SII-SWORD/CoKE huggingface dataset:
Pfam PF03055: Retinal pigment epithelial membrane protein (repeat)
This family represents a retinal pigment epithelial membrane receptor which is abundantly expressed in retinal pigment epithelium, and binds plasma retinal binding protein.  The family also includes the sequence related neoxanthin cleavage enzyme in plants and lignostilbene-alpha,beta-dioxygenase in bacteria.
Wikipedia: Carotenoid oxygenases are a family of enzymes involved in the cleavage of carotenoids to produce, for example, retinol, commonly known as vitamin A. This family includes an enzyme known as RPE65 which is abundantly expressed in the retinal pigment epithelium where it catalyzed the formation of 11-cis-retinol from all-trans-retinyl esters.
Pfam PF00947: Picornavirus core protein 2A (domain)
This protein is a protease, involved in cleavage of the polyprotein.
Pfam PF03186: CobD/Cbib protein (family)
This family includes CobD proteins from a number of bacteria, in Salmonella this protein is called Cbib. Salmonella CobD is a different protein. This protein is involved in cobalamin biosynthesis and is probably an enzyme responsible for the conversion of adenosylcobyric acid to adenosylcobinamide or adenosylcobinamide phosphate.
Wikipedia: Cobalamin biosynthesis is the process by which bacteria and archea make cobalamin, vitamin B12. Many steps are involved in converting aminolevulinic acid via uroporphyrinogen III and adenosylcobyric acid to the final forms in which it is used by enzymes in both the producing organisms and other species, including humans who acquire it through their diet.
Pfam PF03390: 2-hydroxycarboxylate transporter family (family)
The 2-hydroxycarboxylate transporter family is a family of secondary transporters found exclusively in the bacterial kingdom. They function in the metabolism of the di- and tricarboxylates malate and citrate, mostly in fermentative pathways involving decarboxylation of malate or oxaloacetate.
Pfam PF10811: Protein of unknown function (DUF2532) (family)
This bacterial 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 PF04442: Cytochrome c oxidase assembly protein CtaG/Cox11 (family)
Cytochrome c oxidase assembly protein is essential for the assembly of functional cytochrome oxidase protein.      In eukaryotes it is an integral protein of the mitochondrial inner membrane. Cox11 is essential for the insertion of Cu(I) ions to form the CuB site. This is essential for the stability of other structures in subunit I, for example haems a and a3, and the magnesium/manganese centre.  Cox11 is probably only required in sub-stoichiometric amounts relative to the structural units. The C terminal region of the protein is known to form a dimer. Each monomer coordinates one Cu(I) ion via three conserved cysteine residues (111, 208 and 210) in Saccharomyces cerevisiae ([swissprot:P19516]).  Met 224 is also thought to play a role in copper transfer or stabilising the copper site.
Wikipedia: The enzyme cytochrome c oxidase or Complex IV is a large transmembrane protein complex found in bacteria, archaea, and the mitochondria of eukaryotes.
Pfam PF02355: Protein export membrane protein SecD/SecF, C-terminal (domain)
This entry represents the C-terminal domain of various prokaryotic SecD and SecF protein export membrane proteins and their archaeal  homologues. These SecD and SecF proteins are part of the multimeric protein export complex comprising SecA, D, E, F, G, Y, and YajC. SecD and SecF are required to maintain a proton motive force.
Wikipedia: SecD and SecF are prokaryotic protein export membrane proteins. They are a part of the larger multimeric protein export complex comprising SecA, D, E, F, G, Y, and YajC. SecD and SecF are required to maintain a proton motive force.
Pfam PF11010: Protein of unknown function (DUF2848) (family)
This bacterial 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 PF08428: Rib domain (domain)
The region featured in this family is found repeated in a number of bacterial surface proteins, such as Rib ([swissprot:P72362]) and alpha ([swissprot:Q02192]). These are expressed by group B streptococci, and Rib is thought to confer protective immunity.
Pfam PF03544: Gram-negative bacterial TonB protein C-terminal (domain)
The TonB_C domain is the well-characterised C-terminal region of the TonB receptor molecule. This protein is bound to an inner membrane-bound protein ExbB via a globular domain and has a flexible middle region that is likely to help in positioning the C-terminal domain into the iron-transporter barrel in the outer membrane. TonB_C interacts with the N-terminal TonB box of the outer membrane transporter that binds the Fe3+-siderophore complex. The barrel of the transporter, consisting of 22 beta-sheets and an inside plug, binds the iron complex in the barrel entrance.
Pfam PF11934: Domain of unknown function (DUF3452) (family)
This presumed domain is functionally uncharacterised. This domain is found in bacteria and eukaryotes. This domain is typically between 124 to 150 amino acids in length. This domain is found associated with [pfam:PF01858], [pfam:PF01857]. This domain has a single completely conserved residue W that may be functionally important.
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 PF17864: RuvB AAA lid domain (domain)
The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein. This entry contains the AAA lid domain that is found to the C-terminus of the AAA domain.
Pfam PF11538: Snurportin1 (family)
Snurportin1 is a novel nuclear import receptor which contains an N-terminal importin beta binding domain which is essential for its function of a snRNP-specific nuclear import receptor. Snurportin1 interacts with m3G-cap where it enhances the m3G-cap dependent nuclear import of U snRNPs in Xenopus laevis oocytes and digitonin-permeabilized HeLa cells.
Pfam PF09158: Bacteriophage T4 MotA, C-terminal (domain)
Members of this family adopt a compact alpha/beta structure comprising three alpha-helices and six beta-strands in the order: alpha1-beta1-beta2-beta3-beta4-alpha2-beta5-beta6-alpha3. The beta-strands form a single anti-parallel beta-sheet and the three alpha-helices pack side-by-side onto one surface of the beta-sheet. In this architecture, the domain's hydrophobic core is at the sheet-helix interface, and the second surface of the beta-sheet is completely exposed. The domain is a DNA-binding motif, with a consensus sequence containing nine base pairs (5'-TTTGCTTTA-3'), that appears to bind to various mot boxes, allowing access to the minor groove towards the 5'-end of this sequence and the major groove towards the 3'-end.
Pfam PF13905: Thioredoxin-like (domain)
Thioredoxins are small enzymes that participate in redox reactions, via the reversible oxidation of an active centre disulfide bond.
Wikipedia: Thioredoxin is a class of small redox proteins known to be present in all organisms. It plays a role in many important biological processes, including redox signaling. In humans, thioredoxins are encoded by TXN and TXN2 genes. Loss-of-function mutation of either of the two human thioredoxin genes is lethal at the four-cell stage of the developing embryo. Although not entirely understood, thioredoxin is linked to medicine through their response to reactive oxygen species (ROS). In plants, thioredoxins regulate a spectrum of critical functions, ranging from photosynthesis to growth, flowering and the development and germination of seeds. Thioredoxins play a role in cell-to-cell communication.
Pfam PF04713: Poxvirus protein I5 (family)
This entry represents the Poxvirus protein I5, also known as Protein OPG081. In Vaccinia virus, I5 is associated with the membranous components of assembling and mature virions .
Pfam PF03332: Eukaryotic phosphomannomutase (family)
This enzyme [ec:5.4.2.8] is involved in the synthesis of the GDP-mannose and dolichol-phosphate-mannose required for a number of critical mannosyl transfer reactions.
Pfam PF16902: FokI, D3 domain (domain)
Type IIS restriction endonuclease FokI is a member of an unusual class of bipartite restriction enzymes that recognises the double- stranded DNA sequence 5'-GGATG-3' and cleave DNA phosphodiester groups 9 base pairs away on this strand and 13 base pairs away on the complementary strand. FokI contains amino- and carboxy- terminal domains corresponding to the DNA-recognition and cleavage functions, respectively. The recognition domain is made of three smaller subdomains (D1, D2 and D3) which are evolutionarily related to the helix-turn-helix-containing DNA-binding domain of the catabolite gene activator protein CAP. This is the D3 domain which is most similar to CAP and related proteins such as histone H5, HNF-3gamma  and the biotin operon repressor (BirA). Despite its similarity, D3 barely touches the DNA.
Pfam PF03110: SBP domain (domain)
SBP domains (for SQUAMOSA-pROMOTER BINDING PROTEIN) are found in plant proteins.  It is a sequence specific DNA-binding domain. Members of family probably function as transcription factors involved in the control of early flower development. The domain contains 10 conserved cysteine and histidine residues that probably are zinc ligands.
Wikipedia: The SQUAMOSA promoter binding protein-like family of transcription factors are defined by a plant-specific DNA-binding domain. The founding member of the family was identified based on its specific in vitro binding to the promoter of the snapdragon SQUAMOSA gene. SBP proteins are thought to be transcriptional activators.
Pfam PF05919: Mitovirus RNA-dependent RNA polymerase (family)
This family consists of several Mitovirus RNA-dependent RNA polymerase proteins. The family also contains fragment matches in the mitochondria of Arabidopsis thaliana.
Pfam PF16575: mRNA cleavage and polyadenylation factor CLP1 P-loop (domain)
CLP1_P is the P-loop carrying domain of Clp1 mRNA cleavage and polyadenylation factor, Clp1, proteins in eukaryotes. Clp1 is essential for 3'-end processing of mRNAs.  This region carries the P-loop suggesting it is the region that binds adenine or guanine nucleotide.
Pfam PF19481: Family of unknown function (DUF6017) (domain)
This presumed domain is functionally uncharacterised. It is found to the C-terminus of a helix-turn-helix domain which strongly suggests that it is a transcriptional regulatory protein. These domains associated with HTH domains often bind to a ligand. This domain family is found in firmicutes, and is approximately 150 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 PF00938: Lipoprotein (domain)
This family of lipoproteins is Mycoplasma specific.
Pfam PF02224: Cytidylate kinase (domain)
Cytidylate kinase [ec:2.7.4.14] catalyses the phosphorylation of cytidine 5'-monophosphate (dCMP) to cytidine 5'-diphosphate (dCDP) in the presence of ATP or GTP.
Pfam PF20578: Atrophied bacterial Ig domain (domain)
This domain is related to [pfam:PF02368] a bacterial immunoglobulin-like domain. According to structure predictions members of this domain family have lost several beta strands found on one sheet of the Ig domain. This domain is found in a wide range of bacterial cell surface proteins.
Pfam PF20096: Family of unknown function (DUF6486) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 30 amino acids in length. There is a conserved IAVASA sequence motif.
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 PF18588: Polysaccharide biosynthesis enzyme WcbI (domain)
Capsular polysaccharides (CPSs) are protective structures on the surfaces of many Gram-negative bacteria. wcbI is one of several genes in the CPS biosynthetic cluster whose deletion leads to significant attenuation of the pathogen. Structural analysis and biophysical assays suggest that WcbI functions as an acetyltransferase enzyme but it requires another functional module to carry out this function. WcbI adopts a predominantly helical fold where the N-terminal 100 amino acids form a ligand-binding domain and binds tightly to coenzyme A and its derivative acetyl-CoA.
Pfam PF02382: N-terminal domain in RTX protein (domain)
The RTX family of bacterial toxins are a group of cytolysins and cytotoxins that have RTX (Repeat in ToXin repeats) [pfam:PF00353]. This is a hydrophobic pore-forming domain found at the N-terminal of these proteins.
Pfam PF14296: O-antigen polysaccharide polymerase Wzy (family)
This family includes O-antigen polysaccharide polymerases. These enzymes link O-units via a glycosidic linkage to form a long O-antigen. These enzymes vary in specificity and sequence.
Pfam PF16329: Pestivirus envelope glycoprotein E2 (domain)
Pestiviruses have an outer lipid envelope bearing two glycoproteins, E1 and E2, required for cell entry . This entry represent the E2 protein, which consists of two Ig-like domains followed by an elongated Î²-stranded domain with a new fold .
Pfam PF13248: zinc-ribbon domain (domain)
This family consists of a single zinc ribbon domain, ie half of a pair as in family DZR. [pfam:PF12773].
Pfam PF22207: MCM3 winged helix domain (domain)
This entry represents the C-terminal winged helix domain found in yeast MCM3 protein.
Pfam PF13270: Coiled-coil domain-containing protein 28 (family)
This entry includes CCDC28A and CCDC28B. CCDC28B modulates mTORC2 complex assembly and function, possibly enhances AKT1 phosphorylation.
Pfam PF15392: Joubert syndrome-associated (family)
This family of proteins is domain of unknown function, which is found in eukaryotes. However, mutations in the gene lead to Joubert's Syndrome, indicating that the protein that the gene encodes for is vital for correct ciliogenesis.
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 PF23716: Family of unknown function (DUF7158) (family)
This domain is found at the N-terminal end of a group of uncharacterised sequences from actinobacteria.
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 PF15505: Vexin domain (domain)
Proteins containing this domain include Xenopus laevis Vexin and its human homologue, C8orf46. Vexin is transiently expressed in differentiating progenitors in the developing central nervous system (CNS) and is required for neurogenesis in the neural plate and retina. This entry corresponds to a presumed SH3 domain.
Pfam PF02136: Nuclear transport factor 2 (NTF2) domain (domain)
This family includes the NTF2-like Delta-5-3-ketosteroid isomerase proteins.
Pfam PF10386: Protein of unknown function (DUF2441) (family)
This is a family of highly conserved, predicted, proteins from Bacillus species. The structure forms a homo-dimer. The function is unknown.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF19819: Family of unknown function (DUF6302) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000703) is described by MIBiG as an example of the following biosynthetic class, saccharide, in particular the  kanamycin biosynthetic gene cluster from Streptomyces kanamyceticus.
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 PF00923: Transaldolase/Fructose-6-phosphate aldolase (domain)
Transaldolase (TAL) is an enzyme of the pentose phosphate pathway (PPP) found almost ubiquitously in the three domains of life (Archaea, Bacteria, and Eukarya). TAL shares a high degree of structural similarity and sequence identity with fructose-6-phosphate aldolase (FSA). They both belong to the class I aldolase family. Their protein structures have been revealed.
Wikipedia: Transaldolase is an enzyme of the non-oxidative phase of the pentose phosphate pathway. In humans, transaldolase is encoded by the TALDO1 gene.
Pfam PF16316: Domain of unknown function (DUF4956) (family)
This family consists of uncharacterized proteins around 220 residues in length and is mainly found in various Bacteroides species. The function of this protein is unknown.
Pfam PF24167: Family of unknown function (DUF7411) (family)
This is a family of unknown function mainly found in archaea but also in some bacterial species. They may have a Rossmann-like alpha/beta/alpha 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 PF04453: LPS transport system D (family)
Lipopolysaccharide (LPS) is essential for most Gram-negative bacteria and has crucial roles in protection of the bacteria from harsh environments and toxic compounds, including antibiotics. This family includes members such as LPTD found in Shigella flexneri and Yersinia pestis. Structural analysis indicates that LptD forms a novel 26-stranded beta-barrel. It interacts with LPTE where LptE adopts a roll-like structure located inside the barrel of LptD. The LPS translocon LptD is unable to fold properly in the absence of LptE and the two proteins form a unique barrel and plug architecture for LPS transport and insertion. LptD is an essential outer membrane protein that mediates the final transport of lipopolysaccharide (LPS) to outer leaflet. It has been suggested that LptD is a promising target for the development of effective vaccines and antibody-based therapies to control Vibrio infection.
Pfam PF03646: FlaG protein (family)
Although important for flagella the exact function of this protein is unknown.
Pfam PF22232: TraI helicase-associated ssDNA bd, N-terminal (domain)
This entry      represents the N-terminal fragment of the helicase-associated   ssDNA binding domain of the conjugative transfer relaxase/helicase TraI. This     domain adopts a globular   structure that closely resembles that of the RecD N-terminal despite little sequence similarity. It is part of a larger domain, referred to as vestigial helicase domain, that functions as a ssDNA binding domain. This region doesn't have helicase activity or measurable DNA binding affinity itself but it may play a role in either DNA unwinding or regulation of ssDNA transfer from host to recipient cell.
Pfam PF06284: Cytomegalovirus UL84 protein (family)
This family consists of several Cytomegalovirus UL84 proteins. The open reading frame UL84 of human cytomegalovirus encodes a multifunctional regulatory protein which is required for viral DNA replication and binds with high affinity to the immediate-early transactivator IE2-p86. This protein interacts with DNA sequences in oriLyt containing several CCAAT/enhancer binding protein (C/EBPalpha) transcription factor binding sites, which is essential for its amplification.
Pfam PF19570: Family of unknown function (DUF6088) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found primarily in bacteria. Proteins in this family are typically between 197 and 228 amino acids in length. This family appears to be distantly related to [pfam:PF13338] suggesting proteins in this family may be an antitoxin component of a toxin/antitoxin system.
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 PF25027: RECK-like, EGF-like 1 domain (domain)
This domain is found in human Reversion-inducing cysteine-rich protein with Kazal motifs (RECK) and similar animal proteins. RECK is involved in the selective response of brain endothelial cells to Wnt7 signals. RECK consists of five repeats of an uncommon domain with six cysteines (the CC domain, [pfam:PF22961], [pfam:PF23332], [pfam:PF23332]), a Frizzled-like cysteine-rich domain (Fz-like CRD, [pfam:PF23298]), two epidermal growth factor-like domains (EGF-like 1, represented by this entry, and 2, [pfam:PF22955]), and three Kazal-like motifs (Kazal-like 1 to 3, [pfam:PF07648]).