SII-SWORD/CoKE huggingface dataset:
Pfam PF12524: dsDNA virus glycoprotein L C terminal (family)
This domain family is found in viruses, and is typically between 55 and 80 amino acids in length. The family is found in association with [pfam:PF05259]. This family is the C terminal of glycoprotein L from various types of double stranded DNA viruses (dsDNA).
Pfam PF20748: RecJ C-terminal domain, Deinococci (domain)
This domain is found at the C terminus of Single-stranded-DNA- specific exonuclease RecJ from Deinococci. This protein has four domains that form a molecule with an O-like structure. The fourth domain (this entry) binds the C-terminal region of Single-stranded DNA-binding protein ([pfam:PF00436]) to efficiently process broken DNA ends for homologous recombination.
Pfam PF18717: CxC4 like cysteine cluster associated with KDZ transposases (domain)
A predicted Zinc chelating domain present N-terminal to the KDZ transposase domain.
Pfam PF07461: Nicotine adenine dinucleotide glycohydrolase (NADase) (family)
This family consists of several bacterial nicotine adenine dinucleotide glycohydrolase (NGA) proteins which appear to be specific to Streptococcus pyogenes. NAD glycohydrolase (NADase) is a potential virulence factor. Streptococcal NADase may contribute to virulence by its ability to cleave beta-NAD at the ribose-nicotinamide bond, depleting intracellular NAD pools and producing the potent vasoactive compound nicotinamide.
Pfam PF04796: Plasmid encoded RepA protein (family)
Family of plasmid encoded proteins involved in plasmid replication.  The role of RepA in the replication process is not clearly understood.
Pfam PF16770: Regulator of Ty1 transposition protein 107 BRCT domain (domain)
This is the fifth BRCT domain of regulator of Ty1 transposition protein 107 (RTT107). It is involved in binding phosphorylated histone H2A.
Pfam PF06244: Coiled-coil domain-containing protein 124 /Oxs1 (family)
Oxs1 (oxidative stress transcription corepressor Oxs1) and Pap1 form a complex to regulate transcription when cells are exposed to diamide or Cd that causes disulfide stress. In fission yeast such as S. pombe, heterologous Oxs1-like proteins can enhance diamide stress tolerance. Furthermore, human and arabidopsis Oxs1 can interchangeably bind Pap1 or Pap1 homologues from human (cJun) and arabidopsis (bZIP10), suggesting that Oxs1 may be a component of an evolutionarily-conserved stress response pathway. Family members found in human such as Ccdc124 (Coiled-Coil Domain Containing Protein 124), were identified as a novel component of the centrosome during interphase and G2/M transition and is involved in cytokinesis.
Pfam PF23317: Calcium channel YVC1-like, C-terminal (domain)
This domain is found at the C-terminal of Calcium channel YVC1 from Saccharomyces cerevisiae, a transient receptor potential (TRP) channel required for release of calcium ions from the vacuole in response to hyperosmotic shock. This domain adopts an all-alpha configuration. It is often found associated with [pfam:PF23190].
Pfam PF16246: Domain of unknown function (DUF4903) (family)
A small family of uncharacterized proteins around 210 residues in length and found in various Bacteroides and Prevotella species. The function of this family is unknown.
Pfam PF22710: Short NACHT-associated C-Terminal domain, family 1 (domain)
The SNaCT domains are a rapidly evolving, monophyletic assemblage of domains found C-terminal to the NACHT module in several bacterial NACHT conflict systems. They contain a well-conserved aspartate near the N-terminus of the domain. SNaCT domains are thought to occlude the NTP-binding region, potentially until they interact with phage-encoded bNACHT inhibitors.
Pfam PF15687: Nuclear receptor-interacting protein 1 repression 1 (family)
This domain is the first (N-terminal) repression domain of nuclear receptor-interacting protein 1.
Wikipedia: Nuclear receptor-interacting protein 1 (NRIP1) also known as receptor-interacting protein 140 (RIP140) is a protein that in humans is encoded by the NRIP1 gene.
Pfam PF12289: Rotavirus VP1 C-terminal domain (domain)
This domain is the C-terminal bracelet domain of the rotavirus VP1 RNA-directed RNA polymerase. It surrounds the exit tunnel for dsRNA produced by replication and for the RNA template for transcription.
Pfam PF11611: Domain of unknown function (DUF4352) (family)
Members of these family are putative lipoproteins that fall into the Antigen MPT63/MPB63 (immunoprotective extracellular protein) 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 PF22194: F-93, winged-helix domain (domain)
This entry represents a WH-like domain (PDB: 1tbx) found in a putative transcription factor called F-93 from Sulfolobus spindle-shaped viruses (SSVs) ([swissprot:P20222]). Members of this family appear to be related to MarR ([pfam:PF01047]) and PadR ([pfam:PF03551]) families of prokaryotic transcription factors.
Pfam PF21514: FimA-like major fimbrial subunit protein, C-terminal domain (domain)
This domain is found at the C-terminal end of FimA-like major fimbrial subunit protein from Bacteroides stercoris and similar proteins found predominately in bacteroidetes. It is normally found associated with [pfam:PF06321].
Pfam PF05644: Mitochondrial and peroxisomal fission factor Mff (family)
This protein has a role in mitochondrial and peroxisomal fission.
Pfam PF15691: Protein phosphatase 1 regulatory subunit 32 (family)
PPP1R32 is a family of eukaryotic proteins thought to be involved in the interactome of protein phosphatase-1.
Pfam PF13718: GNAT acetyltransferase 2 (family)
This domain has N-acetyltransferase activity. It has a GCN5-related N-acetyltransferase (GNAT) fold.
Pfam PF15580: Immunity protein 53 (family)
A predicted immunity protein with an alpha+beta fold and a conserved tryptophan, and WE and PGW motifs. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, usually containing a domain of the Ntox24 or Ntox10 families.
Pfam PF09110: HAND (domain)
The HAND domain adopts a secondary structure consisting of four alpha helices, three of which (H2, H3, H4) form an L-like configuration. Helix H2 runs antiparallel to helices H3 and H4, packing closely against helix H4, whilst helix H1 reposes in the concave surface formed by these three helices and runs perpendicular to them. The domain confers DNA and nucleosome binding properties to the protein.
Wikipedia: In molecular biology, the HAND domain is a protein domain which adopts a secondary structure consisting of four alpha helices, three of which form an L-like configuration. Helix H2 runs antiparallel to helices H3 and H4, packing closely against helix H4, whilst helix H1 reposes in the concave surface formed by these three helices and runs perpendicular to them. This domain confers DNA and nucleosome binding properties to the proteins in which it occurs. It is named the HAND domain because its 4-helical structure resembles an open hand.
Pfam PF09941: Uncharacterized conserved protein (DUF2173) (family)
This domain, found in various hypothetical prokaryotic 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 PF10996: Beta-Casp domain (domain)
The beta-CASP domain is found C terminal to the beta-lactamase domain in pre-mRNA 3'-end-processing endonuclease.  The active site of this enzyme is located at the interface of these two domains.
Pfam PF22789: Protein of unknown function (DUF4026) C-terminal (domain)
This domain is found in uncharacterised bacterial proteins. It is usually associated with [pfam:PF13218] and [pfam:PF10077] that flank this domain from N- and C-terminal ends, respectively. This domain is distantly related to SUFU-like domains.
Pfam PF19212: Coronavirus replicase NSP2, C-terminal (family)
This entry corresponds to a presumed domain found at the C-terminus of Coronavirus non-structural protein 2 (NSP2). NSP2 is encoded by ORF1a/1ab and proteolytically released from the pp1a/1ab polyprotein and its function is unclear. Viral-host protein interaction studies in SARS-CoV and SARS-CoV-2 found that this protein could interact with several host proteins, including prohibitin 1 (PHB1) and PHB2, which are implicated in a number of cellular functions, including cellular migration, differentiation and apoptosis. This presumed domain is found in two copies in some viral NSP2 proteins. This domain is found in both alpha and betacoronaviruses.
Pfam PF02615: Malate/L-lactate dehydrogenase (family)
This family consists of bacterial and archaeal Malate/L-lactate dehydrogenase. L-lactate dehydrogenase, [ec:1.1.1.27], catalyses the reaction (S)-lactate + NAD(+)  pyruvate + NADH. Malate dehydrogenase, [ec:1.1.1.37] and [ec:1.1.1.82], catalyses the reactions: (S)-malate + NAD(+)  oxaloacetate  + NADH, and (S)-malate + NADP(+)  oxaloacetate + NADPH respectively.
Pfam PF17461: Family of unknown function (DUF5423) (family)
This is a domain of unknown function found in Chlamydia. Family members have 4 predicted trans-membrane regions.
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 PF21035: Coiled-coil domain-containing protein 138, C-terminal domain (repeat)
This is the C-terminal domain of coiled-coil domain-containing protein 138 (CCDC138), which adopts an alpha-solenoid structure. CCDC138 function is not yet clear. However, it has been localised to basal bodies, suggesting to play a role in centrosomal and ciliary biology.
Pfam PF11299: Protein of unknown function (DUF3100) (family)
Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently no function is known.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF03932: CutC family (domain)
Copper homeostasis protein CutC was originally thought to be involved in copper tolerance in Escherichia coli, as mutation in the corresponding gene lead to an increased copper sensitivity. However, this phenotype has been later reported to depend on the levels of he mRNA-interfering complementary RNA regulator MicL, which is transcribed from a promoter located within the coding sequence of the cutC gene in enterobacteria. In the plant pathogen Xylella fastidiosa, this protein has been reported as specific for copper efflux. The structure of this protein in the bacteria Shigella flexneri showed a monomer structure that adopts a common TIM beta/alpha barrel with eight beta strands surrounded by eight alpha-helices. The human homologue of this protein, whose structure showed a potential copper-binding site, has an important role in intracellular copper homeostasis.
Pfam PF20681: Domain of unknown function (DUF6818) (domain)
This presumed domain is functionally uncharacterised. It is found in proteins from eukaryotes, and is typically between 39 and 76 amino acids in length. There are  several conserved motifs, Y/FxN, KF and KPTG and a highly conserved W residue at the N-terminal. Structural predictions indicate this domain may fold into three alpha helices.
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 PF03989: DNA gyrase C-terminal domain, beta-propeller (repeat)
This repeat is found as 6 tandem copies at the C-termini of GyrA and ParC DNA gyrases. It is predicted to form 4 beta strands and to probably form a  beta-propeller structure. This region has been shown to bind DNA non-specifically and may stabilise the DNA-topoisomerase complex.
Pfam PF19952: Domain of unknown function (DUF6414) (domain)
This entry represents a family of uncharacterised proteins found in bacteria. These proteins share a conserved beta barrel domain with extensive variable insertions. The N and C-terminus of these proteins are the most conserved regions and interact with each other.
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 PF04041: beta-1,4-mannooligosaccharide phosphorylase (repeat)
This is a family of glycosyl-hydrolases of the CAZy GH130 family. Several have been characterised as mannosylglucose phosphorylase. This enzyme is part of the mannan catalytic pathway and feeds into the glycolysis cycle. Specifically it catalyses the reversible phosphorolysis of beta-1,4-D-mannosyl-N-acetyl-D-glucosamine. This family was noted to belong to the Beta fructosidase superfamily in.
Pfam PF16435: Domain of unknown function (DUF5032) (family)
This family consists of several uncharacterized proteins around 270 in length and is mainly found in various Bacteroides and Parabacteroides species. The function of this family 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 PF07270: Protein of unknown function (DUF1438) (family)
This family consists of several hypothetical proteins of around 170 residues in length which appear to be mouse specific. The function of this family 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 PF07643: Protein of unknown function (DUF1598) (family)
A family of Rhodopirellula baltica hypothetical proteins of 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 PF19304: D-3-phosphoglycerate dehydrogenase intervening domain (domain)
This domain is found in the D-3-phosphoglycerate dehydrogenase enzyme. In the structure of the Mycobacterium tuberculosis enzyme this domain was described as the intervening domain, also known as the allosteric substrate binding domain (ASB). The intervening domain between the substrate-binding and regulatory domains is not present in E. coli PGDH. This domain is closely related to [pfam:PF03315]. It serves as an anion-binding site and may function as an allosteric site for the control of enzyme activity.
Pfam PF13974: YebO-like protein (domain)
This short protein is uncharacterized. It seems likely to be of phage origin as it is found in [swissprot:Q9MCU2] and [swissprot:Q9MCS4]. The protein is also found in a variety of enteric bacteria.
Pfam PF21393: Decoration protein pb10 N-terminal domain (domain)
Bacteriophage capsids constitute icosahedral shells of exceptional stability that protect the viral genome. Many capsids display on their surface decoration proteins whose structure and function remain largely unknown. The decoration protein pb10 of phage T5 binds at the centre of the 120 hexamers formed by the major capsid protein. Pb10 consists of an N-terminal alpha-helical capsid-binding domain (this entry) and an Ig-like domain.
Pfam PF20638: Autophagy protein ATG5, UblA domain (domain)
This is the N-terminal ubiquitin-like domain, termed UblA, from autophagy protein ATG5. ATG5 comprises two ubiquitin-like domains (UblA and UblB) that flank a helix-rich domain (HBR). Both UblA and UblB comprise a five-stranded sheet and two-helices.
Pfam PF17472: Family of unknown function (DUF5425) (family)
This is a family of unknown function found in Borreliella burgdorferi.
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 PF05950: Orthopoxvirus A36R protein (family)
This family consists of several Orthopoxvirus A36R proteins. The A36R protein is predicted to be a type Ib membrane protein.
Pfam PF02867: Ribonucleotide reductase, barrel domain (family)
Ribonucleotide reductase (RNR, 1.17.4.1)  catalyses the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs divide into three classes on the basis of their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, bacteriophage and viruses, use a diiron-tyrosyl radical, Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in anaerobic bacteria and bacteriophage, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes.

Ribonucleotide reductase is an oligomeric enzyme composed of a large subunit (700 to 1000 residues) and a small subunit (300 to 400 residues) - class II RNRs are less complex, using the small molecule B12 in place of the small chain .

The reduction of ribonucleotides to deoxyribonucleotides involves the transfer of free radicals, the function of each metallocofactor is to generate an active site thiyl radical. This thiyl radical then initiates the nucleotide reduction process by hydrogen atom abstraction from the ribonucleotide . The radical-based reaction involves five cysteines: two of these are located at adjacent anti-parallel strands in a new type of ten-stranded Î±/Î²-barrel; two others reside at the carboxyl end in a flexible arm; and the fifth, in a loop in the centre of the barrel, is positioned to initiate the radical reaction . There are several regions of similarity in the sequence of the large chain of prokaryotes, eukaryotes and viruses spread across 3 domains: an N-terminal domain common to the mammalian and bacterial enzymes; a C-terminal domain common to the mammalian and viral ribonucleotide reductases; and a central domain common to all three .
This entry represents the C-terminal region of the large (alpha) subunit of RNRs from all domains in life.
Wikipedia: Ribonucleotide reductase (RNR), also known as ribonucleoside diphosphate reductase, is an enzyme that catalyzes the formation of deoxyribonucleotides from ribonucleotides. It catalyzes this formation by removing the 2'-hydroxyl group of the ribose ring of nucleoside diphosphates. This reduction produces deoxyribonucleotides. Deoxyribonucleotides in turn are used in the synthesis of DNA. The reaction catalyzed by RNR is strictly conserved in all living organisms. Furthermore, RNR plays a critical role in regulating the total rate of DNA synthesis so that DNA to cell mass is maintained at a constant ratio during cell division and DNA repair. A somewhat unusual feature of the RNR enzyme is that it catalyzes a reaction that proceeds via a free radical mechanism of action. The substrates for RNR are ADP, GDP, CDP and UDP. dTDP is synthesized by another enzyme from dTMP.
Pfam PF01693: Ribonuclease H1 N-terminal domain (domain)
This domain is found at the N-terminal of ribonuclease H1 from human, its fungal orthologues and in various caulimovirus viroplasmin proteins. This domain consists of three-stranded antiparallel beta-sheet and two short alpha-helices that pack onto opposite faces of the beta-sheet and is structurally similar to ribosomal protein L9 which binds to 23 S ribosomal RNA. RNase H1 belong to the family of ribonuclease H enzymes that recognise RNA:DNA hybrids and degrade the RNA component. The viroplasmin protein is encoded by gene VI and is the main component of viral inclusion bodies or viroplasms. Inclusions are the site of viral assembly, DNA synthesis and accumulation. Two domains exist within gene VI corresponding approximately to the 5' third and middle third of gene VI, these influence systemic infection in a light-dependent manner.
Pfam PF09686: Plasmid protein of unknown function (Plasmid_RAQPRD) (family)
This entry identifies a family of proteins, which are about 100 amino acids in length, including a predicted signal sequence and a perfectly conserved motif RAQPRD towards the C terminus. Members are found in the Pseudomonas putida TOL plasmid pWW0 and in cryptic plasmid regions of Salmonella enterica subsp. enterica serovar Typhi and Pseudomonas syringae DC3000. The function of these proteins are unknown.
Pfam PF04311: Protein of unknown function (DUF459) (family)
Putative periplasmic protein.
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.