SII-SWORD/CoKE huggingface dataset:
Pfam PF16969: RNA-binding signal recognition particle 68 (family)
SRP68 is a family that is part of the SRP or signal recognition particle complex. This complex, consisting of six proteins and a 7SL-RNA is necessary for guiding the emerging proteins designed for the membrane towards the translocation pore. SRP68 forms a stable heterodimer with SRP72, a protein with a TPR repeat. Specific RNA-binding of SRP68 is mediated by the N-terminal domain of approximately 200 residues of this family.
Pfam PF08734: GYD domain (domain)
This protein is found in a range of bacteria.  It is usually less than 100 amino acids in length. The function of the protein is unknown.  It may belong to the dimeric alpha/beta barrel superfamily.
Pfam PF15981: Envelope glycoprotein GP 5 of equine arteritis virus (family)
EAV_GP5 is a domain family found in equine arteritis virus envelope. It is approximately 80 amino acids in length and is found in association with [pfam:PF00951].
Pfam PF04097: Nup93/Nic96 (repeat)
Nup93/Nic96 is a component of the nuclear pore complex.  It is required for the correct assembly of the nuclear pore complex.  In Saccharomyces cerevisiae, Nic96 has been shown to be involved in the distribution and cellular concentration of the GTPase Gsp1. The structure of Nic96 has revealed a mostly alpha helical structure.
Pfam PF20563: Family of unknown function (DUF6773) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 151 and 172 amino acids in length. This family has a conserved sequence motif DER and two conserved residues, a Tyr and a Gly.
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 PF03465: eRF1 domain 3 (domain)
The release factor eRF1 terminates protein biosynthesis by recognising stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known. The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase centre. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site. This family also includes other proteins for which the precise molecular function is unknown.  Many of them are from Archaebacteria. These proteins may also be involved in translation termination but this awaits experimental verification.
Pfam PF23457: NFP LysM2 domain (domain)
This entry represents the second LysM domain found in proteins from plants, including the NFP from Medicago truncatula. The LysM domain adopt a beta-alpha-alpha-beta fold, according to structure predictions and. NFP/NFR5 class of receptors are crucial for initial lipochitooligosaccharide (LCO) perception and essential for LCO-mediated root nodule symbiosis. The NFP LysM2 domain, and L154 in particular, are crucial for the entry step of rhizobia, suggesting that NFP is involved in specific NF recognition for infection.
Pfam PF10481: Cenp-F N-terminal domain (coiled_coil)
Mitosin or centromere-associated protein-F (Cenp-F) is found bound across the centromere as one of the proteins of the outer layer of the kinetochore. Most of the kinetochore/centromere functions appear to depend upon binding of the C-terminal par to f the molecule, whereas the N-terminal part, here, may be a cytoplasmic player in controlling the function of microtubules and dynein.
Pfam PF04645: Protein of unknown function, DUF603 (family)
This family includes several uncharacterised proteins from Borrelia species.
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 PF14289: Domain of unknown function (DUF4369) (family)
This domain family is found in bacteria, and is approximately 110 amino acids in length. The family is found in association with [pfam:PF00578]. LPAM signal peptide sequence is found in some family members.
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 PF20412: RALGAPB N-terminal domain (domain)
This putative domain is found at the N-terminus of the Ral GTPase-activating protein beta subunit. The function of this region is not 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 PF22575: Virilizer, yeast (repeat)
This entry includes virilizer (Vir1p), the yeast homologue of human virilizer (VIRMA). It is a component of the MIS complex, a complex that mediates N6-methyladenosine (m6A) methylation of meiotic mRNAs and is required for initiation of meiosis, progression through the meiotic divisions and sporulation. In the complex, it plays a scaffolding role, stabilizing the other complex members.
Pfam PF20891: Domain of unknown function (DUF6844) (domain)
This domain is found in proteins predominantly found in Gammaproteobacteria such as Hypothetical protein FTT_1539c from Francisella tularensis. It is located in the centre of the proteins included in this entry.
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 PF11020: Domain of unknown function (DUF2610) (domain)
This family is conserved in Proteobacteria. One member is annotated as being elongation factor P but this could not be confirmed. This domain is related to the Ribbon-helix-helix superfamily so may be a DNA-binding 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.
Pfam PF17019: Domain of unknown function (DUF5096) (family)
This is a family of microsporidial sequences of unknown function. There is a well conserved Asp residue towards the C-terminus which may be functional.
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 PF05641: Agenet domain (domain)
This domain is related to the TUDOR domain [pfam:PF00567]. The function of the agenet domain is unknown. This family now matches both the two Agenet domains in the FMR proteins.
Pfam PF02643: Uncharacterized ACR, COG1430 (family)
Two structures have been solved for members of this large (>500 members) family of bacterial proteins present mostly in environmental bacteria and metagenomes (distant homologues are also present in several Plasmodium species).  TOPSAN analysis for pdb:3pjy shows that there is much similarity with the other solved structure, pdb:3m7a, solved for UniProt:Q2GA55 (Saro_0823), a homologue of Thermotoga maritima TM1668, UniProt:Q9X1Z6., The homologue in Caulobacter crescentus (CC1388), UniProt:Q9A8G6, is associated with CspD, a cold shock protein (CC1387), UniProt:Q9A8G7. However, the genomic context of UniProt:Q2GA55 is most conserved with a putative xylose isomerase, suggesting a possible role in extracellular sugar processing. Saro_0821, UniProt:Q2GA57, is annotated as an AMP-dependent synthetase and ligase. PDB:3m7a structure corresponds to the C-terminal (27-165) fragment of the YP_496102 (Saro_0823) protein and it is structurally unique, as the best hits from Dali have a Z-score of 3.8 (1nt0, 2j1t, 3kq4) and it is thus a likely candidate for a new fold. Interestingly, many of the top Dali hits are involved in sugar metabolism. There are no obvious active site-like cavities on the protein surface of 3m7a (http://www.topsan.org/Proteins/JCSG/).
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 PF03728: Viral DNA-binding protein, zinc binding domain (domain)
This family represents the zinc binding domain of the viral DNA- binding protein, a multi functional protein involved in DNA replication and transcription control.  Two copies of this domain  are found at the C-terminus of many members of the family.
Pfam PF17144: Ribosomal large subunit proteins 60S L5, and 50S L18 (family)
This family contains the large 60S ribosomal L5 proteins from Eukaryota and the 50S L18 proteins from Archaea. It has been shown that the amino terminal 93 amino acids of [swissprot:P09895] are necessary and sufficient to bind 5S rRNA in vitro, suggesting that the entire family has a function in rRNA binding.
Pfam PF24055: DNA polymerase delta catalytic subunit-like, N-terminal domain (domain)
This domain is found towards the N-terminal of DNA polymerase delta catalytic subunit from Saccharomyces cerevisiae (POL3) and similar eukaryotic protein sequences. POL3 is the catalytic component of DNA polymerase delta (DNA polymerase III), which participates in chromosomal DNA replication. This domain shows an alpha-beta configuration.
Pfam PF16887: Domain of unknown function (DUF5081) (family)
This protein is believed to be involved in the type VII secretion system.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF11741: AMIN domain (family)
This N-terminal domain of various bacterial protein families is crucial for the targetting of periplasmic or extracellular proteins to specific regions of the bacterial envelope. AMIN is derived from the N-terminal domain of AmiC, an N-acetylmuramoyl-l-alanine amidase of Escherichia coli which localises to the septal ring during division and plays a key role in the separation of daughter cells.  The AMIN domain is present in several protein families besides amidases suggesting that AMIN may represent a general targetting determinant involved in the localisation of periplasmic protein complexes.
Pfam PF21839: Domain of unknown function (DUF6898) (domain)
This entry represents a small protein that has a domain with a structure resembling a double stranded RNA-binding domain such as [pfam:PF00035]. Thus suggesting this protein may also have a dsRNA binding function. This is supported by the presence of several conserved positively charged residues.
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 PF06039: Malate:quinone oxidoreductase (Mqo) (family)
This family consists of several bacterial Malate:quinone oxidoreductase (Mqo) proteins ([ec:1.1.99.16]). Mqo takes part in the citric acid cycle. It oxidises L-malate to oxaloacetate and donates electrons to ubiquinone-1 and other artificial acceptors or, via the electron transfer chain, to oxygen. NAD is not an acceptor and the natural direct acceptor for the enzyme is most likely a quinone. The enzyme is therefore called malate:quinone oxidoreductase, abbreviated to Mqo. Mqo is a peripheral membrane protein and can be released from the membrane by addition of chelators.
Pfam PF08881: CVNH domain (domain)
CyanoVirin-N Homology domains are found in the sugar-binding antiviral protein cyanovirin-N (CVN) as well as filamentous ascomycetes and in the fern Ceratopteris richardii.
Wikipedia: In molecular biology, the CVNH domain is a conserved protein domain. It is found in the sugar-binding antiviral protein cyanovirin-N (CVN) as well as proteins from filamentous ascomycetes and in the fern Ceratopteris richardii.
Pfam PF10320: Serpentine type 7TM GPCR chemoreceptor Srsx (family)
Chemoreception is mediated in Caenorhabditis elegans by members of the seven-transmembrane G-protein-coupled receptor class (7TM GPCRs) of proteins which are of the serpentine type. Srsx is a solo family amongst the superfamilies of chemoreceptors. Chemoperception is one of the central senses of soil nematodes like C. elegans which are otherwise 'blind' and 'deaf'.
Pfam PF10772: Bacteriophage HP1, Orf24 (family)
This family is represented by Bacteriophage HP1, Orf24, whose function is unknown. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Pfam PF08526: Protein-arginine deiminase (PAD) N-terminal domain (domain)
This family represents the N-terminal non-catalytic domain of protein-arginine deiminase. This domain has a cupredoxin-like fold.
Pfam PF24332: Family of unknown function (DUF7500) (family)
This entry represents a family of uncharacterised archaeal proteins. They contain three highly conserved negatively charged (aspartate and glutamate) residues.
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 PF10474: Syndetin, C-terminal (repeat)
The function of this domain is unknown but it is found at the C terminus of syndetin (VPS50), a unique component of the endosome-associated retrograde protein (EARP) complex. The EARP complex otherwise shares four of its five subunits with the Golgi-associated retrograde protein (GARP) complex. The EARP complex is localised to recycling to endosomes where it acts as a tethering complex for recycling of plasma membrane receptors.
Pfam PF13857: Ankyrin repeats (many copies) (repeat)
The ankyrin repeat is one of the most common protein-protein interaction motifs in nature. Ankyrin repeats are tandemly repeated modules of about 33 amino acids. They occur in a large number of functionally diverse proteins mainly from eukaryotes. The few known examples from prokaryotes and viruses may be the result of horizontal gene transfers. The repeat has been found in proteins of diverse function such as transcriptional initiators, cell-cycle regulators , cytoskeletal, ion transporters and signal transducers . The ankyrin fold appears to be defined by its structure rather than its function since there is no specific sequence or structure which is universally recognised by it.

The conserved fold of the ankyrin repeat unit is known from several crystal and solution structures . Each repeat folds into a helix-loop-helix structure with a Î²-hairpin/loop region projecting out from the helices at a 90oangle. The repeats stack together to form an L-shaped structure .
Wikipedia: The ankyrin repeat is a 33-residue motif in proteins consisting of two alpha helices separated by loops, first discovered in signaling proteins in yeast Cdc10 and Drosophila Notch. Domains consisting of ankyrin tandem repeats mediate protein–protein interactions and are among the most common structural motifs in known proteins. They appear in bacterial, archaeal, and eukaryotic proteins, but are far more common in eukaryotes. Ankyrin repeat proteins, though absent in most viruses, are common among poxviruses. Most proteins that contain the motif have four to six repeats, although its namesake ankyrin contains 24, and the largest known number of repeats is 34, predicted in a protein expressed by Giardia lamblia.
Pfam PF21402: NLR family member X1, C-terminal domain (domain)
This domain is found at the C-terminal end of NLR family member X1 from humans (NLRX1) and similar proteins from vertebrates. NLRX1 is both a proinflammatory activator that stimulates the production of reactive oxygen species (ROS) via TNFalpha activation and is able to down-regulate inflammatory responses through interaction with the mitochondrial antiviral signaling adaptor and TRAF6-IKK. This domain is organised into a three subdomains: an N-terminal helical domain, a central LRR motifs and a C-terminal three-helix bundle. The interaction of this domain with RNA ligands plays a key role in NLRX1-mediated ROS activation.
Pfam PF17289: Terminase RNaseH-like domain (domain)
This entry represents the C-terminal domain found in the terminase large subunits. Terminase is a component of the molecular motor that translocates genomic DNA into empty capsids during DNA packaging . The large subunit heterodimerises with the small terminase protein, which is docked on the capsid portal protein. The latter forms a ring through which genomic DNA is translocated into the capsid. The terminase protein has endonuclease activity to cleave DNA after encapsidation .

Proteins containing this domain include gp17 from bacteriophage T4 (P17312).
Pfam PF18941: Family of unknown function (DUF5688) (family)
This is a family of unknown function 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 PF21001: Inner membrane protein YqiJ, N-terminal (domain)
This entry represents a presumed helical domain found at the N-terminal of several bacterial proteins, including the inner membrane protein YqiJ from E. coli, whose function is not clear.
Pfam PF18151: Domain of unknown function (DUF5601) (domain)
This domain is found in the catalytic core RABEX-5 present in Homo sapiens. RABEX, also known as Rab GTPase exchange factors, regulate endocytic trafficking through activation of the Rab families RAB5, RAB21 and RAB22. The domain is helical in nature.
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 PF10741: Type II secretion system (T2SS), protein M subtype b (family)
The T2SMb family is conserved in Proteobacteria and Actinobacteria, and differs from the T2SM proteins in Vibrio spp. ([pfam:PF04612]).
Pfam PF14917: Coiled coil protein 74, C terminal (coiled_coil)
This is a C-terminal conserved domain of coiled-coil proteins from vertebrates. The function is not known. Expression levels in humans are elevated in breast cancer [].
Pfam PF20438: Stage IV sporulation protein A, middle domain (domain)
This is the structural middle domain of Stage IV sporulation protein A (SpoIVA) which follows the ATPase domain and the predicted secondary structure suggests that it is composed of two symmetrical units containing alpha-helices and beta-strands. SpoIVA acts in the mother cell compartment and plays a role in spore coat morphogenesis. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species.
Pfam PF12186: Acyl-CoA dehydrogenase C terminal (domain)
This domain family is found in bacteria, and is approximately 110 amino acids in length. The family is found in association with [pfam:PF02770], [pfam:PF00441], [pfam:PF02771]. There is a conserved ARRL sequence motif. The C terminal domain is an alpha helical domain. The flavin ring of Acyl-CoA dehydrogenase is buried in the crevice between the two alpha helical domains and the beta-sheet domain of one subunit, and the adenosine pyrophosphate moiety is stretched into the subunit junction of a neighbouring subunit, composed of two C terminal domains.
Pfam PF04340: Protein of unknown function, DUF484 (family)
This family consists of several proteins of uncharacterised 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 PF08732: HIM1 (family)
HIM1 (high induction of mutagenesis protein 1) plays a role in the control of spontaneous and induced mutagenesis.  It is thought to participate in the control of processing of mutational intermediates appearing during error-prone bypass of DNA damage.
Pfam PF14632: Acidic N-terminal SPT6 (family)
The N-terminus of SPT6 is highly acidic. The full SPT6 protein is a transcription regulator, but the exact function of this acidic region is not certain.