SII-SWORD/CoKE huggingface dataset:
Pfam PF12299: Protein of unknown function (DUF3627) (family)
This domain family is found in bacteria and viruses, and is approximately 90 amino acids in length. The family is found in association with [pfam:PF02498].
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 PF22383: AVR-Pik-like, HMA interaction domain (domain)
This entry represents the HMA interaction domain of AVR-Pik, an effector protein from the rice blast fungus Pyricularia oryzae which binds and stabilizes rice HMA-domain containing NLR proteins to co-opt their function to suppress immunity. AVR-Pik adopts a six-stranded beta-sandwich structure.
Pfam PF20949: Influenza RNA polymerase PB2 middle domain (domain)
Influenza virus encodes a large, multidomain RNA-dependent RNA polymerase that can both transcribe and replicate the viral RNA genome. In influenza virus, the polymerase is composed of three polypeptides: PB1, PB2 and PA/P3. PB1 houses the polymerase active site, whereas PB2 and PA/P3 contain, respectively, cap-binding and endonuclease domains required for transcription initiation by cap-snatching. This entry represents the middle domain in Flu PB2 protein.
Pfam PF02797: Chalcone and stilbene synthases, C-terminal domain (domain)
This domain of chalcone synthase is reported to be structurally similar to domains in thiolase and beta-ketoacyl synthase.   The differences in activity are accounted for by differences  in the N-terminal domain.
Wikipedia: Chalcone synthase or naringenin-chalcone synthase (CHS) is an enzyme ubiquitous to higher plants and belongs to a family of polyketide synthase enzymes (PKS) known as type III PKS. Type III PKSs are associated with the production of chalcones, a class of organic compounds found mainly in plants as natural defense mechanisms and as synthetic intermediates. CHS was the first type III PKS to be discovered. It is the first committed enzyme in flavonoid biosynthesis.
The enzyme catalyzes the conversion of 4-coumaroyl-CoA and malonyl-CoA to naringenin chalcone.
Pfam PF00630: Filamin/ABP280 repeat (domain)
The many different actin cross-linking proteins share a common architecture, consisting of a globular actin-binding domain and an extended rod. Whereas their actin-binding domains consist of two calponin homology domains (see IPR001715), their rods fall into three families.

The rod domain of the family including the Dictyostelium discoideum (Slime mould) gelation factor (ABP120) and human filamin (ABP280). It is constructed from tandem repeats of a 100-residue motif that is glycine and proline rich . The gelation factor's rod contains 6 copies of the repeat, whereas filamin has a rod constructed from 24 repeats. The resolution of the 3D structure of rod repeats from the gelation factor has shown that they consist of a Î²-sandwich, formed by two Î²-sheets arranged in an immunoglobulin-like fold . The repeat structure is common to the members of the gelation factor/filamin family.

This entry represents the entire filamin/ABP280 repeat.
Pfam PF18482: Fungal Pih1 CS domain (domain)
The Pih1 protein is part of the R2TP complex. The CS domain of Pih1 binds to the unstructured region of Tah1. The C-terminal domain of Pih1 consists of a seven-stranded beta sandwich with the topology of a CS domain, a structural motif also found in Hsp90 cochaperones such as p23/Sba1 and Sgt1.
Pfam PF05540: Serpulina hyodysenteriae variable surface protein (family)
This family consists of several variable surface proteins from Serpulina hyodysenteriae.
Pfam PF13739: Deacetylase PdaC (domain)
This domain forms an alpha-beta-two layer sandwich. It is found in the Bacillus subtilis proteins anti-sigma-V factor RsiV, which downregulates SigV activity, and peptidoglycan-N-acetylmuramic acid deacetylase PdaC, which catalyzes the deacetylation of N-acetylmuramic acid which makes the peptidoglycan resistant to lysosyme. It is found in association with Heat-shock cognate 70kd protein 44kd ATPase, [pfam:PF11738].
Pfam PF21777: Short chain dehydrogenase-like protein (domain)
This family of uncharacterised proteins appear to be related to known short-chain dehydrogenase enzymes. They are rather short having a Rossmann fold domain which consists of only four beta-strands. Proteins in this family are primarily found in Proteobacteria.
Pfam PF25102: Family of unknown function (DUF7810) (family)
This entry represents uncharacterised plant proteins that share detectable similarity with members of the Glycosyl transferase clan GT-B.
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 PF10911: Bacteriophage T7-like gene 6.5 (family)
Members in this family of proteins are annotated as gene 6.5 protein, however, currently there is no known function.
Pfam PF23980: Putative phage tail tube initiator protein (family)
This entry represents a family of uncharacterised phage proteins. Based on structure prediction these proteins show similarity to the Pam3 gp17 the tail tube initiator protein. Six gp17 subunits form a hexameric ring that initiates tail tube polymerization from the baseplate.
Pfam PF13330: Mucin-2 protein WxxW repeating region (family)
This family is repeating region found on mucins 2 and 5. The function is not known, but the repeat can be present in up to 32 copies, as in [swissprot:C3Y5K5], from Branchiostoma floridae. The region carries a highly conserved WxxW sequence motif and also has at least six well conserved cysteine residues.
Pfam PF08520: Mitofissin (family)
This is a family of fungal proteins identified as mitochondrial fission factors (mitofissin, also referred to as Atg44) which are essential for mitophagy. Mitofissin directly binds to lipid membranes to drive mitochondrial fission required for mitophagy.
Pfam PF15862: Coilin N-terminus (family)
Coilin is a nuclear phosphoprotein that serves as an assembly centre in Cajal bodies (CBs) and has a role in small nuclear ribonucleoprotein (snRNP) biogenesis, involved in the modification and assembly of nucleoplasmic snRNPs . Coilin also acts to repress polymerase I activity in response to cisplatin-induced DNA damage, which could indicate a link between the DNA damage response and the inhibition of rRNA synthesis .
Conservation at the amino acid level is highest within coilin's N- and C-termini. The first N-terminal 92-amino acid domain have been shown to self-interact and to be essential for proper targeting of coilin to CBs .
Wikipedia: Coilin is a protein that in humans is encoded by the COIL gene. Coilin got its name from the coiled shape of the Cajal bodies in which it is found. It was first identified using human autoimmune serum.
Pfam PF15125: TMEM238 protein family (family)
The function of this family of transmembrane proteins, TMEM238; has not, as yet, been determined. Members of this family are as yet uncharacterised. This family of proteins is found in eukaryotes. Proteins in this family are typically between 61 and 153 amino acids in length.
Pfam PF03625: Domain of unknown function DUF302 (domain)
Domain is found in an undescribed set of proteins. Normally occurs uniquely within a sequence, but is found as a tandem repeat ([swissprot:Q9X8B8]). Shows interesting phylogenetic distribution with majority of examples in bacteria and archaea, but it is also found in some fungal proteins. The hypothetical protein TT1751 from Thermus thermophilus has a beta-alpha-beta(4)-alpha structural 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 PF17468: Phage gene product 52 (family)
This is a family of unknown function found in Mycobacterium phage.
Pfam PF22586: ANCHR-like B-box zinc-binding domain (domain)
This entry represents a B-box domain found in ANCHR, ZFYV1 and TRIM proteins, which is characterised by C6H2 zinc-binding consensus motif.
Pfam PF03700: Sorting nexin, N-terminal domain (family)
These proteins bins to the cytoplasmic domain of plasma membrane receptors. and are involved in endocytic protein trafficking. The N-terminal domain appears to be specific to sorting nexins 1 and 2.
Wikipedia: Sorting nexins are a large group of proteins that are localized in the cytoplasm and have the potential for membrane association either through their lipid-binding PX domain or through protein–protein interactions with membrane-associated protein complexes Some members of this family have been shown to facilitate protein sorting.
Pfam PF14401: RimK-like ATPgrasp N-terminal domain (family)
An uncharacterized alpha+beta fold domain that is mostly fused to a RimK-like ATP-grasp and is found in bacteria and euryarchaea. Members of this family are almost always associated in gene  neighborhoods with a GNAT-like acetyltransferase fused to a  papain-like petidase. Additionally M20-like peptidases, GCS2,  4Fe-4S Ferredoxins, a distinct metal-sulfur cluster protein and ribosomal proteins are found in the gene neighborhoods. Contextual analysis suggests a role for these in peptide biosynthesis.
Pfam PF13774: Regulated-SNARE-like domain (domain)
Longin is one of the approximately 26 components required for transporting proteins from the ER to the plasma membrane, via the Golgi apparatus. It is necessary for the steps of the transfer from the ER to the Golgi complex. Longins are the only R-SNAREs that are common to all eukaryotes, and they are characterised by a conserved N-terminal domain with a profilin-like fold called a longin domain.
Pfam PF13409: Glutathione S-transferase, N-terminal domain (domain)
This family is closely related to [pfam:PF02798].
Wikipedia: Glutathione S-transferases (GSTs), previously known as ligandins, are a family of eukaryotic and prokaryotic phase II metabolic isozymes best known for their ability to catalyze the conjugation of the reduced form of glutathione (GSH) to xenobiotic substrates for the purpose of detoxification. The GST family consists of three superfamilies: the cytosolic, mitochondrial, and microsomal—also known as MAPEG—proteins. Members of the GST superfamily are extremely diverse in amino acid sequence, and a large fraction of the sequences deposited in public databases are of unknown function. The Enzyme Function Initiative (EFI) is using GSTs as a model superfamily to identify new GST functions.
Pfam PF05192: MutS domain III (domain)
This domain is found in proteins of the MutS family (DNA mismatch repair proteins) and is found associated with [pfam:PF00488], [pfam:PF05188], [pfam:PF01624] and [pfam:PF05190]. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair; other members of the family included the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have various roles in DNA repair and recombination. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. The aligned region corresponds with domain III, which is central to the structure of Thermus aquaticus MutS as characterised in.
Pfam PF19169: Family of unknown function (DUF5851) (family)
This is a family of uncharacterised proteins of unknown function predominantly found in Mimiviridae.
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 PF00451: Scorpion short toxin, BmKK2 (domain)
Members of this family, which are found in various scorpion toxins, confer potassium channel blocking activity.
Wikipedia: Agitoxin is a toxin found in the venom of the scorpion Leiurus quinquestriatus hebraeus. Other toxins found in this species include charybdotoxin (CTX). CTX is a close homologue of Agitoxin.
Pfam PF11522: Yeast phosphatidylinositol-4-OH kinase Pik1 (family)
Pik1 is a regulator of membrane traffic and participates in the mating-pheromone signal-transduction cascade. The protein is localised to the nucleus and cytoplasm in the Golgi. Pik1 is thought to have an actin-independent role in membrane transport.
Pfam PF21482: GLD-3 2nd KH domain (aka KH3) (domain)
This KH domain is found in the C. elegans GLD-3 protein. GLD-3 is a protein required maternally for germline survival and embryogenesis. This domain is known as the KH3 domain based on a prior identification of five KH domains in the GLD-3 protein. However, based on recent structure predictions using AlphaFold is appears that the KH1 domain is not a KH domain at all. Therefore the 2nd KH domain is known as KH3. This is the second KH domain of the globular structure unit also formed by KH2, KH4 and KH5.
Pfam PF06850: PHB de-polymerase C-terminus (family)
This family represents the C-terminus of bacterial poly(3-hydroxybutyrate) (PHB) de-polymerase. This degrades PHB granules to oligomers and monomers of 3-hydroxy-butyric acid.
Pfam PF11423: Regulatory protein Mnt (family)
Mnt is a repressor which is involved in the genetic switch between lysogenic and lytic growth in bacteriophage P22. The C-terminal domain of the protein consists of a dimer of two antiparallel coiled coils with a right handed twist, which is both stronger and has closer inter-helical separation compared with those found in left-handed coiled coils.
Pfam PF19834: Family of unknown function (DUF6314) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 138 and 177 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 PF07595: Planctomycete extracellular (conserved_site)
This motif is conserved as the N terminus of several Rhodopirellula baltica proteins predicted to be extracellular.
Pfam PF18797: Adenomatous polyposis coli (APC) repeat (repeat)
Adenomatous polyposis coli contains an armadillo repeat and uses its highly conserved surface groove to recognize the APC-binding region (ABR) of Asef. This entry represents a single repeat unit of the  Armadillo region.
Pfam PF23552: ParB dimerisation domain (domain)
This entry represents the C-terminal dimerisation domain found in ParB proteins.  The ParB family proteins are key players in bacterial chromosome partitioning, a critical process for cell division and genetic material distribution. Members of the ParB family are involved in recognizing and binding to specific DNA sequences at the origin of replication. They localise to the cell poles after DNA replication is complete, ensuring proper segregation of chromosomes into daughter cells during cell division. These proteins may interact with other partitioning proteins and DNA sites to facilitate the orderly distribution of chromosomes.
Pfam PF23833: Family of unknown function (DUF7203) (family)
These proteins are found in various phages infecting bacteria from the Enterobacteriaceae family, such as Escherichia, Salmonella, Shigella, Klebsiella, and Yersinia. They are typically around 100 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 PF01490: Transmembrane amino acid transporter protein (domain)
This transmembrane region is found in many amino acid transporters  including UNC-47 and MTR. UNC-47 encodes a vesicular amino butyric acid (GABA) transporter, (VGAT). UNC-47 is predicted to have 10 transmembrane  domains [swissprot:P34579]. MTR is a N system amino acid transporter system protein involved in methyltryptophan resistance [swissprot:P38680]. Other members of this family include proline transporters and amino acid permeases.
Wikipedia: An amino acid transporter is a membrane transport protein that transports amino acids. They are mainly of the solute carrier family.
Pfam PF22687: BRCA2 TR2 domain (domain)
This domain is found near the C terminus of BRCA2 homologues. It is likely that the TR2 domain is largely disordered and does not fold into a globular structure. It contains a highly conserved proline-rich region which is preceded by a conserved stretch of positively charged residues. This domain is known to interact with meiosis-specific recombinase DMC1 and RAD51.
Pfam PF21720: MIOS, WD40 repeat (repeat)
GATOR complex protein MIOS, a component of the GATOR subcomplex GATOR2 which consists of MIOS, SEC13, SEH1L, WDR24 and WDR59, and it activates mTORC1 and the TORC1 signaling pathway through the inhibition of the GATOR1 subcomplex. Sea4 is the counterpart from yeast, a component of the SEA complex which coats the vacuolar membrane and is involved in intracellular trafficking, autophagy, response to nitrogen starvation, and amino acid biogenesis. This entry represents the N-terminal WD40 repeat domain of these proteins.
Pfam PF20577: Phage ORF5 protein (domain)
This family of proteins is found in bacteriophage such as Bacteriophage phiMH2K and Bacteriophage Chp1. Proteins in this family are typically between 81 and 96 amino acids in length. These proteins appear to have a role in phage packaging.
Pfam PF03437: BtpA family (family)
The BtpA protein is tightly associated with the thylakoid membranes, where it stabilises the reaction centre proteins of photosystem I.
Wikipedia: In molecular biology, the BtpA protein family is a family of proteins which includes BtpA. BtpA appears to play a role in the stabilisation of photosystem I. It is an extrinsic membrane protein located on the cytoplasmic side of the thylakoid membrane. Homologs of BtpA are found in the Thermoproteota and "Euryarchaeota", where their function remains unknown. The Ycf4 protein is firmly associated with the thylakoid membrane, presumably through a transmembrane domain. Ycf4 co-fractionates with a protein complex larger than PSI upon sucrose density gradient centrifugation of solubilised thylakoids. The Ycf3 protein is loosely associated with the thylakoid membrane and can be released from the membrane with sodium carbonate. This suggests that Ycf3 is not part of a stable complex and that it probably interacts transiently with its partners. Ycf3 contains a number of tetratricopeptide repeats (TPR); TPR is a structural motif present in a wide range of proteins, which mediates protein-protein interactions.
Pfam PF07522: DNA repair metallo-beta-lactamase (domain)
The metallo-beta-lactamase fold contains five sequence motifs. The first four motifs are found in [pfam:PF00753] and are common to all metallo-beta-lactamases.  The fifth motif appears to be specific to function.          This entry represents the fifth motif from metallo-beta-lactamases involved in DNA repair.
Pfam PF08072: BDHCT (NUC031) domain (domain)
This is a C-terminal domain in Bloom's syndrome DEAD helicase subfamily.
Pfam PF21884: Zuotin-like, zuotin homology domain (domain)
This domain is found in Zuotin from Saccharomyces cerevisiae (ZUO1) and in similar eukaryotic sequences. ZUO1 is a component of the ribosome-associated complex (RAC), a heterodimeric chaperone complex involved in regulation of accurate translation termination and in folding or maintaining nascent polypeptides in a folding-competent state. This entry represents its zuotin homology domain (ZHD), which is functionally important for association with ribosomes. It folds into four helices, including a three helix bundle. It is normally found C-terminal to [pfam:PF00226].
Pfam PF10203: Cytochrome c oxidase assembly protein PET191 (family)
Pet191_N is the conserved N-terminal of a family of conserved proteins found from nematodes to humans. It carries six highly conserved cysteine residues. Pet191 is required for the assembly of active cytochrome c oxidase but does not form part of the final assembled complex.
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 PF09855: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082) (family)
This domain, found in various hypothetical prokaryotic proteins, as well as some Zn-ribbon nucleic-acid-binding proteins has no known function.
Pfam PF23277: Deleted in lung and esophageal cancer protein 1 Ig domain (domain)
This domain is found in the human Deleted in lung and esophageal cancer protein 1 (Dlec1) and realted proteins. Dlec1 is essential for spermatogenesis and male fertility. This protein may play an important role in sperm head and tail formation. This domain is predicted to fold into a beta-sandwich with an Ig-like topology. It shares significant sequence similarity with Ig-like domains found in Cep192 and hydin.
Pfam PF07058: Microtubule-associated protein 70 (family)
This family represents a family of plant microtubule-associated proteins of size 70 kDa. The proteins contain four predicted coiled-coil domains, and truncation studies identify a central domain that targets the proteins to microtubules. It has no predicted trans-membrane domains, and the region between the coils from approximately residues 240-483 is the targetting region.
Pfam PF05114: RiPP precursor modification enzyme MbnB/TglH/ChrH (domain)
This entry represents a family of multinuclear iron-containing proteins which are post-translational modification enzymes involved in the biosynthesis of ribosomally synthesized and post-translationally modified peptide (RiPP) natural products, including the precursor modification enzymes MbnB, TglH, and ChrH, formerly known as DUF692.
Pfam PF21583: BAdV-4, Fiber, head domain (domain)
This domain is found at the C-terminal end of proteins from adenovirus, including Fiber from Bovine adenovirus 4 (BAdV-4), which is essential for host cell interaction. This domain shows a beta- sandwich with two four-stranded sheets and an alpha-helix in a loop.
Pfam PF08686: PLAC (protease and lacunin) domain (domain)
The PLAC (protease and lacunin) domain is a short six-cysteine region that is usually found at the C terminal of proteins.  It is found in a range of proteins including PACE4 (paired basic amino acid cleaving enzyme 4) and the extracellular matrix protein lacunin.
Pfam PF05924: SAMP Motif (conserved_site)
This short region is found repeated in the mid region of the adenomatous polyposis proteins (APCs). This motif binds axin.