SII-SWORD/CoKE huggingface dataset:
Pfam PF05949: Bacterial protein of unknown function (DUF881) (family)
This family consists of a series of hypothetical bacterial proteins. One of the family members [swissprot:Q45543] from Bacillus subtilis is thought to be involved in cell division and sporulation.
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 PF22697: SOS1/NGEF-like PH domain (domain)
This is a PH domain found in a diverse group of animal proteins such as Ephexin-1, SOS1 from human and related RhoGEFs.
Pfam PF05034: Methylaspartate ammonia-lyase N-terminus (family)
Methylaspartate ammonia-lyase [ec:4.3.1.2] catalyses the second step of fermentation of glutamate. It is a homodimer. This family represents the N-terminal region of Methylaspartate ammonia-lyase. This domain is structurally related to [pfam:PF03952]. This domain is associated with the catalytic domain [pfam:PF07476].
Pfam PF13959: ATP-dependent rRNA helicase SPB4-like, C-terminal extension (domain)
This short domain is found at the C-terminus of many helicase proteins, including ATP-dependent rRNA helicase SPB4 from Saccharomyces cerevisiae, which is involved in the biogenesis of 60S ribosomal subunits. SPB4 is organised into four domains: dual RecA domains ([pfam:PF00270] and [pfam:PF00271]), a C-terminal extension (CTE, represented by this entry) and a C-terminal tail ([pfam:PF23681]). This domain packs closely onto the catalytic core and engages the four nucleotides immediately 5' to those within the RNA binding pocket. It shows a mainly alpha- helical structure.
Pfam PF18323: Cop9 signalosome subunit 5 C-terminal domain (domain)
The COP9 (Constitutive photomorphogenesis 9) signalosome (CSN), a large multiprotein complex that resembles the 19S lid of the 26S proteasome, plays a central role in the regulation of the E3-cullin RING ubiquitin ligases (CRLs). The catalytic activity of the CSN complex is carried by subunit 5 (CSN5), also known as c-Jun activation domain-binding protein-1 (Jab1). This entry is the C-terminal domain found in CSN5 proteins. CSN5, whose two C-terminal helices form an antiparallel hairpin, inserts its final C-terminal helix (helix II) into the central CSN6 framework at the core of the bundle. Deletion of the C-terminal helices has a pronounced effect on CSN integrity.
Pfam PF08186: Wound-inducible basic protein family (family)
This family consists of the wound-inducible basic proteins  from plants. The metabolic activities of plants are  dramatically altered upon mechanical injury or pathogen  attack. A large number of proteins accumulates at wound or  infection sites, such as the wound-inducible basic proteins.  These proteins are small, 47 amino acids in length, has no  signal peptides and are hydrophilic and basic.
Pfam PF15445: acidic terminal segments, variant surface antigen of PfEMP1 (domain)
ATS is the intracellular and relatively conserved acidic terminal segment of the Plasmodium falciparum erythrocyte membrane protein-1 (PfEMP1). this domain appears to be present in all variants of the highly polymorphic PfEMP1 proteins.
Wikipedia: Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) is a family of proteins present on the membrane surface of red blood cells that are infected by the malarial parasite Plasmodium falciparum. PfEMP1 is synthesized during the parasite's blood stage inside the RBC, during which the clinical symptoms of falciparum malaria are manifested. Acting as both an antigen and adhesion protein, it is thought to play a key role in the high level of virulence associated with P. falciparum. It was discovered in 1984 when it was reported that infected RBCs had unusually large-sized cell membrane proteins, and these proteins had antibody-binding (antigenic) properties. An elusive protein, its chemical structure and molecular properties were revealed only after a decade, in 1995. It is now established that there is not one but a large family of PfEMP1 proteins, genetically regulated (encoded) by a group of about 60 genes called var. Each P. falciparum is able to switch on and off specific var genes to produce a functionally different protein, thereby evading the host's immune system. RBCs carrying PfEMP1 on their surface stick to endothelial cells, which facilitates further binding with uninfected RBCs, ultimately helping the parasite to both spread to other RBCs as well as bringing about the fatal symptoms of P. falciparum malaria.
Pfam PF09776: Mitochondrial ribosomal protein L55 (family)
Members of this family are involved in mitochondrial biogenesis and G2/M phase cell cycle progression. They form a component of the mitochondrial ribosome large subunit (39S) which comprises a 16S rRNA and about 50 distinct proteins.
Pfam PF13271: Domain of unknown function (DUF4062) (family)
This presumed domain is functionally uncharacterised. This domain family is found in bacteria, archaea and eukaryotes, and is approximately 80 amino acids in length. There is a conserved SST sequence motif.
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 PF13797: Post-transcriptional regulator (family)
This family includes post-transcriptional regulators.
Pfam PF19859: Family of unknown function (DUF6333) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000274) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the  tetarimycin A biosynthetic gene cluster from uncultured bacterium.
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 PF19810: HFX_2341-like, N-terminal (domain)
This domain is found at the N-terminal of HFX_2341 from Haloferax mediterranei and similar archaeal proteins. HFX_2341 is a global regulator involved in cas gene regulation. This domain contains a conserved sequence motif HxxPxxG and a conserved asparagine residue. It is often found associated with [pfam:PF22665].
Pfam PF03271: EB1-like C-terminal motif (family)
This motif is found at the C-terminus of proteins that are related to the EB1 protein.  The EB1 proteins contain an N-terminal CH domain [pfam:PF00307]. The human EB1 protein was originally discovered as a protein interacting with the C-terminus of the APC protein. This interaction is often disrupted in colon cancer, due to deletions affecting the  APC C-terminus. Several EB1 orthologues are also included in this family.  The interaction between EB1 and APC has been shown to have a potent synergistic effect on microtubule polymerisation. Neither of EB1 or APC alone has this effect. It is thought that EB1 targets APC to the + ends of microtubules, where APC promotes microtubule polymerisation. This process is regulated by APC phosphorylation by Cdc2, which disrupts APC-EB1 binding. Human EB1 protein can functionally substitute for the yeast EB1 homologue Mal3. In addition, Mal3 can substitute for human EB1 in promoting microtubule polymerisation with APC.
Pfam PF08877: MepB-like (domain)
In Staphylococcus aureus MepB is encoded by the MepRAB operon. This operon has been shown to play a role in drug resistance and, although the functions of MepR and MapA are known, there is still little information regarding MepB's function. Structural studies have shown that this protein is structural similar to the PD-(D/E)XK family of endonucleases, although PD-(D/E)XK's catalytic active site residues are not conserved in MepB. MepB binds DNA and RNA, with a higher affinity for RNA and single stranded DNA than for double stranded DNA. The association of MepB with this drug resistance operon suggests that this protein is involved in antimicrobial response, role which is believed to be carried out through its interactions with nucleic acids.
Pfam PF22107: Pch2 N-terminal domain (domain)
Pch2/TRIP13 belongs to a family of proteins known as AAA-ATPases and via an adaptor protein binds to the closed form of MAD2. Pch2/TRIP13 then unfolds a part of the MAD2 protein, converting MAD2 into the open form. The C.elegans ortholog Pch2 forms a stable hexamer and its structure consists of a N-terminal domain and a AAA-ATPase module composed of two subdomains. This entry represents the N-terminal domain that consists of a four-stranded beta-sheet and an alpha-helix packed on it. The structure of this domain shows a clear relationship to the N-terminal substrate recognition domains of a AAA+ classic remodeller sub-family that includes NSF, p97, and PEX1.
Pfam PF22590: CRISPR-associated nuclease/helicase Cas3, C-terminal (domain)
This entry represents the C-terminal domain of CRISPR-associated nuclease/helicase Cas3 subtype I-F/YPEST from Pseudomonas aeruginosa (Cas3), a DNA-degradation enzyme that forms part of the CRISPR-Cas bacterial immune system. Cas3 contains a Cas2 domain, an HD nuclease domain ([pfam:PF18019]), RecA1, RecA2, a long linker region, and a C-terminal domain (this entry). This domain contains two alpha-helices and two six-stranded beta-blades.
Pfam PF23473: LYK4/5 LysM3 domain (domain)
This entry represents the third LysM domain found in proteins from plants, including LYK4/5 from Arabidopsis thaliana. The LysM domain adopt a beta-alpha-alpha-beta fold, according to structure predictions. LYK4 is a chitin-binding protein and contributes to chitin-triggered immunity. LYK5 has been identified as a receptor with a very high affinity to chitooligosaccharides.
Pfam PF09938: Uncharacterized protein conserved in bacteria (DUF2170) (family)
This domain, found in various hypothetical prokaryotic proteins, has no known function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF23138: Armc9, CTLH-like domain (domain)
This entry represents a domain that is found C-terminal to LisH motif in Armc9 and related proteins. The human Armc9 protein is involved in ciliogenesis and it is required for appropriate acetylation and polyglutamylation of ciliary microtubules, and regulation of cilium length. This domain is distantly related to the CTLH/CRA domain ([pfam:PF10607]) found in proteins components of ubiquitin-protein ligase complex.
Pfam PF10859: Protein of unknown function (DUF2660) (family)
This is a family of proteins with unknown 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 PF08146: BP28CT (NUC211) domain (domain)
This C terminal domain is found in BAP28-like nucleolar proteins.
Pfam PF12376: Protein of unknown function (DUF3654) (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 193 and 612 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 PF19292: Phosphorylase b kinase C-terminal domain (domain)
This entry represents the C-terminal domain found in Phosphorylase b kinase regulatory alpha and beta subunits, which control the catalytic activity of the Phosphorylase kinase catalytic gamma subunit. this domain has been proposed as the second calcineurin B-like (CBL-2) domain containing a gamma subunit-binding site.
Pfam PF20614: Homologues of viral RNAse III, found in viruses infecting fungi (domain)
This domain is found in viruses infecting fungi (mycoviruses), either as a standalone domain in short proteins (e.g. in deltaflexiviruses), or in polyproteins (e.g. endornaviruses or hypoviruses). It is homologous to RNAse III domains ([pfam:PF14622], [pfam:PF00636], [pfam:PF11469]) as seen using sequence-based searches. Its function is unknown.
Pfam PF06663: Connector enhancer of kinase suppressor of ras 2/3 domain (domain)
This family represents a conserved region of unknown function within Connector enhancer of kinase suppressor of ras 2 (CNK2, also known MAGUIN), Connector enhancer of kinase suppressor of ras 3 (CNK3) and CNK3/IPCEF1 fusion protein. This region is situated between the PDZ [pfam:PF00595] and PH [pfam:PF00169] domains in CNK2 and CNK3/IPCEF1, and after the PDZ domain in CNK3. All family members also contain an N-terminal [pfam:PF00536] domain. CNK2 is predominantly expressed in neural tissues, being critical for postsynaptic density morphology, implicated in X-linked intellectual disability (ID). CNK2 was first described as a regulator of Ras/MAPK signalling that lead to further studies concluding that it act as a scaffold for multiple signal cascades. It is able to direct the localisation of regulatory proteins within the cell and influences the behaviour of important regulatory molecules. CNK3 regulates aldosterone-induced and epithelial sodium channel (ENaC)-mediated sodium transport through regulation of ENaC cell surface expression, acting as a scaffold protein that coordinates the assembly of an ENaC-regulatory complex (ERC). CNK3/IPCEF1 is required for hepatocyte growth factor (HGF)-dependent activation of Arf6 and HGF-stimulated cell migration.
Pfam PF16555: Gram-positive pilin subunit D1, N-terminal domain (domain)
GramPos_pilinD1 is the first subunit domain of Gram-positive pilins from Strep.pneumoniae. There are three major pilin subunits that form the polymeric backbone of the pilin from S. pneumoniae, constructed of three Ig-like, CnaB, domains along with a crucial N-terminal domain, D1. The three IG-like domains are stabilised by internal Lys-Asn isopeptide bonds, but this N-terminal domain makes few contact with the rest of the molecule due to the different orientation of its G beta-strand. Strand G of D1 also carries the YPKN motif that provides the essential Lys residue for the sortase-mediated intermolecular linkages along the pilus shaft.  Gram-positive pili are formed from a single chain of covalently linked subunit proteins (pilins), usually comprising an adhesin at the distal tip, a major pilin that forms the polymer shaft and a minor pilin that mediates cell wall anchoring at the base.
Pfam PF01318: Bromovirus coat protein (domain)
This family consists of Bromovirus coat proteins. RNA-protein interactions stabilise many viruses and also the nucleoprotein cores of enveloped animal viruses (e.g. retroviruses). The nucleoprotein particles are frequently pleomorphic and generally unstable due to the lack of strong protein-protein interactions in their capsids.

The structure is known for Cowpea chlorotic mottle virus (CCMV) . It shows novel quaternary structure interactions based on interwoven carboxyterminal polypeptides that extend from canonical capsid Î²-barrel subunits. Additional particle stability is provided by intercapsomere contacts between metal ion mediated carboxyl cages and by protein interactions with regions of ordered RNA.
Pfam PF21345: PcRGLX-like protein central beta sandwich domain (domain)
This family of proteins includes Exo-rhamnogalacturonan lyase from Penicillium chrysogenum 31B (PcRGLX). The family also includes YetA from B. subtilis is functionally uncharacterised. This family of proteins is found in Actinobacteria, Firmicutes, Proteobacteria and fungi. Proteins in this family are typically between 863 and 928 amino acids in length.  This entry represents the central beta-sandwich domain. Members of this family share a 3 domain architecture.
Pfam PF03916: Polysulphide reductase, NrfD (family)
NrfD is an integral transmembrane protein with loops in both the periplasm and the cytoplasm.  NrfD is thought to participate in the transfer of electrons, from the quinone pool into the terminal  components of the Nrf pathway.
Wikipedia: Polysulfide reductase (NrfD) is an integral transmembrane protein with loops in both the periplasm and the cytoplasm. NrfD is thought to participate in the transfer of electrons, from the quinone pool into the terminal components of the Nrf pathway.
Pfam PF21519: Tailspike protein, C-terminal (domain)
Tailspike protein from Shigella phage Sf6 specifically mediates the attachment to their hosts. Its structure revealed a conserved architecture with a central, right-handed beta-helix. The C-terminal domain adopts a beta-sandwich fold, is represented in this entry, and is reminiscent of viral capsid proteins.
Pfam PF21478: Glycine dehydrogenase, C-terminal domain (domain)
This entry includes Glycine dehydrogenases, also known as glycine cleavage system P protein, which bind the alpha-amino group of glycine through its pyridoxal phosphate cofactor; CO2 is released and the remaining methylamine moiety is then transferred to the lipoamide cofactor of the H protein. The monomer consists of two domains, a large domain and a small domain. This entry represents the small domain, which has a complex alpha/beta structure.
Pfam PF07638: ECF sigma factor (family)
These proteins are probably RNA polymerase sigma factors belonging to the extra-cytoplasmic function (ECF) subfamily and show sequence similarity to [pfam:PF04542] and [pfam:PF04545].
Pfam PF23537: Apicomplexa microprotein (family)
This protein family includes uncharacterised microproteins encoded by small open reading frames (smORFs) from apicomplexa, including [swissprot:A7AXD5] from the parasite Babesia bovis.
Pfam PF08059: SEP domain (domain)
The SEP domain is named after Saccharomyces cerevisiae Shp1, Drosophila melanogaster eyes closed gene (eyc), and vertebrate p47.  In p47, the SEP domain has been shown to bind to and inhibit the cysteine protease cathepsin L.  Most SEP domains are succeeded closely by a UBX domain.
Pfam PF23568: E3 ubiquitin-protein ligase LIN-like, ARM repeat (repeat)
This region is found in a group of plant proteins, including soybean E3 ubiquitin-protein ligase LIN. It is predicted to fold into ARM-like repeats.
Pfam PF10058: ER junction formation factor lunapark, zinc ribbon finger (family)
This zinc ribbon domain is found in Endoplasmic reticulum junction formation protein (LNP1) and other related eukaryotic proteins. LNP1 plays a role in endoplasmic reticulum  (ER) network formation. It binds to the reticulons and Yop1p and resides at ER tubule junctions in both yeast and mammalian cells. Lnp1 dimerises in vitro via this zinc finger domain and this is required for proper ER structure but not for the nuclear pore complex (NPC) integrity. The latter role is determined by the interactions with other ER components, including Rtn1, Yop1, Pom33, and Per33.
Pfam PF22252: N-glycanase peptide, N-terminal domain (domain)
This domain is found at the N-terminal end of N-glycanase peptide from Elizabethkingia meningoseptica (PNGase F-II) and other bacterial sequences mainly found in flavobacteriales. This is often found associated with [pfam:PF09112] and [pfam:PF09113].
Pfam PF04646: Protein of unknown function, DUF604 (family)
This family includes a conserved region found in several uncharacterised plant 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 PF20399: PH domain (domain)
This entry represents a PH domain found in a variety of fungal proteins.
Wikipedia: Pleckstrin homology domain or (PHIP) is a protein domain of approximately 120 amino acids that occurs in a wide range of proteins involved in intracellular signaling or as constituents of the cytoskeleton.
Pfam PF08614: Autophagy protein 16 (ATG16) (coiled_coil)
Autophagy is a ubiquitous intracellular degradation system for eukaryotic cells.                                During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. ATG16 (also known as Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate in the yeast autophagy pathway.
Pfam PF17715: Family of unknown function (DUF5560) (family)
This is a family of unknown function found in primates.
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 PF20775: Tag1 N-terminal domain (domain)
This entry represents the N-terminal domain of Tag1. Tag1 is a vacuolar membrane protein involved in termination of autophagy. It regulates autophagy termination during persistent nitrogen starvation through Atg1p-mediated re-phosphorylation of Atg13p and PAS disassembly. It shows homology to LEA-2 domain, and together with TMEM106B from humans and Vac7 from yeast, are all predicted to be lipid transfer proteins. Tag1 has 3 tandemly repeated LEA-2 domains.
Pfam PF20829: Anti-CRISPR protein Acr30-35/AcrF1 (family)
Pseudomonas phages have diverse anti-CRISPR (Acr) proteins that subvert the immune systems in their hosts. These systems depend on a  CRISPR RNA (crRNA)-guided surveillance complex (Csy) for the degradation of foreign DNA. This family represents AcrF1, which inhibits DNA recognition of the Csy complex by interfering with base pairing between the DNA target strand and crRNA spacer. AcrF1 can use different mechanisms to block target DNA recognition.
Pfam PF00846: Hantavirus nucleocapsid protein (family)
Hantaviruses are ssRNA negative-strand viruses. The nucleocapsid protein is an internal protein of the virus particle .