SII-SWORD/CoKE huggingface dataset:
Pfam PF15047: Protein of unknown function (DUF4533) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in mammals. This family includes two human proteins: C12orf60 and C12orf69.
Pfam PF07052: Hepatocellular carcinoma-associated antigen 59 (family)
This family represents a conserved region approximately 100 residues long within mammalian hepatocellular carcinoma-associated antigen 59 (HCA59). Family members are found in a variety of eukaryotes, such as fission yeast where telomere length and silencing protein 1 (Tls1) is required for telomeric heterochromatin assembly as well as telomere length control. Homologs in Arabidopsis are known as Cop1 suppressor 2 (CSU2). Csu2 inhibits constitutive photomorphogenic 1 (COP1) E3 ubiquitin ligase activity. Furthermore, CSU2 is required for primary root development under normal light growth condition.
Pfam PF11433: Protein of unknown function (DUF3198) (family)
Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently, this archaeal family 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 PF12207: Domain of unknown function (DUF3600) (domain)
This family of proteins is found in bacteria. Proteins in this family are approximately 230 amino acids in length. This domain is the C terminal of the putative ecf-type sigma factor negative effector.
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 PF05019: Coenzyme Q (ubiquinone) biosynthesis protein Coq4 (family)
Coq4p was shown to peripherally associate with the matrix face of the mitochondrial inner membrane. The putative mitochondrial- targeting sequence present at the amino-terminus of the polypeptide efficiently imported it to mitochondria. The function of Coq4p is unknown, although its presence is required to maintain a steady-state level of Coq7p, another component of the Q biosynthetic pathway.  The overall structure of Coq4 is alpha helical and shows resemblance to haemoglobin/myoglobin (information from TOPSAN).
Pfam PF07773: Tectonic domain DUF1619 (domain)
This is a conserved domain found in tectonic proteins (TCTN1/2/3) which contains a Cys rich N-terminal region. Although its function is currently unknown (this domain is also known as DUF1619), studies in TCTN2 suggest that it is indispensable for normal functions. These proteins form a complex required for hedgehog signalling transduction.
Pfam PF13986: Domain of unknown function (DUF4224) (domain)
This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 50 amino acids in length. The protein is likely to be of phage origin and is found as protein Gp02 [swissprot:C8CLF5] in the Xylella phage Xfas53.
Pfam PF08007: JmjC domain (domain)
This entry includes proteins with a JmjC domain that belong to the cupin superfamily, including Bifunctional lysine-specific demethylase and histidyl-hydroxylase NO66, Ribosomal oxygenase 1/2, and 50S ribosomal protein L16 3-hydroxylase from Escherichia coli. Proteins are bifunctional, acting as histone lysine demethylases and ribosomal histidine hydroxylases.
Wikipedia: The cupin superfamily is a diverse superfamily of proteins named after its conserved barrel domain. The superfamily includes a wide variety of enzymes as well as non-enzymatic seed storage proteins.
Pfam PF01524: Geminivirus V2 protein (family)
Disruption of the V2 gene in Tomato yellow leaf curl virus (TYLCV) stopped its ability to systemically infect tomato plants, suggesting that the V2 gene product is required for successful infection of the host.
Pfam PF04481: Protein of unknown function (DUF561) (family)
Protein of unknown function found in a cyanobacterium, and the chloroplasts of algae.
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 PF14619: Snf2-ATP coupling, chromatin remodelling complex (domain)
This domain appears to play a crucial role in chromatin remodelling for yeast SWI/SNF. It binds histones. It is required for mobilising nucleosomes and lies within the catalytic subunit of the yeast SWI/SNF. It is found to be universally conserved.
Pfam PF18369: Polyketide synthase dimerisation element domain (domain)
This is the dimerisation element domain found in bacterial modular polyketide synthase ketoreductases. The dimerization element (DE) domain is N-terminal to the KR domain [pfam:PF08659]. DE domain is necessary for KR function, presumably because the dimeric DE orients the KR domains for optimal activity within a module.
Pfam PF09810: Exonuclease V - a 5' deoxyribonuclease (family)
Exonuclease V is a monomeric 5' deoxyribonuclease that is localised in the nucleus. It degrades single-stranded, but not double-stranded, DNA from the 5'-end, and the products are dinucleotides, except the 3'-terminal tri- and tetranucleotides, which are not degraded. The initial hydrolytic cut of exonuclease V on the dephosphorylated substrate produces a mixture of dinucleoside monophosphates and trinucleoside diphosphates. The enzyme is processive in action. Exo5 is specific for single-stranded DNA and does not hydrolyze RNA. However, Exo5 has the capacity to slide across 5' double-stranded DNA or 5' RNA sequences and resume cutting two nucleotides downstream of the double-stranded-to-single-stranded junction or RNA-to-DNA junction, respectively.
Pfam PF18308: N-terminal extension of GAT domain (family)
This region is found in the N-terminal region of the GGA and Tom1 (GAT) domain in Golgi-localizing gamma-adaptin ARF-binding protein 1 (GGA1) present in Homo sapiens. The GAT domain is the key region in GGA that interacts with ARF. ARF plays a crucial role in docking adaptor proteins to membranes. This region is referred to as N-GAT and it interacts extensively with ARF.
Pfam PF06261: Actinobacillus actinomycetemcomitans leukotoxin activator LktC (family)
This family consists of several Actinobacillus actinomycetemcomitans leukotoxin activator (LktC) proteins. Actinobacillus actinomycetemcomitans is a Gram-negative bacterium that has been implicated in the etiology of several forms of periodontitis, especially localised juvenile periodontitis. LktC along with LktB and LktD are thought to be required for activation and localisation of the leukotoxin.
Pfam PF21556: Excretory-secretory protein 2 (family)
This protein family represents a group of proteins from nematodes, including Excretory-secretory protein 2 from Ancylostoma ceylanicum (AceES-2), a highly immunoreactive molecule secreted by adult worms at the site of intestinal attachment. AceES-2 folds into a five-stranded beta-barrel flanked by short N- and C-terminal alpha-helices that lie parallel to each other on one side of the beta-barrel, adopting a netrin-like (NTR) domain, similar to the C-terminal domain of netrins.
Pfam PF20852: Non-structural protein 3, zinc-binding domain (domain)
This domain is found in Non-structural protein 3 (nsP3) from Chikungunya virus (CHIKV) and similar proteins from Alphavirus. The function of nsP3, one of the four products of the polyprotein P1234, is still unknown. This protein consists of three domains: an amino-terminal Macro domain ([pfam:PF01661]), a central zinc- binding domain (ZBD, this entry), and a hypervariable-sequence carboxyl terminus. ZBD is essential for viral replication. It has two cysteines in a loop between alpha-helices and the other two cysteines at the end of two parallel beta-strands, which represent a structural scaffold for zinc-ion coordination.
Pfam PF25030: Serine/threonine-protein kinase ATR, M-HEAT region (repeat)
This region of HEAT repeats is found in human Serine/threonine -protein kinase ATR and similar eukaryotic proteins. ATR acts as a DNA damage sensor and is associated with severe disorders such as Seckel syndrome 1. This protein is organised into a large N-terminal alpha solenoid containing HEAT repeats, a FAT (FRAP, ATM, TRRAP) domain ([pfam:PF02259]), a kinase domain ([pfam:PF00454]), and a C-terminal short segment referred to as FATC ([pfam:PF02260]). The N-terminal part has two continuous HEAT repeat regions, the N-HEAT and the M-HEAT. This entry represents the M-HEAT region.
Pfam PF06956: Regulator of RNA terminal phosphate cyclase (family)
RtcR is a sigma54-dependent enhancer binding protein that activates transcription of the rtcBA operon. The product of the rtcA gene is an RNA 3'-terminal phosphate cyclase. This domain is found at the N terminus of the RtcR sequence. RtcR, and other sigma54-dependent activators, contain [pfam:PF00158] in the central region of the protein sequence.
Pfam PF07905: Purine catabolism regulatory protein-like family (family)
The bacterial proteins found in this family are similar to the purine catabolism regulatory protein expressed by Bacillus subtilis (PucR, [swissprot:O32138]). PucR is thought to be a transcriptional activator involved in the induction of the purine degradation pathway, and may contain a LysR-like DNA-binding domain.  It is similar to LysR-type regulators in that it represses its own expression. The other members of this family are also annotated as being putative regulatory proteins.
Pfam PF16889: Heparinase II/III N-terminus (repeat)
This is the N-terminal domain of heparinase II/III proteins. It is a toroid-like domain.
Pfam PF11243: Protein of unknown function (DUF3045) (family)
Members in this family of proteins are annotated as gene protein 30.1. Currently no function is 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 PF00281: Ribosomal protein L5 (domain)
This entry represents the N-terminal domain of the ribosomal protein uL5.
Large ribosomal subunit protein uL5, previously known as Ribosomal protein L5, is ~180 amino acids in length. In Escherichia coli, uL5 is known to be involved in binding 5S RNA to the large ribosomal subunit .
Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.

Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome .
Pfam PF02183: Homeobox associated leucine zipper (coiled_coil)
This region is a plant specific leucine zipper that is always found associated with a homeobox .
Pfam PF04090: RNA polymerase I-specific transcription initiation factor Rrn11 (repeat)
The RNA polymerase I specific transcription initiation factor Rrn11 is a member of a multiprotein complex essential for the initiation of transcription by RNA polymerase I, together with Rrn6 and Rrn7 subunits. Binding to the DNA template is dependent on the initial binding of other factors. Rrn11 contains a tetratricopeptide repeats (TPRs) and interacts with Rrn6 and Rrn7 to form the core factor (CF), which which resembles a right hand holding the DNA molecule between the fingers and the palm.     The palm is composed of the N-terminal regions of both Rrn11 and Rrn6, the thumb is composed of the C-terminal of Rrn11, and the fingers and knuckles are composed of Rrn7 and the C-terminal half of Rrn6, respectively.
Pfam PF10865: Domain of unknown function (DUF2703) (domain)
This family of protein has no known function, but it may be distantly related to the thioredoxin fold. It contains the CXXC motif that is characteristic of thioredoxins.
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 PF16442: Domain of unknown function (DUF5039) (family)
This family consists of several uncharacterized proteins around 240 residues in length and is mainly found in various Bacteroides species. The function of this family is unknown.
Pfam PF21370: Cyclic-di-AMP phosphodiesterase GdpP-like, PAS domain (domain)
This domain is found at the N-terminal region of Cyclic-di-AMP phosphodiesterase GdpP from Geobacillus thermodenitrificans. GdpP is a stress signaling protein with phosphodiesterase activity against cyclic-di-AMP (c-di-AMP). This protein contains three protein domains in addition to the two N-terminal transmembrane helices: a Per-ARNT-Sim (PAS) domain (this entry), a GGDEF domain, and a DHH/DHHA1 domain ([pfam:PF01368] and [pfam:PF02272]). This domain adopts the typical alpha-beta-PAS domain fold formed by several short and distorted alpha-helices and one five-stranded antiparallel beta- sheet. Noticeably, three of the strands and one of the helices are shorter than those found in other typical PAS domains. This domain is also found at the N-terminal of the membrane protein-large ribosomal subunit bL9 fusion protein from phytoplasma which have a large N-terminal domain structurally similar to this group of sequences, although not functionally related.
Pfam PF03141: Putative S-adenosyl-L-methionine-dependent methyltransferase (family)
This family is a putative S-adenosyl-L-methionine (SAM)-dependent methyltransferase.
Pfam PF18082: N-acyltransferase N-terminal domain (domain)
This is the N-terminal all helix domain found in N-acyltransferases (NATs), the gene products orf11 and dbv8. The all-helix domain is composed of eight helices with two helix-turn-helix motifs in tandem. It is structurally akin to the AAA+ protein family (ATPases associated with diverse cellular activities).
Pfam PF12630: Poxvirus poly(A) polymerase N-terminal domain (domain)
This domain is found at the N-terminus of the pox virus Poly(A) polymerase protein. According to SCOP this domain contains a helix-hairpin-helix motif.
Pfam PF19507: Family of unknown function (DUF6041) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000260) is described by MIBiG as an example of the following biosynthetic class, polyketide. This family includes a protein from the prodigiosin biosynthetic gene cluster from  Hahella chejuensis KCTC 2396
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 PF03318: Clostridium epsilon toxin ETX/Bacillus mosquitocidal toxin MTX2 (family)
This family appears to be distantly related to [pfam:PF01117].
Pfam PF17735: Biofilm surface layer A (family)
This family includes members such as BslA (previously called YuaB). Secreted BslA from Bacillus subtillis has been shown to form surface layers around the biofilm self-assembling at interfaces of B. subtilis biofilms, forming an elastic film. structural analysis revealed that BslA consists of an Ig-type fold with the addition of an unusual, extremely hydrophobic cap region. The hydrophobic cap exhibits physiochemical properties similar to the hydrophobic surface found in fungal hydrophobins; thus, BslA is defined as member of a class of bacterially produced hydrophobins.
Pfam PF01372: Melittin (family)
Allergies are hypersensitivity reactions of the immune system to specific substances called allergens (such as pollen, stings, drugs, or food) that, in most people, result in no symptoms. A nomenclature system has been established for antigens (allergens) that cause IgE-mediated atopic allergies in humans [WHO/IUIS Allergen Nomenclature Subcommittee King T.P., Hoffmann D., Loewenstein H., Marsh D.G., Platts-Mills T.A.E., Thomas W. Bull. World Health Organ. 72:797-806(1994)]. This nomenclature system is defined by a designation that is composed of the first three letters of the genus; a space; the first letter of the species name; a space and an Arabic number. In the event that two species names have identical designations, they are discriminated from one another by adding one or more letters (as necessary) to each species designation.

The allergens in this family include allergens with the following designations: Api m 3.

Melittin is the principal protein component of the venom of the honeybee, Apis mellifera. It inhibits protein kinase C, Ca2+/calmodulin-dependent protein kinase II, myosin light chain kinase and Na+/K+-ATPase (synaptosomal membrane) and is a cell membrane lytic factor. Melittin is a small peptide with no disulphide bridge; the N-terminal part of the molecule is predominantly hydrophobic and the C-terminal part is hydrophilic and strongly basic.

The molecular mechanisms underlying the various effects of melittin on membranes have not been completely defined and much of the evidence indicates that different molecular mechanisms may underlie different actions of the peptide .

Extensive work with melittin has shown that the venom has multiple effects, probably, as a result of its interaction with negatively changed phospholipids. It inhibits well known transport pumps such as the Na+-K+-ATPase and the H+-K+-ATPase. Melittin increases the permeability of cell membranes to ions, particularly Na+and indirectly Ca2+, because of the Na+-Ca2+-exchange. This effect results in marked morphological and functional changes, particularly in excitable tissues such as cardiac myocytes. In some other tissues, e.g., cornea, not only Na+but Cl- permeability is also increased by melittin. Similar effects to melittin on H+-K+-ATPase have been found with the synthetic amphipathic polypeptide Trp-3 .

The study of melittin in model membranes has been useful for the development of methodology for determination of membrane protein structures. A molecular dynamics simulation of melittin in a hydrated dipalmitoylphosphatidylcholine (DPPC) bilayer was carried out. The effect of melittin on the surrounding membrane was localised to its immediate vicinity, and its asymmetry with respect to the two layers may be a result of the fact that it is not fully transmembranal. Melittin's hydrophilic C terminus anchors it at the extracellular interface, leaving the N terminus "loose" in the lower layer of the membrane .
Wikipedia: Melittin is the main component and the major pain-producing substance of honeybee venom. Melittin is a basic peptide consisting of 26 amino acids.
Pfam PF15568: Immunity protein 39 (family)
A predicted immunity protein with an alpha+beta fold and conserved GR, and GxK motifs. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, usually containing a domain of the Tox-URI2 family of nucleases.
Pfam PF10798: Biofilm development protein YmgB/AriR (family)
YmgB is part of the three gene cluster ymgABC which has a role in biofilm development and stability. YmgB represses biofilm formation in rich medium containing glucose, decreases cellular motility and also protects the cell from acid which indicates that YmgB has an important function in acid-resistance. YmgB binds as a dimer to genes which are important for biofilm formation via a ligand. Due to its important function in acid resistance it is also known as AriR (regulator of acid resistance influenced by indole).
Pfam PF21660: Filamentous archaeal viruses coat protein, C-terminal (domain)
This entry represents the C-terminal domain of a major coat protein from Acidianus filamentous virus 1 which adopts a four-helix bundle fold.
Pfam PF23135: TRI4 N-terminal (domain)
This entry represents a presumed domain found at the N-terminal of TRIP4 (also known as ASC-1) from human and related sequences. TRIP4 is the orthologue of yeast RQT4 and is part of the RQC trigger (RQT) complex that activates the ribosome quality control (RQC) pathway, a pathway that degrades nascent peptide chains during problematic translation. TRIP4 has also been described as a transcription coactivator which associates with nuclear receptors and transcriptional coactivators including EP300, CREBBP and NCOA1, and basal transcription factors like TBP and TFIIA to facilitate nuclear receptors-mediated transcription. The function of this domain is known. According to structure predictions, this domain may adopt a four helical bundle fold.
Pfam PF07791: Immunity protein family (Imm11) (family)
This family formerly known as DUF1629 was identified to be an immunity protein.