) and similar bacterial proteins. This protein adopts an alpha+beta fold described as an 'open jaw', which shares some similarity to the PR-1-like fold. NuiA regulates the activity of Nuclease A (NucA). The NucA inhibition by NuiA involves an unusual divalent metal ion bridge that connects the nuclease with its inhibitor. A highly conserved glutamate extends into the active site, mimicking the charge of a phosphate. In addition, a second interaction site located on one of the two 'jaws' of the NuiA structure, contribute to the specificity and strength of the NuiA-NucA interaction.
Pfam PF01581: FMRFamide related peptide family (family)
The neuroactive peptide Phe-Met-Arg-Phe-NH2 (FMRF-amide) has a variety of effects on both mammalian and invertebrate tissues.
Pfam PF01008: Initiation factor 2 subunit family (family)
This family includes initiation factor 2B alpha, beta and delta subunits from eukaryotes, initiation factor 2B subunits 1 and 2 from archaebacteria and some proteins of unknown function from prokaryotes. Initiation factor 2 binds to Met-tRNA, GTP and the small ribosomal subunit. Members of this family have also been characterised as 5-methylthioribose- 1-phosphate isomerases, an enzyme of the methionine salvage pathway. The  crystal structure of Ypr118w, a non-essential, low-copy number gene  product from Saccharomyces cerevisiae, reveals a dimeric protein with  two domains and a putative active site cleft.
Pfam PF21188: Pre-mRNA-splicing helicase BRR2 plug domain (domain)
This entry represents the Plug domain from the Brr2 RNA helicase protein. The Brr2 helicase provides the key remodelling activity for spliceosome catalytic activation, during which it disrupts the U4/U6 di-snRNP (small nuclear RNA protein). The plug domain is a small alpha helical bundle domain found near the N-terminus of the Brr2 protein.
Pfam PF16110: Domain of unknown function (DUF4828) (family)
This family consists of uncharacterized proteins around 120 residues in length and is mainly found in various Enterococcus and Lactobacillus species. The function of this family is unknown.
Pfam PF14871: Hypothetical glycosyl hydrolase 6 (family)
GHL6 is a family of hypothetical glycoside hydrolases.
Pfam PF21464: Flagellar hook protein FlgE, D3 domain (domain)
This domain is found in Flagellar hook protein FlgE from Campylobacter jejuni and similar proteins found in Epsilonproteobacteria. Around 100 copies of FlgE polymerise to form a tubular helical structure: the bacterial flagellar hook. This protein is organised into five domains. This entry represents domain D3, which is made of two discontinuous segments. It shows a set of eight beta-strands separated into two groups by two alpha-helices that form an alpha-beta barrel. This domain is not conserved in other bacterial FlgE proteins.
Pfam PF11822: SANT and BTB domain regulator of CSR, BTB domain (domain)
Class switch recombination (CSR) is the process by which B cells switch production from IgM/IgD to other immunoglobulin isotypes in the immune response process. This entry represents the BTB domain found at the N-terminal half of the protein SANT and BTB domain regulator of class switch recombination (SANBR, previously known as KIAA1841). This domain is responsible for the negative regulation of CSR.
Pfam PF02620: Large ribosomal RNA subunit accumulation protein YceD (family)
This family is nearly universally conserved in bacteria and plants except the Chlorophyceae algae. Thus far, mutantional analysis in bacteria have not established a function. In contrast, mutants have embryo lethal phenotypes in maize and Arabidopsis. In maize, the mutant embryos arrest at an early transition stage.It has been suggested that family members specifically affect 23S rRNA accumulation in plastids as well as bacteria.
Pfam PF00261: Tropomyosin (coiled_coil)
Tropomyosin is an alpha-helical protein that forms a coiled-coil structure of 2 parallel helices containing 2 sets of 7 alternating actin binding sites. The protein is best known for its role in regulating the interaction between actin and myosin in muscle  contraction, but is also involved in the organisation and dynamics of the cytoskeleton in non-muscle cells. There are multiple cell-specific isoforms, expressed by alternative promoters and alternative RNA processing of at least four genes. Muscle  isoforms of tropomyosin are characterised by having 284 amino acid residues and a highly conserved N-terminal region, whereas non-muscle forms are generally smaller and are heterogeneous in their N-terminal region.
Wikipedia: Tropomyosin is a two-stranded alpha-helical, coiled coil protein found in many animal and fungal cells. In animals, it is an important component of the muscular system which works in conjunction with troponin to regulate muscle contraction. It is present in smooth and striated muscle tissues, which can be found in various organs and body systems, including the heart, blood vessels, respiratory system, and digestive system. In fungi, tropomyosin is found in cell walls and helps maintain the structural integrity of cells.
Pfam PF21530: DNA helicase Pif1, 2B domain (domain)
Pif1 is a DNA helicase conserved from bacteria to humans. It suppresses both G-quadruplex-associated DNA damage and telomere lengthening. In budding yeast, it exists in two forms, nuclear and mitochondrial forms. Its nuclear form inhibits telomerase, while its mitochondrial is involved in repair and recombination of mitochondrial DNA. These proteins belong to the helicase superfamily 1 (SF1) and contain RecA-like domains (1A and 2A) which, together with two additional domains, 1B and 2B, form the helicase core. This entry represents domain 2B, which adopts a SH3-like fold.
Pfam PF04010: Protein of unknown function (DUF357) (family)
Members of this family are short (less than 100 amino acid) proteins found in archaebacteria.  The function of these proteins is unknown.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF21844: Family of unknown function (DUF6903) (family)
This entry represents a family of small putative integral membrane proteins with two transmembrane helices.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF03227: Gamma interferon inducible lysosomal thiol reductase (GILT) (family)
This family includes the two characterised human gamma-interferon-inducible lysosomal thiol reductase (GILT) sequences: [swissprot:P13284] and [swissprot:Q9UL08]. It also contains several other eukaryotic putative proteins with similarity to GILT. The aligned region contains three conserved cysteine residues. In addition, the two GILT sequences possess a C-X(2)-C motif that is shared by some of the other sequences in the family. This motif is thought to be associated with disulphide bond reduction.
Pfam PF18169: SMODS and SLOG-associating 2TM effector domain 6 (domain)
The SLATT domain contains two transmembrane helices. SLATT domains are generally predicted to function as pore-forming effectors in a class of conflict systems which are reliant on the production of second messenger nucleotide or nucleotide derivatives. SLATT domains are predicted to initiate cell suicide responses upon their activation. This SLATT family associates with a SMODS nucleotide synthetase domain fused to the predicted AGS-C sensor domain. It is sometimes further coupled to R-M systems.
Pfam PF19085: Choline-binding repeat (repeat)
this entry contains a pair of presumed choline-binding repeats that are often found adjacent to [pfam:PF01473].
Pfam PF14169: Cold-inducible protein YdjO (family)
This family includes the B. subtilis YdjO protein [swissprot:O34759], which is functionally uncharacterised. This is not a homologue of E. coli YdjO, [swissprot:P76210].  B. subtilis YdjO is cold-inducible. Its expression is induced by the extracytoplasmic function sigma factor sigma-W.  This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length.
Pfam PF02958: Ecdysteroid kinase-like family (family)
This family includes ecdysteroid 22-kinase, an enzyme responsible for the phosphorylation of ecdysteroids (insect growth and moulting hormones) at C-22, to form physiologically inactive ecdysteroid 22-phosphates. Most insects contain 12 to 105 genes encoding this family and yet so far only one enzyme (ecdysteroid 22-kinase from Bombyx mori) has characterised substrates (2-deoxyecdysone, ecdysone, 20-hydroxyecdysone). There are good reasons to believe that this family includes kinases that act on other small molecule substrates and that they may function in detoxification processes.