SII-SWORD/CoKE huggingface dataset:
Pfam PF05172: Nup53/35/40-type RNA recognition motif (domain)
Members of this family belong to the nucleor pore complex, NPC, the only gateway between the nucleus and the cytoplasm. The NPC consists of several subcomplexes each one of which is made up of multiple copies of several individual Nup, Nic or Sec protein subunits. In yeast, this Nup or nucleoporin subunit is numbered Nup53, Nup40 in Schizo. pombe and in vertebrates as Nup35. This subunit forms part of the inner ring within the membrane and interacts directly with Nup-Ndc1, considered to be an anchor for the NPC in the pore membrane. This region of the Nup is the RNA-recognition region.
Pfam PF21983: Mobilization protein NikA (family)
This family includes homologs of mobilisation protein NikA as well as MobC, MobB and MobA. These proteins are involved in mobilisation and replication functions of plasmids. They are distantly related to accessory factor PcfF and likely adopt similar homo-dimeric structure consisting of N-terminal DNA-binding ribbon-helix-helix (RHH) domain and a C-terminal stalk domain.
Pfam PF00582: Universal stress protein family (domain)
The universal stress protein UspA [swissprot:P28242]  is a small cytoplasmic  bacterial protein whose expression  is enhanced when the cell is exposed to stress agents. UspA enhances the rate of cell survival during  prolonged exposure to such conditions, and may provide a general "stress endurance" activity.  The crystal structure of Haemophilus influenzae UspA reveals  an  alpha/beta fold similar to that of the Methanococcus jannaschii  MJ0577 protein, which binds ATP, though UspA lacks ATP-binding activity.
Wikipedia: The universal stress protein (USP) domain is a superfamily of conserved genes which can be found in bacteria, archaea, fungi, protozoa and plants. Proteins containing the domain are induced by many environmental stressors such as nutrient starvation, drought, extreme temperatures, high salinity, and the presence of uncouplers, antibiotics and metals.
Pfam PF07236: Phytoreovirus S7 protein (family)
This family consists of several Phytoreovirus S7 proteins which are thought to be viral core proteins.
Pfam PF11357: Cell cycle regulatory protein (family)
Speedy (Spy1) is a cell cycle regulatory protein which activates CDK2, the major kinase that allows progression through G1/S phase and further replication events. Spy1 expression overcomes a p27-induced cell cycle arrest to allow for DNA synthesis, so cell cycle progression occurs due to an interaction between Spy1 and p27. Spy1 is also known as Ringo protein A.
Pfam PF19208: Family of unknown function (DUF5880) (family)
This is a family of uncharacterised proteins of unknown function predominantly found in Phycodnaviridae. This family also includes uncharacterised proteins found in Archaea and Eukaryotes.
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 PF11690: Protein of unknown function (DUF3287) (family)
This eukaryotic family of proteins has no known function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF17527: Phage ALC protein (family)
During the course of infection of Escherichia coil by bacteriophage T4, transcription of viral late genes does not take place unless template DNA contains hydroxymethyl cytosine (hmCyt), a modification normally effected by virus-encoded enzymes. Bacteriophage T4 Alc protein acts as a site-specific termination factor participating in shutting off host transcription after infection of E. coli, while the bacteriophage T4 transcription is protected from the action of Alc by overall substitution of cytosine with 5-hydroxymethyl cytosine in T4 DNA. Based on genetic studies, Alc is thought to bind directly to the beta sub-unit dispensable region 1 (bDR1) of E.coli RNAP. However, immune-isolation experiments show that Alc binds both core and sigma 70-holoenzyme of RNAP.
Pfam PF14887: HMG (high mobility group) box 5 (family)
Nucleolar transcription factor/upstream binding factor contains six HMG box domains. This is the fifth HMG box domain in these proteins. This domain has lost DNA-binding ability.
Pfam PF16159: FOXP coiled-coil domain (domain)
This domain, approximately 60-70 residues in length, is  mainly found in Forkhead box proteins in various Mammalia  species. It is a coiled-coil domain, which modulates  the dimeric associations of FOXP transcription factors.  Several key disease mutations, for instance those found in  the IPEX syndrome are located in this domain
Pfam PF14797: Serine-rich region of AP3B1, clathrin-adaptor complex (disordered)
This short low-complexity, highly serine-rich region lies on clathrin-adaptor complex 3 beta-1 subunit proteins, between family Adaptin_N, [pfam:PF01602] and a C-terminal domain, AP3B1_C,[pfam:PF14796].
Pfam PF22224: Amylase-binding protein AbpA (domain)
Amylase binding streptococci only colonize hosts that produce amylase in their saliva. In Streptococcus gordonii, amylase binding is mediated by amylase-binding protein A (AbpA). This protein folds into an elongated structure that consists of two domains: an N-terminal helical domain and a small C-terminal alpha/beta domain consisting of a three-stranded beta-sheet packed with helix. The helical domain has shown to be responsible for the amylase binding while the C-terminal domain interacts with SrtB.
Pfam PF23879: Family of unknown function (DUF7232) (family)
This entry represents an uncharacterised phage family. A structure prediction suggests that the proteins consist of a three stranded beta meander followed by a C-terminal Alpha helix.
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 PF05997: Nucleolar protein,Nop52 (family)
Nop52 believed to be involved in the generation of 28S rRNA.
Pfam PF14916: Coiled-coil domain of unknown function (coiled_coil)
This domain family is found in eukaryotes, and is approximately 60 amino acids in length. The function is not known and the proteins carry no other domains.
Pfam PF08710: Coronavirus replicase NSP9 (domain)
Nsp9 is a single-stranded RNA-binding viral protein involved in RNA synthesis. Several crystallographic structures of nsp9 have shown that it is composed of seven beta strands and a single alpha helix. Nsp9 proteins have N-finger motifs and highly conserved GXXXG motifs that both play critical roles in dimerisation. The conserved helix-helix dimer interface containing a GXXXG protein-protein interaction motif is biologically relevant to SARS-CoV replication.
Pfam PF11662: Protein of unknown function (DUF3263) (family)
This family of proteins with unknown function appears to be restricted to Actinobacteria.
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 PF11225: Domain of unknown function (DUF3024) (domain)
This family of proteins has no known function. The proteins are composed of a compact alpha/beta fold with five beta strands and two alpha helices. STRING networks suggest this protein may play a role in nitrogen fixation.
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 PF03852: DNA mismatch endonuclease Vsr (family)
This entry represents VSR (very short patch repair) endonucleases occurring in a variety of bacteria and some archaeal species, including DNA mismatch endonuclease Vsr from Escherichia coli. VSR recognises a TG mismatched base pair, generated after spontaneous deamination of methylated cytosines, and cleaves the phosphate backbone on the 5' side of the thymine . GT mismatches can lead to C-to-T transition mutations if not repaired. VSR repairs the mismatches in favour of the G-containing strand. In Escherichia coli, this endonuclease nicks double-stranded DNA within the sequence CT(AT)GN or NT(AT)GG next to the thymidine residue, which is mismatched to 2'-deoxyguanosine . The incision is mismatch-dependent and strand specific. The structure of VSR is similar to the core structure of restriction endonucleases, which have a 3-layer Î±/Î²/Î± topology .
Wikipedia: Very short patch (VSP) repair is a DNA repair system that removes GT mismatches created by the deamination of 5-methylcytosine to thymine. This system exists because the glycosylases which normally target deaminated bases cannot target thymine.
Pfam PF22360: SbsC,spectrin-like repeat (domain)
This entry represents a Spectrin-like domain present in the bacterial S-layer protein SbsC from Geobacillus stearothermophilus. This  domain shows structural similarity to the Spectrin domain ([pfam:PF00435]).
Pfam PF08153: NGP1NT (NUC091) domain (domain)
This N terminal domain is found in a subfamily of hypothetical nucleolar GTP-binding proteins similar to human NGP1.
Pfam PF07071: KDGP aldolase (domain)
DgaF is part of the dga operon required for wild-type growth of Salmonella Typhimurium with D-glucosaminate. It catalyses the conversion of keto-3-deoxygluconate 6-phosphate (KDGP) to yield pyruvate and glyceraldehyde-3-phosphate. Orthologues of the dga genes are largely restricted to certain enteric bacteria and a few species in the phylum Firmicutes.
Pfam PF18449: Pesticidal crystal protein Cry1Aa, domain IV (domain)
This entry represents a domain is found in the protoxin portion of insecticidal proteins (parasporins, or Cry proteins) such as Cry1Aa from Bacillus thuringiensis (Bt) and related species. These proteins contain a proteolytically labile protoxin segment (in the C-terminal region) and a three-domain toxic core at the N terminus (domains I-III). This entry describes domain IV, one of the four protoxin domains (domains IV-VII). Domains IV and VI are alpha-helical bundles that resemble structural/interaction domains such as spectrin or bacterial fibrinogen-binding complement inhibitor. The structure of full length Cry1Aa is determined.
Wikipedia: Cry1Ac protoxin is a crystal protein produced by the gram-positive bacterium, Bacillus thuringiensis (Bt) during sporulation. Cry1Ac is one of the delta endotoxins produced by this bacterium which act as insecticides. Because of this, the genes for these have been introduced into commercially important crops by genetic engineering in order to confer pest resistance on those plants.
Pfam PF09403: Adhesion protein FadA (coiled_coil)
FadA (Fusobacterium adhesin A) is an adhesin which forms two alpha helices that form an intra-molecular coiled-coil arrangement.
Pfam PF01147: Crustacean CHH/MIH/GIH neurohormone family (family)
Arthropod express a family of neuropeptides  which so far consist of the following types of neurohormones:
 * Crustacean hyperglycemic hormone (CHH). CHH is primarily involved in blood sugar regulation, but also plays a role in the control of molting and reproduction.
 * Molt-inhibiting hormone (MIH). MIH inhibits Y-organs where molting hormone (ecdysteroid) is secreted. A molting cycle is initiated when MIH secretion diminishes or stops.
 * Gonad-inhibiting hormone (GIH), also known as vitellogenesis-inhibiting hormone (VIH) because of its role in inhibiting vitellogenesis in female animals.
 * Mandibular organ-inhibiting hormone (MOIH). MOIH represses the synthesis of methyl farnesoate, the precursor of insect juvenile hormone III in the mandibular organ.
 * Ion transport peptide (ITP) from locust. ITP stimulates salt and water reabsorption and inhibits acid secretion in the ileum of the locust.

These neurohormones are peptides of 70 to 80 residues which are processed from larger size precursors. They contain six conserved cysteines that are involved in disulphide bonds, as shown in the following schematic representation.
Alpha-latrotoxin associated low molecular weight proteins (LMWPs) are a family of uncharacterised venom peptides associated with alpha-latrotoxin, a black widow spider neurotoxin, which are probably also expressed in the venoms of other Latrodectus and Steatoda species .

This entry also includes proteins from Nematoda, such as Caenorhabditis elegans hypothetical protein ZC168.2.
Wikipedia: In molecular biology, the crustacean neurohormone family of proteins is a family of neuropeptides expressed by arthropods. The family includes the following types of neurohormones:Crustacean hyperglycaemic hormone (CHH). CHH is primarily involved in blood sugar regulation, but also plays a role in the control of moulting and reproduction.
Moult-inhibiting hormone (MIH). MIH inhibits Y-organs where moulting hormone (ecdysteroid) is secreted. A moulting cycle is initiated when MIH secretion diminishes or stops.
Gonad-inhibiting hormone (GIH), also known as vitellogenesis-inhibiting hormone (VIH) because of its role in inhibiting vitellogenesis in female animals.
Mandibular organ-inhibiting hormone (MOIH). MOIH represses the synthesis of methyl farnesoate, the precursor of insect juvenile hormone III in the mandibular organ.
Ion transport peptide (ITP) from locust. ITP stimulates salt and water reabsorption and inhibits acid secretion in the ileum of the locust.
Caenorhabditis elegans uncharacterised protein ZC168.2.
Pfam PF25076: FHL2/3 N-terminal LIM domain (domain)
This entry represents the N-terminal LIM domain of Four and a half LIM domains proteins 2/3 (FHL2/3) and related sequences. FHL3 is recruited by SOX15 to FOXK1 promoters where it acts as a transcriptional coactivator of FOXK1. FHL2 may function as a molecular transmitter linking various signaling pathways to transcriptional regulation. It inhibits the transcriptional activity of FOXO1 and its apoptotic function by enhancing the interaction of FOXO1 with SIRT1 and OXO1 deacetylation.
Pfam PF22948: MINAR1, N-terminal helical domain (domain)
This entry represents a N-terminal conserved domain found in the Major intrinsically disordered Notch2-binding receptor 1 (MINAR1) family. MINAR1 is a Notch2-binding protein that has been shown to inhibit angiogenesis and breast cancer growth.
Pfam PF12009: Telomerase ribonucleoprotein complex - RNA binding domain (domain)
Telomeres in most organisms are comprised of tandem simple sequence repeats. The total length of telomeric repeat sequence at each chromosome end is determined in a balance of sequence loss and sequence addition. One major influence on telomere length is the enzyme telomerase. It is a reverse transcriptase that adds these simple sequence repeats to chromosome ends by copying a template sequence within the RNA component of the enzyme. The RNA binding domain of telomerase - TRBD - is made up of twelve alpha helices and two short beta sheets. How telomerase and associated regulatory factors physically interact and function with each other to maintain appropriate telomere length is poorly understood. It is known however that TRBD is involved in formation of the holoenzyme (which performs the telomere extension) in addition to recognition and binding of RNA.
Pfam PF23195: Ubiquilin-1-like domain (domain)
This domain is found in human Ubiquilin-1 (UBQLN1) and similar eukaryotic sequences. UBQLN1 plays an important role in the regulation of different protein degradation mechanisms and pathways including ubiquitin-proteasome system (UPS), autophagy and endoplasmic reticulum-associate protein degradation (ERAD) pathway. This domain, often found associated to [pfam:PF00240] and [pfam:PF00627], is predicted to adopt an all-alpha helical structure.
Pfam PF16190: Ubiquitin-activating enzyme E1 FCCH domain (domain)
This domain is found in the ubiquitin-activating E1 family enzymes.
Pfam PF04648: Yeast mating factor alpha hormone (family)
The hormone is excreted into the culture medium by haploid cells of the alpha mating type and acts on cells of the opposite mating type (type A). It inhibits DNA synthesis in type A cells synchronising them with type alpha, and so mediates the conjugation process.
Pfam PF08930: Domain of unknown function (DUF1912) (domain)
This domain has no known function. It is found in various Streptococcal 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 PF10360: Protein of unknown function (DUF2433) (family)
This is a conserved 120 residue region of a family of proteins found in fungi. The function 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 PF16548: Flagellar assembly protein T, N-terminal domain (domain)
FlgT_N is the N-terminal domain of a family of flagellar proteins that make up part of the basal body of the flagellum. The flagellum is a large macromolecular assembly composed of three major parts: the basal body, the hook, and the filament. The basal body has two unique ring structures, the T ring and the H ring. FlgT is required to form and stabilise both ring structures. FlgT-N contributes to the construction of the H-ring structure, and adopts a two-layer alpha-beta sandwich architecture composed of a four-stranded anti-parallel beta-sheet and two alpha helices.
Pfam PF24690: NTCP5/P3 N-terminal domain (domain)
This entry represents the N-terminal domain of Sodium/bile acid cotransporter 5 (NTCP5) and protein P3 from animals, which may have bile acid:sodium symporter activity. This domain may adopt a beta-sandwich fold.
Pfam PF14006: YqzL-like protein (family)
The YqzL-like protein family includes the B. subtilis YqzL protein [swissprot:C0H452] which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 50 amino acids in length.
Pfam PF23088: Domain of unknown function (DUF7047) (domain)
This is a domain of unknown function mostly found in arthropods. This domain may adopt a three helical bundle fold. These sequences might be related to reverse transcriptase polymerases.
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 PF21788: TNP-like, GTP-binding insertion domain (domain)
This entry represents a GTP-binding insertion domain (GBD) from Transposable element P transposase from Drosophila and its human homologue, THAP9. This domain is inserted in the RNaseH domain and adopts a mostly alpha-helical fold, similar to that in Hermes, Tn5 or RAG1 proteins. This domain is involved in protein-DNA interactions.
Pfam PF16732: Type IV minor pilin ComP, DNA uptake sequence receptor (domain)
ComP-DUS is the DNA-uptake sequence receptor of pathogenic Proteobacteria. ComP is a type IV minor pilin -site on the minor type IV pilin, C one of three minor (low abundance) pilins in pathogenic Proteobacteria Neisseria species (with PilV and PilX). These modulate Tfp-mediated properties without affecting Tfp biogenesis. ComP plays a prominent role in competence at the level of DNA uptake. Comp is exposed on the surface of Neisseria filaments, and it is this that recognises homotypic DNA through genus-specific DNA uptake sequence (DUS) motifs.
Pfam PF19174: Family of unknown function (DUF5856) (family)
This is a family of uncharacterised proteins of unknown function predominantly found in viruses. This family was also 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 PF21078: Glutamate dehydrogenase, helical motif 3 (conserved_site)
Glutamate dehydrogenases (GDHs) are a broadly distributed group of enzymes that catalyse the reversible oxidative deamination of glutamate to ketoglutarate and ammonia. The structure of GDH from Mycobacterium smegmatis revealed that it has a long N- and C-terminal segments flanking the catalytic core, comprising several domains. The flexible N-terminal domain comprises ACT-like and PAS-type domains which could act as metabolic sensors for allosteric regulation. It also includes three helical motifs (HM1-3), HM3 is represented in this entry.
Pfam PF12822: ECF transporter, substrate-specific component (family)
Energy-coupling factor (ECF) transporters consist of a substrate-specific component (known as the S component),  and an energy-coupling module. The substrate-binding  component is a small integral membrane protein which  captures specific substrates and forms an active transporter  in the presence of the energy-coupling AT module.
Pfam PF19410: Family of unknown function (DUF5980) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000666) is described by MIBiG as an example of the following biosynthetic class, terpene.
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.