SII-SWORD/CoKE huggingface dataset:
Pfam PF16586: Domain of unknown function (DUF5060) (domain)
This is the N-terminal domain of a putative glycoside hydrolase, DUF4038. It is found in a number of different bacterial orders.
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 PF10208: ARMET, C-terminal (domain)
This is the C-terminal domain of ARMET (also known as mesencephalic astrocyte-derived neurotrophic factor (MANF) or arginine-rich protein). This domain is well conserved among Armet family proteins whose structure is composed of a basic-helix-loop-helix (bHLH) motif. ARMET is a small protein of approximately 170 residues. It is soluble protein resident in the endoplasmic reticulum and induced by ER stress. It appears to be involved with dealing with mis-folded proteins in the ER, thus in quality control of ER stress.
Pfam PF05339: Protein of unknown function (DUF739) (family)
This family contains several bacteriophage proteins. Some of the proteins in this family have been labeled putative cro repressor 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 PF06487: Sin3 associated polypeptide p18 (SAP18) (family)
This family consists of several eukaryotic Sin3 associated polypeptide p18 (SAP18) sequences. SAP18 is known to be a component of the Sin3-containing complex which is responsible for the repression of transcription via the modification of histone polypeptides. SAP18 is also present in the ASAP complex  which is thought to be involved in the regulation of splicing during the execution of programmed cell death.
Pfam PF11500: Cut12 conserved domain (domain)
This is the central coiled-coil region of the spindle pole body-associated protein cut12 also found in other fungi, barring S. cerevisiae. The full protein has two predicted coiled-coil regions, and one consensus phosphorylation site for p34cdc2 and two for MAP kinase. During fission yeast mitosis, the duplicated spindle pole bodies (SPBs) nucleate microtubule arrays that interdigitate to form the mitotic spindle. Cut12 is localised to the SPB throughout the cell cycle, predominantly around the inner face of the interphase SPB, adjacent to the nucleus. Cut12 associates with Fin1 and is important in this context for the activity of Plo1.
Pfam PF00577: Outer membrane usher protein (family)
In Gram-negative bacteria the biogenesis of fimbriae (or pili) requires a two- component assembly and transport system which is composed of a periplasmic chaperone and an outer membrane protein which has been termed a molecular 'usher'.  The usher protein is rather large (from 86 to 100 Kd) and seems to be mainly composed of membrane-spanning beta-sheets, a structure reminiscent of porins. Although the degree of sequence similarity of these proteins is not very high they share a number of characteristics. One of these is the presence of two pairs of cysteines, the first one located in the N-terminal part and the second at the C-terminal extremity that are probably involved in disulphide bonds. The best conserved region is located in the central part of these proteins.
Wikipedia: The fimbrial usher protein is involved in biogenesis of the pilus in Gram-negative bacteria. The biogenesis of some fimbriae requires a two-component assembly and transport system which is composed of a periplasmic chaperone and a pore-forming outer membrane protein which has been termed a molecular 'usher'; this is the chaperone-usher pathway.
Pfam PF07067: Protein of unknown function (DUF1340) (family)
This family consists of several hypothetical Streptococcus thermophilus bacteriophage proteins of around 235 residues in length. The function of this family 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 PF15084: Domain of unknown function (DUF4550) (family)
This presumed domain is functionally uncharacterised. This domain family is found in eukaryotes, and is approximately 100 amino acids in length. This domain contains an N-terminal HXE motif.
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 PF09940: Domain of unknown function (DUF2172) (domain)
This domain, found in various hypothetical prokaryotic proteins, has no known function. An aminopeptidase domain is conserved within the family, but its relevance has not been established yet. Rebuilding from PDB:3kt9 shows this is an inserted (nested domain within the amino-peptidase). The function of this small domain is not known.
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 PF17042: Nucleotide-binding C-terminal domain (domain)
This is the C-terminal domain found in proteins in a range of Proteobacteria as well as the Gram-positive Oceanobacillus iheyensis. Structural analysis of the whole protein indicates the N- and C-termini act together to produce a surface into which a threonate-ADP complex is bound, demonstrating that a sugar binding site is on the N-terminal domain, and a nucleotide binding site is in the C-terminal domain. There is a critical motif, DDXTG, at approximately residues 22-25. Proteins containing this domain have been predicted as kinases. Some members are associated with PdxA2 by physical clustering and gene fusion with PdxA2. Some members that are fused with PdxA2 have been shown to be involved in L-4-hydroxythreonine (4HT) phosphorylation, part of the alternative pathway to make PLP (pyridoxal 5'-phosphate) out of a toxic metabolite, 4HT. However, 4HT phosphorylation might not be the main function of this group of proteins. Moreover, some members that are not associated with pdxA2, and even one that is associated with pdxA2, have lost 4HT kinase activity. Functional analysis demonstrate that family members include D-Threonate kinases (DtnK), D-Erythronate kinases (DenK) and 3-Oxo-tetronate kinases (OtnK).
Pfam PF20700: Mutator-like transposase (domain)
This is a transposase domain of the mutator superfamily.
Pfam PF20031: Family of unknown function (DUF6437) (domain)
This family of proteins is functionally uncharacterised. This family of proteins is found in Alphaproteobacteria. Proteins in this family are typically between 76 and 122 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 PF10385: RNA polymerase beta subunit external 1 domain (domain)
RNA polymerases catalyse the DNA-dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared with three in eukaryotes (not including mitochondrial or chloroplast polymerases). This domain in prokaryotes spans the gap between domains 4 and 5 of the yeast protein. It is also known as the external 1 region of the polymerase and is bound in association with the external 2 region.
Pfam PF12807: Translation initiation factor eIF3 subunit 135 (family)
Translation initiation factor eIF3 is a multi-subunit protein complex required for initiation of protein biosynthesis in eukaryotic cells. The complex promotes ribosome dissociation, the binding of the initiator methionyl-tRNA to the 40 S ribosomal subunit, and mRNA recruitment to the ribosome. The protein product from TIF31 genes in yeast is p135 which associates with the eIF3 but does not seem to be necessary for protein translation initiation.
Pfam PF03542: Tuberin (family)
Tuberous sclerosis complex (TSC) is an autosomal dominant disorder and is characterised by the presence of hamartomas in many organs, such as brain, skin, heart, lung, and kidney. It is caused by mutation either TSC1 or TSC2 tumour suppressor gene. The TSC2 gene codes for tuberin and interacts with hamartin [pfam:PF04388] , containing two coiled-coil regions, which have been shown to mediate binding to tuberin. These two proteins function within the same pathway(s) regulating cell cycle, cell growth, adhesion, and vesicular trafficking.
Pfam PF13927: Immunoglobulin domain (domain)
This family contains immunoglobulin-like domains.
Wikipedia: The immunoglobulin domain, also known as the immunoglobulin fold, is a type of protein domain that consists of a 2-layer sandwich of 7-9 antiparallel β-strands arranged in two β-sheets with a Greek key topology, consisting of about 125 amino acids.
Pfam PF01970: Tripartite tricarboxylate transporter TctA family (family)
This family, formerly known as DUF112, is a family of bacterial and archaeal tripartite tricarboxylate transporters of the extracytoplasmic solute binding receptor-dependent transporter group of families, distinct from the ABC and TRAP-T families. TctA is part of the tripartite TctABC system which, as characterised in S. typhimurium, is a secondary carrier that depends for activity on the extracytoplasmic tricarboxylate-binding receptor TctC as well as two integral membrane proteins, TctA and TctB. complete three-component systems are found only in bacteria. TctA is a large transmembrane protein with up to 12 predicted membrane spanning regions in bacteria and up to 11 such in archaea, with the N-terminal within the cytoplasm. TctA is thought to be a permease, and in most other bacteria functions without TctB and TctC molecules.
Pfam PF06635: Type 3 secretion system stator protein (family)
This family consists of Type 3 secretion system (T3SS) stator protein, previously known as nodulation protein NolV, from different Rhizobium species. The function of this family is unclear, however, it has been suggested that this protein is a component of the T3SS, which is used to inject bacterial effector proteins into eukaryotic host cells.
Pfam PF01857: Retinoblastoma-associated protein B domain (domain)
The crystal structure of the Rb pocket bound to a nine-residue E7 peptide containing the LxCxE motif, shared by other Rb-binding viral and cellular proteins, shows that the LxCxE peptide binds a highly conserved groove on the B domain. The B domain has a cyclin fold.
Pfam PF19688: Family of unknown function (DUF6189) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000807) is described by MIBiG as an example of the following biosynthetic class, saccharide. It includes a member of  the phosphonoglycans biosynthetic gene cluster from Stackebrandtia  nassauensis DSM 44728.
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 PF09788: Transmembrane protein 55A (family)
Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Pfam PF16053: Mitochondrial 28S ribosomal protein S34 (family)
This entry represents ribosomal protein S34 from the mitochondrial 28S subunit .
Wikipedia: Ribosomes are macromolecular machines, found within all cells, that perform biological protein synthesis. Ribosomes link amino acids together in the order specified by the codons of messenger RNA molecules to form polypeptide chains. Ribosomes consist of two major components: the small and large ribosomal subunits. Each subunit consists of one or more ribosomal RNA molecules and many ribosomal proteins. The ribosomes and associated molecules are also known as the translational apparatus.
Pfam PF09876: Predicted metal-binding protein (DUF2103) (family)
This domain, found in various putative metal binding prokaryotic proteins, has no known 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 PF00031: Cystatin domain (domain)
Very diverse family.  Attempts to define separate sub-families failed.  Typically, either the N-terminal or C-terminal end is very divergent.  But splitting into two domains would make very short families. All members except [swissprot:Q03196] and [swissprot:Q10993] are found. [pfam:PF00666] are related to this family but have not been included.
Wikipedia: The cystatins are a family of cysteine protease inhibitors which share a sequence homology and a common tertiary structure of an alpha helix lying on top of an anti-parallel beta sheet. The family is subdivided as described below.
Pfam PF09963: Uncharacterized protein conserved in bacteria (DUF2197) (family)
This domain, found in various hypothetical bacterial proteins, has no known 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 PF23745: LRRK2 ANK repeat (repeat)
This entry represents the ankyrin repeat (ANK) found towards the N-terminal in Leucine-rich repeat serine/threonine-protein kinase 2 (LRRK2) from eukaryotes, between the ARM repeat domain ([pfam:PF23744]) and the LRR domain ([pfam:PF13855]). LRRK2 is a serine/threonine-protein kinase which phosphorylates a broad range of proteins involved in multiple processes such as neuronal plasticity, primary ciliogenesis, autophagy, and vesicle trafficking. Mutations in LRRK2 are the most common genetic cause of Parkinson's disease. LRRK2 phosphorylates a group of Rab GTPase proteins including Rab29. The ANK domain plays a key role in this process, as conserved leucine residues within the ANK domain are required for Rab29 binding, which mediates Golgi recruitment and kinase activation.
Pfam PF14297: Lin1244/Lin1753-like, N-terminal (domain)
The function of this domain is not known. It is found at the N-terminal of the uncharacterized phage-related protein Lin1244/Lin1753 which contains a DnaD domain ([pfam:PF07261]) at the C-terminal.
Pfam PF12006: Protein of unknown function (DUF3500) (family)
This family of proteins is functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 335 to 438 amino acids in length. This protein has a conserved GHH sequence motif. This protein has two completely conserved G residues 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 PF21784: 4-fold beta flower protein (domain)
This family of proteins have a repetitive structure composed of pairs of beta strands. In this family the proteins usually have four copies of the beta hairpin repeat.
Pfam PF13454: FAD-NAD(P)-binding (domain)
This entry represents the FAD/NAD(P)-binding domain found in a group of proteins, including HpyO from Xanthomonas campestris pv. campestris (FAD-dependent urate hydroxylase) and L-aspartate N-monooxygenase CreE from Streptomyces cremeus. HpyO catalyses the hydroxylation of urate to 5-hydroxyisourate (HIU) . CreE is involved in the biosynthesis of cremeomycin, a light-sensitive o-diazoquinone with antibacterial and antiproliferative effects. It catalyses the iterative oxidation of L-aspartic acid to nitrosuccinic acid (2-nitrobutanedioate) .
Pfam PF18879: EspA/EspE family (family)
This family of proteins includes Mycobacterium tuberculosis EspA and EspE proteins.
Pfam PF06732: Pescadillo N-terminus (family)
This family represents the N-terminal region of Pescadillo. Pescadillo protein localises to distinct substructures of the interphase nucleus including nucleoli, the site of ribosome biogenesis. During mitosis pescadillo closely associates with the periphery of metaphase chromosomes and by late anaphase is associated with nucleolus-derived foci and prenucleolar bodies. Blastomeres in mouse embryos lacking pescadillo arrest at morula stages of development, the nucleoli fail to differentiate and accumulation of ribosomes is inhibited. It has been proposed that in mammalian cells pescadillo is essential for ribosome biogenesis and nucleologenesis and that disruption to its function results in cell cycle arrest. This family is often found in conjunction with a [pfam:PF00533] domain.
Pfam PF21330: Complement component C7, Kazal domain (domain)
Factor I-like modules (FIMs) are present in complement proteins C6, C7, and factor I, and participate in protein-protein interactions that critical to the progress of a complement-mediated immune response. Complement component C7 contains a FIM pair at the C-terminal, FIM1 and FIM2; each of them consists of a small N-terminal FOLN subdomain and a larger C-terminal KAZAL domain. This entry represents the KAZAL domain of FIM1.
Pfam PF11052: Trans-sialidase of Trypanosoma hydrophobic C-terminal (conserved_site)
This is a highly conserved sequence motif that is the very C-terminus of a number of more diverse proteins from Trypanosoma cruzi. All members of the family are annotated putatively as being trans-sialidase but this appears to be a diverse group.
Pfam PF06365: CD34/Podocalyxin family (family)
This family consists of several mammalian CD34 antigen proteins. The CD34 antigen is a human leukocyte membrane protein expressed specifically by lymphohematopoietic progenitor cells. CD34 is a phosphoprotein. Activation of protein kinase C (PKC) has been found to enhance CD34 phosphorylation. This family contains several eukaryotic podocalyxin proteins. Podocalyxin is a major membrane protein of the glomerular epithelium and is thought to be involved in maintenance of the architecture of the foot processes and filtration slits characteristic of this unique epithelium by virtue of its high negative charge. Podocalyxin functions as an  anti-adhesin that maintains an open filtration pathway between neighbouring foot processes in the glomerular epithelium by charge repulsion.
Wikipedia: Podocalyxin, a sialoglycoprotein, is thought to be the major constituent of the glycocalyx of podocytes in the glomerulus in the kidneys. It is a member of the CD34 family of transmembrane sialomucins. It coats the secondary foot processes of the podocytes. It is negatively charged and thus functions through charge repulsion to keep adjacent foot processes separated, thereby keeping the urinary filtration barrier open. This function is further supported by knockout studies in mice which reveal an essential role in podocyte morphogenesis and a role in the opening of vascular lumens and regulation of vascular permeability. Of note, this is the only cell surface sialomucin knockout known to display a lethal phenotype.
Pfam PF03693: Bacterial antitoxin of ParD toxin-antitoxin type II system and RHH (domain)
ParD is the antitoxin of a bacterial toxin-antitoxin gene pair. The cognate toxin is ParE in, [pfam:PF05016]. The family contains several related antitoxins from Cyanobacteria, Proteobacteria and Actinobacteria.  Antitoxins of this class carry an N-terminal ribbon-helix-helix domain, RHH, that is highly conserved across all type II bacterial antitoxins, which dimerises with the RHH domain of a second VapB molecule. A hinge section follows the RHH, with an additional pair of flexible alpha helices at the C-terminus. This C-terminus is the toxin-binding region of the dimer, and so is specific to the cognate toxin, whereas the RHH domain has the specific function of lying across the RNA-binding groove of the toxin dimer and inactivating the active-site - a more general function of all type II antitoxins.
Wikipedia: A toxin-antitoxin system consists of a "toxin" and a corresponding "antitoxin", usually encoded by closely linked genes. The toxin is usually a protein while the antitoxin can be a protein or an RNA. Toxin-antitoxin systems are widely distributed in prokaryotes, and organisms often have them in multiple copies. When these systems are contained on plasmids – transferable genetic elements – they ensure that only the daughter cells that inherit the plasmid survive after cell division. If the plasmid is absent in a daughter cell, the unstable antitoxin is degraded and the stable toxic protein kills the new cell; this is known as 'post-segregational killing' (PSK).
Pfam PF07622: Protein of unknown function (DUF1583) C domain (domain)
Most of these Rhodopirellula baltica hypothetical proteins also match [pfam:PF07619].
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 PF16463: Phage tail tube protein family (family)
This is a small family of Siphoviridae phage tail tube proteins. The tube protein polymerises to form the shaft through which the infecting DNA passes into the host.