SII-SWORD/CoKE huggingface dataset:
Pfam PF02233: NAD(P) transhydrogenase beta subunit (family)
This family corresponds to the beta subunit of NADP transhydrogenase in prokaryotes, and either the protein N- or C terminal in eukaryotes.  The domain is often found in conjunction with [pfam:PF01262]. Pyridine  nucleotide transhydrogenase catalyses the reduction of NAD+ to NADPH. A complete loss of activity occurs upon  mutation of Gly314 in  E. coli.
Wikipedia: In enzymology, a NAD(P)+ transhydrogenase (Re/Si-specific (EC 1.6.1.2) is an enzyme that catalyzes the chemical reactionNADPH + NAD+  NADP+ + NADH
Pfam PF17186: Lipocalin-like domain (domain)
This family contains the members of the old Pfam family DUF2006. Structural characterisation of family member [swissprot:Q82US3] (from DUF2006 now merged into this family) has revealed a lipocalin-like fold with domain duplication. This entry represents the C-terminal domain of the pair.
Pfam PF22863: TraI-like middle domain (domain)
This entry represents a domain found in the middle region of TraI-like proteins (such as [swissprot:I1YLR9]), following the N-terminal relaxase domain.
Pfam PF01543: Hepatitis C virus capsid protein (family)
Although Hepatitis A virus, Hepatitis B virus, and Hepatitis C virus have similar names, because they all cause liver inflammation, these are distinctly different viruses both genetically and clinically. The Hepatitis C virus (HCV) is a small (50-80 nm in diameter), enveloped, single-stranded, positive sense RNA virus. It is member of the family Flaviviridae. There are seven genotypes and a number of subtypes with diverse geographic distributions. The genome of HCV consists of a single open reading frame. At the 5' and 3' ends of the RNA are the UTR regions that are not translated into proteins but are important to translation and replication of the viral RNA. The 5' UTR has a ribosome binding site (IRES - Internal ribosome entry site) that starts the translation of unique polyprotein that is later cut by cellular and viral proteases into 10 active structural and non-structural smaller proteins .
The HCV core protein is located at the N terminus of the polyprotein and is followed by the signal sequence located between the core protein and the E1 envelope glycoprotein. This signal sequence targets the nascent HCV polyprotein to the endoplasmic reticulum (ER), allowing the translocation of E1 to the ER lumen. Cleavage by a signal peptidase in the ER lumen releases the N-terminal end of E1, leaving the 191-amino acids (aa) core protein anchored by its C-terminal signal peptide . This 191aa polypeptide, also known as p23, is the immature form of the core protein; p23 is further processed by an intramembrane protease, the signal peptide peptidase (SPP), that removes the ER anchor , releasing p21, the N-terminal 179aa mature form of the core protein . Core protein (p21) is responsible for packaging viral RNA to form a viral nucleocapsid, and it also promotes virion budding .
This entry covers domain I of the core protein.
Pfam PF12123: PlyG Cell wall binding domain (domain)
This domain is found in bacteria and viruses. This domain is about 50 amino acids in length. This domain is thought to be a cell wall binding domain.
Pfam PF24149: K1 capsule-specific polysaccharide lyase, Rider domain (domain)
This entry represents the so-called Rider domain of K1 capsule-specific polysaccharide lyase and related proteins. K1-lyase functions as a receptor binding protein (RBP) and mediates the attachment to the host capsular exopolysaccharides. This enzyme possesses a lyase activity that specifically degrades the K1-type polysaccharides of Klebsiella pneumoniae capsule. The Rider domain folds into a beta-barrel, participates in polysaccharide binding to both carbohydrate-binding sites of the enzyme and makes an important contribution to the structural stability of the trimeric K1-lyase.
Pfam PF23587: Kalirin, SH3 (domain)
This SH3 (src Homology-3) domain is found in human Kalirin (KALRN) and similar proteins predominantly found in animals. KALRN is involved in various signalling mechanisms that regulate neuronal shape, growth, and plasticity, through their effects on the actin cytoskeleton.
Pfam PF15483: Domain of unknown function (DUF4641) (disordered)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 201 and 519 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 PF21218: Formamidopyrimidine-DNA glycosylase-like, C-terminal domain (domain)
This domain is found in Formamidopyrimidine-DNA glycosylase-like from Arabidopsis thaliana (Fpg) and similar proteins from plants. Fpg is involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. It catalyses the hydrolysis of the N-glycosylic bond between the damaged base and the deoxyribose (glycosylase activity) before cleaving the DNA backbone (lyase activity). This entry represents the C-terminal domain, which shows four alpha- helices, two of them forming the helix-two-turn-helix (H2TH) motif, and two antiparallel beta-strands involved in a structural motif mimicking an antiparallel beta-hairpin zinc finger.
Pfam PF15453: Protein incorporated later into Tight Junctions (family)
Pilt is a family of eukaryotic tight junction-proteins that binds to guanylate-kinase. Pilt is a component of TJs (Tight junctions) rather than AJs (Adhesin junctions). The protein is incorporated into TJs after TJ strands are formed, thereby suggesting the name Pilt for 'protein incorporated later into TJs'. Pilt binds to the guanylate-kinase region of hDlg otherwise known as Disk large homologue.
Pfam PF17966: Muc B2-like domain (domain)
This entry corresponds to the Muc B2 domain. This domain is related to the Muc B1 domain [pfam:PF17965]. This domain may be involved in mucin binding. This domain is often found associated with the related [pfam:PF17965] in bacterial cell surface proteins.
Pfam PF21104: Glycosyl hydrolase family 78 alpha-rhamnosidase N-terminal domain (domain)
This entry represents the N-terminal domain of glycosyl hydrolase family 78 alpha-rhamnosidase proteins. This domain is involved in dimerisation of the enzyme.
Pfam PF11763: Cell-wall adhesin ligand-binding C-terminal (family)
The DIPSY domain is characterised by the distinctive D*I*PSY motif at the very C-terminus of yeast cell-wall glycoproteins. It appears not to be conserved in any other species, however. In fungi, cell adhesion is required for flocculation, mating and virulence, and is mediated by covalently bound cell wall proteins termed adhesins. Map4, an adhesin required for mating in Schizosaccharomyces pombe, is N-glycosylated and O-glycosylated, and is an endogenous substrate for the mannosyl transferase Oma4p. Map4 has a modular structure with an N-terminal signal peptide, a serine and threonine (S/T)-rich domain that includes nine repeats of 36 amino acids (rich in serine and threonine residues, but lacking glutamines), and a C-terminal DIPSY domain with no glycosyl-phosphatidyl inositol (GPI)-anchor signal. The N-terminal S/T-rich regions, are required for cell wall attachment, but the C-terminal DIPSY domain is required for agglutination and mating in liquid and solid media.
Pfam PF17798: TRIF N-terminal domain (domain)
The N-terminal domain of TRIF/TICAM-1 has a structure that consists of eight antiparallel helices. This domain believed to be involved in self-regulation of TRIF by interacting with its TIR domain.
Pfam PF05365: Ubiquinol-cytochrome C reductase, UQCRX/QCR9 like (family)
The UQCRX/QCR9 protein is the 9/10 subunit of complex III, encoding a protein of about 7-kDa. Deletion of QCR9 results in the inability of cells  to grow on grow on-fermentable carbon source n yeast.
Wikipedia: The coenzyme Q : cytochrome c – oxidoreductase, sometimes called the cytochrome bc1 complex, and at other times complex III, is the third complex in the electron transport chain, playing a critical role in biochemical generation of ATP. Complex III is a multisubunit transmembrane protein encoded by both the mitochondrial and the nuclear genomes. Complex III is present in the mitochondria of all animals and all aerobic eukaryotes and the inner membranes of most bacteria. Mutations in Complex III cause exercise intolerance as well as multisystem disorders. The bc1 complex contains 11 subunits, 3 respiratory subunits, 2 core proteins and 6 low-molecular weight proteins.
Pfam PF15038: Jiraiya (family)
Jiraiya inhibits bone morphogenetic protein (BMP) signaling during embryogenesis. The human member of this family is TMEM221.
Pfam PF17842: Double-stranded RNA binding domain 2 (domain)
This domain is found in HEN1 proteins from Arabidopsis. Structural characterization reveal that small RNA substrate bind to two double-stranded RNA (dsRNA)-specific binding domains, dsRBD1 and dsRBD2. This entry relates to dsRBD2 which together with dsRBD1 forms a strong grip on the duplex region of the small RNA substrate, and these interactions help position the other duplex terminus towards the MTase domain [pfam:PF13847].
Pfam PF16973: Flagellar motor switch protein FliN N-terminal (domain)
FliN is one of three proteins that form a switch-complex at the base of the basal body of the flagellum; the switch regulates the flagellum-motor.
Pfam PF13203: Putative metallopeptidase domain (domain)
This domain, found in various hypothetical bacterial proteins, has no known function. However, it is related to [pfam:PF01435].
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 PF05341: Per os infectivity factor 6 (family)
Family members include Autographa californica nuclear polyhedrosis virus (AcMNPV) Orf68 (also known as per os infectivity factor 6, PIF6 or ac68). PIF6 is present in both the budded virus (BV) and the occluded-derived virus (ODV). The ac68 gene overlaps the lef3 gene which encodes the single-stranded DNA binding protein, and knockout experiments of ac68 have to ensure that a functional lef3 gene is present. In ac68KO experiments, viral DNA replication and BV levels were unaffected as were mortality rates if caterpillars were injected with BV directly into the hemolymph bypassing the gut. However, in oral bioassays the ac68KO occlusion bodies failed to kill larvae, indicating that PIF6 is a per os infectivity factor.
Pfam PF24398: Family of unknown function (DUF7542) (family)
This entry represents a family of small uncharacterised proteins found mainly in Halobacteria. They are predicted to adopt a globular alpha/beta structure consisting of three-stranded beta-sheet and two alpha-helices one of which is packed on the beta-sheet.
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 PF14454: Prokaryotic Ubiquitin (family)
A Ubiquitin-superfamily protein that is present across several bacterial lineages, and found in gene neighborhoods with components of the ubiquitin modification system such as the E1, E2 and JAB  proteins, and a novel alpha-helical protein, which is predicted  to be enzymatic.
Pfam PF22837: Type II methyltransferase M.Eco57I, C-terminal domain (domain)
This domain is found at the C-terminal of the gamma subtype methylase Type II methyltransferase M.Eco57I from Escherichia coli. This domain is predicted to adopt an alpha-beta configuration and is often found associated with [pfam:PF07669].
Pfam PF05639: Pup-like protein (family)
This family consists of several short bacterial proteins formely known as (DUF797).  It was recently shown that Mycobacterium tuberculosis contains a small protein, Pup (Rv2111c), that is covalently conjugated to the e-NH2 groups of lysines on several target proteins (pupylation) such as the malonyl CoA acyl carrier protein (FabD). Pupylation of FabD was shown to result in its recruitment to the mycobacterial proteasome and subsequent degradation analogous to eukaryotic ubiquitin-conjugated proteins. Searches recovered Pup orthologs in all major actinobacteria lineages including the basal bifidobacteria and also sporadically in certain other bacterial lineages. The Pup proteins were all between 50-90 residues in length and a multiple alignment shows that they all contain a conserved motif with a G [EQ] signature at the C-terminus. Thus, all of them are suitable for conjugation via the terminal glutamate or the deamidated glutamine (as shown in the case of the Mycobacterium Pup). The conserved globular core of Pup is predicted to form a bihelical unit with the extreme C-terminal 6-7 residues forming a tail in the extended conformation. Thus, Pup is structurally unrelated to the ubiquitin fold and has convergently evolved the function of protein modifier.
Wikipedia: Prokaryotic ubiquitin-like protein (Pup) is a functional analog of ubiquitin found in the prokaryote Mycobacterium tuberculosis. Like ubiquitin, Pup serves to direct proteins to the proteasome for degradation in the Pup-proteasome system (PPS). However, the enzymology of ubiquitylation and pupylation is different, owing to their distinct evolutionary origins. In contrast to the three-step reaction of ubiquitylation, pupylation requires only two steps, and thus only two enzymes are involved in pupylation. The enzymes involved in pupylation are descended from glutamine synthetase.
Pfam PF21202: Structure-specific endonuclease subunit SLX1, C-terminal (domain)
Slx1 is a catalytic subunit of the SLX1-SLX4 structure-specific endonuclease that resolves DNA secondary structures generated during DNA repair and recombination. It has endonuclease activity towards branched DNA substrates, introducing single-strand cuts in duplex DNA close to junctions with ss-DNA. This is the RING zinc finger domain.
Pfam PF05375: Pacifastin inhibitor (LCMII) (family)
Structures of members of this family show that they are comprised of a triple-stranded antiparallel beta-sheet connected by three disulfide bridges, which defines this as a novel family of serine protease inhibitors.
Wikipedia: Pacifastin is a family of serine proteinase inhibitors found in arthropods. Pacifastin inhibits the serine peptidases trypsin and chymotrypsin.
Pfam PF08660: Oligosaccharide biosynthesis protein Alg14 like (family)
Alg14 is involved dolichol-linked oligosaccharide biosynthesis and anchors the catalytic subunit Alg13 to the ER membrane.
Pfam PF05859: Mis12 protein (family)
Kinetochores are the chromosomal sites for spindle interaction and play a vital role in chromosome segregation. Fission yeast kinetochore protein Mis12, is required for correct spindle morphogenesis, determining metaphase spindle length. Thirty-five to sixty percent extension of metaphase spindle length takes place in Mis12 mutants. It has been shown that Mis12  genetically interacts with Mal2, another inner centromere core  complex protein in S. pombe.
Pfam PF20462: Domain of unknown function (DUF6715) (domain)
This putative domain is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 200 amino acids in length. This domain appears to belong to the NTF2 superfamily.
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 PF19131: Family of unknown function (DUF5814) (family)
This is a family of proteins that are thought to have helicase activity, predominantly found in Halobacteria and Methanomicrobia.
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 PF09401: Coronavirus RNA synthesis protein NSP10 (family)
Non-structural protein 10 (NSP10) is involved in RNA synthesis. It is synthesised as a polyprotein whose cleavage generates many non-structural proteins. NSP10 contains two zinc binding motifs and forms two anti-parallel helices which are stacked against an irregular beta sheet. A cluster of basic residues on the protein surface suggests a nucleic acid-binding function. NSP10 interacts with NSP14 and NSP16 and regulates their respective ExoN and 2-O-MTase activities. When binding to the N-terminal of NSP14, NSP10 allows the ExoN active site to adopt a stably closed conformation and is an allosteric regulator that stabilizes NSP16. The structure of the SARS-CoV-2 NSP10/NSP16 heterodimer revealed that it is extremely similar to that of its SARS-CoV-1 homologue. One NSP10 residue, Tyr-96 is of particular interest as it plays a crucial role in the NSP10-NSP16/NSP14 interaction. This residue is specific for SARS-CoV NSP10 and is a phenylalanine in most other Coronavirus homologues.
Pfam PF16125: Domain of unknown function (DUF4837) (family)
This family consists of uncharacterized proteins around 350 residues in length and is mainly found in various Bacteroides species. The function of this family is unknown.
Pfam PF11317: Protein of unknown function (DUF3119) (family)
This family of proteins has no known function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF17548: Histone-like Protein p6 (family)
Family members such as protein p6 from Bacillus subtilis phage phi29 bind double-stranded DNA, forming a large nucleoprotein complex all along the viral genome, and have been proposed to be an architectural protein with a global role in genome organization. P6 is also involved in viral transcriptional control, repressing the C2 early promoter located at the right DNA end,and together with the viral regulatory protein p4, repressing early promoters A2b/A2c and activating late promoter A3.
Pfam PF24519: Nucleoporin pom152-like, first immunoglobulin-like domain (domain)
This is the first immunoglobulin-like (Ig-like) domain found in Nucleoporin pom152 from Schizosaccharomyces pombe and similar fungal proteins. Pom152 functions as a component of the nuclear pore complex (NPC).
Pfam PF13497: Domain of unknown function (DUF4121) (family)
Based on Bacteroides thetaiotaomicron gene BT_2588, a putative uncharacterised protein. As seen in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2231), it appears to be upregulated in the presence of host or vs when in culture.
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 PF07478: D-ala D-ala ligase C-terminus (family)
This family represents the C-terminal, catalytic domain of the D-alanine--D-alanine ligase enzyme [ec:6.3.2.4]. D-Alanine is one of the central molecules of the cross-linking step of peptidoglycan assembly. There are three enzymes involved in the D-alanine branch of peptidoglycan biosynthesis: the pyridoxal phosphate-dependent D-alanine racemase (Alr), the ATP-dependent D-alanine:D-alanine ligase (Ddl), and the ATP-dependent D-alanine:D-alanine-adding enzyme (MurF).
Pfam PF22650: Glyoxalase At5g48480-like C-terminal domain (domain)
This entry includes plant sequences that belong to the Lactoylglutathione lyase/glyoxalase I family. They are poorly characterised and contain two characteristic VOC domains. Members of this entry contain conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping. This entry represents the C-terminal domain.
Pfam PF09844: Uncharacterized conserved protein (COG2071) (family)
This conserved protein (similar to YgjF), found in various prokaryotes, 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 PF16406: Domain of unknown function (DUF5014) (family)
This small family of proteins is functionally uncharacterised. This family is found in various Bacteroides species. Proteins in this family are around 630 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 PF21491: Mimivirus sulfhydryl oxidase R596-like, C-terminal domain (domain)
This domain is found at the C-terminal end of the FAD-linked sulfhydryl oxidase R596 from Acanthamoeba polyphaga mimivirus (APMV) and similar proteins predominantly found in giant viruses. This protein is a member of the Erv family of sulfhydryl oxidases. This is an ORFan domain that folds into six alpha-helices forming a compact domain.
Pfam PF13063: Protein of unknown function (DUF3925) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 70 amino acids in length.
Pfam PF04760: Translation initiation factor IF-2, N-terminal region (domain)
This conserved feature at the N-terminus of bacterial translation initiation factor IF2 has recently had its structure solved.  It shows structural similarity to the tRNA anticodon Stem Contact Fold domains of the methionyl-tRNA and glutaminyl-tRNA synthetases, and a similar fold is also found in the B5 domain of the phenylalanine-tRNA synthetase.