SII-SWORD/CoKE huggingface dataset:
Pfam PF13042: Protein of unknown function (DUF3902) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 170 amino acids in length. There is a conserved LGI sequence motif.
Pfam PF20832: Reovirus VP3 protein, Methyltransferase domain 2 (domain)
Cytoplasmic polyhedrosis virus (CPV) has a turreted single-layer capsid consisting of 12 pentameric turrets on the five-fold vertices. Each turret has one Turret protein (TP), also known as VP3, which shows a polyhedrin-binding domain (PBD), a guanylyltransferase (GTase) domain ([pfam:PF20790]), two methyltransferase domains and a bridge domain. This entry represents the second methyltransferase domain, which is found at the C-terminal end of the protein.
Pfam PF11506: Protein of unknown function (DUF3217) (family)
This family of proteins with unknown function appears to be restricted to Mycoplasma and Ruminococcus spp. The structure of Uncharacterized protein MG376 homolog from Mycoplasma pneumoniae shows an OB fold with six beta-strands and three loops forming a beta-barrel that is capped by one alpha-helix. Its specific function is still 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 PF18319: PriA DNA helicase Cys-rich region (CRR) domain (domain)
This is a cys-rich region (CRR) domain found in PriA DNA helicases. In bacteria, the replication restart process is orchestrated by the PriA DNA helicase, which identifies replication forks via structure-specific DNA binding and interactions with fork-associated ssDNA-binding proteins (SSBs). The CRR region which is embedded within the C-terminal helicase lobe has been identified to bind two Zn2+ ions. This 50-residue insertion forms a structure on the surface of the helicase core in which two Zn2+ ions are coordinated by invariant Cys residues. Biochemical experiments have shown that sequence changes to Zn2+-binding Cys residues in the PriA CRR can eliminate helicase, but not ATPase, activity and can block assembly of PriB onto DNA-bound PriA, implicating the CRR in multiple functions in PriA.
Pfam PF20851: SidM, Rab1-activation domain (domain)
This domain is found in the type IV virulence effector SidM/DrrA from Legionella pneumophila. This protein has dual GEF and GDF activity specifically toward Rab1, a key regulator for endoplasmic reticulum (ER)-to-Golgi vesicle trafficking. SidM consists of an N-terminal helical domain, a Rab1-activation domain (this entry), and a C- terminal phosphatidylinositol 4-phosphate-binding (P4M) domain ([pfam:PF14860]). The Rab1-activation domain strongly interacts with Rab1 switch regions leading to substantial conformational changes on SidM binding. This domain is organized into two layers of helices.
Pfam PF22170: Phosphocholine transferase AnkX insertion domain (domain)
This entry represents the insertion domain of AnkX, a Legionella pneumophila PC transferase that mediates the recruitment of Rab1 to the cytosolic face of the Legionella-containing vacuole (LCVs). It is a virulence factor that modifies host RAB1 (RAB1A, RAB1B, or RAB1C) and RAB35 leading to the displacement of GDP dissociation inhibitors (GDI) and impairs accessibility to the GTPase effector LepB. It consists of two distinct structural units. The N-terminal contains a FIC domain, which encompasses the CDP-choline binding pocket and a C-terminal ankyrin repeats-containing domain.  Unlike other FIC enzymes, AnkX comprises an additional insert domain located in the conserved beta-hairpin which consists of alpha-helices and beta-sheets that protrudes from the enzyme and adapts a rigid, thorn-like structure.
Pfam PF01406: tRNA synthetases class I (C) catalytic domain (domain)
This entry represents the catalytic (Rossmann-fold) domain found in  cysteinyl tRNA synthetases which is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It  contains the characteristic class I HIGH and KMSKS motifs, which are  involved in ATP binding. Cysteine-tRNA ligase (also known as cysteinyl-tRNA synthetase)  (6.1.1.16) is an alpha monomer and belongs to class Ia. It  aminoacylates the 2'-OH of the nucleotide at the 3' of the  appropriate tRNA. It is highly specific despite not possessing the  amino acid editing activity characteristic of many other tRNA  ligases.
Pfam PF00489: Interleukin-6/G-CSF/MGF family (domain)
This entry represents interleukin-6 (IL6), also refered to as B-cell stimulatory factor-2 (BSF-2) and interferon beta-2, it is a cytokine involved in a wide variety of biological functions . It plays an essential role in the final differentiation of B-cells into IG-secreting cells, as well as inducing myeloma/plasmacytoma growth, nerve cell differentiation and, in hepatocytes, acute phase reactants .

This entry also includes the interleukin-6 homologue from human herpesvirus 8 type P which binds to interleukin-6 receptor subunit beta IL6ST and initiates a signal transduction. It is able to induce blood to lymphatic endothelial cell differentiation and, in infected primary effusion lymphoma cells, it promotes cell proliferation, protects them from apoptosis, and promotes immune evasion of interferon activity .
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 PF21095: CarD, C-terminal domain (domain)
This entry represents the C-terminal helical domain of CarD from Mycobacterium tuberculosis, a RNAP-binding protein that regulates transcription and essential processes. This domain binds DNA in a non-specific manner.
Pfam PF06439: 3-keto-disaccharide hydrolase (domain)
This family has structural similarity to an endo-1,3-1,4-beta glucanase belonging to glycoside hydrolase family 16. A member containing this domain, BT2157 from B. thetaiotaomicron, hydrolyses 3-ketotrehalose during trehalose degradation that proceeds through a 3-keto-glycoside intermediate. Other members containing this domain are involved in disaccharide catabolism with 3-ketoglycoside intermediates.
Pfam PF15871: Junction-mediating and -regulatory protein (family)
JMY, Junction-mediating and -regulatory protein is also a WASP homolog-associated protein with actin, membranes and microtubules. This middle region is the coiled-coil region that putatively binds microtubules to the scaffold. This ability to interact with microtubules plays a role in membrane tubulation.
Pfam PF24644: Domain of unknown function (DUF7638) (domain)
This domain is found in uncharacterised bacterial proteins. It is predicted to adopt an alpha/beta structure consisting of curved beta-sheet and alpha-helices packed on the concave side of it.
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 PF04200: Lipoprotein associated domain (domain)
This presumed domain is about 100 amino acids in length. It is found in lipoprotein of unknown function and is greatly expanded in Mycoplasma pulmonis.  The domain is found in up to five copies in some proteins. This family also includes the Mycoplasma arthritidis MAA2 variable surface protein. MAA2 is implicated in in cytoadherence and virulence and has been shown to exhibit both size and phase variability.
Pfam PF24204: Domain of unknown function (DUF7428) (domain)
This entry represents a small family of uncharacterised phage proteins. The structure of this family is predicted to be composed of a four stranded beta sheet and a single alpha helix.
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 PF05167: Uncharacterised ACR (DUF711) (family)
The proteins in this family are functionally uncharacterised. The proteins are around 450 amino acids long and includes Streptococcus pneumoniae Sp0239 which is structurally similar to ribonucleotide reductase (RNR) and pyruvate formate lyase (PFL). It is likely that this family represents a group of glycerol-3-phosphate dehydrogenases.
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 PF22456: PQQ synthase PqqF-like, C-terminal lobe domain 4 (domain)
This entry represents domain 4 from the C-terminal lobe of PQQ synthase PqqF, a protein required for coenzyme pyrroloquinoline quinone (PQQ) biosynthesis. It consists of four structurally similar domains organised in N-terminal (domain 1 represented in Pfam: PF00675 and domain 2 in [pfam:PF22454]) and C-terminal (domain 3 and domain 4) lobes. This domain is also found in other Peptidase M16 members, such as Nardilysin and insulin degrading enzymes from human.
Pfam PF00930: Dipeptidyl peptidase IV (DPP IV) N-terminal region (repeat)
This family is an alignment of the region to the N-terminal side of the active site. The Prosite motif does not correspond to this Pfam entry.
Wikipedia: In molecular biology, the dipeptidyl-peptidase IV family is a family of serine peptidases which belong to MEROPS peptidase family S9, subfamily S9B. The protein fold of the peptidase domain for members of this family resembles that of serine carboxypeptidase D, the type example of clan SC. The type example of this family is Dipeptidyl peptidase-4.
Pfam PF22017: LPP20 lipofamily protein, C-terminal domain (domain)
This domain is found at the C-terminal end of LPP20 lipofamily protein [swissprot:K2KM35] from Helicobacter pylori (HP1454) and similar sequences predominantly found in epsilonproteobacteria. HP1454 is a secreted protein composed of three distinct domains: the N-terminal [pfam:PF02169], the middle domain Pfam: PF22018 and this domain, which shows a beta-sheet flanked by two alpha-helices.
Pfam PF20894: Small heat shock protein Tsp36, N-terminal domain (domain)
This domain is found at the N-terminal end of Small heat shock protein Tsp36 from the parasitic flatworm Taenia saginata and similar proteins from worms. Tsp36 is organised into two alpha-crystallin domains, two repeat segments on the N-terminal side, a linker region, and a long N-terminal segment of about 80 residues (this entry). This domain consists of a series of helices with sharp turns between them marked by prolines.
Pfam PF07535: DBF zinc finger (domain)
This domain is predicted to bind metal ions and is often found associated with [pfam:PF00533] and [pfam:PF02178]. It was first identified in the Drosophila chiffon gene product, and is associated with initiation of DNA replication.
Pfam PF16692: Folliculin C-terminal domain (domain)
This is the C-terminal domain of folliculin. It has guanine nucleotide exchange factor (GEF) activity.
Wikipedia: The tumor suppressor gene FLCN encodes the protein folliculin, also known as Birt–Hogg–Dubé syndrome protein, which functions as an inhibitor of Lactate Dehydrogenase-A and a regulator of the Warburg effect. Folliculin (FLCN) is also associated with Birt–Hogg–Dubé syndrome, which is an autosomal dominant inherited cancer syndrome in which affected individuals are at risk for the development of benign cutaneous tumors (folliculomas), pulmonary cysts, and kidney tumors.
Pfam PF10887: Protein of unknown function (DUF2686) (family)
Some members in this family of proteins are annotated as yjfZ however 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 PF00429: ENV polyprotein (coat polyprotein) (family)
Enveloped viruses such as Human immunodeficiency virus 1, influenza virus, and Ebola virus sp. express a surface glycoprotein that mediates both cell attachment and fusion of viral and cellular membranes. The ENV polyprotein (coat polyprotein) usually contains two coat proteins which differ depending on the source.

The structure of a number of the ENV polyprotein domains have been determined:


 * The crystal structure of an extraviral segment of the Moloney murine leukemia virus (MoMuLV) transmembrane (TM) subunit has been determined to 1.7-A resolution. This segment contains a trimeric coiled coil, with a hydrophobic cluster at its base and a strand that packs in an antiparallel orientation against the coiled coil. This structure serves as a model for a wide range of viral fusion proteins; key residues in this structure are conserved among C- and D-type retroviruses and the filovirus ebola .
 * An essential step in retrovirus infection is the binding of the virus to its receptor on a target cell. The structure of the receptor-binding domain of the envelope glycoprotein from Friend murine leukemia virus (F-MuLV) has been determined determined to 2.0-A resolution. The core of the domain is an antiparallel Î² sandwich, with two interstrand loops forming a helical subdomain atop the sandwich. The residues in the helical region, but not in the Î² sandwich, are highly variable among mammalian C-type retroviruses with distinct tropisms, indicating that the helical subdomain determines the receptor specificity of the virus .
Pfam PF03181: BURP domain (family)
The BURP domain is found at the C-terminus of several different plant proteins. It was named after the proteins in which it was first  identified: the BNM2 clone-derived protein from Brassica napus [swissprot:O65009]; USPs and USP-like proteins [swissprot:P21746] [swissprot:P21747] [swissprot:Q06765]  [swissprot:O24482]; RD22 from Arabidopsis thaliana [swissprot:Q08298]; and PG1beta from Lycopersicon esculentum [swissprot:Q40161]. This domain is around 230 amino acid residues long. It possesses the following conserved features: two phenylalanine residues at its N-terminus; two cysteine residues; and four repeated cysteine-histidine motifs, arranged as: CH-X(10)-CH-X(25-27)-CH-X(25-26)-CH, where X can be any amino acid. The function of this domain is unknown.
Wikipedia: In molecular biology, the BURP domain is a ~230-amino acid protein domain, which has been named for the four members of the group initially identified, BNM2, USP, RD22, and PG1beta. It is found in the C-terminal part of a number of plant cell wall proteins, which are defined not only by the BURP domain, but also by the overall similarity in their modular construction. The BURP domain proteins consists of either three or four modules: (i) an N-terminal hydrophobic domain - a presumptive transit peptide, joined to (ii) a short conserved segment or other short segment, (iii) an optional segment consisting of repeated units which is unique to each member, and (iv) the C-terminal BURP domain. Although the BURP domain proteins share primary structural features, their expression patterns and the conditions under which they are expressed differ. The presence of the conserved BURP domain in diverse plant proteins suggests an important role for this domain. It is possible that the BURP domain represents a general motif for localization of proteins within the cell wall matrix. The other structural domains associated with the BURP domain may specify other target sites for intermolecular interactions.
Pfam PF20843: Rax2 third domain (domain)
This entry represents the third domain in Rax 2 which is found inserted within the first beta propeller domain.  Diploid yeast cells repeatedly polarise and bud from their poles, due probably to the presence of highly stable membrane markers, and Rax2 is one such marker. It is inherited immutably at the cell cortex for multiple generations, and has a half-life exceeding several generations. The persistent inheritance of cortical protein markers would provide a means of coupling a cell's history with the future development of a precise morphogenetic form. Both Rax1 and Rax2 localise to the distal pole as well as to the division site and they interact both with each other and with Bud8p and Bud9p in the establishment and/or maintenance of the cortical markers for bipolar budding. Thus Rax2 is likely to control cell polarity during vegetative growth, and in fission yeast this is done by regulating the localisation of for3p.
Pfam PF06006: Bacterial protein of unknown function (DUF905) (family)
This family consists of several short hypothetical Enterobacteria proteins of unknown function. Structural analysis of the surface features of the protein YvyC has revealed a single cluster of highly conserved residues on the surface. Additionally, these residues fall into two groups which lie within the two largest of the three cavities identified over the surface. The conclusion from this is that these two cavities with, Leu 58, Glu 75, Ile 82, and Glu 83 and Pro 86, conserved, are likely to be important for the molecular function and reflect the cavities found on the surface of the FlaG proteins in [pfam:PF03646].
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 PF08666: SAF domain (domain)
This domain family includes a range of different proteins. Such as antifreeze proteins and flagellar FlgA proteins, and CpaB pilus proteins.
Pfam PF04279: Intracellular septation protein A (family)
Inner membrane-spanning protein YciB (also known as intracellular septation protein A) is a family of proteins which are essential for both normal cell division and bacterial virulence and are believed to play a role in the septation process. These proteins play a role in cell envelope biogenesis, maintenance of cell envelope integrity and membrane homeostasis.
Pfam PF13708: Domain of unknown function (DUF4942) (domain)
The function of this family 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 PF00555: delta endotoxin (repeat)
This family contains insecticidal toxins produced by Bacillus species of bacteria.  During spore formation the bacteria produce crystals of this protein.  When an insect ingests these proteins they are activated by proteolytic cleavage.  The N terminus is cleaved in all of the proteins and a C terminal extension is cleaved in some members.  Once activated the endotoxin binds to the gut epithelium and causes cell lysis leading to death.  This activated region of the delta endotoxin is composed of three structural domains.  The N-terminal helical domain is involved in membrane insertion and pore formation. The second and third domains are involved in receptor binding.
Wikipedia: Delta endotoxins (δ-endotoxins) are a family of pore-forming toxins produced by Bacillus thuringiensis species of bacteria. They are useful for their insecticidal action and are the primary toxin produced by the genetically modified (GM) Bt maize/corn and other GM crops. During spore formation the bacteria produce crystals of such proteins that are also known as parasporal bodies, next to the endospores; as a result some members are known as a parasporin. The Cyt (cytolytic) toxin group is another group of delta-endotoxins formed in the cytoplasm. VIP toxins are formed at other stages of the life cycle.
Pfam PF22441: CLIC-like N-terminal domain (domain)
This entry represents the N-terminal domain of chloride ion channels CLIC and related sequences.
Pfam PF08050: Tetracycline resistance leader peptide (family)
This family consists of the tetracycline resistance leader peptide. The presence of 3 inverted repeats  which can form 2 different conformations of mRNA  suggests that the tetracycline resistance (TcR) region is regulated by a translational attenuation mechanism. A Rho-independent transcriptional terminator structure is present immediately after the translational stop codon  of the TET protein.
Pfam PF10336: Protein of unknown function (DUF2420) (family)
This is a family of proteins conserved in fungi.  The function 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 PF12487: Protein of unknown function (DUF3703) (family)
This family of proteins is found in bacteria. Proteins in this family are typically between 113 and 135 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 PF20117: Family of unknown function (DUF6507) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 115 and 135 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.