SII-SWORD/CoKE huggingface dataset:
Pfam PF18266: Nicastrin small lobe (domain)
This domain is part of the protein Nicastrin, a component of gamma secretase present in Homo sapiens. Gamma-secretase is thought to contribute to Alzheimer's disease development by generating beta-amyloid peptides. This domain is the known as the small lobe which forms the 'lid'. The lid is an extended surface loop that covers the hydrophilic pocket that is thought to be responsible for substrate recruitment. On substrate binding, the large lobe is thought to rotate relative to the small lobe.
Pfam PF01779: Ribosomal L29e protein family (family)
This entry represents the large ribosomal subunit protein eL29 family.
Ribosomal protein eL29 forms part of the 60S ribosomal subunit . This family is found in eukaryotes. There are there are 20 to 22 copies of the eL29 gene in Rattus norvegicus (Rat). Rat eL29 is related to yeast ribosomal protein YL43 .
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 PF03173: Putative carbohydrate binding domain (domain)
This domain represents the N terminal domain in chitobiases and beta-hexosaminidases [ec:3.2.1.52]. It is composed of a beta sandwich structure that is similar in structure to the cellulose binding domain of cellulase from Cellulomonas fimi.  This suggests that this may be a carbohydrate binding domain.
Wikipedia: In molecular biology, the CHB HEX N-terminal domain represents the N-terminal domain in chitobiases and beta-hexosaminidases. Chitobiases degrade chitin, which forms the exoskeleton in insects and crustaceans, and which is one of the most abundant polysaccharides on earth. Beta-hexosaminidases are composed of either a HexA/HexB heterodimer or a HexB homodimer, and can hydrolyse diverse substrates, including GM(2)-gangliosides; mutations in this enzyme are associated with Tay–Sachs disease. HexB is structurally similar to chitobiase, consisting of a beta sandwich structure; this structure is similar to that found in the cellulose-binding domain of cellulase from Cellulomonas fimi. This domain may function as a carbohydrate binding module.
Pfam PF01402: Ribbon-helix-helix protein, copG family (domain)
The structure of this protein repressor, which is the shortest reported to date and the first isolated from a plasmid, has a homodimeric ribbon-helix-helix arrangement. The helix-turn-helix-like structure is involved in dimerisation and not DNA binding as might have been expected.
Pfam PF11529: Melampsora lini avirulence protein AvrL567-A (family)
AvrL567-A is a protein from the fungal pathogen flax which induces plant disease resistance in flax plants. The protein has a novel fold.
Pfam PF09784: Mitochondrial ribosomal protein L31 (family)
This is a family of mitochondrial ribosomal proteins.  L31 is essential for mitochondrial function in yeast.
Wikipedia: A ribosomal protein is any of the proteins that, in conjunction with rRNA, make up the ribosomal subunits involved in the cellular process of translation. E. coli, other bacteria and Archaea have a 30S small subunit and a 50S large subunit, whereas humans and yeasts have a 40S small subunit and a 60S large subunit. Equivalent subunits are frequently numbered differently between bacteria, Archaea, yeasts and humans.
Pfam PF17549: Gene Product 17 (family)
Family members such as protein 17 (gene product 17/gp17) found in Bacillus phage phi29, is involved in DNA replication and in pulling the phage DNA into the cell during the injection process.
Pfam PF00333: Ribosomal protein S5, N-terminal domain (domain)
Small ribosomal subunit protein uS5 is one of the proteins from the small ribosomal subunit, and is a protein of 166 to 254 amino acid residues. In Escherichia coli, uS5 is known to be important in the assembly and function of the 30S ribosomal subunit. Mutations in uS5 have been shown to increase translational error frequencies. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities , groups bacterial, cyanelle, red algal chloroplast, archaeal and fungal mitochondrial uS5; cytoplasmic mammalian, Caenorhabditis elegans, Drosophila and plant uS5 (also known as S2); mitochondrial uS5m (MRPS5) and yeast uS5 (also known as S4 or SUP44).

This entry represents the N-terminal domain of ribosomal protein S5, which has an Î±-Î²(3)-Î± structure that folds into two layers, Î±/Î².
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 PF02949: 7tm Odorant receptor (family)
This family is composed of 7 transmembrane receptors, that are probably drosophila odorant receptors.
Pfam PF11413: Hypoxia-inducible factor-1 (family)
HIF-1 is a transcriptional complex and controls cellular systemic homeostatic responses to oxygen availability. In the presence of oxygen HIF-1 alpha is targeted for proteasomal degradation by pHVL, a ubiquitination complex.
Wikipedia: Hypoxia-inducible factors (HIFs) are transcription factors that respond to decreases in available oxygen in the cellular environment, or hypoxia. They also respond to instances of pseudohypoxia, such as thiamine deficiency. Both hypoxia and pseudohypoxia leads to impairment of adenosine triphosphate (ATP) production by the mitochondria.
Pfam PF19035: CCN3 Nov like TSP1 domain (domain)
This entry represents a sub-type of TSP1 domains found in matricellular CCN proteins that have an alternative disulphide binding pattern compared to the canonical TSP1 domains.
Pfam PF18645: Family of unknown function (DUF5631) (domain)
This is an alpha helical domain found at the C-terminal region of the hypothetical protein Rv3899c from Mycobacterium tuberculosis which is conserved across mycobacteria.
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 PF17608: Family of unknown function (DUF5504) (family)
This is a family of unknown function found in Lactobacillus. Family members have 4 predicted trans-membrane 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 PF20120: Family of unknown function (DUF6510) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 90 amino acids in length. There is a conserved RCP sequence motif. These proteins are predicted to resemble zinc beta-ribbon domains.
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 PF20789: Acyl-CoA thioesterase C-terminal domain (domain)
This family contains a wide variety of enzymes, principally thioesterases. These enzymes are part of the Hotdog fold superfamily. This domain represents the C-terminal domain in a pair of HotDog domains, usually found with [pfam:PF13622].
Pfam PF11531: Coactivator-associated arginine methyltransferase 1 N terminal (domain)
CARM1 is an arginine methyltransferase which methylates a variety of different proteins and plays a role in gene expression. This is the N terminal domain of the protein which has a PH domain, normally present to regulate protein-protein interactions.A molecular switch is also present on the N terminal domain.
Pfam PF05802: SPI-2 type 3 secretion system translocon protein SctB (family)
This entry represents a protein family that includes SPI-2 type 3 secretion system translocon protein SctB from Salmonella typhimurium (SctB2) and similar bacterial sequences. SctB2 is required for the translocation of SPI-2 effector proteins and for systemic Salmonella infection of the mouse. It is also essential for SpvB-induced actin depolymerisation in the host cell cytoplasm.
Pfam PF14933: CEP19-like protein (family)
This family includes the centrosomal protein of 19 kDa found in eukaryotes. In humans, it is encoded for by the gene CEP19 which is also known as C3orf34. These proteins localize in the centrosomes. Centrosomes are dynamic organelles that assemble around the centrioles. They organise the microtubule cytoskeleton and mitotic spindle apparatus and are required for cell division and cell migration. C3orf34 localizes near the centrosome in early interphase, to spindle poles during mitosis, and to distinct foci oriented towards the midbody at telophase.
Pfam PF17775: YchJ, middle NTF2-like domain (domain)
This entry represents the NTF2-like domain found in the functionally uncharacterised YchJ family protein from Psychrobacter arcticus  and related proteins.  This domain is usually found flanked by either ([pfam:PF21612]) and ([pfam:PF02810]) at the N and C terminus or flanked on both sides by ([pfam:PF02810]]). The structure of YchJ shows that this domain adopts structure typical for Nuclear transport factor 2 (NTF2) that consists of a curved three-stranded beta-sheet and array of alpha-helices packed on one side of it. The function of this domain is unknown.
Pfam PF08033: Sec23/Sec24 beta-sandwich domain (domain)
COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex . COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation .

Sec23 p and Sec24p are structurally related, folding into five distinct domains: a Î²-barrel, a zinc-finger (IPR006895), an Î±/Î² trunk domain (IPR006896), an all-helical region (IPR006900), and a C-terminal gelsolin-like domain (IPR007123). This entry describes part of the Sec23/24 Î²-barrel domain, which is formed from approximately 180 residues from three segments of the polypeptide. The strands of the barrel are oriented roughly parallel to the membrane such that one end of the barrel forms part of the inner surface of the coat and the other end part of the membrane-distal surface. The barrel is constructed from two opposed sheets: a six-stranded Î²-sheet facing partly towards the zinc finger domain and partly towards the solvent, and a five-stranded Î²-sheet facing the helical domain.
Pfam PF04539: Sigma-70 region 3 (family)
Region 3 forms a discrete compact three helical domain within the sigma-factor.  Region is not normally involved in the recognition of promoter DNA, but as some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role.  Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme.
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 PF24133: Domain of unknown function (DUF7400) (repeat)
This entry represents a domain of unknown function found towards the N-terminal of some PRiA4b ORF-3-like proteins from bacteria, such as SwissProt:A0A1I7K0M5. This domain may adopt a TPR-like fold and is generally associated to PriA4_ORF3 ([pfam:PF07929]) domain.
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 PF19517: Family of unknown function (DUF6050) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found mainly in Clostridia. Proteins in this family are typically between 103 and 122 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 PF18023: BDBT FKBP like N-terminal (domain)
This is the N-terminal domain of the beta chain found in Drosophila melanogaster protein BDBT (a FK506-Binding Protein) which stimulates the DBT circadian function. The domain contains the DBT-binding site. The domain is structurally homologous to the peptidyl prolyl isomerase (PPIase) regions of FK506-binding proteins despite low sequence homology. BDBT is structurally related to the immunophilin FKBP51 and it shares a common domain organization consisting of PPIase-like and TPR domains with noncanonical immunophilins such as FKBP38 or FKBPL.
Pfam PF10635: DisA bacterial checkpoint controller linker region (domain)
The DisA protein is a bacterial checkpoint protein that dimerises into an octameric complex. The protein consists of three distinct domains. the first, N-terminal region, from 1-145 is globular and is represented by family DisA_N, [pfam:PF02457]; the next 146-289 residues is this domain that consists of an elongated bundle of three alpha helices (alpha-6, alpha-10, and alpha-11), one side of which carries an additional three helices (alpha7-9), thus forming a spine like-linker between domains 1 and 3. The C-terminal residues of domain 3 are family HHH, [pfam:PF00633], the specific DNA-binding domain. The octameric complex thus has structurally linked nucleotide-binding and DNA-binding HhH domains and the nucleotide-binding domains are bound to a cyclic di-adenosine phosphate such that DisA is a specific di-adenylate cyclase. The di-adenylate cyclase activity is strongly suppressed by binding to branched DNA, but not to duplex or single-stranded DNA, suggesting a role for DisA as a monitor of the presence of stalled replication forks or recombination intermediates via DNA structure-modulated c-di-AMP synthesis.
Pfam PF17478: Rotavirus VP4 helical domain (domain)
This entry represents the C-terminal domain of VP4 . VP4 and VP7 are the two protein components of the outer protein layer of the virion of Rotavirus .
Pfam PF24147: SHIP1/2 second C2 domain (domain)
This entry represents the second C2 domain of Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatases 1/2. The C2 domains of these proteins modulate the activity of the phosphatase domain.
Pfam PF17681: Gamma tubulin complex component N-terminal (domain)
This is the N-terminal domain found in components of the gamma-tubulin complex proteins (GCPs). Family members include spindle pole body (SBP) components such as Spc97 and Spc98 which function as the microtubule-organizing center in yeast. Furthermore, family members such as human GCP4 (Gamma-tubulin complex component 4) have been structurally elucidated [swissprot:Q9UGJ1]. Functional studies have shown that the N-terminal domain defines the functional identity of GCPs, suggesting that all GCPs are incorporated into the helix of gamma-tubulin small complexes (gTURCs) via lateral interactions between their N-terminal domains. Thereby, they define the direct neighbors and position the GCPs within the helical wall of gTuRC. Sequence alignment of human GCPs based on the GCP4 structure helped delineate conserved regions in the N- and C-terminal domains. In addition to the conserved sequences, the N-terminal domains carry specific insertions of various sizes depending on the GCP, i.e. internal insertions or N-terminal extensions. These insertions may equally contribute to the function of individual GCPs as they have been implied in specific interactions with regulatory or structural proteins. For instance, GCP6 carries a large internal insertion phosphorylated by Plk4 and containing a domain of interaction with keratins, whereas the N-terminal extension of GCP3 interacts with the recruitment protein MOZART1.
Pfam PF01057: Parvovirus non-structural protein NS1 (domain)
This family also contains the NS2 protein. Parvoviruses encode two non-structural proteins, NS1 and NS2. The mRNA for NS2 contains the coding sequence for the first 87 amino acids of NS1, then by an alternative splicing mechanism mRNA from a different reading frame, encoding the last 78 amino acids, makes up the full length of the NS2 mRNA. NS1, is the major non-structural protein.  It is essential for DNA replication. It is an 83-kDa nuclear phosphoprotein.  It has DNA helicase and ATPase activity.
Pfam PF23579: Tubulin-specific chaperone D-like, ARM repeat (repeat)
This region is found at the N-terminal end of human Tubulin -specific chaperone D (TBCD), which is required for tubulin complex assembly and involved in the regulation of microtubule polymerisation or depolymerisation. It is predicted to fold into ARM-like repeats.
Pfam PF14327: Hinge domain of cleavage stimulation factor subunit 2 (family)
The hinge domain of cleavage stimulation factor subunit 2 proteins, CSTF2, is necessary for binding to the subunit CstF-77 within the polyadenylation complex and subsequent nuclear localisation. This suggests that nuclear import of a pre-formed CSTF complex is an essential step in polyadenylation. Accurate and efficient polyadenylation is essential for transcriptional termination, nuclear export, translation, and stability of eukaryotic mRNAs. CSTF2 is an important regulatory subunit of the polyadenylation complex.
Pfam PF18787: CRM1 / Exportin repeat 3 (repeat)
Chromosome region maintenance 1 / Exportin 1 mediates the nuclear  transport of proteins bearing a leucin-rich nuclear export signal  (NES). It contains helical repeats that are structurally similar to HEAT repeats, but share little sequence similarity with them. N-, C-terminal and central repeats show slightly different structural arrangements, with N- and C- terminal repeats interacting with each  other. This Pfam entry includes some CRM1 repeats that fail to be  detected with the PF18777 model.
Pfam PF14685: Tricorn protease PDZ domain (domain)
This domain is the PDZ domain of tricorn protease.
Pfam PF09926: Uncharacterized small protein (DUF2158) (family)
Members of this family of prokaryotic proteins have 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.