SII-SWORD/CoKE huggingface dataset:
Pfam PF20188: Family of unknown function (DUF6551) (family)
This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 200 amino acids in length. Many sequences are related to ParB proteins, annotated as ParB-like or ParB domain-containing proteins. It contains the conserved motifs YQR, DGQH and EAxxF.
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 PF18020: TIG domain found in plexin (domain)
This entry represents a TIG domain found in plexin proteins. TIG domains have an Ig-like fold.
Pfam PF07101: Protein of unknown function (DUF1363) (family)
This family consists of several Trypanosoma brucei putative variant specific antigen proteins of around 80 residues in length.
Pfam PF12468: Type III secretion system leucine rich repeat protein (repeat)
This domain family is found in bacteria, and is approximately 50 amino acids in length. There are two completely conserved residues (Y and W) that may be functionally important. This family consists of leucine-rich repeat proteins involved in type III secretion.
Pfam PF09028: Mac 1 (domain)
The bacterial protein Mac 1 adopts an alpha/beta fold, with 14 beta strands and 9 alpha helices. The N-terminal domain is made up predominantly of alpha helices, whereas the C-terminal domain consists predominantly of beta sheets. Mac 1 blocks polymorphonuclear opsonophagocytosis, inhibits the production of reactive oxygen species and contains IgG endopeptidase activity.
Pfam PF08852: Protein of unknown function (DUF1822) (repeat)
This family of proteins are 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 PF09049: Stannin transmembrane (domain)
Members of this family consist of a single highly hydrophobic transmembrane helix that transverses the lipid bilayer at a 20 degree angle with respect to the membrane normal. They contain a conserved cysteine residue (Cys32) that, together with Cys34 found in the stannin unstructured linker domain, constitutes the putative trimethyltin-binding site that resides at the end of the transmembrane domain close to the lipid/solvent interface.
Wikipedia: Stannins are small proteins that consist of a single transmembrane helix, an unstructured linker domain, and a cytoplasmic domain. The transmembrane region contains a conserved cysteine residue (Cys32) that, together with Cys34 found in the stannin unstructured linker domain, constitutes the putative trimethyltin-binding site, close to the lipid/solvent interface.
Pfam PF01599: Ribosomal protein S27a (domain)
This family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesised as a C-terminal extension of ubiquitin (CEP). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis.  The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins.
Pfam PF00368: Hydroxymethylglutaryl-coenzyme A reductase (family)
The HMG-CoA reductases catalyse the conversion of HMG-CoA to mevalonate, which is the rate-limiting step in the synthesis of isoprenoids like cholesterol. Probably because of the critical role of this enzyme in cholesterol homeostasis, mammalian HMG-CoA reductase is heavily regulated at the transcriptional, translational, and post-translational levels.
Wikipedia: In molecular biology, the HMG-CoA reductase family is a family of enzymes which participate in the mevalonate pathway, the metabolic pathway that produces cholesterol and other isoprenoids.
Pfam PF24308: Family of unknown function (DUF7487) (repeat)
This entry represents a group of uncharacterised sequences from viruses. They may have a novel repeat fold consisting of two domains at the N- and C-terminal with beta-hairpin-beta-alpha configuration that are connected by nine alpha-helices linked by loops.
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 PF10284: Luciferase helical bundle domain (domain)
This domain is found associated with the the catalytic domain of dinoflagellate luciferase . Luciferase is involved in catalysing the light emitting reaction in bioluminescence. The structure of this domain has been solved. This domain has a three helix bundle structure that holds four important histidines that are thought to play a role in the pH regulation of the enzyme.
Pfam PF13837: Myb/SANT-like DNA-binding domain (domain)
This presumed domain appears to be related to other Myb/SANT-like DNA binding domains. In particular [pfam:PF10545] seems most related.  This family is greatly expanded in plants and appears in several proteins annotated as transposon proteins.
Pfam PF23412: Vps8 RING zinc finger (domain)
Vps8 is one of the Golgi complex components necessary for vacuolar sorting. It is the core component of the endosomal tethering complex CORVET (class C core vacuole/endosome tethering). Vps8 co-operates with Vps21-GTP to mediate endosomal clustering in a reaction that is dependent on Vps3. Vps8 is the only CORVET subunit that is enriched on late endosomes, suggesting that it is a marker for the maturation of late endosomes. These proteins consist of a beta-propeller at the N-terminal followed by a long, central TPR domain and a RING zinc finger at the C-terminal. This entry represents the RING zinc finger found in Vps8 from mammals and similar sequences.
Pfam PF16718: Immunity factor for SPN (domain)
Immunity factor for SPN (IFS) binds to and inhibits the SPN toxin.
Pfam PF08971: Glycogen synthesis protein (domain)
Members of this family are involved in glycogen synthesis in Enterobacteria. The structure of the polypeptide chain comprises a bundle of two parallel amphipathic helices, alpha-1 and alpha-3, and a short hydrophobic helix alpha-2 sandwiched between them.
Pfam PF18840: Large polyvalent protein associated domain 25 (domain)
This is an alpha and beta fold domain found in polyvalent proteins of conjugative elements.
Pfam PF02983: Alpha-lytic protease prodomain (domain)
Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Many families of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases .

Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) .
The alpha-lytic protease prodomain is associated with serine peptidases, specifically the alpha-lytic endopeptidases and streptogrisin A, B, C, D and E, which are bacterial enzymes and which belong to MEROPS peptidase subfamily S1A (IPR001316). The protease precursor in Gram-negative bacterial proteases may be a general property of extracellular bacterial proteases . The proteases are encoded with a large (166 amino acid) N-terminal pro region that is required transiently bothin vivoandin vitrofor the correct folding of the protease domain . The pro region also acts as a potent inhibitor of the mature enzyme .
Pfam PF15181: Spermatid-specific manchette-related protein 1 (family)
This family of proteins, SMRP1, is thought to have a role in spermatogenesis and may be involved in differentiation or function of ciliated cells. This family of proteins is found in eukaryotes. Proteins in this family are typically approximately 260 amino acids in length.
Pfam PF20806: Integrin alpha Ig-like domain 3 (domain)
This domain is found in integrin alpha and integrin alpha precursors to the C terminus of a number of [pfam:PF01839] repeats and to the N-terminus of the [pfam:PF00357] cytoplasmic region. This region is composed of an immunoglobulin-like domain.
Wikipedia: Integrins are transmembrane receptors that help cell–cell and cell–extracellular matrix (ECM) adhesion. Upon ligand binding, integrins activate signal transduction pathways that mediate cellular signals such as regulation of the cell cycle, organization of the intracellular cytoskeleton, and movement of new receptors to the cell membrane. The presence of integrins allows rapid and flexible responses to events at the cell surface.
Pfam PF20979: Arginosuccinate synthase C-terminal domain (domain)
This entry represents the C-terminal domain of the Arginosuccinate synthase enzyme.
Wikipedia: Argininosuccinate synthase or synthetase is an enzyme that catalyzes the synthesis of argininosuccinate from citrulline and aspartate. In humans, argininosuccinate synthase is encoded by the ASS gene located on chromosome 9.
Pfam PF03419: Sporulation factor SpoIIGA (family)
Sporulation in bacteria such as Bacillus subtilis involves the formation of a polar septum, which divides the sporangium into a mother cell and a forespore. The sigma E factor, which is encoded within the spoIIG operon, is a cell-specific regulatory protein that directs gene transcription in the mother cell. Sigma E is synthesised as an inactive proprotein pro-sigma E, which is converted to the mature factor by the processing enzyme SpoIIGA, releasing an N-terminal peptide .

The SpoIIGA peptidase (MEROPS peptidase family A36) is assumed to be an aspartic peptidase because of the presence of an Asp-Thr/Ser-Gly motif in which the Asp is an active site residue. The peptidase is active as a homodimer . SpoIIGA has five transmembrane helices at the N-terminal half of the molecule; the proteolytic activity is in the C-terminal half . Its tertiary structure is not known.
Pfam PF10814: Cell wall synthesis protein CwsA (family)
Cell wall synthesis protein CwsA is required for cell  division, cell wall synthesis and cell shape maintenance.
Pfam PF15209: Interleukin 31 (family)
This entry represents interleukin 31 (IL-31), it is a four-helix bundle cytokine that is preferentially produced by T helper type 2 cells . It is associated with pruritus, a characteristic feature of atopic dermatitis , and with other types of allergic contact dermatitis-provoked skin inflammation .
Wikipedia: Interleukin-31 (IL-31) is a protein that in humans is encoded by the IL31 gene that resides on chromosome 12. IL-31 is an inflammatory cytokine that helps trigger cell-mediated immunity against pathogens. It has also been identified as a major player in a number of chronic inflammatory diseases, including atopic dermatitis.
Pfam PF15370: NOP protein chaperone 1 (family)
This entry includes NOPCHAP1 from animals and New4 from fission yeast. NOPCHAP1 is a client-loading PAQosome/R2TP complex cofactor that selects NOP58 to promote box C/D small nucleolar ribonucleoprotein (snoRNP) assembly. The function of New4 is not clear.
Pfam PF13953: PapC C-terminal domain (domain)
The PapC C-terminal domain is a structural domain found at the C-terminus of the E. coli PapC protein. Pili are assembled using the chaperone usher system. In E.coli this is composed of the chaperone PapD and the usher PapC. This domain represents the C-terminal domain from PapC and its homologues. This domain has a beta-sandwich structure similar to the plug domain of PapC.
Pfam PF05045: Rhamnan synthesis protein F (family)
This family consists of a group of proteins which are related to the Streptococcus rhamnose-glucose polysaccharide assembly protein (RgpF). Rhamnan backbones are found in several O polysaccharides of phytopathogenic bacteria and are regarded as pathogenic factors.
Pfam PF18718: CxC5 like cysteine cluster associated with KDZ transposases (domain)
A predicted Zinc chelating domain present N-terminal to the KDZ transposase domain.
Pfam PF18606: Zap helix turn helix N-terminal domain (domain)
Zinc-finger antiviral protein (ZAP) is a host factor that specifically inhibits the replication of certain viruses, such as HIV-1, by targeting viral mRNA for degradation. This domain is a helix turn helix domain found at the N-terminal region constituting the top cockpit layer of the protein.
Pfam PF16076: Acyltransferase C-terminus (family)
This domain is found at the C-terminus of several different acyltransferases including 1-acyl-sn-glycerol-3-phosphate acyltransferase, acyl-CoA:lysophosphatidylglycerol acyltransferase 1 and lysocardiolipin acyltransferase 1.
Pfam PF05121: Gas vesicle protein K (domain)
These proteins are involved in the formation of gas vesicles ().
Pfam PF03746: LamB/YcsF family (family)
This family includes LamB. The lam locus of Aspergillus nidulans consists of two divergently transcribed genes, lamA and lamB, involved in the utilisation of lactams such as 2-pyrrolidinone. Both genes are under the control of the positive regulatory gene amdR and are subject to carbon and nitrogen metabolite repression. The exact molecular function of the proteins in this family is unknown.
Pfam PF20933: Haptoglobin-hemoglobin receptor (family)
Haptoglobin-hemoglobin receptor (HpHbR), a protein found within the variant surface glycoprotein (VSG) from trypanosomes, plays a key role in determining if humans can be infected by these parasites developing sleeping sickness. HpHbR is responsible for the acquisition of haem, an important growth factor for these organism that are deficient in its biosynthesis. This protein folds into an elongated three alpha-helical bundle with a small head structure containing the ligand-binding site that is distal to the C-terminal GPI-anchor attachment site. This structure appears to be conserved among trypanosome species.
Pfam PF12453: Protein tyrosine phosphatase N terminal (family)
This domain family is found in eukaryotes, and is approximately 30 amino acids in length. The family is found in association with [pfam:PF00041]. There is a single completely conserved residue L that may be functionally important. This family consists of various protein tyrosine phosphatase haematopoietic receptors, e.g. CD45, which dephosphorylate growth stimulating proteins. This limits growth signalling in haematopoietic cells.
Pfam PF02747: Proliferating cell nuclear antigen, C-terminal domain (domain)
N-terminal and C-terminal domains of PCNA are topologically identical.  Three PCNA molecules are tightly associated to form a closed ring encircling duplex DNA.
Wikipedia: A DNA clamp, also known as a sliding clamp, is a protein complex that serves as a processivity-promoting factor in DNA replication. As a critical component of the DNA polymerase III holoenzyme, the clamp protein binds DNA polymerase and prevents this enzyme from dissociating from the template DNA strand. The clamp-polymerase protein–protein interactions are stronger and more specific than the direct interactions between the polymerase and the template DNA strand; because one of the rate-limiting steps in the DNA synthesis reaction is the association of the polymerase with the DNA template, the presence of the sliding clamp dramatically increases the number of nucleotides that the polymerase can add to the growing strand per association event. The presence of the DNA clamp can increase the rate of DNA synthesis up to 1,000-fold compared with a nonprocessive polymerase.
Pfam PF08498: Sterol methyltransferase C-terminal (family)
This domain is found to the C-terminus of a methyltransferase domain ([pfam:PF08241]) in fungal and plant sterol methyltransferases.
Pfam PF14326: Domain of unknown function (DUF4384) (family)
This presumed domain is functionally uncharacterised. This domain family is found in bacteria and archaea, and is approximately 80 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 PF05119: Phage terminase, small subunit (family)
This group of sequences are a family of phage (and integrated prophage) putative terminase small subunit sequences. Members tend to be encoded by the gene adjacent to the phage terminase large subunit gene.
Pfam PF13344: Haloacid dehalogenase-like hydrolase (domain)
This family is part of the HAD superfamily.
Pfam PF14821: Threonine synthase N terminus (domain)
This domain is found at the N-terminus of many threonine synthase enzymes.
Pfam PF16198: tRNA pseudouridylate synthase B C-terminal domain (family)
This C-terminal region is found on a subset of TruB_B protein family members [pfam:PF01509].  It is found from bacteria and archaea to fungi, plants and human.
Pfam PF19156: Family of unknown function (DUF5838) (family)
This family of unknown function is associated with  the biosynthetic gene cluster for anacyclamide A10. The family appears to be restricted to Cyanobacteria. Some matches also contain a methyltransferase domain  at the N terminus.
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 PF15395: Domain of unknown function (DUF4617) (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 702 and 1745 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 PF05988: Bacterial protein of unknown function (DUF899) (family)
This family consists of several uncharacterised bacterial proteins of unknown function.
Pfam PF21234: Protein-tyrosine-phosphatase-like, N-terminal domain (domain)
This domain is found at the N-terminal of a group of bacterial phosphatases and arsenate reductases, including Protein-tyrosine- phosphatase from Corynebacterium glutamicum. This domain, often found associated to [pfam:PF01451], forms a three-helical bundle that interacts with the active site of the other chain in the dimeric interface.
Pfam PF18553: PheRS DNA binding domain 3 (domain)
This is a DNA-binding fold domain found in Phenylalanyl-tRNA Synthetase N-terminal region. This domain belongs to a superfamily of 'winged helix' DNA-biding domains. The topology of DBD-1 and DBD-3 closely resembles the topology of the Z-DNA-binding domain Zalpha of double-stranded RNA (dsRNA) adenosine deaminase and other domains from DNA-binding proteins. Mutational analysis indicate that DBD-1, 2 and 3 play critical roles in tRNAPhe binding and recognition, i.e., from the drastic reduction of aminoacylation activity seen upon removal of the N-terminal domains.
Pfam PF16552: D-ornithine 4,5-aminomutase alpha-subunit (domain)
OAM_alpha is the 12.8kDa, alpha subunit of d-ornithine 4,5-aminomutase, or OAM, an enzyme that converts d-ornithine to 2,4-diaminopentanoic acid by way of radical propagation from an adenosylcobalamin to a pyridoxal 5'-phosphate cofactor. OAM is an alpha2-beta2 heterodimer comprising two strongly associating subunits. The packing of the alpha subunits against the beta helps to form the substrate and co-factor binding-regions.
Pfam PF18072: Formylglycinamide ribonucleotide amidotransferase linker domain (domain)
This is the linker domain found in Formylglycinamide ribonucleotide amidotransferase (FGAR-AT), also known as Phosphoribosylformylglycinamidine synthase ([ec:6.3.5.3]), PurL and formylglycinamidine ribonucleotide (FGAM) synthase. This enzyme catalyzes the ATP-dependent conversion of formylglycinamide ribonucleotide (FGAR) and glutamine to formylglycinamidine ribonucleotide (FGAM), ADP, Pi, and glutamate in the fourth step of the purine biosynthetic pathway. The structure analysis of Salmonella typhimurium FGAR-AT reveals that this linker domain is made up of a long hydrophilic belt with an extended conformation.
Pfam PF21786: 6-fold beta flower protein (domain)
This family of proteins have a repetitive structure composed of pairs of beta strands. In this family the proteins usually have six copies of the beta hairpin repeat with a central alpha helix in the barrel.
Pfam PF02756: GYR motif (conserved_site)
The GYR motif is found in several drosophila proteins. Its function is unknown, however the presence of completely conserved tyrosine residues may suggest it could be a substrate for tyrosine kinases.
Pfam PF07299: Elongation factor G-binding protein, N-terminal (domain)
This domain can be found in the N terminus of the FusB, FusC, and FusD proteins from Staphylococcus aureus. They are elongation  factor G (EF-G) binding proteins that are linked to the fusidic  acid (FA) resistance in S. aureus. The FusB proteins are two-domain metalloproteins, and this N-terminal domain forms a four-helical bundle whose helices help to stabilise the conformation of the treble-clef zinc-finger in the C-terminal domain. FA is an antibiotic that binds to EF-G, preventing its release from the ribosome, thus stalling bacterial protein synthesis. The FusB proteins provide FA resistance by preventing formation or facilitating dissociation of the FA-locked EF-G-ribosome complex during elongation and ribosome recycling.