SII-SWORD/CoKE huggingface dataset:
Pfam PF09878: Predicted membrane protein (DUF2105) (family)
This domain, found in various hypothetical archaeal 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 PF15832: FAM27 D and E protein family (family)
FAM27 is a family of proteins found in eukaryotes. Proteins in this family are typically between 57 and 131 amino acids in length.
Pfam PF19857: Family of unknown function (DUF6332) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001598) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide, in particular the foxicins A-D biosynthetic gene cluster  from Streptomyces diastatochromogenes. This family appears to  be predominantly found in 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 PF23728: Tubby C-terminal like domain (domain)
This entry represents a bacterial protein domain that is structurally similar to the C-terminal domain of the tubby protein. It consists of 12 beta strands organised into a barrel with a central C-terminal Alpha helix. This family shows distant sequence similarity to both the Tubby C-terminal domain and the LURP 1 family.
Pfam PF13367: PrsW family intramembrane metalloprotease (family)
This family includes members such as the experimentally characterized PrsW protease from Bacillus subtilis [swissprot:P50738]. PrsW mediates site-1 cleavage of anti-sigma factor RsiW, and it senses antimicrobial peptides that damage the cell membrane and other agents that cause cell envelope stress. PrsW proteases, CPBP family (type II CAAX Proteases and Bacteriocin Processing enzymes), YhfC intramembrane metalloprotease, and APH-1 are distantly related. They share four predicted core transmembrane segments and possess similar, yet distinct sets of sequence motifs. The first N-terminal motif in PrsW bears the consensus signature of 'EExxK' the second motif 'FxxxE' and the third motif possess a conserved histidine. The fourth motif, 'HxxxB', is shared by the PrsW proteases and the CPBP, APH-1 and the YhfC families. Site-directed mutagenesis indicates that either double point mutation of the two conserved glutamates in the first motif (E75A/E76A), or a single mutation of the conserved histidine in the fourth motif (H175A), are of functional importance.
Pfam PF01641: SelR domain (domain)
Methionine sulfoxide reduction is an important process, by which cells regulate biological processes and cope with oxidative stress. MsrA, a protein involved in the reduction of methionine sulfoxides in proteins, has been known for four decades and has been extensively characterised with respect to structure and function. However, recent studies revealed that MsrA is only specific for methionine-S-sulfoxides. Because oxidised methionines occur in a mixture of R and S isomers in vivo, it was unclear how stereo-specific MsrA could be responsible for the reduction of all protein methionine sulfoxides. It appears that a second methionine sulfoxide reductase, SelR, evolved that is specific for methionine-R-sulfoxides, the activity that is different but complementary to that of MsrA. Thus, these proteins, working together, could reduce both stereoisomers of methionine sulfoxide. This domain is found both in SelR proteins and fused with the peptide methionine sulfoxide reductase enzymatic domain [pfam:PF01625]. The domain has two conserved cysteines and histidines. The domain binds both selenium and zinc. The final cysteine is found to be replaced by the rare amino acid selenocysteine in some members of the family. This family has methionine-R-sulfoxide reductase activity.
Pfam PF17923: Tetracyclin repressor-like, C-terminal domain (domain)
TetR family regulators are involved in the transcriptional control of multidrug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity. The TetR proteins identified in overm ultiple genera of bacteria and archaea share a common helix-turn-helix (HTH) structure in their DNA-binding domain. However, TetR proteins can work in different ways: they can bind a target operator directly to exert their effect (e.g. TetR binds Tet(A) gene to repress it in the absence of tetracycline), or they can be involved in complex regulatory cascades in which the TetR protein can either be modulated by another regulator or TetR can trigger the cellular response. TetR regulates the expression of the membrane-associated tetracycline resistance protein, TetA, which exports the tetracycline antibiotic out of the cell before it can attach to the ribosomes and inhibit protein synthesis. TetR blocks transcription from the genes encoding both TetA and TetR in the absence of antibiotic. The C-terminal domain is multi-helical and is interlocked in the homodimer with the helix-turn-helix (HTH) DNA-binding domain. This entry represents the C-terminal domain present in TetR transcriptional regulations found in proteobacteria.
Pfam PF15737: Domain of unknown function (DUF4685) (family)
This domain family is found in eukaryotes, and is typically between 106 and 131 amino acids in length. There are two conserved sequence motifs: SGE and VRF.
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 PF21935: Tetracyclin repressor-like, C-terminal domain (domain)
This domain is found at the C-terminal end of CprB from Streptomyces coelicolor ([swissprot:O66122]) and similar bacterial transcriptional regulators. This region is the ligand-binding domain (LBD). It is often found associated with [pfam:PF00440].
Pfam PF04681: Blastomyces yeast-phase-specific protein (domain)
The molecular function of this protein is not known. Its expression is specific to the high temperature, unicellular yeast morphology (as opposed to the lower temperature, multicellular mycelium form).
Pfam PF21252: Glycosyl hydrolase 109, C-terminal domain (domain)
This domain is found at the C-terminal end of the group of bacterial glycosyl hydrolases 109, including Alpha-N-acetylgalactosaminidase from Elizabethkingia meningoseptica. This domain shows a large open-faced, seven-stranded, anti-parallel beta-sheet, adjacent to nine alpha-helices and an alpha-helical bundle covering the dinucleotide-binding tunnel.
Pfam PF18800: Attenuator of Hedgehog (family)
Attenuator of Hedgehog is a integral membrane protein of the tetraspan family that functions as a negative regulator of Hedgehog signaling.
Pfam PF08254: Threonine leader peptide (family)
Threonine leader peptide of the Threonine operon thrA1A2BC.  It as been sequenced in different bacteria: E. coli, Serratia marcescens, Salmonella typhi.
Pfam PF13705: TRC8 N-terminal domain (domain)
This region is found at the N-terminus of the TRC8 protein [swissprot:Q8WU17]. TRC8 is an E3 ubiquitin-protein ligase also known as RNF139. This region contains 12 transmembrane domains. This region has been suggested to contain a sterol sensing domain. It has been found that TRC8 protein levels are sterol responsive and that it binds and stimulates ubiquitylation of the endoplasmic reticulum anchor protein INSIG.
Pfam PF14965: Negative regulator of p53/TP53 (family)
This family of transmembrane proteins is found in eukaryotes. Proteins in this family are typically between 213 and 245 amino acids in length. It is found in various tissues, including the brain, liver and kidneys. It was first discovered as a functional unknown gene, murine brain I3 (BRI3). This protein is also known as HCCRBP-1 and it plays a role in tumourigenesis, as it binds to an oncogene, HCCR-1, and acts as a negative regulator of p53/TP53 tumour suppressor. BRI3BP induces tumourigenesis by activating protein kinase C (PKC) activity but decreasing the pro-apoptotic PKC-alpha and PKC-delta isoform levels. BRI3BP is over-expressed in many tumours.
Pfam PF12606: Tumour necrosis factor receptor superfamily member 19 (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 49 and 288 amino acids in length. There are two completely conserved residues (K and Y) that may be functionally important. The members of tumor necrosis factor receptor (TNFR) superfamily have been designated as the 'guardians of the immune system' due to their roles in immune cell proliferation, differentiation, activation, and death (apoptosis). The messenger RNA of RELT is especially abundant in hematologic tissues such as spleen, lymph node, and peripheral blood leukocytes as well as in leukemias and lymphomas. RELT is able to activate the NF-kappaB pathway and selectively binds tumor necrosis factor receptor-associated factor 1. RELT is a TNF receptor family member that is expressed in hematological tissues and can stimulate the proliferation of T-cells, the p38 and JNK MAPK pathways, and serves as a substrate for the closely related kinases OSR1 and SPAK. Furthermore, family members include the homologues RELL1 and RELL2 (RELT-like protein 1 and 2 respectively). RELT, RELL1 and RELL2 bind to each other in vitro and co-localize with one another at the plasma membrane. Functional studies of the role of RELT, show that overexpression of RELT in epithelial cells induces cell death by promoting cell rounding and DNA fragmentation.
Pfam PF09729: Gti1/Pac2 family (family)
In S. pombe the gti1 protein promotes the onset of gluconate uptake upon glucose starvation. In S. pombe the Pac2 protein controls the onset of sexual development, by inhibiting the expression of ste11, in a pathway that is independent of the cAMP cascade.
Pfam PF01322: Cytochrome C' (domain)
Cytochromes c (cytC) can be defined as electron-transfer proteins having one or several haem c groups, bound to the protein by one or, more generally, two thioether bonds involving sulphydryl groups of cysteine residues. The fifth haem iron ligand is always provided by a histidine residue. CytC possess a wide range of properties and function in a large number of different redox processes. Ambler  recognised four classes of cytC.
Wikipedia: Cytochromes c  cytochromes, or heme-containing proteins, that have heme C covalently attached to the peptide backbone via one or two thioether bonds. These bonds are in most cases part of a specific Cys-X-X-Cys-His (CXXCH) binding motif, where X denotes a miscellaneous amino acid. Two thioether bonds of cysteine residues bind to the vinyl sidechains of heme, and the histidine residue coordinates one axial binding site of the heme iron. Less common binding motifs can include a single thioether linkage, a lysine or a methionine instead of the axial histidine or a CXnCH binding motif with n&gt;2. The second axial site of the iron can be coordinated by amino acids of the protein, substrate molecules or water. Cytochromes c possess a wide range of properties and function as electron transfer proteins or catalyse chemical reactions involving redox processes. A prominent member of this family is mitochondrial cytochrome c.
Pfam PF17717: Family of unknown function (DUF5562) (family)
This is a family of unknown function found in mammals. Family members have one or several predicted transmembrane regions.
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 PF04500: FLYWCH zinc finger domain (domain)
Mutations in the mod(mdg4) gene have effects on variegation (PEV), the properties of insulator sequences, correct path-finding of growing nerve cells, meiotic pairing of chromosomes, and apoptosis. The  occurrence of FLYWCH motifs in mod(mdg4) gene product and other proteins is discussed in.
Wikipedia: In molecular biology, the FLYWCH zinc finger is a zinc finger domain. It is found in a number of eukaryotic proteins. FLYWCH is a C2H2-type zinc finger characterised by five conserved hydrophobic residues, containing the conserved sequence motif: F/Y-X(n)-L-X(n)-F/Y-X(n)-WXCX(6-12)CX(17-22)HXH
Pfam PF05274: Occlusion-derived virus envelope protein E25 (family)
This family consists of several nucleopolyhedrovirus occlusion-derived virus envelope E25 proteins.
Pfam PF04258: Signal peptide peptidase (family)
The members of this family are membrane proteins. In some proteins this region is found associated with [pfam:PF02225]. This family corresponds with Merops subfamily A22B, the type example of which is signal peptide peptidase. There is a sequence-similarity relationship with [pfam:PF01080].
Wikipedia: In molecular biology, the Signal Peptide Peptidase (SPP) is a type of protein that specifically cleaves parts of other proteins. It is an intramembrane aspartyl protease with the conserved active site motifs 'YD' and 'GxGD' in adjacent transmembrane domains (TMDs). Its sequences is highly conserved in different vertebrate species. SPP cleaves remnant signal peptides left behind in membrane by the action of signal peptidase and also plays key roles in immune surveillance and the maturation of certain viral proteins.
Pfam PF24083: Putative phage ssDNA-binding domain (domain)
This entry represents a small family of phage proteins that show structural similarity to other phage ssDNA-binding proteins. Structure prediction shows a plausible ssDNA binding pocket on the surface of the domain. This domain has an OB fold.
Pfam PF02058: Guanylin precursor (family)
This entry represents the guanylin family. Its members include guanylate cyclase activator 2A and 2B. They are endogenous activators of intestinal guanylate cyclases.
Wikipedia: Guanylin is a 15 amino acid peptide that is secreted by goblet cells in the colon. Guanylin acts as an agonist of the guanylyl cyclase receptor GC-C and regulates electrolyte and water transport in intestinal and renal epithelia. Upon receptor binding, guanylin increases the intracellular concentration of cGMP, induces chloride secretion and decreases intestinal fluid absorption, ultimately causing diarrhoea. The peptide stimulates the enzyme through the same receptor binding
region as the heat-stable enterotoxins.
Pfam PF13156: Restriction endonuclease (family)
Prokaryotic family found in type II restriction enzymes containing the hallmark (D/E)-(D/E)XK active site. Presence of catalytic residues implicates this region in the enzymatic cleavage of DNA
Pfam PF04987: Phosphatidylinositolglycan class N (PIG-N) (family)
Phosphatidylinositolglycan class N (PIG-N) is a mammalian homologue of the yeast protein MCD4P and is expressed in the endoplasmic reticulum. PIG-N is essential for glycosylphosphatidylinositol anchor synthesis. Glycosylphosphatidylinositol (GPI)-anchored proteins are cell surface-localised proteins that serve many important cellular functions.
Pfam PF13592: Winged helix-turn helix (domain)
This helix-turn-helix domain is often found in transferases and is likely to be DNA-binding.
Pfam PF00827: Ribosomal L15 (family)
A number of eukaryotic and archaebacterial ribosomal proteins can be grouped on the basis of sequence similarities . One of these families consists of:


 * Mammalian eL15.
 * Insect eL15.
 * Plant eL15.
 * Yeast YL10 (L13) (Rp15r).
 * Archaebacterial eL15 (known as L15e).


These proteins have about 200 amino acid residues.
Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.

Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome .
Pfam PF13858: Protein of unknown function (DUF4199) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 167 and 182 amino acids in length.
Pfam PF07899: Frigida-like protein (family)
This family is composed of plant proteins that are similar to FRIGIDA protein expressed by Arabidopsis thaliana ([swissprot:Q9FDW0]). This protein is probably nuclear and is required for the regulation of flowering time in the late-flowering phenotype. It is known to increase RNA levels of flowering locus C. Allelic variation at the FRIGIDA locus is a major determinant of natural variation in flowering time.
Pfam PF21085: CusS sensor domain (domain)
This entry represents a periplasmic sensor domain found in CusS from E. coli. The overall structure of the domain shows a PAS like topology.
Pfam PF15305: Intraflagellar transport protein 43 (family)
Intraflagellar transport protein 43 (IFT43) is a subunit of the IFT complex A (IFT-A) machinery of primary cilia.
Pfam PF04904: NAB conserved region 1 (NCD1) SAM domain (domain)
Nab1 and Nab2 are co-repressors that specifically interact with and repress transcription mediated by the three members of the NGFI-A (Egr-1, Krox24, zif/268) family of transcription  factors. This region consists of the N-terminal NAB conserved region 1, which  interacts with the EGR1 inhibitory domain (R1). It may also mediate multimerisation. This domain is related to the SAM domain.
Pfam PF19216: Coronavirus replicase NSP15, middle domain (domain)
This entry represents the non-catalytic middle domain from coronavirus non-structural protein 15 (NSP15). NSP15 is encoded by ORF1a/1ab and proteolytically released from the pp1a/1ab polyprotein. This domain is formed by ten beta strands organised into three beta hairpins.
Pfam PF15509: Domain of unknown function (DUF4650) (family)
This family of vertebrate proteins lies to the C-terminus of Ubiquitin-specific peptidase-like protein family peptidase_C98, [pfam:PF15499]. It might be acting as the exosite for the peptidase.
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 PF00990: Diguanylate cyclase, GGDEF domain (domain)
This domain is found linked to a wide range of non-homologous domains in a variety of bacteria. It has been shown to be homologous to the adenylyl cyclase catalytic domain and has diguanylate cyclase activity. This observation correlates with the functional information available on two GGDEF-containing proteins, namely diguanylate cyclase and phosphodiesterase A of Acetobacter xylinum, both of which regulate the turnover of cyclic diguanosine monophosphate. In the WspR protein of Pseudomonas aeruginosa, the GGDEF domain acts as a diguanylate cyclase, PDB:3bre, when the whole molecule appears to form a tetramer consisting of two symmetrically-related dimers representing a biological unit. The active site is the GGD/EF motif, buried in the structure, and the cyclic dimeric guanosine monophosphate (c-di-GMP) bind to the inhibitory-motif RxxD on the surface. The enzyme thus catalyses the cyclisation of two guanosine triphosphate (GTP) molecules to one c-di-GMP molecule.
Wikipedia: In molecular biology, the GGDEF domain is a protein domain which appears to be ubiquitous in bacteria and is often linked to a regulatory domain, such as a phosphorylation receiver or oxygen sensing domain. Its function is to act as a diguanylate cyclase and synthesize cyclic di-GMP, which is used as an intracellular signalling molecule in a wide variety of bacteria. Enzymatic activity can be strongly influenced by the adjacent domains. Processes regulated by this domain include exopolysaccharide synthesis, biofilm formation, motility and cell differentiation.
Pfam PF18977: Family of unknown function (DUF5713) (family)
This is a family of unknown function, mainly 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 PF10821: Protein of unknown function (DUF2567) (family)
This is a bacterial 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 PF23531: Apicomplexa microprotein (family)
This protein family includes uncharacterised microproteins encoded by small open reading frames (smORFs) from apicomplexa, including [swissprot:A7AW80] from the parasite Babesia bovis.