SII-SWORD/CoKE huggingface dataset:
Pfam PF03460: Nitrite/Sulfite reductase ferredoxin-like half domain (repeat)
Sulfite and Nitrite reductases are key to both biosynthetic assimilation of sulfur and nitrogen and dissimilation of oxidised anions for energy transduction. Two copies of this repeat are found in Nitrite and Sulfite reductases and form a single structural domain.
Pfam PF22735: NACHT N-terminal Helical domain 3 (domain)
This is an helical domain found at the N-terminus of bacterial NACHT conflict systems. This position is frequently occupied by an effector domain.
Pfam PF17668: Acetyltransferase (GNAT) domain (domain)
N-acetyltransferases catalyse the transfer of acetyl groups from acetyl-CoA to arylamines. This acetyltransferase (GNAT) domain is found in Eis from Mycobacterium  and other N-acetyltransferases still uncharacterized.
Pfam PF11460: Protein of unknown function (DUF3007) (family)
This is a family of uncharacterised proteins found in bacteria and eukaryotes.
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 PF10552: ORF6C domain (domain)
This domain was identified by Iyer and colleagues.
Pfam PF13552: Protein of unknown function (DUF4127) (family)
This family of uncharacterised bacterial proteins are about 500 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 PF03441: FAD binding domain of DNA photolyase (domain)
This entry represents a multi-helical domain found in the C terminus of the cryptochrome proteins and DNA photolyases. It acts as a FAD-binding domain .

The cryptochrome and photolyase families consist of structurally related flavin adenine dinucleotide (FAD) proteins that use the absorption of blue light to accomplish different tasks. The photolyasess use the blue light for light-driven electron transfer to repair UV-damaged DNA, while the cryptochromes are blue-light photoreceptors involved in the circadian clock for plants and animals .
Wikipedia: Photolyases are DNA repair enzymes that repair damage caused by exposure to ultraviolet light. These enzymes require visible light both for their own activation and for the actual DNA repair. The DNA repair mechanism involving photolyases is called photoreactivation. They mainly convert pyrimidine dimers into a normal pair of pyrimidine bases. Photo reactivation, the first DNA repair mechanism to be discovered, was described initially by Albert Kelner in 1949 and independently by Renato Dulbecco also in 1949.
Pfam PF15102: TMEM154 protein family (family)
The function of this family of transmembrane proteins has not, as yet, been determined. However, it is thought to be a therapeutic target for ovine lentivirus infection. This family of proteins is found in eukaryotes and members are typically between 138 and 320 amino acids in length.
Pfam PF24687: Type III Secretion system protein OrgC (family)
This entry represents the type III Secretion system protein OrgC from Salmonella Typhimurium and related proteins. OrgC is a protein encoded within the T3SS gene cluster that is secreted by the T3SS. It interacts with the needle filament subunit PrgI and accelerates its polymerization into filaments in vitro. OrgC structure consists of array of four alpha-helices.
Pfam PF12653: Protein of unknown function (DUF3785) (domain)
This family of proteins is functionally uncharacterised.This family of proteins is found in bacteria. Proteins in this family are approximately 140 amino acids in length. These proteins share two CXXC motifs suggesting these are zinc binding proteins. This protein is found in clostridia in an operon with three signalling proteins, suggesting this protein may be a DNA-binding transcription regulator downstream of an as yet unknown signalling pathway (Bateman A pers obs).
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 PF12573: 2-oxoisovalerate dehydrogenase E1 alpha subunit N terminal (family)
This domain family is found in bacteria, and is approximately 40 amino acids in length. The family is found in association with [pfam:PF00676].  There are two conserved sequence motifs: VPEP and RPG. This family is the alpha subunit of the E1 component of 2-oxoisovalerate dehydrogenase. This is the enzyme complex responsible for metabolism of pyruvate, 2-oxoglutarate, branched chain 2-oxo acids and acetoin. The E1 component is a heterotetramer of alpha2beta2. The homodimerised beta subunits are flanked by two alpha subunits in a 'vise' structure.
Pfam PF15078: Domain of unknown function (DUF4545) (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between and 417 amino acids in length. The human member of this family is C1orf141.
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 PF19825: Domain of unknown function (DUF6306) (domain)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 137 and 172 amino acids in length. Protein in this family belong to the ferritin clan.
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 PF03899: ATP synthase I chain (family)
The atp operon of alkaliphilic Bacillus pseudofirmus OF4, as in most prokaryotes, contains the eight structural genes for the F-ATPase (ATP synthase), which are preceded by an atpI gene that encodes a membrane protein with 2 TMSs. A tenth gene, atpZ, has been found in this operon, which is upstream of and overlapping with atpI.  AtpI is a Ca2+/Mg2+ transporter.
Pfam PF04562: Dictyostelium spore coat protein, N terminus (family)
The Dictyostelium spore coat is a polarised extracellular matrix composed of glycoproteins and cellulose. Four of the major coat glycoproteins exist as a multi-protein complex within the prespore vesicles before secretion.  Of these, SP96 and SP70 are members of this family. The presence of SP96 and SP70 in the complex is necessary for the cellulose binding activity of the complex, which is in turn necessary for normal spore coat assembly. The function of this region of these proteins is not known.
Pfam PF03157: High molecular weight glutenin subunit (disordered)
Members of this family include high molecular weight subunits of glutenin. This group of gluten proteins is thought to be largely responsible for the elastic properties of gluten, and hence, doughs. Indeed, glutenin high molecular weight subunits are classified as elastomeric proteins, because the glutenin network can withstand significant deformations without breaking, and return to the original conformation when the stress is removed. Elastomeric proteins differ considerably in amino acid sequence, but they are all polymers whose subunits consist of elastomeric domains, composed of repeated motifs, and non-elastic domains that mediate cross-linking between the subunits. The elastomeric domain motifs are all rich in glycine residues in addition to other hydrophobic residues.  High molecular weight glutenin subunits have an extensive central elastomeric domain, flanked by two terminal non-elastic domains that form disulphide cross-links. The central elastomeric domain is characterised by the following three repeated motifs: PGQGQQ, GYYPTS[P/L]QQ, GQQ. It possesses overlapping beta-turns within and between the repeated motifs, and assumes a regular helical secondary structure with a diameter of approx. 1.9 nm and a pitch of approx. 1.5 nm [see 1, fig.2].
Pfam PF21223: Tripeptidyl-peptidase II, first Ig-like domain (domain)
Tripeptidyl peptidase II (TPPII)  is a crucial component of the proteolytic cascade acting downstream of the 26S proteasome in the ubiquitin-proteasome pathway. It is an amino peptidase belonging to the subtilase family removing tripeptides from the free N terminus of oligopeptides. This protein adopts a dimeric assembly. Each monomer is organised into three main parts: the N-terminal subtilisine-like domain ([pfam:PF00082]) a central domain and C-terminal domain ([pfam:PF12583]). The central domain can be subdivided into two Ig-like domains and a GBD-like domain ([pfam:PF21316]). This entry represents the first Ig-like domain, while [pfam:PF12580] represents the second one.
Pfam PF06058: Dcp1-like decapping family (domain)
An essential step in mRNA turnover is decapping.  In yeast, two proteins have been identified that are essential for decapping, Dcp1 (this family) and Dcp2 ([pfam:PF05026]).  The precise role of these proteins in the decapping reaction have not been established. Evidence suggests that the Dcp1 may enhance the function of Dcp2.
Pfam PF22450: T4SS protein CagL (family)
This family includes CagL from Helicobacter pylori ([swissprot:O25272]), a type IV secretion system (T4SS) pilus protein that interacts with several integrins through an helical RGD motif. It shows an all-alpha structure that undergoes specific conformational changes depending on pH variations. These changes also affect the exposure of the RGD motif and therefore modulate its binding capacity to host cell integrins.
Pfam PF07035: Regulator of MON1-CCZ1 complex, C-terminal (domain)
This family represents the C-terminus (approximately 160 residues) of a number of Regulator of MON1-CCZ1 complex (RMC1, also known as colon cancer-associated protein Mic1). This is an alpha-helical region that serves as a scaffold for CCZ1-MON1 recruitment and bridges the membrane and GEF complex.
Pfam PF11873: Membrane-bound lytic murein transglycosylase C, N-terminal domain (family)
This domain is found associated with [pfam:PF01464]. It is the N-terminal structural domain of MltC (Membrane-bound lytic murein transglycosylase C), one of the seven lytic transglycosylases found in the genome of the Gram-negative bacterium Escherichia coli. The role of the N-terminal domain is suggested to be important not as a mere structural extension of the active site beyond what is seen in other lytic transglycosylases but one that creates a peptide-binding site at position +2.
Pfam PF20245: Family of unknown function (DUF6600) (family)
This entry represents a bacterial protein of unknown function. It is rich in conserved tryptophan residues and contains a central HYGRW motif that may be of functional importance.
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 PF24594: Family of unknown function (DUF7618) (family)
This entry represents a small family of uncharacterised phage 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 PF08912: Rho Binding (coiled_coil)
Rho Binding Domain is responsible for the recognition and binding of Rho binding domain-containing proteins (such as ROCK) to Rho, resulting in activation of the GTPase which in turn modulates the phosphorylation of various signalling proteins. This domain is within an amphipathic alpha-helical coiled-coil and interacts with Rho through predominantly hydrophobic interactions.
Pfam PF10530: Toxin with inhibitor cystine knot ICK or Knottin scaffold (family)
Spider toxins of the CSTX family are ion channel toxins containing an inhibitor cystine knot (ICK) structural motif or Knottin scaffold. The four disulfide bonds present in the CSTX spider toxin family are arranged in the following pattern: 1-4, 2-5, 3-8 and 6-7. CSTX-1 is the most important component of C. salei venom in terms of relative abundance and toxicity and therefore is likely to contribute significantly to the overall toxicity of the whole venom. CSTX-1 blocked rat neuronal L-type, but no other types of HVA Cav channels. Interestingly, the omega-toxins from Phoneutria nigriventer venom (another South American species also belonging to the Ctenidae family) are included as they carry the same disulfide bond arrangement. suggestive that CSTX-1 may interact with Cav channels. Calcium ion voltage channel heteromultimer containing an L-type pore-forming alpha1-subunit is the most probable candidate for the molecular target of CSTX-1 and these toxins.
Wikipedia: Spider toxins are a family of proteins produced by spiders which function as neurotoxins. The mechanism of many spider toxins is through blockage of calcium channels.
Pfam PF13664: Domain of unknown function (DUF4149) (domain)
This entry represents a transmembrane domain found in TMEM205 from animals , its homologue from yeast YPR098C and in uncharacterised bacterial sequences. This domain is functionally uncharacterised.
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 PF23497: YmiD (family)
This protein family includes the uncharacterised protein YmiD from Escherichia coli, a 42-residues micropeptide encoded by a small open reading frame (smORF). Proteins 50 or fewer residues-long have been shown to regulate the functions of larger proteins in a variety of organisms.
Pfam PF08046: IlvGEDA operon leader peptide (family)
This family consists of the leader peptides of ilvGEDA  operon. The expression of the ilvGEDA operon of E coli  K-12 is multivalently controlled by the three branched -chain amino acids. Regulation is thought to occur by  attenuation of transcription in response to the changing  levels of the cognate tRNAs. Transcription of this operon  is usually terminated at the end of the leader (regulatory)  region.
Pfam PF17338: Gene product 88 (domain)
This family of unknown function is found in Bacteria and phage. These domains for a partial Tim barrel fold.
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 PF14485: Domain of unknown function (DUF4431) (domain)
This domain of unknown function is found in 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 PF20943: Domain of unknown function (DUF4785) C-terminal domain (domain)
This family of proteins is found in bacteria. Proteins in this family are typically between 392 and 442 amino acids in length. This entry represents the C-terminal immunoglobulin-like domain.
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 PF05571: JNK1/MAPK8-associated membrane protein (family)
This family consists of several eukaryotic proteins including JAMP, a Jun N-terminal kinase 1 (JNK1)-associated membrane protein. It associates with JNK1 through its C-terminal domain and regulates the duration of JNK1 activity in response to diverse stress stimuli. It is an important component for coordinated clearance of misfolded proteins from the ER.
Pfam PF05941: Chordopoxvirus A20R protein (family)
This family consists of several Chordopoxvirus A20R proteins. The A20R protein is required for DNA replication, is associated with the processive form of the viral DNA polymerase, and directly interacts with the viral proteins encoded by the D4R, D5R, and H5R open reading frames. A20R may contribute to the assembly or stability of the multiprotein DNA replication complex.
Pfam PF06286: Coleoptericin (family)
This family consists of several insect Coleoptericin, Acaloleptin, Holotricin and Rhinocerosin proteins which are all known to be antibacterial proteins.
Pfam PF12228: Protein of unknown function (DUF3604) (family)
This family of proteins is found in bacteria. Proteins in this family are typically between 621 and 693 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 PF14057: GGGtGRT protein (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are approximately 330 amino acids in length and contain many highly conserved residues including a GGGtGRT motif.
Pfam PF00212: Atrial natriuretic peptide (family)
Atrial natriuretic peptides (ANPs) are vertebrate hormones that play an important role in the control of cardiovascular homeostatis, and sodium and water balance in general . There are different NPs that vary in length but share a common core. All are processed from a single precursor. A disulphide bond resident in the C-terminal section is required for full activity of atriopeptins. The family of NPs includes structurally-related peptides that elicit similar pharmacological spectra. Amongst these are brain natriuretic peptide (BNP); C-type natriuretic peptide (CNP); ventricular natriuretic peptide (VNP) ; and green mamba natriuretic peptide (DNP) .
Pfam PF17388: Mycobacteriophage tail assembly protein (family)
Bacteriophages (viruses of bacteria) use a specialised organelle called a tail to deliver their genetic material and proteins across the cell envelope during infection. This family represents tail assembly proteins found in phages from Siphoviridae family, which includes Mycobacteriophage L5, D29 and Lamina13. This phages have long non-contractile tails. This proteins are likely to interact with the tape measure protein.
Pfam PF25093: Family of unknown function (DUF7807) (family)
This entry represents uncharacterised worm proteins. They are predicted to fold into two alpha-hairpins arranged in V-shape.
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 PF21135: Oxidoreductase DRL, catalytic domain (domain)
This domain is found in DRL from Brucella abortus ([swissprot:Q2YIM3]) and other bacterial putative oxidoreductases and homoserine dehydrogenases. DRL is involved in isoprenoid biosynthesis. This protein is organised into three structural domains: N-terminal, central, (catalytic, this entry), and C-terminal. The catalytic domain shows an alpha/beta fold with a central four-stranded mixed beta-sheet. The active site lid is formed by a protusion made of two antiparallel helices connected by a short loop.
Pfam PF03368: Dicer dimerisation domain (domain)
This domain is found in members of the Dicer protein family which function in RNA interference, an evolutionarily conserved mechanism for gene silencing using double-stranded RNA (dsRNA) molecules.  It is essential for the activity of Dicer. It is a divergent double stranded RNA-binding domain. The N-terminal alpha helix of this domain is in a different orientation to that found in canonical dsRNA-binding domains. This results in a change of charge distribution at the potential dsRNA-binding surface and in the N- and C-termini of the domain being in close proximity. This domain has weak dsRNA-binding activity. It mediates heterodimerisation of Dicer proteins with their respective protein partners.
Pfam PF06282: Protein of unknown function (DUF1036) (family)
This family consists of several hypothetical bacterial proteins 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.