SII-SWORD/CoKE huggingface dataset:
Pfam PF00855: PWWP domain (domain)
The PWWP domain is named after a conserved Pro-Trp-Trp-Pro motif. The domain binds to Histone-4 methylated at lysine-20, H4K20me, suggesting that it is methyl-lysine recognition motif. Removal of two conserved aromatic residues in a hydrophobic cavity created by this domain within the full-length protein, Pdp1, abolishes the interaction o f the protein with H4K20me3. In fission yeast, Set9 is the sole enzyme that catalyses all three states of H4K20me, and Set9-mediated H4K20me is required for efficient recruitment of checkpoint protein Crb2 to sites of DNA damage. The methylation of H4K20 is involved in a diverse array of cellular processes, such as organising higher-order chromatin, maintaining genome stability, and regulating cell-cycle progression.
Pfam PF18290: Nudix hydrolase domain (domain)
This domain is found just before the N-terminal region of nucleoside diphosphate-linked moiety (Nudix) hydrolases ([pfam:PF00293]). Nudix hydrolases catalyze the hydrolysis of nucleoside diphosphates which are often toxic metabolic intermediates and signalling molecules.
Pfam PF17117: Domain of unknown function (DUF5104) (family)
This is a family of gut microbes of unknown function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF13523: Acetyltransferase (GNAT) domain (domain)
This domain catalyses N-acetyltransferase reactions.
Wikipedia: An acetyltransferase is any of a class of transferase enzymes that transfers an acetyl group in a reaction called acetylation. In biological organisms, post-translational modification of a protein via acetylation can profoundly transform its functionality by altering various properties like hydrophobicity, solubility, and surface attributes. These alterations have the potential to influence the protein's conformation and its interactions with substrates, cofactors, and other macromolecules.
Pfam PF14113: Type VI secretion system (T6SS), amidase effector protein 4 (domain)
Tae4 is a new form of toxin-antitoxin system protein for a type VI secretion system, T6SS. T6SS has roles in interspecies interactions, as well as higher order host-infection, by injecting effector proteins into the periplasmic compartment of the recipient cells of closely related species. Pseudomonas aeruginosa produces at least three effector proteins to other cells and thus has three specific cognate immunity proteins to protect itself. Tae4, or type VI amidase effector 4, in Enterobacter cloacae has a cognate Tai4 or type VI amidase immunity 4 protein. The immunity protein is Tai4, [pfam:PF16695].
Pfam PF16349: Domain of unknown function (DUF4978) (family)
This family consists of uncharacterised proteins around 540 residues in length and is mainly found in various Bacteroides and Prevotella species. Several proteins in this family are annotated as Glycoside hydrolases, but the function of this protein is unknown.
Pfam PF14018: Domain of unknown function (DUF4234) (family)
This presumed integral membrane protein domain is functionally uncharacterised. This domain family is found in bacteria and archaea, and is approximately 70 amino acids in length.
Pfam PF17672: Fertilisation-influencing membrane protein (family)
In mice, 4930451I11Rik encodes two isoforms: a transmembrane (TM) form and a secreted form. FIMP is the TM form. It is a sperm-specific transmembrane protein that is essential for the sperm-oocyte fusion process.
Pfam PF18910: Domain of unknown function (DUF5665) (family)
This entry represents a functionally uncharacterised family of integral membrane proteins. This protein family is found in bacteria, and is approximately 60 amino acids in length. There are several conserved glycines in the first transmembrane helix that may be functionally important.
Pfam PF10261: Fat storage-inducing transmembrane protein (family)
This entry represents transmembrane proteins which belong to the Fat storage-inducing transmembrane protein family (FIT/FITM, also known as Acyl-coenzyme A diphosphatase). The members are conserved from yeasts to humans and are localised to the endoplasmic reticulum where they are involved in triglyceride lipid droplet formation, important for maintaining ER structure and for lipid droplets (LDs) biogenesis,  involved in maintaining lipid and energy homeostasis. In mammals there are two FIT proteins, FIT1, which is muscle specific and FIT2, which is expressed in most other tissues. Yeast has two FIT2 orthologues, called Scs3p and Yft2.
Pfam PF10699: Male gamete fusion factor (domain)
The gene encoding Arabidopsis HAP2 is allelic with GCS1 (Generative cell-specific protein 1). HAP2 is expressed only in the haploid sperm and is required for efficient guidance of the pollen tube to the ovules. In Arabidopsis the protein is a predicted membrane protein with an N-terminal secretion signal, a single transmembrane domain and a C-terminal histidine-rich domain. HAP2-GCS1 is found from plants to lower eukaryotes and is necessary for the fusion of the gametes in fertilisation. Studies in the green alga Chlamydomonas and the malaria organism Plasmodium showed that it is involved in a novel mechanism for gamete fusion where a first species-specific protein binds male and female gamete membranes together after which a second, broadly conserved protein, either directly or indirectly, causes fusion of the two membranes together. The broadly conserved protein is represented by this HAP2-GCS1 domain, conserved from plants to lower eukaryotes. In Plasmodium berghei the protein is expressed only in male gametocytes and gametes, having a male-specific function during the interaction with female gametes, and being indispensable for parasite fertilisation. The gene in plants and eukaryotes might well have originated from acquisition of plastids from red algae.
Pfam PF24396: Family of unknown function (DUF7541) (family)
This entry represents a family of uncharacterised proteins found mainly in Halobacteria. They are predicted to adopt a structure consisting of four alpha-helices.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF12079: Protein of unknown function (DUF3558) (family)
This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 177 to 195 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 PF18079: Archaeal glycosylation protein B long peripheral domain (domain)
This domain is found in Archaeal Glycosylation B protein (AglB-Long) in A. fulgidus. When the domain, known as peripheral l (Pl), is combined with the central core (CC) and insertion (IS) sub-units, they form the C-terminal domain. It is thought that the C-terminal domain may contribute toward the increased thermal stability of the AglB proteins in the hyper-thermophilic.
Pfam PF20344: Family of unknown function (DUF6639) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 218 and 231 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 PF05506: Bacterial phospholipase C, C-terminal domain (domain)
This domain is found, normally as a tandem repeat, at the C-terminus of bacterial phospholipase C proteins.
Pfam PF09308: LuxQ, periplasmic (domain)
Members of this family constitute the periplasmic sensor domain of the prokaryotic protein LuxQ, and assume a structure consisting of two tandem Per/ARNT/Simple-minded (PAS) folds.
Pfam PF09601: Protein of unknown function (DUF2459) (family)
This conserved hypothetical protein of unknown function is found in several Proteobacteria. Its function is unknown and its genome context is not well-conserved. It is found amid urease genes in at least one species.
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 PF24363: Family of unknown function (DUF7519) (family)
This family includes a group of proteins from archaea. Members are predicted to adopt a mainly alpha-helical 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 PF14964: Integrator complex subunit 15 (family)
Integrator complex subunit 15 (C7orf26) is likely a component of the Integrator (INT) complex, which is involved in the small nuclear RNAs (snRNA) U1 and U2 transcription and in their 3'-box-dependent processing.
Pfam PF19726: Family of unknown function (DUF6218) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000696) is described by MIBiG as an example of the following biosynthetic class, saccharide. It includes a member from the gentamicin biosynthetic gene cluster from Micromonospora  echinospora.
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 PF20583: Family of unknown function (DUF6786) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 397 and 433 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 PF20273: Domain observed between E2 and E1 domains (domain)
Certain prokaryotic Ubiquitin systems contain this domain between E2 and E1 fusion proteins. Many of these systems are secondary effector modules associating with nucleotide-activated effector systems.
Pfam PF02710: Hemagglutinin domain of haemagglutinin-esterase-fusion glycoprotein (family)
Haemagglutinin-esterase fusion glycoprotein (HEF) is a multi-functional protein embedded in the viral envelope of several viruses, including influenza C virus, coronaviruses and toroviruses . HEF is required for infectivity, and functions to recognise the host cell surface receptor, to fuse the viral and host cell membranes, and to destroy the receptor upon host cell infection. The haemagglutinin region of HEF is responsible for receptor recognition and membrane fusion, and bears a strong resemblance to the sialic acid-binding haemagglutinin found in influenza A and B viruses, except that it binds 9-O-acetylsialic acid. The esterase region of HEF is responsible for the destruction of the receptor, an action that is carried out by neuraminidase in influenza A and B viruses. The esterase domain is similar in structure to Streptomyces scabies esterase, and to acetylhydrolase, thioesterase I and rhamnogalacturonan acetylesterase.

The haemagglutinin-esterase glycoprotein HEF must be cleaved by the host's trypsin-like proteases to produce two peptides (HEF1 and HEF2) in order for the virus to be infectious. Once HEF is cleaved, the newly exposed N-terminal of the HEF2 peptide then acts to fuse the viral envelope to the cellular membrane of the host cell, which allows the virus to infect the host cell.

The haemagglutinin-esterase glycoprotein is a trimer, where each monomer is composed of three domains: an elongated stem active in membrane fusion, an esterase domain, and a receptor-binding domain, where the stem and receptor-binding domains together resemble influenza A virus haemagglutinin. Two of these domains are composed of non-contiguous sequence: the receptor-binding haemagglutinin domain is inserted into a surface loop of the esterase domain, and the esterase domain is inserted into a surface loop of the haemagglutinin stem.

This entry represents the receptor-binding haemagglutinin domain of the haemagglutinin-esterase glycoprotein.
Pfam PF17243: POTRA domain TamA domain 1 (domain)
This family represents the POTRA domain found in the membrane insertase TamA.
Pfam PF13696: Zinc knuckle (domain)
This is a zinc-binding domain of the form CxxCxxxGHxxxxC from a variety of different species.
Wikipedia: A zinc finger is a small protein structural motif that is characterized by the coordination of one or more zinc ions (Zn2+) which stabilizes the fold. It was originally coined to describe the finger-like appearance of a hypothesized structure from the African clawed frog (Xenopus laevis) transcription factor IIIA. However, it has been found to encompass a wide variety of differing protein structures in eukaryotic cells. Xenopus laevis TFIIIA was originally demonstrated to contain zinc and require the metal for function in 1983, the first such reported zinc requirement for a gene regulatory protein followed soon thereafter by the Krüppel factor in Drosophila. It often appears as a metal-binding domain in multi-domain proteins.
Pfam PF09632: Rac1-binding domain (domain)
The Rac1-binding domain is the C-terminal portion of YpkA from Yersinia. It is an all-helical molecule consisting of two distinct subdomains connected by a linker. the N-terminal end, residues 434-615, consists of six helices organised into two three-helix bundles packed against each other. This region is involved with binding to GTPases. The C-terminal end, residues 705-732. is a novel and elongated fold consisting of four helices clustered into two pairs, and this fold carries the helix implicated in actin activation. Rac1-binding domain mimics host guanidine nucleotide dissociation inhibitors (GDIs) of the Rho GTPases, thereby inhibiting nucleotide exchange in Rac1 and causing cytoskeletal disruption in the host. It is usually found downstream of [pfam:PF00069].
Pfam PF15343: Decidual protein induced by progesterone family (family)
DEPP is a family of proteins expressed in various tissues, including pancreas, placenta, ovary, testis and kidney. High levels are found during the first trimester.  Its expression is induced by progesterone, testosterone and, to a much lower extent, oestrogen. The family is alternatively known as fasting-induced gene protein, FIG.
Pfam PF08528: Whi5 like (conserved_site)
In metazoans, cyclin-dependent kinase(CDK) dependent phosphorylation of the retinoblastoma Tudor suppressor protein (Rb) alleviates repression of E2F and thereby activates G1/S transcription. The cell size regulator Whi5 appears to be an analogous target of CDK activity during G1 phase.
Pfam PF12055: Domain of unknown function (DUF3536) (family)
This presumed domain is functionally uncharacterised. This domain is found in bacteria and archaea. This domain is typically between 274 to 285 amino acids in length. This domain is found associated with [pfam:PF03065].
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 PF18937: Family of unknown function (DUF5685) (family)
This is a family of unknown function mostly found in bacteria.
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 PF21645: Fatty acid kinase subunit A-like, middle domain (domain)
This domain is found in fatty acid kinase subunit A (FakA) from a bacterial fatty acid kinase (Fak) system and it is localised between [pfam:PF02734] and [pfam:PF13684]. Two major human pathogens, Staphylococcus and Streptococcus, use this machinery to scavenge host fatty acids. The Fak complex consists of an ATP-binding subunit FakA, which interacts with varied FakB (fatty acid-binding protein) isoforms, and synthesises acyl-phosphate from extracellular fatty acids. FakA comprises three domains, denoted as FakA_N, FakA_M and FakA_C in of which the middle domain is represented in this entry. It consists of four alpha-helices, four beta-strands and several long loops, containing a zinc finger motif. It shows similarities to the yeast copper chaperone ATX1, a metallochaperone/metal-binding protein.
Pfam PF05484: LRV protein FeS4 cluster (repeat)
This Iron sulphur cluster is found at the N-terminus of some proteins containing [pfam:PF01816] repeats.
Wikipedia: A leucine-rich repeat (LRR) is a protein structural motif that forms an α/β horseshoe fold. It is composed of repeating 20–30 amino acid stretches that are unusually rich in the hydrophobic amino acid leucine. These tandem repeats commonly fold together to form a solenoid protein domain, termed leucine-rich repeat domain. Typically, each repeat unit has beta strand-turn-alpha helix structure, and the assembled domain, composed of many such repeats, has a horseshoe shape with an interior parallel beta sheet and an exterior array of helices. One face of the beta sheet and one side of the helix array are exposed to solvent and are therefore dominated by hydrophilic residues. The region between the helices and sheets is the protein's hydrophobic core and is tightly sterically packed with leucine residues.
Pfam PF23903: Phage zinc binding domain (domain)
This entry represents a family of uncharacterised phage proteins that likely binds to zinc.
Pfam PF13335: Magnesium chelatase, subunit ChlI C-terminal (family)
This is a family of the C-terminal of putative bacterial magnesium chelatase subunit ChlI proteins. Most members have the associated [pfam:PF01078].
Pfam PF16204: BDHCT-box associated domain on Bloom syndrome protein (family)
This family is found on Bloom syndrome-associated DEAD-box helicases in higher eukaryotes. It lies between the BDHCT, and DEAD-box families, [pfam:PF08072] and [pfam:PF00270].
Pfam PF23700: YsdD (family)
This protein family includes Protein YsdD from Escherichia coli, a 26-residues long sequence.
Pfam PF04389: Peptidase family M28 (domain)
This domain is found in metallopeptidases belonging to the MEROPS peptidase family M28 (aminopeptidase Y, clan MH)  and in non-peptidase homologues such as transferrin receptor proteins. Members containing this domain, also contain a transferrin receptor-like dimerisation domain (IPR007365) and a protease-associated PA domain (IPR003137).
Over 70 metallopeptidase families have been identified to date. In these enzymes a divalent cation which is usually zinc, but may be cobalt, manganese or copper, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. In some families of co-catalytic metallopeptidases, two metal ions are observed in crystal structures ligated by five amino acids, with one amino acid ligating both metal ions. The known metal ligands are His, Glu, Asp or Lys. At least one other residue is required for catalysis, which may play an electrophillic role. Many metalloproteases contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site . The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases .
Pfam PF22135: Cell wall binding protein Cwp8 domain 3 (domain)
This entry represents the third domain (D3) of cell wall protein Cwp8 found in C. difficile. This domain folds into an alpha/beta structure consisting of a four-stranded antiparallel beta-sheet packed on one side with alpha-helices. This domain is related to domain 1 (D1) of the cell wall protein Cwp2 from the same organism.
Pfam PF11360: Protein of unknown function (DUF3110) (family)
This family of 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 PF01378: B domain (domain)
This domain is found as a tandem repeat in Streptococcal cell surface proteins, such as the IgG binding protein G.