SII-SWORD/CoKE huggingface dataset:
Pfam PF07235: Protein of unknown function (DUF1427) (family)
This family consists of several bacterial proteins of around 100 residues in length. 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 PF15883: Domain of unknown function (DUF4736) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in insects. Proteins in this family are typically between 186 and 228 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 PF21957: Zinc beta-ribbon finger, putative (family)
This domain is about 60 amino acids in length and is found N-terminal to [pfam:PF19898] that resembles a DNA primase core domain. This domain has remote similarity to the zinc-ribbon domain of DNA primase and it is predicted to adopt the same structure. It has four nearly invariant Cys residues, two of which located in unusual conserved motif VGRCxxxxxCGYH.
Pfam PF15364: PAXIP1-associated-protein-1 C term PTIP binding protein (family)
This protein domain family is the C-terminal domain of PAXIP1-associated-protein-1, which also goes by the name PTIP-associated protein 1. This family of proteins is found in eukaryotes. The function of this protein is to localise at the site of DNA damage and form foci with PTIP at the DNA break point. Furthermore, studies have shown that depletion of PA1 increases cellular sensitivity to ionizing radiation. Proteins in this family are typically between 122 and 254 amino acids in length.
Pfam PF09169: BRCA2, helical (domain)
Members of this family adopt a helical structure, consisting of a four-helix cluster core (alpha 1, alpha 8, alpha 9, alpha 10) and two successive beta-hairpins (beta 1 to beta 4). An approx. 50-amino acid segment that contains four short helices (alpha 2 to alpha 4), meanders around the surface of the core structure. In BRCA2, the alpha 9 and alpha 10 helices pack with BRCA-2_OB1 ([pfam:PF09103]) through van der Waals contacts involving hydrophobic and aromatic residues, and also through side-chain and backbone hydrogen bonds. The domain binds the 70-amino acid DSS1 (deleted in split-hand/split foot syndrome) protein, which was originally identified as one of three genes that map to a 1.5-Mb locus deleted in an inherited developmental malformation syndrome.
Wikipedia: BRCA2 and BRCA2 are human genes and their protein products, respectively. The official symbol and the official name are maintained by the HUGO Gene Nomenclature Committee. One alternative symbol, FANCD1, recognizes its association with the FANC protein complex. Orthologs, styled Brca2 and Brca2, are common in other vertebrate species. BRCA2 is a human tumor suppressor gene, found in all humans; its protein, also called by the synonym breast cancer type 2 susceptibility protein, is responsible for repairing DNA.
Pfam PF08317: Spc7 kinetochore protein (coiled_coil)
This domain is found in cell division proteins which are required for kinetochore-spindle association.
Pfam PF11007: Spore coat associated protein JA (CotJA) (family)
CotJA is part of the CotJ operon which contains CotJA and CotJC. The operon encodes spore coat proteins. Interaction of CotJA with CotJC is required for the assembly of both CotJA and CotJC into the spore coat.
Pfam PF05570: Circovirus protein of unknown function (DUF765) (family)
This family consists of several short (27-30aa) porcine and bovine circovirus ORF6 proteins of unknown function.
Pfam PF19727: Family of unknown function (DUF6219) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001575) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide). It  includes a member from the dipeptide aldehydes biosynthetic gene  cluster from Ruminococcus sp. 5_1_39BFAA. This family appears to be predominantly found in bacteria.
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 PF08883: Dopa 4,5-dioxygenase family (domain)
This family of proteins are related to [swissprot:P87064] a DOPA 4,5-dioxygenase that is involved in synthesis of betalain. DOPA-dioxygenase is the key enzyme involved in betalain biosynthesis. It converts 3,4-dihydroxyphenylalanine to betalamic acid, a yellow chromophore.
Pfam PF16635: Unstructured region on APC between SAMP and APC_crr (disordered)
APC_u14 is a short region of natively unstructured sequence lying between the second SAMP [pfam:PF05924], and the fifth creatine-rich region, APC_crr, [pfam:PF05923], on APC or adenomatous polyposis coli proteins in higher eukaryotes. The function is not known.
Pfam PF12252: SidE phosphodiesterase (PDE) domain (domain)
This entry represents the phosphodiesterase (PDE) domain found in the bacterial ubiquitinating enzymes, which belong to the SidE family. This domain catalyses the conjugation of ADP-ribosylated ubiquitin (ADPR-Ub), previously synthesised by the mono-ADP-ribosyltransferase (mART) domain, to a serine residue on substrates to generate a protein-phosphoribosyl-Ub (PR-Ub) product. These pathogen proteins are secreted bacterial effector proteins, which are translocated inside the host cell using the Dot/Icm secretion system. The SidE family of enzymes carry out ubiquitination of host cell proteins in an E1/E2-independent manner.
Pfam PF22564: HAAS (domain)
This entry represents the HAAS (HTH-associated alpha-helical signaling) domain, found N-terminal to DUF1700 ([pfam:PF08006]) which represents the transmembrane segment (Preprint https://doi.org/10.1101/2020.09.24.301986).
Pfam PF02024: Leptin (domain)
Leptin, a metabolic monitor of food intake and energy need, is expressed by the ob obesity gene. The protein may function as part of a signalling pathway from adipose tissue that acts to regulate the size of the body fat depot , the hormone effectively turning the brain's appetite message off when it senses that the body is satiated. Obese humans have high levels of the protein, suggesting a similarity to type II (adult onset) diabetes, in which sufferers over-produce insulin, but can't respond to it metabolically - they have become insulin resistant. Similarly, it is thought that obese individuals may be leptin resistant.
Wikipedia: Leptin, also known as obese protein, is a protein hormone predominantly made by adipocytes. Its primary role is likely to regulate long-term energy balance.
Pfam PF20760: Thermus phage P23-45 gp39, N-terminal domain (domain)
This domain is found at the N terminus in the protein gp35 from Thermus phage P23-45 and similar sequences from tailed bacteriophages. This protein binds the host's DNA-dependent RNA polymerase (RNAP), inhibiting host gene transcription while allowing transcription of phage genes. Structural studies show this core domain of the protein binds to the RNA beta-flap domain. It consists of a central beta sheet and a N-terminal helix.
Pfam PF20985: Legumain, prodomain (domain)
This domain is found in the proenzyme form of Vacuolar-processing enzyme (VPE), known as legumain. VPE is an asparagine-specific endopeptidase that plays important roles in many physiological processes, including the maturation of toll-like receptors 3/7/9. The mature active form of VPE is generated by autoproteolytic maturation at acidic pH. In the three-dimensional structure of the proenzyme, this prodomain is located on top of the protease domain, blocking access to the active site. It shows an entirely alpha-helical fold, with an activation peptide and a region that assemblies into a death domain-like fold at its C-terminal end.
Pfam PF24224: Family of unknown function (DUF7440) (family)
This entry represents a protein family of unknown function found in various bacterial phage proteins. The family typically consists of proteins around 140-160 amino acids in length. It is found in phages that infect bacteria such as Salmonella, Escherichia, Shigella, and Dickeya. The function of this family remains unclear.  Some members of this family are annotated as uncharacterized or hypothetical proteins.  AlphaFold predictions suggest the proteins in this family contain two distinct domains, with a central domain composed of a three stranded beta sheet and a C-terminal small 3-helix bundle domain.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF16671: Actin cross-linking domain (domain)
This domain is found in Vibrio cholerae RtxA toxin and VgrG1 protein. This domain cross-links to G-actin leading to cytoskeletal changes.
Pfam PF21930: Gp138, beta helical trimerization domain (repeat)
This domain is found in Gp138 from Escherichia phage phi92 ([swissprot:I7HXF9]) and similar sequences found in tailed bacteriophages and prophages from proteobacteria. Gp138 forms an spike-shaped trimer with three highly intertwined chains. Each polypeptide has an oligonucleotide/oligosaccharide-binding (OB-fold) domain (Pfam: PF18352) and a long beta-helical C-terminal domain (this entry), which initiates the contact with the host cell membrane. The trimeric beta-helix is composed of three antiparallel beta-sheets, which swap three C-terminal beta-strands with each other around the threefold axis.
Pfam PF13654: LonB-like, AAA domain (domain)
This entry includes a wide variety of AAA domains, including some that have lost essential nucleotide binding residues in the P-loop. This domain is found in Lon proteases from archaea and bacteria.
Wikipedia: AAA proteins are a large group of protein family sharing a common conserved module of approximately 230 amino acid residues. This is a large, functionally diverse protein family belonging to the AAA+ protein superfamily of ring-shaped P-loop NTPases, which exert their activity through the energy-dependent remodeling or translocation of macromolecules.
Pfam PF02186: TFIIE beta subunit core domain (domain)
General transcription factor TFIIE consists of two subunits, TFIIE alpha [pfam:PF02002] and TFIIE beta. TFIIE beta has been found to bind to the region where the promoter starts to open to be single-stranded upon transcription initiation by RNA polymerase II. The structure of the DNA binding core region has been solved and has a winged helix fold.
Pfam PF04661: Poxvirus I3 ssDNA-binding protein (family)
The 34kDa protein encoded by the I3 gene of vaccinia virus, named Protein OPG079, is expressed at early and intermediate times post-infection and is phosphorylated on serine residues. I3 protein demonstrates a striking affinity for single-stranded, but not for double-stranded, DNA. Electrophoretic mobility shift assays indicate that numerous I3 molecules can bind to a template, reflecting the stoichiometric interaction of I3 with DNA. Sequence analysis reveals that a pattern of aromatic and charged amino acids common to many replicative single-stranded DNA binding proteins (SSBs) is conserved in I3 . This protein plays an essential role in viral DNA replication .
Pfam PF07910: Peptidase family C78 (family)
This family formerly known as DUF1671 has been shown to be a cysteine peptidase called (Ufm1)-specific protease.
Pfam PF24214: Putative phage head-tail joining protein (domain)
This entry represents a putative phage head to tail joining protein.
Pfam PF20414: Family of unknown function (DUF6698) (family)
This entry represents an uncharacterised family of fungal proteins.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF00386: C1q domain (domain)
C1q is  a subunit of the C1 enzyme complex that activates the serum complement system.
Wikipedia: The complement component 1q is a protein complex involved in the complement system, which is part of the innate immune system. C1q together with C1r and C1s form the C1 complex.
Pfam PF11304: Protein of unknown function (DUF3106) (family)
Some members in this family of proteins are annotated as transmembrane 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 PF00714: Interferon gamma (domain)
Interferon gamma (IFN-gamma) is produced by lymphocytes activated by specific antigens or mitogens. IFN-gamma shows antiviral activity and has important immunoregulatory functions. It is a potent activator of microphages and had antiproliferative effects on transformed cells. It can potentiate the antiviral and antitumor effects of the type I interferons.

The crystal structures of a number IFN-gamma proteins have been solved, including bovine interferon-gamma at 2.0-A  and human IFN-gamma at 2.9-A .
Wikipedia: Interferon gamma is a dimerized soluble cytokine that is the only member of the type II class of interferons. The existence of this interferon, which early in its history was known as immune interferon, was described by E. F. Wheelock as a product of human leukocytes stimulated with phytohemagglutinin, and by others as a product of antigen-stimulated lymphocytes. It was also shown to be produced in human lymphocytes. or tuberculin-sensitized mouse peritoneal lymphocytes challenged with Mantoux test (PPD); the resulting supernatants were shown to inhibit growth of vesicular stomatitis virus. Those reports also contained the basic observation underlying the now widely employed interferon gamma release assay used to test for tuberculosis. In humans, the IFNG protein is encoded by the IFNG gene.
Pfam PF17147: Pyruvate:ferredoxin oxidoreductase core domain II (domain)
PFOR_II is a core domain of the anaerobic enzyme pyruvate:ferredoxin oxidoreductase and is necessary for inter subunit contacts in conjunction with domains I and IV.
Pfam PF21543: Virulence regulatory factor CvfB, second domain (domain)
This domain is found in the virulence regulatory factor CvfB from Streptococcus pneumoniae and in similar proteins predominantly found in Firmicutes. CvfB is composed of three consecutive S1 RNA-binding domains and a winged-helix (WH) domain ([pfam:PF17783]). This entry represents the second S! domain, an RNA-binding module that adopts the typical S1 fold that consists of a five-stranded, antiparallel beta-sheet forming a beta-barrel.
Pfam PF21046: Rad26-like, C-terminal domain (domain)
This domain is found at the C-terminal end of Rad26 from Myceliophthora thermophila ([swissprot:G2QDY6]), a functional subunit of the Rad3-Rad26 complex that is responsible for bringing the kinase to sites of DNA damage. This domain consists of the last three helices in the structure. Together with the flexible C-terminal kinase-docking motif it plays a role in the binding of Rad3.
Pfam PF14953: Domain of unknown function (DUF4504) (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 253 and 329 amino acids in length. There are two conserved sequence motifs: LLGYP and SFS.
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 PF22982: ATP-dependent helicase HRQ1, winged helix domain (domain)
This domain is found in the homologues of ATP-dependent helicase HRQ1. HRQ1 is a helicase with 3'-5' helicase activity involved in genome stability. Hrq1 is able to unwind relatively long duplex DNA up to 120-bp and is significantly stimulated by a preexisting fork structure. This domain is predicted to form a globular structure with significant similarity to Winged helix HTH domains.
Pfam PF02831: gpW (family)
gpW is a 68 residue protein known to be present in  phage particles. Extracts of phage-infected cells lacking gpW contain DNA-filled heads, and active tails, but no infectious virions. gpW is required for the addition of gpFII to the head, which is, in turn, required for the attachment of tails. Since gpFII and tails are known to be attached at the connector, gpW is also likely to assemble at this site. The addition of gpW to filled heads increases the DNase resistance of the packaged DNA, suggesting that gpW either forms a plug at the connector to prevent ejection of the DNA, or binds directly to the DNA. The large number of positively charged residues in gpW (its calculated pI is 10.8) is consistent with a role in DNA interaction.
Pfam PF02397: Bacterial sugar transferase (domain)
This Pfam family represents a conserved region from a number of different bacterial sugar transferases, involved in diverse biosynthesis pathways.
Pfam PF23878: ELP1 TPR domain (repeat)
This entry represents the TPR domain found within the C-terminal dimerization domain of Elongator complex protein 1 (ELP1), from eukaryotes. Elongator is a conserved protein complex implicated in multiple processes including regulation of transcription, alpha-tubulin acetylation and tRNA modification. Mutations in the ELP1 gene have been shown to cause the neurodegenerative disease familial dysautonomia. The C-terminal dimerization domain consists of 28 alpha-helices organised in three domains: an elongated alpha-solenoid domain (helices 1 to 14); the TPR domain, formed by six double-helix repeats (helices 15 to 26) that act as an interface for protein dimerization; and a three-helix bundle, C-terminal cap (helices 26 to 28). ELP1 self-association contributes to its stability and is important for Elongator assembly. ELP1 is considered to function both as a scaffold, for Elongator complex ELP2 and ELP3 binding, and as a docking site for various factors that regulate Elongator activity. Also known as IKAP, ELP1 acts as a regulator of IkB kinase complex involved in proinflammatory cytokine signalling.
Pfam PF02217: Origin of replication binding protein (domain)
This domain of large T antigen binds to the SV40 origin of DNA replication.
Pfam PF23784: Smacovirus capsid protein (family)
This entry represents the capsid protein of smacoviruses, a family of small, circular single-stranded DNA viruses. The capsid protein is typically around 300-400 amino acids in length. Smacoviruses have been identified in the fecal matter of a variety of mammals, including humans, non-human primates, pigs, and other domestic and wild animals. The viruses are currently not known to be associated with any disease.
Pfam PF07873: YabP family (family)
This family of proteins is involved in spore coat assembly during the process of sporulation. Proteins in this family consist of five anti-parallel beta strands.
Pfam PF07471: Phage DNA packaging protein Nu1 (family)
Terminase, the DNA packaging enzyme of bacteriophage lambda, is a  heteromultimer composed of subunits Nu1 and A.  The smaller Nu1 terminase subunit has  a low-affinity ATPase stimulated by non-specific DNA.
Pfam PF14349: Motility related/secretion protein (family)
This domain is found repeated three times in the N-terminal half of the gliding motility-related SprA proteins. The role of this domain in motility is uncertain. It is also found in proteins required for secretion.
Pfam PF20276: C-terminal domain 1 of the ABC-three component (ABC-3C) systems (domain)
C-terminal domains (CTDs) of ABC-3C systems, contain distinct patterns of charged and polar residues and are not yet unifiable with known domains. These domains are found at the C-terminus of the effector component of the systems, which are upstream of the Middle Component and ABC ATPase components on the genome. Due to the typically large size of these CTDs relative to the actual effector and MC domains, the CTDs are predicted to serve as the platform on which the remaining two components assemble. Therewith, conformational changes transmitted by the ABC ATPase-mediated detection of invasive elements like DNA viruses would result in an unfurling and activation of the CTD-associated effector.
Pfam PF21250: Glycoside phosphorylase supersandwich domain (domain)
Glycoside phosphorylases catalyze the phosphorolysis of oligosaccharides into sugar phosphates. This domain is the second of four domains (nDom2) found in the L. phytofermentans SOGP (sophoro-oligosaccharide beta-1,2-gluco-phosphorylase). This domain shows structural similarity to nDom1.  The third domain is the catalytic GH94 domain.
Pfam PF18470: Cas9 alpha-helical lobe domain (domain)
This is an alpha-helical lobe domain found in Cas9 proteins. Cas9 enzymes adopt a bilobed architecture composed of a nuclease lobe containing juxtaposed RuvC and HNH nuclease domains and a variable alpha-helical lobe likely to be involved in nucleic acid binding. Amino acid residues located in both the nuclease and alpha-helical lobe clefts are highly conserved within type II-A Cas9 proteins.
Pfam PF16224: DOmain of unknown function (DUF4883) (family)
This family consists of several uncharacterized proteins around 160 residues in length and is mainly found in various Clostridium species. The function of this family is unknown.
Pfam PF12851: Oxygenase domain of the 2OGFeDO superfamily (domain)
A double-stranded beta helix (DSBH) fold domain of the 2-oxoglutarate (2OG)-Fe(II)-dependent dioxygenase (2OGFeDO) superfamily found in  various eukaryotes, bacteria and bacteriophages. Members of this  family catalyze nucleic acid modifications, such as thymidine hydroxylation during base J synthesis in kinetoplastids, and the conversion of 5 methyl-cytosine (5-mC) to 5-hydroxymethyl-cytosine  (hmC), or further oxidation to 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). Metazoan TET proteins contain a cysteine-rich region inserted into the core of the DSBH fold. Vertebrate TET proteins are oncogenes that are mutated in various  myeloid cancers. Fungal and algal versions of this family are  linked to a predicted transposase and show lineage-specific  expansions.
Pfam PF17093: Penicillin-binding protein N-terminus (family)
This domain occurs at the N-terminus of some penicillin-binding proteins in Caulobacter species.