SII-SWORD/CoKE huggingface dataset:
Pfam PF20110: Family of unknown function (DUF6500) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 70 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 PF17532: Family of unknown function (DUF5451) (family)
This is a family of unknown function found in Epstein-Barr virus.
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 PF13677: Membrane MotB of proton-channel complex MotA/MotB (domain)
This is the MotB member of the E.coli MotA/MotB proton-channel complex that forms the stator of the bacterial membrane flagellar motor. Key residues act as a plug to prevent premature proton flow. The plug is in the periplasm just C-terminal to the MotB TM, consisting of an amphipathic alpha helix flanked by Pro-52 and Pro-65, eg in [swissprot:D3V2T1]. In addition to the Pro residues, Ile-58, Tyr-61, and Phe 62 are also essential for plug function.
Pfam PF00090: Thrombospondin type 1 domain (domain)
This repeat was first described in 1986 by Lawler and Hynes . It was found in the thrombospondin protein where it is repeated 3 times. Now a number of proteins involved in the complement pathway (properdin, C6, C7, C8A, C8B, C9)  as well as extracellular matrix protein like mindin, F-spondin , SCO-spondin and even the circumsporozoite surface protein 2 and TRAP proteins of Plasmodium  contain one or more instance of this repeat. It has been involved in cell-cell interaction, inhibition of angiogenesis  and apoptosis .

The intron-exon organisation of the properdin gene confirms the hypothesis that the repeat might have evolved by a process involving exon shuffling . A study of properdin structure provides some information about the structure of the thrombospondin type I repeat .
Thrombospondins are multimeric multidomain glycoproteins that function at cell surfaces and in the extracellular matrix milieu. They act as regulators of cell interactions in vertebrates. They are divided into two subfamilies, A and B, according to their overall molecular organisation. The subgroup A proteins TSP-1 and -2 contain an N-terminal domain, a VWFC domain, three TSP1 repeats, three EGF-like domains, TSP3 repeats and a C-terminal domain. They are assembled as trimer. The subgroup B thrombospondins, designated TSP-3, -4, and COMP (cartilage oligomeric matrix protein, also designated TSP-5) are distinct in that they contain unique N-terminal regions, lack the VWFC domain and TSP1 repeats, contain four copies of EGF-like domains, and are assembled as pentamers . EGF, TSP3 repeats and the C-terminal domain are thus the hallmark of a thrombospondin.
Wikipedia: Thrombospondins (TSPs) are a family of secreted glycoproteins with antiangiogenic functions. Due to their dynamic role within the extracellular matrix they are considered matricellular proteins. The first member of the family, thrombospondin 1 (THBS1), was discovered in 1971 by Nancy L. Baenziger.
Pfam PF01659: Luteovirus putative VPg genome linked protein (family)
This family consists of several putative genome linked proteins. The genomic RNA of luteoviruses are linked to virally encoded genome proteins (VPg).  Open reading frame 4 is thought to encode the VPg  in Soybean dwarf luteovirus. Luteoviruses have isometric capsids that contain a positive stand ssRNA genome, they have no DNA stage during their replication.
Pfam PF15248: Domain of unknown function (DUF4587) (family)
This protein family is a domain of unknown function. The precise function of this protein domain remains to be elucidated. This domain family is found in eukaryotes, and is typically between 64 and 79 amino acids in length. There are two conserved sequence motifs: QNAQ and HHH. In humans, it is found in the position, chromosome 21 open reading frame 58.
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 PF11688: Protein of unknown function (DUF3285) (family)
This family of proteins with unknown function appears to be restricted to Cyanobacteria.
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 PF02420: Insect antifreeze protein repeat (repeat)
This family of extracellular proteins is involved in stopping the formation of ice crystals at low temperatures. The proteins are composed of a 12 residue repeat that forms a structural repeat. The structure of the repeats is a beta helix. Each repeat contains two cys residues that form a disulphide bridge.
Wikipedia: Antifreeze proteins (AFPs) or ice structuring proteins refer to a class of polypeptides produced by certain animals, plants, fungi and bacteria that permit their survival in temperatures below the freezing point of water. AFPs bind to small ice crystals to inhibit the growth and recrystallization of ice that would otherwise be fatal. There is also increasing evidence that AFPs interact with mammalian cell membranes to protect them from cold damage. This work suggests the involvement of AFPs in cold acclimatization.
Pfam PF11437: Vanadium-binding protein 2 (family)
The Vanadium binding protein, Vanabin2, contains four alpha-helices connected by nine disulphide bonds. Vanadium accumulates in Ascidians however the biological reason remains unclear.
Pfam PF13929: mRNA stabilisation (family)
This domain is an mRNA stabilisation factor.
Pfam PF16312: Coiled-coil region of Oberon (coiled_coil)
Oberon_cc is the coiled-coil region of Oberon proteins from plants. Oberon is necessary for maintenance and/or establishment of both the shoot and root apical meristems in Arabidopsis. Most Oberon proteins carry a PHD finger domain, [pfam:PF07227] and this coiled-coil domain. Oberon proteins mediate the TMO7 (the direct target of MP) expression through modification of, or binding to, chromatin at the TMO7 locus. TMO7 stands for the target of Monopteros 7 (or Auxin response factor 7).
Pfam PF21634: Helicase MOV-10, beta-barrel domain (domain)
Helicase MOV-10 is a 5'-3' RNA helicase required for RNA-mediated gene silencing by the RNA-induced silencing complex (RISC). It is involved in mRNA metabolism and translation, modulation of viral infectivity, inhibition of retrotransposition and regulation of synaptic transmission. It interacts with FMRP1 and regulates miRNA-mediated translational repression by AGO2. This entry represents a presumed domain found in MOV-10 and its homologues, which, according to structure predictions, it seems to form a beta-barrel, closely related to the OB fold. This domain is found prior to the helicase domain.
Pfam PF17146: PIN domain of ribonuclease (domain)
This is a PIN domain found in eukaryotic ribonuclease Nob1 and archaeal ribonuclease VapC1. Budding yeast Nob1 is involved in proteasomal and 40S ribosomal subunit biogenesis. VapC1 is a toxic component and a ribonuclease of a toxin-antitoxin (TA) module. PIN domains are small protein domains identified by the presence of three strictly conserved acidic residues. Apart from these three residues, there is poor sequence conservation. PIN domains are found in eukaryotes, eubacteria and archaea. In eukaryotes they are ribonucleases involved in nonsense mediated mRNA decay and in processing of 18S ribosomal RNA. In prokaryotes, they are the toxic components of toxin-antitoxin (TA) systems, their toxicity arising by virtue of their ribonuclease activity. The PIN domain TA systems are now called VapBC TAs(virulence associated proteins), where VapB is the inhibitor and VapC, the PIN-domain ribonuclease toxin.
Pfam PF24992: Domain of unknown function (DUF7777) (domain)
This domain is found exclusively in Trichomonas proteins. It is predicted to fold into an alpha/beta structure.
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 PF17925: Tetracyclin repressor-like, C-terminal domain (domain)
TetR family regulators are involved in the transcriptional control of multidrug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity. The TetR proteins identified in overm ultiple genera of bacteria and archaea share a common helix-turn-helix (HTH) structure in their DNA-binding domain. However, TetR proteins can work in different ways: they can bind a target operator directly to exert their effect (e.g. TetR binds Tet(A) gene to repress it in the absence of tetracycline), or they can be involved in complex regulatory cascades in which the TetR protein can either be modulated by another regulator or TetR can trigger the cellular response. TetR regulates the expression of the membrane-associated tetracycline resistance protein, TetA, which exports the tetracycline antibiotic out of the cell before it can attach to the ribosomes and inhibit protein synthesis. TetR blocks transcription from the genes encoding both TetA and TetR in the absence of antibiotic. The C-terminal domain is multi-helical and is interlocked in the homodimer with the helix-turn-helix (HTH) DNA-binding domain. This entry represents the C-terminal domain present the transcriptional regulator KstR that regulates a large set of genes responsible for cholesterol catabolism. This is important for Mycobacterium tuberculosis during infection, both at an early stage in the macrophage phagosome and later within the necrotic granuloma.
Pfam PF00688: TGF-beta propeptide (family)
This propeptide is known as latency associated peptide (LAP) in TGF-beta. LAP is a homodimer which is disulfide linked to TGF-beta binding protein.
Pfam PF07281: Insulin-induced protein (INSIG) (family)
This family contains a number of eukaryotic Insulin-induced proteins (INSIG-1 and INSIG-2) approximately 200 residues long. INSIG-1 and INSIG-2 are found in the endoplasmic reticulum and bind the sterol-sensing domain of SREBP cleavage-activating protein (SCAP), preventing it from escorting SREBPs to the Golgi. Their combined action permits feedback regulation of cholesterol synthesis over a wide range of sterol concentrations.
Pfam PF12047: Cytosine specific DNA methyltransferase replication foci domain (domain)
This domain is part of a cytosine specific DNA methyltransferase enzyme. It functions non-catalytically to target the protein towards replication foci. This allows the DNMT1 protein to methylate the correct residues. This domain targets DMAP1 and HDAC2 to the replication foci during the S phase of mitosis. They are thought to have some importance in conversion of critical histone lysine moieties.
Pfam PF08759: Glycosyltransferase GT-D fold (domain)
This domain is found at the C terminus of proteins such as the probable glycosyltransferase Gly ([swissprot:Q9AEU2]) that also contain the glycosyl transferase domain at the N terminus. It is also found N-terminal in numerous putative glycosyltransferases such as GalT1. GalT1 has been shown to catalyse the third step of Fap1  glycosylation. This domain is structurally distinct from all known GT folds of glycosyltransferases and contains a metal binding site. This new glycosyltransferase fold has been named GT-D.
Pfam PF05737: Collagen binding domain (domain)
The domain fold is a jelly-roll, composed of two antiparallel beta-sheets and two short alpha-helices. A groove on beta-sheet I exhibited the best surface complementarity to the collagen. This site partially overlaps with the peptide sequence previously shown to be critical for collagen binding. Recombinant proteins containing single amino acid mutations designed to disrupt the surface of the putative binding site exhibited significantly lower affinities for collagen.
Pfam PF02792: Mago nashi protein (family)
This family was originally identified in Drosophila and called mago nashi, it is a strict maternal effect, grandchildless-like, gene. The human homologue has been shown to interact with an RNA binding protein [swissprot:Q9Y5S9]. An RNAi knockout of the C. elegans homologue causes masculinization of the germ line (Mog phenotype) hermaphrodites, suggesting it is involved in hermaphrodite germ-line sex determination. Mago nashi has been found to be part of the exon-exon junction complex that binds 20 nucleotides upstream of exon-exon junctions.
Pfam PF21230: Nakanori-like protein (domain)
This entry include the Nakanori protein a nontoxic mushroom protein that specifically binds to a complex of sphingomyelin, a major sphingolipid in mammalian cells, and cholesterol.
Pfam PF14236: Druantia protein DruA (family)
Druantia type I is an antiviral defense system composed of DruA, DruB, DruC, DruD and DruE. Expression of Druantia in E.coli (strain MG1655) confers resistance to phage lambda, SECphi18, SECphi27 and T4. This entry represents DruA.
Pfam PF05272: Virulence-associated protein E-like domain (domain)
This domain is found in VapE (virulence-associated protein E, [swissprot:Q46554]) from Dichelobacter nodosus and similar proteins, mainly from bacteria. These proteins contain a P-loop motif.
Pfam PF11794: 4-hydroxyphenylacetate 3-hydroxylase N terminal (family)
HpaB [swissprot:Q57160] encodes part of the 4-hydroxyphenylacetate 3-hydroxylase from Escherichia coli. HpaB is part of a heterodimeric enzyme that also requires HpaC. The enzyme is NADH-dependent and uses FAD as the redox chromophore. This family also includes PvcC [swissprot:O30372] may play a role in one of the proposed hydroxylation steps of pyoverdine chromophore biosynthesis.
Pfam PF22678: Cytochrome c-type protein NrfB-like (domain)
This entry includes Cytochrome c-type protein NrfB and similar proteins, which plays a role in nitrite reduction. These proteins contain several copies of the CXXCH haem-binding motif.
Pfam PF16779: DNA-mimic protein (domain)
This is a family of DNA-mimic proteins expressed by Neisseria species. In its monomeric form DMP12 interacts with the Neisseria dimeric form of the bacterial histone-like protein HU. HU proteins promote the assembly of higher-order DNA-protein structures, The interaction between DMP12 and HU protein may be instrumental in controlling the stability of the nucleoid in Neisseria as DMP12 prevents Neisseria HU protein from being digested by trypsin.
Pfam PF12500: TRSP domain C terminus to PRTase_2 (domain)
This domain occurs C-terminal to PRTase_2 and has highly conserved GXXE and TRSP signatures. It is found in bacteria. These genes are found in the biosynthetic operon associated with the Ter stress response operon and are predicted to be involved in the biosynthesis of a ribo-nucleoside involved in stress response.
Pfam PF00667: FAD binding domain (domain)
This domain is found in sulfite reductase, NADPH cytochrome P450 reductase, Nitric oxide synthase and methionine synthase reductase.
Wikipedia: Flavoprotein pyridine nucleotide cytochrome reductases catalyse the interchange of reducing equivalents between one-electron carriers and the two-electron-carrying nicotinamide dinucleotides. The enzymes include ferredoxin-NADP+ reductases, plant and fungal NAD(P)H:nitrate reductases, cytochrome b5 reductases, cytochrome P450 reductases, sulphite reductases, nitric oxide synthases, phthalate dioxygenase reductase, and various other flavoproteins.
Pfam PF01229: Glycosyl hydrolases family 39 (domain)
This entry represents the N-terminal catalytic domain of Glycoside hydrolase family 39 proteins.
Glycoside hydrolase family 39 (GH39) comprises enzymes with several known activities such as alpha-L-iduronidase (3.2.1.76), beta-xylosidase (3.2.1.37), and alpha-1,4-L-rhamnosidase .

The most highly conserved regions in these enzymes are located in their N-terminal parts. These contain a glutamic acid residue which, on the basis of similarities with other families of glycosyl hydrolases , probably acts as the proton donor in their catalytic mechanism.
Wikipedia: In molecular biology, glycoside hydrolase family 39 is a family of glycoside hydrolases.
Pfam PF14565: Interleukin 22 IL-10-related T-cell-derived-inducible factor (domain)
Interleukin-22 is distantly related to interleukin (IL)-10, and is produced by activated T cells. IL-22 is a ligand for CRF2-4, a member of the class II cytokine receptor family.
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 PF03261: Cyclin-dependent kinase 5 activator protein (family)
These proteins are neuron specific activators of cyclin-dependent kinase 5 (CDK5) . They form a heterodimer with the catalytic subunit (CDK5) .
Pfam PF00113: Enolase, C-terminal TIM barrel domain (domain)
Enolase (2-phospho-D-glycerate hydrolase) is an essential, homodimeric enzyme that catalyses the reversible dehydration of 2-phospho-D-glycerate to phosphoenolpyruvate as part of the glycolytic and gluconeogenesis pathways . The reaction is facilitated by the presence of metal ions . In vertebrates, there are 3 different, tissue-specific isoenzymes, designated alpha, beta and gamma. Alpha is present in most tissues, beta is localised in muscle tissue, and gamma is found only in nervous tissue. The functional enzyme exists as a dimer of any 2 isoforms. In immature organs and in adult liver, it is usually an alpha homodimer, in adult skeletal muscle, a beta homodimer, and in adult neurons, a gamma homodimer. In developing muscle, it is usually an alpha/beta heterodimer, and in the developing nervous system, an alpha/gamma heterodimer . The tissue specific forms display minor kinetic differences. Tau-crystallin, one of the major lens proteins in some fish, reptiles and birds, has been shown  to be evolutionary related to enolase.

Neuron-specific enolase is released in a variety of neurological diseases, such as multiple sclerosis and after seizures or acute stroke. Several tumour cells have also been found positive for neuron-specific enolase. Beta-enolase deficiency is associated with glycogenosis type XIII defect.
Wikipedia: Phosphopyruvate hydratase, usually known as enolase, is a metalloenzyme (EC 4.2.1.11) that catalyses the conversion of 2-phosphoglycerate (2-PG) to phosphoenolpyruvate (PEP), the ninth and penultimate step of glycolysis. The chemical reaction is:2-phospho-D-glycerate  phosphoenolpyruvate + H2O
Pfam PF01918: Alba (family)
Alba is a novel chromosomal protein that coats archaeal DNA without compacting it.
Pfam PF13707: RloB-like protein (domain)
This family includes the RloB protein that is found within a bacterial restriction modification operon.  This family includes the AbiLii protein that is found as part of a plasmid encoded phage abortive infection mechanism. Deletion within abiLii abolished the phage resistance. The family includes some proteins annotated as CRISPR Csm2 proteins.
Pfam PF01848: Hok/gef family (family)
The hok/gef family of Gram-negative bacterial proteins are toxic to cells when overexpressed, killing the cells from within by interfering with a vital function in the cell membrane . Some family members (flm) increase the stability of unstable RNA , some (pnd) induce the degradation of stable RNA at higher than optimum growth temperatures , while others affect the release of cellular magnesium by membrane alterations . The proteins are short (50-70 residues), consisting of an N-terminal hydrophobic (possibly membrane spanning) domain, and a C-terminal periplasmic region, which contains the toxic domain. The C-terminal region contains a conserved cysteine residue that mediates homo-dimerisation in the gef protein, although dimerisation is not necessary for the toxic effect .
Wikipedia: The hok/sok system is a postsegregational killing mechanism employed by the R1 plasmid in Escherichia coli. It was the first type I toxin-antitoxin pair to be identified through characterisation of a plasmid-stabilising locus. It is a type I system because the toxin is neutralised by a complementary RNA, rather than a partnered protein.
Pfam PF04257: Exodeoxyribonuclease V, gamma subunit (family)
The Exodeoxyribonuclease V enzyme is a multi-subunit enzyme comprised of the proteins RecB, RecC (this family) and  RecD. This enzyme plays an important role in homologous genetic recombination, repair of double strand DNA breaks resistance to UV irradiation and chemical DNA-damage. The enzyme ([ec:3.1.11.5]) catalyses ssDNA or dsDNA-dependent ATP hydrolysis, hydrolysis of ssDNA or dsDNA and unwinding of dsDNA. This subunit recognises and binds DNA forks containing Chi sequences in a sequence specific manner while Chi interactions with the phosphodiester backbone (mainly arginine side chains) stabilise the twisted conformation of the DNA. These interactions induce conformational changes that switch RecBCD from bacteriophage destruction and CRISPR spacer acquisition, to constructive host DNA repair.
Pfam PF09022: Staphostatin A (domain)
The staphostatin A polypeptide chain folds into a slightly deformed, eight-stranded beta-barrel, with strands beta-4 through beta-8 forming an antiparallel sheet while the N-terminus forms a a psi-loop motif. Members of this family constitute a class of cysteine protease inhibitors distinct in the fold and the mechanism of action from any known inhibitors of these enzymes.
Pfam PF03128: CXCXC repeat (repeat)
This repeat contains the conserved pattern CXCXC where X can be any amino acid.  The repeat is found in up to five copies in Vascular endothelial growth factor C. In the salivary glands of the dipteran Chironomus tentans, a specific messenger ribonucleoprotein (mRNP) particle, the Balbiani ring (BR) granule, can be visualised during its assembly on the gene and during its nucleocytoplasmic transport. This repeat is found over 70 copies in the balbiani ring protein 3 [swissprot:Q03376]. It is also found in some silk proteins.
Pfam PF10033: Autophagy-related protein 13 (family)
Members of this family of phosphoproteins are involved in cytoplasm to vacuole transport (Cvt), and more specifically in Cvt vesicle formation. They are probably involved in the switching machinery regulating the conversion between the Cvt pathway and autophagy. Finally, ATG13 is also required for glycogen storage.