SII-SWORD/CoKE huggingface dataset:
Pfam PF11160: Hypervirulence associated proteins TUDOR domain (domain)
Family members include Cryptococcus neoformans HVA1 (hypervirulence-associated protein 1) whose absence is associated with a hypervirulent phenotype in mice. Metabolomics analysis suggests that when HVA1 is absent there is a block in the citric acid cycle, while structural analysis of the Hva1 protein suggests a potential interaction with NADPH. The structural architecture of Hva1 bears similarity with Tudor domains.
Wikipedia: In molecular biology, a Tudor domain is a conserved protein structural domain originally identified in the Tudor protein encoded in Drosophila. The Tudor gene was found in a Drosophila screen for maternal factors that regulate embryonic development or fertility. Mutations here are lethal for offspring, inspiring the name Tudor, as a reference to the Tudor King Henry VIII and the several miscarriages experienced by his wives.
Pfam PF11467: Lens epithelium-derived growth factor (LEDGF) (domain)
LEDGF is a chromatin-associated protein that protects cells from stress-induced apoptosis. It is the binding partner of HIV-1 integrase in human cells. The integrase binding domain (IBD) of LEDGF is a compact right-handed bundle composed of five alpha-helices. The residues essential for the interaction with the integrase are present in the inter-helical loop regions of the bundle structure.
Pfam PF22906: L-gulonolactone oxidase 2-like, C-terminal domain (domain)
This domain is found at the C-terminal end of L-gulonolactone oxidase 2 from Arabidopsis thaliana (GULLO2), which catalyses the oxidation of L-gulono-1,4-lactone to ascorbic acid. This short domain is predicted to contain a beta-hairpin and have structural similarity with omega toxins.
Pfam PF15855: Domain of unknown function (DUF4726) (family)
This family of proteins is found in vertebrates. Proteins in this family are typically between 40 and 110 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 PF24590: Domain of unknown function (DUF7615) (domain)
This domain is found in uncharacterised proteins mainly from plants. This domain is predicted to fold into an alpha-helical hairpin.
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 PF07499: RuvA, C-terminal domain (domain)
Homologous recombination is a crucial process  in all living organisms.  In bacteria, this process the RuvA, RuvB, and RuvC proteins are involved. More specifically the proteins process the Holliday junction DNA. RuvA is comprised of three distinct domains. The domain represents the C-terminal domain and plays a significant role in the ATP-dependent branch migration of the hetero-duplex  through direct contact with RuvB. Within the Holliday junction, the C-terminal domain  makes no interaction with DNA.
Pfam PF10766: Multidrug efflux pump-associated protein AcrZ (family)
AcrZ is associated with the AcrA-TolC multidrug efflux pump, it may enhance the ability of the pump to recognise and export certain substrates.
Pfam PF09527: Putative F0F1-ATPase subunit Ca2+/Mg2+ transporter (family)
This model represents a protein found encoded in F1F0-ATPase operons in several genomes, including Methanosarcina barkeri (archaeal) and Chlorobium tepidum (bacterial). It is a small protein (about 100 amino acids) with long hydrophobic stretches and is presumed to be a subunit of the enzyme. It carries two transmembrane helices and is a magnesium or calcium uniporter. The atp operon of alkaliphilic Bacillus pseudofirmus OF4, as in most prokaryotes, contains the eight structural genes for the F-ATPase (ATP synthase), which are preceded by an atpI gene that encodes a membrane protein with 2 TMSs. A tenth gene, atpZ, has been found in this operon, which is upstream of and overlapping with atpI.
Pfam PF10445: Protein of unknown function (DUF2456) (family)
This is a family of uncharacterised 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 PF14572: Phosphoribosyl synthetase-associated domain (domain)
This family includes several examples of enzymes from class [ec:2.7.6.1], phosphoribosyl-pyrophosphate transferase.
Wikipedia: Ribose-phosphate diphosphokinase is an enzyme that converts ribose 5-phosphate into phosphoribosyl pyrophosphate (PRPP). It is classified under EC 2.7.6.1.
Pfam PF16772: Telomeric repeat-binding factor 2 Rap1-binding motif (domain)
This domain, found in telomeric repeat-binding factor 2, binds to the C-terminus of repressor activator protein 1 (RAP1) (telomeric repeat-binding factor 2-interacting protein 1).
Pfam PF07402: Human herpesvirus U26 protein (family)
This family consists of several Human herpesvirus U26 proteins of around 300 residues in length. The function of this family is unknown.
Pfam PF01123: Staphylococcal/Streptococcal toxin, OB-fold domain (domain)
This entry represents an OB-fold domain found in enterotoxins.
Wikipedia: In the field of molecular biology, enterotoxin type B, also known as Staphylococcal enterotoxin B (SEB), is an enterotoxin produced by the gram-positive bacteria Staphylococcus aureus. It is a common cause of food poisoning, with severe diarrhea, nausea and intestinal cramping often starting within a few hours of ingestion. Being quite stable, the toxin may remain active even after the contaminating bacteria are killed. It can withstand boiling at 100 °C for a few minutes. Gastroenteritis occurs because SEB is a superantigen, causing the immune system to release a large amount of cytokines that lead to significant inflammation.
Pfam PF16614: Unstructured region two on RhoGEF 6 and 7 (disordered)
RhoGEF67_u2 is a region of natively unstructured residues on Rho guanine nucleotide exchange factor 6 and 7 proteins. The function is not known. It lies after the PH domain and before the C-terminal coiled-coil.
Pfam PF14192: Domain of unknown function (DUF4314) (family)
This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is typically between 56 and 93 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 PF23895: Phage zinc binding domain (domain)
This small domain is found in a variety of uncharacterised enterobacterial phage proteins. Structure prediction shows that it is likely zinc binding, with an N-terminal conserved CXXC motif and more central CXXXXC motif providing the zing binding residues.  The domain adopts a four stranded beta meander fold.
Pfam PF14763: Hermansky-Pudlak syndrome 3 protein, C-terminal region (repeat)
This domain found in the HPS3 protein is composed a an alpha solenoid repeat.  This region carries a number of tyrosine sorting motifs and the second of two di-leucine sorting boxes at residues 711-717 well as the ER membrane-retention signal KKPL at residues 1000-1003 in SwissProt:Q969F9. There is also reference to a human Mendelian disease at MIM:614072. Mutations in the gene that encode this protein causes Hermansky-Pudlak syndrome 3 (HPS3), a genetically heterogeneous autosomal recessive disorder characterised by oculocutaneous albinism, a bleeding diathesis due to the absence of platelet dense granules and lysosomal storage defects.
Pfam PF21340: Cip1-like, core domain (domain)
This domain is found in Cip1 from Hypocrea jecorina and similar sequences predominantly found in fungi. Cip1 is a cellulose induced protein with a carbohydrate binding module ([pfam:PF00734]) connected via a linker region to a domain with yet unknown function (this entry). This domain shows a beta- sandwich jelly-roll fold with two anti-parallel beta-sheets that consist on eight and seven strands and pack on top of one another. Structural analysis suggest it may function as a lyase.
Pfam PF14291: Domain of unknown function (DUF4371) (family)
This domain is found in animal and 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 PF22626: LysX preATP-grasp domain (domain)
This entry represents the preATP-grasp domain found at the N-terminal of archaeal LysX, ArgX and similar proteins. LysX catalyses the ATP-dependent formation of a covalent bond between the amino group of alpha-aminoadipate (AAA) and the gamma-carboxyl group of the C-terminal glutamate residue in LysW. ArgX catalyses the ATP-dependent formation of a covalent bond between the amino group  of glutamate and the gamma-carboxyl group of the C-terminal glutamate residue in LysW.
Pfam PF05992: SbmA/BacA-like family (family)
The Rhizobium meliloti bacA gene encodes a function that is essential for  bacterial differentiation into bacteroids within plant cells in the symbiosis between R. meliloti and alfalfa. An Escherichia coli homolog of  BacA, SbmA, is implicated in the uptake of microcins and bleomycin.  This family is likely to be a subfamily of the ABC transporter family.
Pfam PF03732: Retrotransposon gag protein (domain)
Gag or Capsid-like proteins from LTR retrotransposons. There is a central motif QGXXEXXXXXFXXLXXH that is common to Retroviridae gag-proteins, but is poorly conserved.
Pfam PF00676: Dehydrogenase E1 component (domain)
This family uses thiamine pyrophosphate as a cofactor. This family includes pyruvate dehydrogenase, 2-oxoglutarate dehydrogenase and 2-oxoisovalerate dehydrogenase.
Pfam PF21522: Archaeal actin homologue MreB-like, C-terminal (domain)
Archaeal actin homologue Ta0583 is an active ATPase at physiological temperatures, which has a propensity to form filaments. It has the core actin structure and is highly homologous to MreB and ParM from bacteria. This entry represents the C-terminal actin-like domain.
Pfam PF24744: CARF-associated HTH (domain)
This is a presumed HTH domain found at the C-terminal of CARF-containing proteins mainly from archaea.
Pfam PF20248: Family of unknown function (DUF6603) (family)
This entry represents a large potential domain found in a wide range of uncharacterised fungal proteins.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF17012: Domain of unknown function (DUF5091) (family)
This is a family of microsporidial-specific sequences of 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 PF00506: Influenza virus nucleoprotein (family)
Influenza virus nucleoprotein (NP) is a structural protein which encapsidates the negative strand viral RNA. NP is one of the main determinants of species specificity. The question of how far the NP gene can cross the species barrier by reassortment and become adapted by mutation to the new host has been discussed .
Wikipedia: Influenza virus nucleoprotein (NP) is a structural protein which encapsidates the negative strand viral RNA. NP is one of the main determinants of species specificity. The question of how far the NP gene can cross the species barrier by reassortment and become adapted by mutation to the new host has been discussed.
Pfam PF14489: QueF-like protein (domain)
This protein is involved in the biosynthesis of queuosine.  In some proteins this domain appears to be fused to [pfam:PF06508].
Pfam PF21254: Beta-agarase/YXIM esterase-like, galactose-binding domain-like (domain)
This entry represents the galactose-binding domain found at the C-terminal of beta-agarase A from Zobellia galactanivorans and the N-terminal of the uncharacterised esterase YXIM from Bacillus subtilis and similar sequences.
Pfam PF19431: MEKK4 N-terminal (family)
This domain represents the regulatory N-terminal non-catalytic region of Mitogen-activated protein kinase kinase kinase 4 (MEKK4) which contains a putative PH-domain. This N-terminal region acts as an autoinhibitory domain that must be dissociated from the catalytic domain to allow the activation of these kinases.
Pfam PF16232: Domain of unknown function (DUF4891) (family)
This family consists of uncharacterized proteins around 140 residues in length and is mainly found in various Bacteroides species. The function of this family is unknown.
Pfam PF10366: Vacuolar sorting protein 39 domain 1 (repeat)
This domain is found on the vacuolar sorting protein Vps39 which is a component of the C-Vps complex.  Vps39 is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole.  In Saccharomyces cerevisiae, Vps39 has been shown to stimulate nucleotide exchange.  The precise function of this domain has not been characterised.
Pfam PF16017: BTB/POZ domain (domain)
This entry represents the BTB/POZ domain found in BTBD10 and KCTD20 proteins.
BTBD10 acts as an activator of AKT family members by inhibiting PPP2CA-mediated dephosphorylation, thereby keeping AKTs activated . KCTD20 is also a positive regulator of Akt .
Pfam PF24380: Family of unknown function (DUF7536) (family)
This family includes a group of short proteins from archaea.
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 PF19971: Ternary complex associated domain 2 (domain)
Novel uncharacterised protein domain found associated with the vWA-MoxR-VMAP ternary systems.
Pfam PF20838: Immunoglobulin D, delta linker region (domain)
The linker region of Immunoglobulin D (IgD), the longest hinge sequence of any immunoglobulin, connects the Fab and Fc fragments. It has up to seven O-linked oligosaccharide sites, which is thought to be related to the flexible T-shape of IgD.
Pfam PF12749: Eukaryotic metallothionein (domain)
This is a family of eukaryotic metallothioneins.
Pfam PF13860: FlgD Ig-like domain (domain)
This domains has an immunoglobulin like beta sandwich fold. It is found in the FlgD protein the flagellar hook capping protein. THe structure for this domain shows that it is inserted within a TUDOR like beta barrel domain.
Pfam PF23413: Vps8 RING zinc finger, fungal (domain)
Vps8 is one of the Golgi complex components necessary for vacuolar sorting. It is the core component of the endosomal tethering complex CORVET (class C core vacuole/endosome tethering). Vps8 co-operates with Vps21-GTP to mediate endosomal clustering in a reaction that is dependent on Vps3. Vps8 is the only CORVET subunit that is enriched on late endosomes, suggesting that it is a marker for the maturation of late endosomes. These proteins consist of a beta-propeller at the N-terminal followed by a long, central TPR domain and a RING zinc finger at the C-terminal. This entry represents the RING zinc finger found in yeast Vps8 and similar sequences.
Pfam PF16233: Domain of unknown function (DUF4893) (family)
This family consists of uncharacterized proteins around 200 residues in length and is mainly found in various Pseudomonas species. The function of this family is unknown.
Pfam PF22884: Telomere ends associated C-terminal domain (domain)
This entry represents the C-terminal domain of protein telomere ends associated (Tea) found in Drosophila species and related fly sequences. Tea protects telomeres from fusion and it likely functions as a component of the MTV complex along with moi and ver. The complex binds single-stranded DNA in a sequence-independent manner and can protect it from DNA degradation. The function of this domain is still unknown. According to structure predictions, it adopts and alpha/beta structure consisting of 7 beta-strands and 3 alpha helices.
Pfam PF07091: Ribosomal RNA methyltransferase (FmrO) (family)
This family consists of several bacterial ribosomal RNA methyltransferase (aminoglycoside-resistance methyltransferase) proteins.
Pfam PF12635: Protein of unknown function (DUF3780) (family)
This family of proteins is functionally uncharacterised.This family of proteins is found in bacteria. Proteins in this family are typically between 189 and 206 amino acids in length. There are two conserved sequence motifs: PEERWWL and GWR. This family is found in a very sporadic set of bacterial species, suggesting that it may have been horizontally transferred. One protein is annotated as plasmid borne.
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 PF10353: Protein of unknown function (DUF2430) (family)
This is a family of short, 111 residue, proteins found in S. pombe.  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 PF12171: Zinc-finger double-stranded RNA-binding (family)
This domain family is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation.
Pfam PF15231: Variable charge X/Y family (disordered)
The variable charge X/Y (VCX/VCY) family of proteins has members on the Human X and Y chromosomes, is expressed in male germ calls and may play a role in spermatogenesis or in sex ratio distortion.
Pfam PF07188: Kaposi's sarcoma-associated herpesvirus (KSHV) K8 protein (family)
This family consists of Kaposi's sarcoma-associated herpesvirus (KSHV) K8 proteins. KSHV is a human Gammaherpesvirus related to Epstein-Barr virus (EBV) and herpesvirus saimiri. KSHV open reading frame K8 encodes a basic region-leucine zipper protein of 237 aa that homodimerises. K8 interacts and co-localises with human [pfam:PF04855], a cellular chromatin-remodelling factor, both in vivo and in vitro. K8 is thought to function as a transcriptional activator under specific conditions and its transactivation activity requires its interaction with the cellular chromatin remodelling factor hSNF5.
Pfam PF12414: Calcitonin gene-related peptide regulator C terminal (family)
This domain family is found in eukaryotes, and is typically between 69 and 99 amino acids in length. The family is found in association with [pfam:PF00076]. This family is the C terminal of Fox-1, a protein involved in the regulation of calcitonin gene-related peptide to mediate the neuron-specific splicing pattern. Fox-1, with Fox-2, functions to repress exon 4 inclusion.
Pfam PF17393: Family of unknown function (DUF5402) (family)
This is a family of unknown function found in Methanobacteria and Methanococci.
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 PF04233: Phage Mu protein F like protein (family)
Members of this family are found in double-stranded DNA bacteriophages, and in some bacteria.  A member of this family is required for viral head  morphogenesis in bacteriophage SPP1 ([swissprot:Q38577]).  This family is  possibly a minor head protein. This family may be related to the family TT_ORF1 ([pfam:PF02956]).
Pfam PF23665: CDCP1 CUB domain (domain)
This domain is found in the human CUB domain-containing protein 1 (CDCP1) and related proteins. CDCP1 may be involved in cell adhesion and cell matrix association. It also play a role in the regulation of anchorage versus migration or proliferation versus differentiation via its phosphorylation. CDCP1 contains a tandem of CUB domains. This entry represents the sixth of the tandem.
Pfam PF03479: Plants and Prokaryotes Conserved (PCC) domain (domain)
This is a Plants and Prokaryotes Conserved (PPC) domain found in proteins that contain AT-hook motifs [pfam:PF02178] which strongly suggests a DNA-binding function for the proteins as a whole. Proteins with PPC domains are found in Bacteria, Archaea and the plant kingdom.The PPC domain has a single alpha-helix packed against an antiparallel beta-sheet, which is formed by five beta-strands. There are three highly conserved histidine residues, eg at 117, 119 and 133 in [swissprot:Q46QL5] which appear to form a zinc-binding site, and the domain has been observed to form homotrimers. The domain co-occurs with a thioredoxin-like domain in uncharacterized cyanobacterial proteins.