SII-SWORD/CoKE huggingface dataset:
Pfam PF16437: Domain of unknown function (DUF5034) (family)
This family consists of several uncharacterized proteins around 190 residues in length and is mainly found in various Bacteroides species. The function of this family is unknown.
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 PF09544: Protein of unknown function (DUF2381) (family)
This family consists of at least 8 paralogs in Myxococcus xanthus, a member of the Deltaproteobacteria. The function is unknown.
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 PF24166: Domain of unknown function (DUF7410) (domain)
This is a C2H2 zinc finger found in a group of uncharacterised 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 PF10951: Protein of unknown function (DUF2776) (family)
This bacterial 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 PF17529: Family of unknown function (DUF5450) (family)
This is a family of unknown function found in Giardia intestinalis.
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 PF16407: PKD-like family (family)
This is a PKD-like family of proteins found in various Bacteroides species.
Pfam PF22216: Spindle assembly abnormal protein 6 homolog, C-terminal coiled coil (domain)
This entry represents the C-terminal coiled-coil (CC) domain found in Spindle assembly abnormal protein 6 homolog from Drosophila melanogaster (Sas-6) and similar sequences found predominantly in arthropods. Sas-6 is a central scaffolding component of the centrioles ensuring their nine-fold symmetry. Sas-6 forms a dimer through this domain to then further homo-oligomerise to form a ring structure from which the CC domains emanate as spokes.
Pfam PF20118: Family of unknown function (DUF6508) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 131 and 449 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 PF08955: BofC C-terminal domain (domain)
The C-terminal domain of the bacterial protein 'bypass of forespore C' contains a three-stranded beta-sheet and three alpha-helices. Its exact function is, as yet, unknown.
Pfam PF18416: N-acetylglucosamine binding protein domain 2 (domain)
This domain can be found in N-acetylglucosamine binding protein (GbpA) from Vibrio cholerae, a bacterial pathogen that colonizes the chitinous exoskeleton of zooplankton as well as the human gastrointestinal tract. GbpA binds to GlcNAc oligosaccharides. Structural comparison show that there are distant structural similarities between domain 2 of GbpA and the beta-domain of the flagellin protein p5. It is suggested that this domain interacts with the bacterial surface, and functions to project an alginate binding domain of the protein from the cell surface.
Pfam PF05475: Pgp3 C-terminal domain (domain)
This family consists of Chlamydia virulence proteins which are thought to be required for growth within mammalian cells. The C-terminal domain shows distant homology to the TNF superfamily.
Pfam PF23013: IML1 N-terminal double psi beta barrel domain (domain)
This entry represents the N-terminal double psi beta barrel domain found in IML1 proteins.  The IML1 protein family is involved in the regulation of the mTORC1 signaling pathway, particularly in response to amino acid availability. Members of this family are components of the GATOR1 complex, which acts as an inhibitor of the amino acid-sensing branch of the mTORC1 pathway. When amino acids are scarce, GATOR1 increases GTP hydrolysis by Rag GTPases, converting them to their inactive GDP-bound state, thus detaching mTORC1 from the lysosomal surface and inhibiting its signaling. This action is crucial for cellular adaptation to nutrient deprivation, promoting catabolic metabolism and autophagy. Conversely, in the presence of abundant amino acids, GATOR1 is negatively regulated by GATOR2, allowing mTORC1 signaling to proceed. The IML1 family proteins interact with the nucleotide-binding pocket of Rag GTPases, coordinating their nucleotide loading states, but do not possess GAP activity themselves.
Pfam PF22751: Active DUF488-N3 subclade (domain)
This entry represents a subclade of DUF488 domains with degenerate C-terminal core strand. Sometimes it is observed adjacent to the DUF488-s subclade, suggesting it preserves a catalytic activity comparable to other active DUF488 subclades.
Pfam PF18004: 26S proteasome regulatory subunit RPN2 C-terminal domain (domain)
This is the C-terminal domain found in S. cerevisiae Rpn2 (26S proteasome regulatory subunit RPN2) as well as other eukaryotic species. A study revealed that the C-terminal 52 residues of the Rpn2 C-terminal domain are responsible for mediating interactions with the ubiquitin-binding subunit Rpn13. Futhermore, the extreme C-terminal 20 or 21 residues of Rpn2 (926-945 or 925-945) of S. cerevisiae, were shown to be equally effective at binding Rpn13. Multiple sequence alignments indicate that Rpn2 orthologs are highly conserved in this C-terminal region and share characteristic acidic, aromatic, and proline residues, suggesting a common function. In the structure of Rpn2 from S. cerevisiae , this region is exposed and disordered, and is thus accessible for associating with Rpn13. The Rpn2 binding surface of human Rpn13 has been mapped by nuclear magnetic resonance titration to one surface of its Pru domain.
Pfam PF17092: Penicillin-binding protein OB-like domain (family)
This entry represents the OB (oligonucleotide/oligosaccharide binding)-fold domain found in penicillin-binding proteins (PBPs). A. baumannii PBP is the first example of a multimodular PBP containing the OB-fold domain. Structure-based sequence alignment suggests that this OB-fold domain may also exist in high molecular mass PBPs of subclass A1 from other Gram-negative bacteria including the respective PBP1a proteins of P. aeruginosa and K. pneumoniae .
Pfam PF08694: Ubiquitin-fold modifier-conjugating enzyme 1 (domain)
Ubiquitin-like (UBL) post-translational modifiers are covalently linked to most, if not all, target protein(s) through an enzymatic cascade analogous to ubiquitylation, consisting of E1 (activating), E2 (conjugating), and E3 (ligating) enzymes. Ubiquitin-fold modifier 1 (Ufm1) a ubiquitin-like protein is activated by a novel E1-like enzyme, Uba5, by forming a high-energy thioester bond. Activated Ufm1 is then transferred to its cognate E2-like enzyme, Ufc1, in a similar thioester linkage. This family represents the E2-like enzyme.
Pfam PF16993: Accessory Sec system protein Asp1 (family)
Asp1, along with SecY2, SecA2, and other proteins forms part of the accessory secretory protein system. The system is involved in the export of serine-rich glycoproteins important for virulence in a number of Gram-positive species, including Streptococcus gordonii and Staphylococcus aureus. This protein family is assigned to transport rather than glycosylation function, but the specific molecular role is unknown. Asp1 is predicted to be cytosolic.
Pfam PF18472: HP1451 C-terminal domain (domain)
HP1451 modulates the ATPase activity of HP0525 H. pylori. It is suggested that HP1451 acts as an inhibitory factor of HP0525 to regulate Cag-mediated secretion. It consists of two domains. The two HP1451 domains (referred to as the KH-domain and S8-domain) interact with each other via two salt bridges. The second domain is structurally homologous to other nucleic acid-binding proteins such as the NTD of ribosomal protein S8 and DNaseI.
Pfam PF01117: Aerolysin toxin (domain)
This family represents the pore forming lobe of aerolysin.
Wikipedia: In molecular biology, aerolysin is a cytolytic pore-forming toxin exported by Aeromonas hydrophila, a Gram-negative bacterium associated with diarrhoeal diseases and deep wound infections. It is also produced by the caterpillar of the moth Megalopyge opercularis, sometimes called the Tree Asp. The mature toxin binds to eukaryotic cells and aggregates to form holes leading to the destruction of the membrane permeability barrier and osmotic lysis. The structure of proaerolysin has been determined to 2.8A resolution and shows the protoxin to adopt a novel fold. Images of an aerolysin oligomer derived from electron microscopy have helped to construct a model of the protein in its heptameric conformation, and to outline a mechanism by which this assembly might insert into lipid bilayers to form ion channels.
Pfam PF13805: Eisosome component PIL1 (family)
In the budding yeast, S. cerevisiae, Pil1 and another cytoplasmic protein, Lsp1, together form large immobile assemblies at the plasma membrane that mark sites for endocytosis, called eisosomes.  Endocytosis functions to recycle plasma membrane components, to regulate cell-surface expression of signalling receptors and to internalise nutrients in all eukaryotic cells.
Pfam PF00070: Pyridine nucleotide-disulphide oxidoreductase (domain)
This family includes both class I and class II oxidoreductases and also NADH oxidases and peroxidases.  This domain is actually a small NADH binding domain within a larger FAD binding domain.
Pfam PF12875: Protein of unknown function (DUF3826) (family)
This is a putative sugar-binding family.
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 PF15559: Domain of unknown function (DUF4660) (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 93 and 189 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 PF24235: Rho GTPase-activating protein 29/45 N-terminal (domain)
This entry represents a domain found at the N-terminal of Rho GTPase-activating protein 29 (RHG29) and 45 (RHG45, also known as HMHA1). These proteins are GTPase activators for the Rho-type GTPases. HMHA1 may be able to negatively regulate the actin cytoskeleton as well as cell spreading.
Pfam PF05433: Glycine zipper 2TM domain (family)
This family includes a putative two transmembrane alpha-helical region that contains glycine zipper motifs. This family includes  several Rickettsia genus specific 17 kDa surface antigen proteins.
Pfam PF01265: Cytochrome c/c1 heme lyase (family)
Holocytochrome c-type synthase (HCCS, also known as cytochrome c-type heme lyase) (4.4.1.17) and holocytochrome-c1 synthase (CC1HL, also known as cytochrome c1 heme lyase)  are mitochondrial enzymes that catalyse the covalent attachment of a haem group on two cysteine residues of cytochrome c and c1. These two enzymes are functionally and evolutionary related. There are two conserved regions, the first is located in the central section and the second in the C-terminal section. These enzymes contain a conserved histidine, which is key to interact with the heme iron and to form the HCCS:heme complex, the platform for interaction with apocytochrome c .
Wikipedia: The enzyme holocytochrome-c synthase catalyzes the chemical reactionholocytochrome c  apocytochrome c + heme
Pfam PF18245: 5-3 exonuclease XRN1 DCP1-binding motif (conserved_site)
This domain is found in the 5'-3' exonuclease (XRN1) present in Drosophila melanogaster. XRN1 degrades deadenylated mRNA that has recently been decapped by decapping enzyme 2 (DCP2). DCP2 associates with decapping activators DCP1 and EDC4. The direct interaction between DCP1 and XRN1 couples mRNA decapping to 5' exonucleolytic degradation. This domain is responsible for binding to DCP1. In particular, the helical C-terminal region of the domain contributes to the binding affinity and the specificity of the interaction.
Pfam PF17177: Pentacotripeptide-repeat region of PRORP (repeat)
Pentatricopeptide repeat (PPR) proteins are a large family of modular RNA-binding proteins which mediate several aspects of gene expression primarily in organelles but also in the nucleus. PPR_long is the region of Arabidopsis protein-only RNase P (PRORP) enzyme that consists of up to eleven alpha-helices. PRORPs are a class of RNA processing enzymes that catalyze maturation of the 5' end of precursor tRNAs in Eukaryotes. All PPR proteins contain tandemly repeated sequence motifs (the PPR motifs) which can vary in number. The series of helix-turn-helix motifs formed by PPR motifs throughout the protein produces a superheros with a central groove that allows the protein to bind RNA. Proteins containing PPR motifs are known to have roles in transcription, RNA processing, splicing, stability, editing, and translation. Over a decade after the discovery of PPR proteins, the super-helical structure was confirmed. The protein-only mitochondrial RNase P crystal structure from Arabidopsis thaliana (PRORP1) confirmed the role of its PPR motifs in pre-tRNA binding and suggest it has evolved independently from other RNase P proteins that rely on catalytic RNA.
Pfam PF07586: Protein of unknown function (DUF1552) (family)
A family of proteins identified in Rhodopirellula baltica.
Pfam PF20496: Double strand break localizing Dbl7 (family)
This family represents the Schizosaccharomyces specific protein double strand break localizing Dbl7. Dbls localize to DNA double-strand breaks (DSBs) and are involved in DSB repair.
Pfam PF22396: Family of unknown function (DUF6976) (family)
This family of uncharacterised proteins is found mainly in Proteobacteria. It is likely to consists of two domains that engage in extensive contacts mainly via hydrophobic residues. The predicted structure of the N-terminal domain has similarity to chorismatases.
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 PF21955: Carbapenem resistance protein CarG-like (family)
This entry represents the carbapenem resistance protein CarG from Serratia sp. and similar sequences mainly found in proteobacteria. CarG shows a unique beta-sandwich fold with short terminal alpha-helices, displaying close structural homology with bacterial inhibitors of invertebrate lysozyme ([pfam:PF16743]).
Pfam PF02751: Transcription initiation factor IIA, gamma subunit (domain)
Accurate transcription in vivo requires at least six general transcription initiation factors, in addition to RNA polymerase II.  Transcription initiation factor IIA (TFIIA) is a multimeric protein which facilitates the binding of TFIID to the TATA box. The C-terminal domain of the gamma subunit is a 12 stranded beta-barrel.
Pfam PF03979: Sigma-70 factor, region 1.1 (family)
Region 1.1 modulates DNA binding by region 2 and 4 when sigma is unbound by the core RNA polymerase. Region 1.1 is also involved in promoter binding
Wikipedia: A sigma factor is a protein needed for initiation of transcription in bacteria. It is a bacterial transcription initiation factor that enables specific binding of RNA polymerase (RNAP) to gene promoters. It is homologous to archaeal transcription factor B and to eukaryotic factor TFIIB. The specific sigma factor used to initiate transcription of a given gene will vary, depending on the gene and on the environmental signals needed to initiate transcription of that gene. Selection of promoters by RNA polymerase is dependent on the sigma factor that associates with it. They are also found in plant chloroplasts as a part of the bacteria-like plastid-encoded polymerase (PEP).
Pfam PF18212: ZNRF-3 Ectodomain (domain)
This domain is found in ZNRF-3 protein present in Danio rerio. ZNRF-3 is a transmembrane E3 ubiquitin ligase that antagonizes Wnt signalling, the signalling system used to mediate Rspo protein actions. ZNFR3 and RNF43, alongside the Rspo proteins, have emerged as a system with therapeutic potential for a number of pathological processes. This domain is known as the ectodomain.
Wikipedia: R-spondin-1 is a secreted protein that in humans is encoded by the RSPO1 gene, found on chromosome 1. In humans, it interacts with WNT4 in the process of female sex development. Loss of function can cause female to male sex reversal. Furthermore, it promotes canonical WNT/β catenin signaling.
Pfam PF16021: Programmed cell death protein 7 (family)
Programmed cell death protein 7 (PDCD7, ES18) may be involved in specific apoptotic processes . This entry also includes Arabodopsis At2g46200 protein, which is predicted to be U11/U12 small nuclear ribonucleoprotein .
Wikipedia: Programmed cell death protein 7 is a protein that in humans is encoded by the PDCD7 gene.
Pfam PF06217: GAGA binding protein-like family (domain)
This family includes gbp a protein from Soybean that binds to GAGA element dinucleotide repeat DNA. It seems likely that the this domain mediates DNA binding. This putative domain contains several conserved cysteines and a histidine suggesting this may be a zinc-binding DNA interaction domain.
Pfam PF17912: MalK OB fold domain (domain)
This entry corresponds to one of two OB-fold domains found in the MalK transport protein.
Pfam PF11229: Focadhesin (repeat)
Focadhesin (FOCAD) is focal adhesion protein with potential tumour suppressor function in gliomas. The structure prediction indicates that it consists in repetitive alpha hairpins that adopt an armadillo-like fold.
Pfam PF11275: Protein of unknown function (DUF3077) (family)
This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
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 PF18328: Fatty acid synthase subunit PfaD N-terminal domain (domain)
This domain is found in N-terminal region of PfaD, an enoyl reductase enzyme present in Bacillus subtilis. PfaD plays a role in the biosynthesis of polyunsaturated fatty acids. The domain is typically found just before the N-terminal region of a nitronate monooxygenase domain ([pfam:PF03060]).
Pfam PF02788: Ribulose bisphosphate carboxylase large chain, N-terminal domain (domain)
The N-terminal domain of RuBisCO large chain adopts a ferredoxin-like fold.
Wikipedia: Ribulose-1,5-bisphosphate carboxylase/oxygenase, commonly known by the abbreviations RuBisCo, rubisco, RuBPCase, or RuBPco, is an enzyme involved in the light-independent part of photosynthesis, including the carbon fixation by which atmospheric carbon dioxide is converted by plants and other photosynthetic organisms to energy-rich molecules such as glucose. It emerged approximately four billion years ago in primordial metabolism prior to the presence of oxygen on Earth. It is probably the most abundant enzyme on Earth. In chemical terms, it catalyzes the carboxylation of ribulose-1,5-bisphosphate.
Pfam PF04468: PSP1 C-terminal conserved region (family)
This region is present in both eukaryotes and eubacteria. The yeast PSP1 protein is involved in  suppressing mutations in the DNA polymerase alpha subunit in yeast.
Pfam PF09305: TACI, cysteine-rich domain (domain)
Members of this family are predominantly found in tumour necrosis factor receptor superfamily, member 13b (TACI), and are required for binding to the ligands APRIL and BAFF.
Wikipedia: In molecular biology, TACI-CRD2 represents the second cysteine-rich protein domain found in the TACI family of proteins. Members of this family are predominantly found in tumour necrosis factor receptor superfamily, member 13b (TACI), and are required for binding to the ligands APRIL and BAFF. TACI-CRD2 stands for Transmembrane Activator and CAML Interactor- Cysteine Rich Domain 2.
Pfam PF24177: Nudivirus polyhedrin (family)
This entry represents the Nudivirus polyhedrin. Its structure consists mainly of array of helices.
Pfam PF09722: Antitoxin Xre/MbcA/ParS C-terminal toxin-binding domain (domain)
This entry represents the C-terminal domain of antitoxin components of a type II toxin-antitoxin (TA) system, including Xre from Pseudomonas putida, MbcA from Mycobacterium sp. and ParS from Sphingobium sp.. This domain interacts with the toxin component and sterically blocks its active site, neutralising its effect. These antitoxins also have a HTH domain at the N-terminal.