SII-SWORD/CoKE huggingface dataset:
Pfam PF01475: Ferric uptake regulator family (family)
This family includes metal ion uptake regulator proteins, that bind to the operator DNA and controls transcription of metal ion-responsive genes.  This family is also known as the FUR family.
Wikipedia: In molecular biology, the ferric uptake regulator family is a family of bacterial proteins involved in regulating metal ion uptake and in metal homeostasis. The family is named for its founding member, known as the ferric uptake regulator or ferric uptake regulatory protein (Fur). Fur proteins are responsible for controlling the intracellular concentration of iron in many bacteria. Iron is essential for most organisms, but its concentration must be carefully managed over a wide range of environmental conditions; high concentrations can be toxic due to the formation of reactive oxygen species.
Pfam PF04421: Mss4 protein (domain)
MSS4 (mammalian suppressor of Sec4) is an evolutionarily highly conserved protein, which is expressed in all mammalian tissues. Although it was first proposed to function as a guanine exchange factor (GEF) for Rab GTPases, it was soon described as a quite inefficient GEF and was thus suggested to function rather as a chaperone, protecting nucleotide free Rabs from degradation, than as a GEF .

The structure of MSS4 revealed a mostly Î² fold stabilized by a Zn(2+) ion coordinated by cysteine residues from two CxxC motifs. The fold of the MSS4 domain consists of a central Î² sheet (betaG-betaK) flanked by a Î² hairpin (betaB-betaC) on one side and a small variable sheet on the other. A single Zn(2+) ion, coordinated by the thiol groups of cysteine residues from two CxxC motifs located in the betaB-betaC and betaI-betaJ loops, appears to play an important structural role by reinforcing the hydrophobic core formed by the betaB-betaC hairpin, the betaG-betaH loop, and the central Î² sheet .
Pfam PF05022: SRP40, C-terminal domain (domain)
This presumed domain is found at the C-terminus of the S. cerevisiae SRP40 protein [swissprot:P32583] and its homologues. SRP40/nopp40 is a chaperone involved in nucleocytoplasmic transport. SRP40 is also a suppressor of mutant AC40 subunit of RNA polymerase I and III.
Pfam PF01705: CX module (family)
This domain has no known function. It is found in several C. elegans proteins. The domain contains 6 conserved cysteines that probably form three disulphide bridges.
Pfam PF08110: Ocellatin family (family)
This family consists of the ocellatin family of antimicrobial peptides. Ocellatins are produced from the electrical-stimulated skin secretions of the South American frog, Leptodactylus ocellatus.  The family consists of three structurally related peptides, ocellatin 1, ocellatin 2 and ocellatin 3.  These peptides present hemolytic activity against human erythrocytes and are also active against Escherichia coli.
Pfam PF07285: Protein of unknown function (DUF1444) (family)
This family contains several hypothetical bacterial proteins of unknown function that are approximately 250 residues long.
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 PF14334: Domain of unknown function (DUF4390) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 192 and 203 amino acids in length.
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 PF19951: Family of unknown function (DUF6413) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001749) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the  epipyriculol biosynthetic gene cluster from Pyricularia oryzae 70-15. This family appears to be predominantly found in fungi.
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 PF00740: Parvovirus coat protein VP2 (family)
This protein, together with VP1 forms a capsomer. Both of these proteins are formed from the same transcript using alternative splicing.                          As a result, VP1 and VP2 differ only in the N-terminal region of VP1.     VP2 is involved in packaging the viral DNA.
Pfam PF09282: Mago binding (domain)
Members of this family adopt a structure consisting of a small globular all-beta-domain, with a three-stranded beta-sheet and a contiguous beta-hairpin. They bind to Mago alpha-helices via extensive electrostatic interactions and at a beta2-beta3 loop via hydrophobic interactions.
Pfam PF05106: Phage holin family (Lysis protein S) (family)
This family represents one of a large number of mutually dissimilar families of phage holins. Holins act against the host cell membrane to allow lytic enzymes of the phage to reach the bacterial cell wall. This family includes the product of the S gene of phage lambda.
Pfam PF21826: Family of unknown function (DUF6887) (family)
This entry represents a family of uncharacterised cyanobacterial 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 PF00121: Triosephosphate isomerase (domain)
Triosephosphate isomerase ([ec:5.3.1.1]) (TIM) is the glycolytic enzyme that catalyses the reversible interconversion of glyceraldehyde 3-phosphate and dihydroxyacetone phosphate. TIM plays an important role in several metabolic pathways and is essential for efficient energy production, present in eukaryotes and prokaryotes. TIM is a dimer of identical subunits, each of which is made up of about 250 amino-acid residues. A glutamic acid residue is involved in the catalytic mechanism. The tertiary structure of TIM has eight beta/alpha motifs folded into a barrel structure. The sequence around the active site residue is perfectly conserved in all known TIM's. Deficiencies in TIM are associated with haemolytic anaemia coupled with a progressive, severe neurological disorder.
Wikipedia: Triose-phosphate isomerase is an enzyme that catalyzes the reversible interconversion of the triose phosphate isomers dihydroxyacetone phosphate and D-glyceraldehyde 3-phosphate.
Pfam PF05611: Caenorhabditis elegans protein of unknown function (DUF780) (family)
This family consists of several short C. elegans proteins of unknown function.
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 PF00733: Asparagine synthase (domain)
This family is always found associated with [pfam:PF00310]. Members of this family catalyse the conversion of aspartate to asparagine.
Pfam PF14428: Double-stranded DNA deaminase toxin A (family)
Members of this family are predicted to function as toxins in bacterial polymorphic toxin systems, including DddA from Burkholderia cenocepacia. DddA is part of the cellular contact- dependent growth inhibition (CDI) system that allows bacteria to communicate with and inhibit the growth of closely related neighbouring bacteria in a contact-dependent fashion. Its deaminase domain has double-stranded DNA cytidine deaminase activity and can be used for CRISPR-free mitochondrial base editing.
Pfam PF19718: Ubiquitin carboxyl-terminal hydrolase 47 C-terminal (domain)
This is the C-terminal domain of Ubiquitin carboxyl-terminal hydrolase 47 (USP47), a ubiquitin-specific protease involved in deubiquitinating of monoubiquitinated DNA polymerase beta (Polbeta), being required for its stability and, therefore, plays a role in DNA base excision repair (BER). The C-terminal domains in USPs mediate protein- protein interactions.
Pfam PF18433: Domain of unknown function (DUF5610) (domain)
This is a domain of unknown function found in bacterial 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 PF18713: Domain of unknown function (DUF5645) (domain)
This is a domain of unknown function found in Diptera. Some family members carry [pfam:PF08445] on their C-terminal.
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 PF00237: Ribosomal protein L22p/L17e (domain)
This family includes L22 from prokaryotes and chloroplasts and L17 from eukaryotes.
Pfam PF05638: Type VI secretion system effector, Hcp (domain)
HCP is a family of proteins which are expressed in up to 1000 copies in Gram-negative bacteria. Together these copies aggregate into a needle-like shaft or tube that will penetrate other bacteria via a puncturing protein attached to its head being part of the type VI secretion system. Initially Hcp forms a hexameric structure with a central channel of 40 Angstroms. These hexamers pile up one on top of each other forming nanotubes resembling the gp19 tail phage tube.
Pfam PF00593: TonB dependent receptor-like, beta-barrel (domain)
This entry represents the beta-barrel domain of TonB-dependent receptors, such as BtuB, CirA, FatA, FcuT, FecA, FepA, among others.
Wikipedia: Outer membrane receptors, also known as TonB-dependent receptors, are a family of beta barrel proteins named for their localization in the outer membrane of gram-negative bacteria. TonB complexes sense signals from the outside of bacterial cells and transmit them into the cytoplasm, leading to transcriptional activation of target genes.
TonB-dependent receptors in gram-negative bacteria are associated with the uptake and transport of large substrates such as iron siderophore complexes and vitamin B12.
Pfam PF06109: Haemolysin E (HlyE) (family)
This family consists of several enterobacterial haemolysin (HlyE) proteins.Hemolysin E (HlyE) is a novel pore-forming toxin of Escherichia coli, Salmonella typhi, and Shigella flexneri. HlyE is unrelated to the well characterised pore-forming E. coli hemolysins of the RTX family, haemolysin A (HlyA), and the enterohaemolysin encoded by the plasmid borne ehxA gene of E. coli 0157. However, it is evident that expression of HlyE in the absence of the RTX toxins is sufficient to give a hemolytic phenotype in E. coli. HlyE is a protein of 34 kDa that is expressed during anaerobic growth of E. coli. Anaerobic expression is controlled by the transcription factor, FNR, such that, upon ingestion and entry into the anaerobic mammalian intestine, HlyE is produced and may then contribute to the colonisation of the host.
Wikipedia: Haemolysin E (HlyE)  is a protein family that consists of several enterobacterial haemolysin (HlyE) proteins. Hemolysin E (HlyE) is a novel pore-forming toxin of Escherichia coli, Salmonella typhi, and Shigella flexneri.
Pfam PF14622: Ribonuclease-III-like (family)
Members of this family are involved in rDNA transcription and rRNA processing. They probably also cleave a stem-loop structure at the 3' end of U2 snRNA to ensure formation of the correct U2 3' end; they are involved in polyadenylation-independent transcription termination. Some members may be mitochondrial ribosomal protein subunit L15, others may be 60S ribosomal protein L3.
Pfam PF06990: Galactose-3-O-sulfotransferase (family)
This family consists of several mammalian galactose-3-O-sulfotransferase proteins. Gal-3-O-sulfotransferase is thought to play a critical role in 3'-sulfation of N-acetyllactosamine in both O- and N-glycans.
Wikipedia: Galactose-3-O-sulfotransferases is a family of several mammalian galactose-3-O-sulfotransferase proteins. Gal-3-O-sulfotransferase is thought to play a critical role in 3'-sulfation of N-acetyllactosamine in both O- and N-glycans.
Pfam PF16364: Cell surface antigen C-terminus (domain)
This repeated domain is found at the C-terminus of cell surface antigens. In the Streptococcus mutans antigen I/II there are three repeats of this domain, a cleft between the first two of these forms a binding site for the human salivary agglutinin (SAG).
Pfam PF19548: Chordin-like protein 1/2 C-terminal (domain)
This is the C-terminal domain of Chordin-like proteins 1 and 2. These proteins can bind BMPs family ligands and inhibit its activity by blocking their interaction with their receptors. They are involved in myoblast and osteoblast differentiation and maturation.
Pfam PF12395: Protein of unknown function (family)
This domain family is found in bacteria, and is approximately 110 amino acids in length. The family is found in association with [pfam:PF08874]. There are two completely conserved residues (D and R) that may be functionally important.
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 PF05525: Branched-chain amino acid transport protein (family)
This family consists of several bacterial branched-chain amino acid transport proteins which are responsible for the transport of leucine, isoleucine and valine via proton motive force.
Pfam PF22987: Lysine-specific demethylase 3B, tudor domain (domain)
This domain is found in Lysine-specific demethylase 3B (KDM3B, also known as JmjC domain-containing histone demethylation protein 2B or JHDM2B) and related proteins. KDM3B is a histone demethylase that specifically demethylates lysine at position 9 of histone H3. This enzyme plays a central role in histone code. This domain is predicted to adopt an open beta-barrel with an SH3-like topology. It has significant sequence and structural similarity to RDM15 tudor domain that is known to specifically recognize the monomethylation (H3K4me1) mark of lysine at position 4 of histone H3.
Pfam PF19248: Family of unknown function (DUF5896) (family)
This is a family of uncharacterised proteins of unknown function predominantly found in Marseillevirus.
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 PF15694: Mediator complex subunit 26 middle domain (domain)
Med26_M is the middle domain of subunit 26 of Mediator. Med19 and Med26 act synergistically to mediate the interaction between REST (a Kruppel-type zinc finger transcription factor that binds to a 21-bp RE1 silencing element present in over 900 human genes) and Mediator.
Wikipedia: Mediator of RNA polymerase II transcription subunit 26 is an enzyme that in humans is encoded by the MED26 gene. It forms part of the Mediator complex.
Pfam PF10624: Plasmid conjugative transfer entry exclusion protein TraS (family)
Entry exclusion (Eex) is a process which prevents redundant transfer of DNA between donor cells.  TraS is a protein involved in Eex.  It blocks redundant conjugative DNA synthesis and transport between donor cells, and it is suggested that TraS interferes with a signalling pathway that is required to trigger DNA transfer.  TraS on the recipient cell is known to form an interaction with TraG on the donor cell.
Pfam PF02041: Auxin binding protein (domain)
Auxin binding protein is located in the lumen of the endoplasmic reticulum (ER). The primary structure contains an N-terminal hydrophobic leader sequence of 30-40 amino acids, which could represent a signal for translocation of the protein to the ER . The mature protein comprises around 165 residues, and contains a number of potential N-glycosylation sites. In vitro transport studies have demonstrated co-translational glycosylation . Retention within the lumen of the ER correlates with an additional signal located at the C terminus, represented by the sequence Lys-Asp-Glu-Leu, known to be responsible for preventing secretion of proteins from the lumen of the ER in eukaryotic cells .
Wikipedia: In molecular biology, the auxin binding protein family is a family of proteins which bind the plant hormone auxin. They are located in the lumen of the endoplasmic reticulum (ER). The primary structure of these proteins contains an N-terminal hydrophobic leader sequence of 30-40 amino acids, which could represent a signal for translocation of the protein to the ER. The mature protein comprises around 165 residues, and contains a number of potential N-glycosylation sites. In vitro transport studies have demonstrated co-translational glycosylation. Retention within the lumen of the ER correlates with an additional signal located at the C terminus, represented by the sequence Lys-Asp-Glu-Leu, known to be responsible for preventing secretion of proteins from the lumen of the ER in eukaryotic cells.
Pfam PF20868: Testis-expressed protein 13, MVPLGDSxSHS repeat (repeat)
This entry represents a repeat found in TEX13 (swiss:A0A0J9YWL9) from human and similar proteins from mammals. These repeats have the conserved pattern MVPLGDSxSHS.
Pfam PF19268: Contractile injection system tape measure protein (family)
This protein is found as part of contractile injection systems. It is the tape measure protein which dictates the length of the syringe tail. It is found in low copy number. This protein is most likely not present in the mature syringes. Deletion of the tape measure protein Pvc14 resulted in large variations in the length of the syringes. The N and C-termini of these proteins are well conserved, but they have a wide length variation in the central region.
Pfam PF16501: S phase cyclin A-associated protein in the endoplasmic reticulum (family)
SCAPER_N is a short highly conserved region close to the N-terminus. SCAPER is localised to the endoplasmic reticulum and is a substrate for cyclin A/Cdk2. It associates with cyclin A and localises to the ER. One theory suggests that SCAPER functions to create a local high concentration of cyclin A2 in the cytoplasm. Alternatively, SCAPER might be acting to sequester a portion of cellular cyclin A2 that could then be readily available for nuclear translocation, which may be needed for exit from G0 phase.
Pfam PF21656: Domain of unknown function (DUF6859) (domain)
This domain is found at the N-terminal of fungal proteins, such as SwissProt:O74728 from S.pombe, a protein thought to be localised in the ER. From AlphaFold structure prediction, it can be inferred that this domain may adopt an alpha/beta structure consisting of six antiparallel beta-strands surrounded by three or four alpha-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 PF22661: Complement C4A/B CUB C-terminal domain (domain)
Complement C4 is organised in 12 structural domains, with eight macroglobulin (MG) domains forming the core of the molecule. They have a thioester domain (TED, [pfam:PF07678]), a large helical domain inserted in the CUB (complement C1r/C1s, Uegf, Bmp1) domain which consists of two antiparallel beta-sheets. This entry covers a fraction of the CUB domain corresponding to the C-terminal part (residues 1323-1389 in human C4A/B) as this domain is made up of residues located apart in these sequences.
Pfam PF07525: SOCS box (domain)
The SOCS box acts as a bridge between specific substrate- binding domains and more generic proteins that comprise a large family of E3 ubiquitin protein ligases.
Pfam PF20421: DHR-2, Lobe C (repeat)
DOCK (dedicator of cytokinesis) proteins are guanine nucleotide exchange factors (GEFs) that activate some small GTPases, such as Rac or Cdc42, by exchanging bound GDP for free GTP to control cell migration, morphogenesis, and phagocytosis. These proteins share a DOCK-type C2 domain (also termed the DOCK-homology region (DHR)-1) at the N-terminal, and the DHR-2 domain (also termed the DOCKER domain) at the C-terminal. DHR-2 is the GEF catalytic domain organised into three lobes A, B and C, with the Rho-family binding site and catalytic centre generated entirely from lobes B and C. This entry represents Lobe C which form an antiparallel four alpha-helical bundle and contains a loop known as the nucleotide sensor characterised by a conserved valine residue essential for catalytic activity.