SII-SWORD/CoKE huggingface dataset:
Pfam PF13840: ACT domain (domain)
The ACT domain is a structural motif of 70-90 amino acids that functions in the control of metabolism, solute transport and signal transduction. They are thus found in a variety of different proteins in a variety of different arrangements. In mammalian phenylalanine hydroxylase the domain forms no contacts but promotes an allosteric effect despite the apparent lack of ligand binding.
Pfam PF16234: Domain of unknown function (DUF4892) (family)
This family consists of uncharacterized proteins around 270 residues in length and is mainly found in various  Pseudomonas aeruginosa species. The function of this family is unknown.
Pfam PF03806: AbgT putative transporter family (family)
AbgT catalyzes the concentration-dependent uptake of p-aminobenzoyl-glutamate (PABA-GLU) into cells. This allows accumulation of PABA-GLU to a concentration enabling AbgAB to catalyze cleavage into p-aminobenzoate and glutamate .
Wikipedia: The p-aminobenzoyl-glutamate transporter (AbgT) family (TC# 2.A.68) is a family of transporter proteins belonging to the ion transporter (IT) superfamily. The AbgT family consists of the AbgT (YdaH; TC# 2.A.68.1.1) protein of E. coli and the MtrF drug exporter (TC# 2.A.68.1.2) of Neisseria gonorrhoeae. The former protein is apparently cryptic in wild-type cells, but when expressed on a high copy number plasmid, or when expressed at higher levels due to mutation, it appeared to allow uptake (Km = 123 nM; see Michaelis–Menten kinetics) and subsequent utilization of p-aminobenzoyl-glutamate as a source of p-aminobenzoate for p-aminobenzoate auxotrophs. p-Aminobenzoate is a constituent of and a precursor for the biosynthesis of folic acid. MtrF was annotated as a putative drug efflux pump.
Pfam PF20417: Gemin6 C-terminal domain (domain)
This entry corresponds to a putative domain found at the C-terminus of several mammalian Gemin6 proteins. This domain appears to be distantly related to [pfam:PF09793] suggesting it may have an RNA-binding function. The exact function of Gemin6 is unknown but it has been found to form part of the [pfam:PF06003] complex. The SMN complex plays a key role in the biogenesis of spliceosomal small nuclear ribonucleoproteins (snRNPs) and other ribonucleoprotein particles.
Pfam PF12351: Ca2+ regulator and membrane fusion protein Fig1 (family)
During the mating process of yeast cells, two Ca2+ influx pathways become activated. The resulting elevation of cytosolic free Ca2+ activates downstream signaling factors that promote long term survival of unmated cells.  Fig1 is a regulator of the low affinity Ca2+ influx system (LACS), and is also required for efficient membrane fusion during yeast mating.
Pfam PF16229: Domain of unknown function (DUF4888) (family)
This family consists of uncharacterized proteins around 190 residues in length and is mainly found in various Staphylococcus species. The function of this family is unknown.
Pfam PF21572: Archaeal Nop5/56-rel, N-terminal domain (domain)
This domain is found at the N-terminal end of a group of archaeal proteins, including Uncharacterized NOP5 family protein MJ0694 from Methanocaldococcus jannaschii. This domain interacts with fibrillarin, the other subunit of a complex that is critical to modify and process ribosomal RNAs. This domain shows a highly conserved folded structure despite low sequence similarity among homologs. It shows four beta-sheets surrounded by four alpha- helices and is found associated with [pfam:PF01798].
Pfam PF06716: Movement protein p6 (family)
This entry represents the movement protein 6 (p6) from Beet yellows virus and related Closterovirus proteins. Movement proteins (MPs) encoded by many virus genera are specialised proteins essential for plant viral genomes or virions transport within and between cells. P6  is a small protein (6kDa) localised in the endoplasmic reticulum. It has a single-span N-terminal transmembrane domain and a C-terminal hydrophilic domain which faces the cytosol. It is involved, together with Hsp70h, CP, CPm, and P64, in cell to cell movement of the viral genome without any budding, being essential for this process. The mechanism of action of this protein is not clear. It is suggested that it also plays a role in virion formation.
Pfam PF09747: Coiled-coil domain containing protein 97-like, C-terminal (coiled_coil)
This domain is found at the C-terminal of CCD97. In some proteins, this domain is found as two conserved domains separated by a region of low complexity, spanning some 200 residues. The function is unknown.
Pfam PF06868: Protein of unknown function (DUF1257) (family)
This family contains hypothetical proteins of unknown function that are approximately 120 residues long. Family members include eukaryotic and bacterial proteins.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF11026: Protein of unknown function (DUF2721) (family)
This family is conserved in bacteria. 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 PF13331: Domain of unknown function (DUF4093) (family)
This domain lies at the C-terminus of primase proteins carrying the TOPRIM, [pfam:PF01751], domain. The exact function of the domain is not known.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF13609: Gram-negative porin (domain)
Porins form aqueous channels for the diffusion of small hydrophillic molecules across the outer membrane . Individual 16-strand anti-parallel Î²-barrels form a central pore, and trimerizes through mainly hydrophobic interactions at the interface. Trimers are stabilized by hytrophillic clamping of Loop L2. Loop 3 bends into the pore, creating an elliptical constriction of about 7 x 11 angstroms, large enough to allow passage of a glucose molecule without steric hindrance. Removal of the C-terminal residue (usually Phe) destabilizes the trimer and removal of the 16th Î²-sheet abolishes trimerization. Unlike typical membrane proteins, porins lack long hydrophobic stretches. Short turns are found at the smooth, periplasmic end, longer irregular loops are found at the rough, extracellular end. The C-terminal residue forms a salt bridge with the N terminus .

This entry represents the structural domain found in Gram-negative bacterial porins.
Wikipedia: General bacterial porins are a family of porin proteins from the outer membranes of Gram-negative bacteria. The porins act as molecular filters for hydrophilic compounds. They are responsible for the 'molecular sieve' properties of the outer membrane. Porins form large water-filled channels which allow the diffusion of hydrophilic molecules into the periplasmic space. Some porins form general diffusion channels that allow any solute up to a certain size to cross the membrane, while other porins are specific for one particular solute and contain a binding site for that solute inside the pores. As porins are the major outer membrane proteins, they also serve as receptor sites for the binding of phages and bacteriocins.
Pfam PF07865: Protein of unknown function (DUF1652) (family)
This is a family containing hypothetical bacterial proteins.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF19184: Family of unknown function (DUF5866) (family)
This is a family of uncharacterised proteins of unknown function predominantly found in Mimiviridae.
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 PF24953: Domain of unknown function (DUF7762) (domain)
This domain is found in uncharacterised proteins mainly from flagellate Discoba. It has detectable similarity to known PDZ domains and it is predicted to adopt similar structure. It is frequently found in multiple tandem copies.
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 PF18980: Family of unknown function (DUF5716) C-terminal (domain)
This is a C-terminal domain found in bacterial sequences 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 PF11921: Domain of unknown function (DUF3439) (repeat)
This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 46 to 94 amino acids in length. This domain is found associated with [pfam:PF01462], [pfam:PF00560].
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 PF05115: Cytochrome B6-F complex subunit VI (PetL) (family)
This family consists of several Cytochrome B6-F complex subunit VI (PetL) proteins found in several plant species. PetL is one of the small subunits which make up The cytochrome b(6)f complex. PetL is strictly required neither for the accumulation nor for the function of cytochrome b6f; in its absence, however, the complex becomes unstable in vivo in aging cells and labile in vitro.  It has been suggested that the N-terminus of the protein is likely to lie in the thylakoid lumen.
Wikipedia: The cytochrome b6f complex (plastoquinol/plastocyanin reductase or plastoquinol/plastocyanin oxidoreductase; EC 7.1.1.6) is an enzyme found in the thylakoid membrane in chloroplasts of plants, cyanobacteria, and green algae, that catalyzes the transfer of electrons from plastoquinol to plastocyanin:plastoquinol + 2 oxidized plastocyanin + 2 H+ [side 1]  plastoquinone + 2 reduced plastocyanin + 4 H+ [side 2].
Pfam PF16625: Unstructured linking region I-set and fnIII on Brother of CDO (disordered)
ISET-FN3_linker is a short section of natively unstructured sequence on Biregional cell adhesion molecule-related/down-regulated by oncogenes (Cdon) binding proteins or Brother of CDO. It is found in higher eukaryotes and lies between the second I-set and the first fnIII domains, [pfam:PF07679] and [pfam:PF00041]. The function is not known.
Pfam PF08250: Sperm-activating peptides (family)
The sperm-activating peptides (SAPs) are isolated in egg-conditioned media (egg jelly) of sea urchins. SAPs have several effects on sea urchin spermatozoa: stimulate sperm respiration and motility through intracellular alkalinization, transient elevation of cAMP, cGMP and Ca++levels in sperm cells.
Pfam PF02656: Domain of unknown function (DUF202) (family)
This family consists of hypothetical proteins some of which are putative membrane proteins.  No functional information or experimental verification of function is known.  This domain is around 100 amino acids long.
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 PF01348: Type II intron maturase (domain)
Group II introns use intron-encoded reverse transcriptase, maturase and DNA endonuclease activities for site-specific insertion into DNA.  Although this type of intron is self splicing in vitro they require a maturase protein for splicing in vivo. It has been shown that a specific region of the aI2 intron is needed for the maturase function. This region was found to be conserved in group II introns and called domain X.
Wikipedia: Group II introns are a large class of self-catalytic ribozymes and mobile genetic elements found within the genes of all three domains of life. Ribozyme activity can occur under high-salt conditions in vitro. However, assistance from proteins is required for in vivo splicing. In contrast to group I introns, intron excision occurs in the absence of GTP and involves the formation of a lariat, with an A-residue branchpoint strongly resembling that found in lariats formed during splicing of nuclear pre-mRNA. It is hypothesized that pre-mRNA splicing may have evolved from group II introns, due to the similar catalytic mechanism as well as the structural similarity of the Group II Domain V substructure to the U6/U2 extended snRNA. Finally, their ability to site-specifically insert into DNA sites has been exploited as a tool for biotechnology. For example, group II introns can be modified to make site-specific genome insertions and deliver cargo DNA such as reporter genes or lox sites
Pfam PF13691: tRNase Z endonuclease (domain)
This is family of tRNase Z enzymes, that are closely related structurally to the Lactamase_B family members. tRNase Z is the endonuclease that is involved in tRNA 3'-end maturation through removal of the 3'-trailer sequences from tRNA precursors. The fission yeast Schizosaccharomyces pombe contains two candidate tRNase Zs encoded by two essential genes. The first, [swissprot:Q10155], is targeted to the nucleus and has an SV40 nuclear localisation signal at its N-terminus, consisting of four consecutive arginine and lysine residues between residues 208 and 211 (KKRK) that is critical for the NLS function. The second, [swissprot:P87168], is targeted to the mitochondria, with an N-terminal mitochondrial targeting signal within the first 38 residues.
Pfam PF07952: Clostridium neurotoxin, Translocation domain (domain)
The Clostridium neurotoxin family is composed of tetanus neurotoxin and seven serotypes of botulinum neurotoxin. The structure of the botulinum neurotoxin reveals a four domain protein.  The N-terminal catalytic domain ([pfam:PF01742]), the central translocation domains and two receptor binding domains. Subsequent to cell surface binding and receptor mediated endocytosis of the neurotoxin, an acid induced conformational change in the neurotoxin translocation domain is believed to allow the domain to penetrate the endosome and from a  pore, thereby facilitating the passage of the catalytic domain across the membrane into the cytosol. The structure of the translocation reveals a pair of helices that are 105 Angstroms long and is structurally distinct from  other pore forming toxins.
Pfam PF17569: Family of unknown function (DUF5475) (family)
This is a family of unknown function found in Alphabaculovirus.
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 PF08596: Lethal giant larvae(Lgl) like, C-terminal (repeat)
The Lethal giant larvae (Lgl) tumour suppressor family is conserved from yeast to mammals.  The Lgl family functions in cell polarity, at least in part, by regulating SNARE-mediated membrane delivery events at the cell surface.  The N-terminal half of Lgl members contains WD40 repeats (see [pfam:PF00400]), while the C-terminal half appears specific to the family.
Pfam PF05071: NADH ubiquinone oxidoreductase subunit NDUFA12 (family)
This family contains the 17.2 kD subunit of complex I (NDUFA12) and its homologues.  The family also contains a second related eukaryotic protein of unknown function, e.g. [swissprot:Q9BV02].
Wikipedia: Respiratory complex I, EC 7.1.1.2 is the first large protein complex of the respiratory chains of many organisms from bacteria to humans. It catalyzes the transfer of electrons from NADH to coenzyme Q10 (CoQ10) and translocates protons across the inner mitochondrial membrane in eukaryotes or the plasma membrane of bacteria.
Pfam PF05599: Deltaretrovirus Tax protein (family)
This family consists of Rex/Tax proteins from human and simian T-cell leukaemia viruses. The exact function of these proteins is unknown. Tax is the viral transactivator; is it a nuclear phosphoprotein that interacts with CREB, coactivator CBP/p300 and PCAF to form a multiprotein complex, which activates viral LTR and stimulates virus expression. Tax is also involved in deregulated expression of numerous cellular genes leading to T-cell leukaemia. Rex is a nucleolar post transcriptional regulator that facilitates export to the cytoplasm of viral RNA not or incompletely spliced [personal communication, Dr. S Nicot].
Pfam PF17427: Phage Single-stranded DNA-binding protein (family)
DNA replication of phi29 and related phages takes place via a strand displacement mechanism, a process that generates large amounts of single-stranded DNA (ssDNA). Consequently, phage-encoded ssDNA-binding proteins (SSBs) are essential proteins during phage phi29-like DNA replication. Single-stranded DNA-binding proteins (SSBs) destabilize double-stranded DNA (dsDNA) and bind without sequence specificity, but selectively and cooperatively, to single-stranded DNA (ssDNA) conferring a regular structure to it, which is recognized and exploited by a variety of enzymes involved in DNA replication, repair and recombination. Phage phi29 protein p5 is the SSB protein active during phi29 DNA replication. It protects ssDNA against nuclease degradation and greatly stimulates dNTP incorporation during phi29 DNA replication process. Binding of the SSB to ssDNA prevents non-productive binding of the viral DNA polymerase to ssDNA, and allows the release DNA polymerase molecules that are already titrated by the ssDNA. This effect would be of particular importance in phi29-like DNA replication systems, where large amounts of ssDNA are generated and SSB binding to ssDNA could favor efficient re-usage of templates. This domain family is found in SSB proteins in phage phi-29, homologues are found in [pfam:PF00436].
Pfam PF00640: Phosphotyrosine interaction domain (PTB/PID) (domain)
Proteins encoding phosphotyrosine binding (PTB) domains function as adaptors or scaffolds to organise the signaling complexes involved in wide-ranging physiological processes including neural development, immunity, tissue homeostasis and cell growth. Due to structural differences, PTB domains are divided into three groups represented by phosphotyrosine-dependent IRS-like, phosphotyrosine-dependent Shc-like, and phosphotyrosine-independent Dab-like PTBs. The last two PTBs have been named as phosphotyrosine interaction domain (PID or PI domain). PID domain has an average length of about 160 amino acids .
The Shc-like PID specifically binds to the Asn-Pro-Xaa-Tyr(P) motif found in many tyrosine-phosphorylated proteins including growth factor receptors. On the other hand the Dab-like PID domain binds to non-phosphorylated tyrosine residue or even a phenylalanine at the same position . Most of the ligands for Shc-like PID domains are RTK or cytokine, whereas phosphotyrosine independent Dab-like PID domains seems to mediate other types of signaling pathways, like endocytosis/processing or exocytosis. This domain binds both peptides and headgroups of phosphatidylinositides, utilising two distinct binding motifs to mediate spatial organisation and localisation within cells .

The 3D structure of PID domain has been solved . It shares a folding pattern, commonly referred to as the PH-domain "superfold". The core "superfold" consists of seven antiparallel Î² strands forming two orthogonal Î² sheets. This Î² sandwich is capped at the C terminus by an Î± helix. It contains a peptide binding pocket (formed by the Î² strand 5 and C-terminal Î± helix) and a highly basic phospholipid binding "crown" (largely composed of residues from loop regions near the N terminus). Both Shc and Dab1 have two additional Î± helices, one of which is located at the N terminus and the other between Î²1 and Î²2 strands.
Pfam PF03336: Poxvirus C4/C10 protein (family)
This family represents proteins found in Poxvirus, including Protein C10 and Protein C4. Vaccinia virus protein C4 plays a role in the inhibition of host NF-kappa-B activation. It blocks the subunit p65/RELA translocation into the host nucleus.
Pfam PF11146: Protein of unknown function (DUF2905) (family)
This is a family of bacterial proteins conserved 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.