SII-SWORD/CoKE huggingface dataset:
Pfam PF00918: Gastrin/cholecystokinin family (family)
Gastrin and cholecystokinin (CCK) are structurally and functionally related peptide hormones that function as hormonal regulators of various digestive processes and feeding behaviors. They are known to induce gastric secretion, stimulate pancreatic secretion, increase blood circulation and water secretion in the stomach and intestine, and stimulate smooth muscle contraction. Originally found in the gut, these hormones have since been shown to be present in various parts of the nervous system. Like many other active peptides they are synthesized as larger protein precursors that are enzymatically converted to their mature forms. They are found in several molecular forms due to tissue-specific post-translational processing. The biological activity of gastrin and CCK is associated with the last five C-terminal residues. One or two positions downstream, there is a conserved sulphated tyrosine residue. The amphibian caerulein skin peptide, the cockroach leukosulphakinin I and II (LSK) peptides, Drosophila melanogaster (Fruit fly) putative CCK-homologues Drosulphakinins I and II, cionin, a Gallus gallus (Chicken) gastrin/cholecystokinin-like peptide and cionin, a neuropeptide from the protochordate Ciona intestinalis belong to the same family.
Wikipedia: Gastrin is a peptide hormone that stimulates secretion of gastric acid (HCl) by the parietal cells of the stomach and aids in gastric motility. It is released by G cells in the pyloric antrum of the stomach, duodenum, and the pancreas.
Pfam PF07804: HipA-like C-terminal domain (domain)
The members of this family are similar to a region close to the C-terminus of the HipA protein expressed by various bacterial species (for example [swissprot:P23874]). This protein is known to be involved in high-frequency persistence to the lethal effects of inhibition of either DNA or peptidoglycan synthesis. When expressed alone, it is toxic to bacterial  cells, but it is usually tightly associated with  HipB, and the HipA-HipB complex may be involved in autoregulation of the hip operon. The hip proteins may be involved in cell division control and may interact with  cell division genes or their products.
Pfam PF21609: Toxofilin-like domain (domain)
This domain is found in a group of sequences from eukaryotic parasites, including Toxofilin from Toxoplasma gondii, an actin-binding protein involved in invasion. This domain interacts with the host mammalian actin. It folds into five helices connected by loops.
Pfam PF15182: Otospiralin (family)
This family of proteins, Otospiralin, has a role in maintaining the neurosensory epithelium of the inner ear. This family of proteins is found in eukaryotes. Proteins in this family are approximately 90 amino acids in length.
Pfam PF11249: Protein of unknown function (DUF3047) (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 PF10014: 2OG-Fe dioxygenase (domain)
This family contains 2-oxoglutarate (2OG) and Fe-dependent dioxygenases. It includes L-isoleucine dioxygenase (IDO).
Pfam PF15767: Armadillo-like helical domain-containing protein 4 (family)
This family represents the Armadillo-like helical domain-containing protein 4, whose function is not clear.
Pfam PF04130: Gamma tubulin complex component C-terminal (domain)
This is the C-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] . Structure-based sequence analysis revealed the existence of an exposed surface area conserved in all human GCPs and in GCP4 orthologs. This area is located in the C-terminal domain of GCP4, which was confirmed in vitro to bind directly to gamma-tubulin. Sequence alignment of human GCPs based on the GCP4 structure helped delineate conserved regions in the N- and C-terminal domains.
Pfam PF12497: Estrogen receptor beta (family)
This domain family is found in eukaryotes, and is approximately 110 amino acids in length. The family is found in association with [pfam:PF00104], [pfam:PF00105]. There is a conserved IPS sequence motif.  There are two completely conserved residues (Y and W) that may be functionally important. ERbeta binds estrogens with an affinity similar to that of ERalpha, and activates expression of reporter genes containing estrogen response elements in an estrogen-dependent manner. ERbeta acts as a transcription factor once bound to its ligand and it can dimerise with ERalpha.
Pfam PF24685: RRP5 OB-fold domain (domain)
This domain is found in the rRNA biogenesis protein RRP5 from Arabidopsis thaliana and related proteins. RRP5 is involved in the biogenesis of ribosomal RNA (rRNA). It is required for the formation of 5.8S rRNA and for normal development of female gametophytes. This domain has a detectable similarity to OB fold domains, in particular to OB domain of 30S ribosomal protein S1 and it is predicted to adopt similar structure.
Pfam PF24825: SNU71 RNA binding domain (domain)
This entry represents the RNA binding domain (RBD, also known as RNA recognition motif, RRM) found in U1 small nuclear ribonucleoprotein component SNU71 from yeast, which is a component of the U1 snRNP particle that recognises and binds the 5'-splice site of pre-mRNA.
Pfam PF18581: Synaptonemal complex 2 armadillo-repeat-like domain (repeat)
Synaptonemal complex protein 2 (SYCP2) N-terminal region contains two separate subdomains an ARLD (armadillo-repeat-like domain) and an SLD (Spt16M-like domain). The ARLD domain belongs to the armadillo-repeat protein family. Armadillo-repeat units often form a superhelix, which typically provides a platform for many protein partners that transduce Wnt signaling, such as beta-catenin. The ARLD of mouse SYCP2 was found to associate with different protein partners, including CENP J and CENP F. ARLD structure is highly similar to that of the 'required for cell differentiation (RCD-1)' protein.
Pfam PF22479: Cyanophage baseplate Pam3 plug gp18 (domain)
This family, previously known as DUF6983, represents Cyanophage baseplate Pam3 plug gp18 and related proteins. Gp18 has structural similarity to a component of the baseplate Complex for Myoviridae Phage XM1. The cyanophage Pam3 has a substantially simpler molecular organisation than the prototypical, contractile-tail bacteriophage T4, but it retains the essential elements required for DNA injection. The baseplate of Pam3 contains six protein components: the trimeric spike gp20, the trimeric hub gp19, the baseplate wedge (six heterotriplexes of gp22-gp23), the plug of six gp18 monomers, and the fibers (12 trimers of gp24). The plug gp18 consists of two-layered beta-sheets and a C-terminal alpha-helix, resembling the immunoglobin fold. Each plug monomer is embedded between the two C-terminal helices of the tube initiator, forming a 'plug' to fix the core helical bundle of the wedge onto the hub
Pfam PF16166: Chloroplast import apparatus Tic20-like (family)
Chloroplast function requires the import of nuclear encoded proteins from the cytoplasm across the chloroplast double membrane. This is accomplished by two protein complexes, the Toc complex located at the outer membrane and the Tic complex located at the inner membrane. The Toc complex recognises specific proteins by a cleavable N-terminal sequence and is primarily responsible for translocation through the outer membrane, while the Tic complex translocates the protein through the inner membrane. This entry represents Tic20, a core member of the Tic complex. This protein is deeply embedded in the inner envelope membrane and is thought to function as a protein- conducting component of the Tic complex.
Pfam PF09750: Alternative splicing regulator (domain)
This entry represents the conserved N-terminal region of SWAP (suppressor-of-white-apricot protein) proteins.  This region contains two highly conserved motifs, viz: DRY and EERY, which appear to be the sites for alternative splicing of exons 2 and 3 of the SWAP mRNA. These proteins are thus thought to be involved in auto-regulation of pre-mRNA splicing. Most family members are associated with two Surp domains [pfam:PF01805] and an Arginine- serine-rich binding region towards the C-terminus.
Pfam PF15897: Domain of unknown function (DUF4741) (family)
Proteins in this family are also known as FAM231. Their 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 PF20452: Calmodulin binding protein C-terminal domain (domain)
The members of this family are putative or actual calmodulin binding proteins expressed by various plant  species. Some members (for example, [swissprot:Q8H6T7]), are known to be involved in the induction of plant defence responses. However, their precise function in this regards is as yet unknown.
Pfam PF09374: Predicted Peptidoglycan domain (domain)
This family contains a potential peptidoglycan binding domain.
Pfam PF20291: ABC-three component (ABC-3C) system Middle Component 5 (family)
Middle Components (MCs) of the ABC-3C biological conflict systems occupy the central position between the catalytic effector and ABC ATPases of the systems. MCs are defined by distinctive patterns of conserved charged residues. As some MCs are HTH domains, they are predicted to function akin to kleisins as DNA-binding partners for the ABC ATPases, assisting in recognition and responding to invasive elements such as DNA viruses.
Pfam PF24936: Domain of unknown function (DUF7753) (domain)
This is a presumed domain found at the C-terminal of a group of worm proteins. This domain may adopt a hairpin fold.
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 PF08177: Small acid-soluble spore protein N family (family)
This family consists of the small acid-soluble spore protein (SASP) N type (sspN). SspN is a 48 residues protein that is expressed only in the forespore compartment of sporulating Bacillus subtilis. The sspN gene is recognised equally by both sigma-G and sigma-F. The role of SspN is still not well-defined.
Pfam PF18190: Polo-like Kinase 4 Polo Box 1 (domain)
This domain is found in Polo-like kinase 4 (Plk4) present in Drosophila melanogaster. Plk4 is a conserved component in the duplication pathway of centrioles which is needed to prevent chromosomal instability. The domain is Polo Box 1 (PB1) and has a pseudo-symmetric dimerization interface across PB1-PB1.
Wikipedia: Polo-like kinases (Plks) are regulatory serine/threonine kinases of the cell cycle involved in mitotic entry, mitotic exit, spindle formation, cytokinesis, and meiosis. Only one Plk is found in the genomes of the fly Drosophila melanogaster (Polo), budding yeast (Cdc5) and fission yeast (Plo1). Vertebrates and other animals, however, have many Plk family members including Plk1, Plk2/Snk, Plk3/Prk/FnK, Plk4/Sak and Plk5. Of the vertebrate Plk family members, the mammalian Plk1 has been most extensively studied. During mitosis and cytokinesis, Plks associate with several structures including the centrosome, kinetochores, and the central spindle.
Pfam PF05299: M61 glycyl aminopeptidase (family)
Glycyl aminopeptidase is an unusual peptidase in that it has a preference for substrates with an N-terminal glycine or alanine. These proteins are found in Bacteria and in Archaea.
Pfam PF10012: Uncharacterized protein conserved in bacteria (DUF2255) (family)
Members of this family of hypothetical bacterial 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.
Pfam PF14710: Respiratory nitrate reductase alpha N-terminal (domain)
This is the N-terminal tail of the respiratory nitrate reductase alpha chain. The nitrate reductase complex is a dimer of heterotrimers each consisting of an alpha, beta and gamma chain. The N-terminal tail of the alpha chain interacts with the beta chain and contributes to the stability of the heterotrimer.
Pfam PF05825: Beta-microseminoprotein (PSP-94) (domain)
This family consists of the mammalian specific protein beta-microseminoprotein. Prostatic secretory protein of 94 amino acids (PSP94), also called beta-microseminoprotein, is a small, nonglycosylated protein, rich in cysteine residues. It was first isolated as a major protein from human seminal plasma. The exact function of this protein is unknown.
Pfam PF24498: TMEM131L third Ig-like domain (domain)
Transmembrane protein 131-like (TMEM131L) was identified as a negative regulator of thymocyte proliferation that acts through mixed Wnt-dependent and independent mechanisms. It has two isoforms, L and S, which have different subcellular localisation. L isoform, the membrane-associated form, inhibits canonical Wnt/beta-catenin signalling through the induction of lysosome-dependent degradation of the active phosphorylated form of the LRP6 coreceptor. This protein was firstly described as containing three conserved homology domains (CHD1, 2 and 3), a transmembrane region and a C-terminal serine-rich region. Using structure prediction models from AlphaFold, it has been possible to identify the CHDs as Ig-like domains. This entry represents the third Ig-like domain of TMEM131L and the fourth in TMEM131. TMEM131 is a collagen binding transmembrane protein involved in collagen secretion by recruiting the ER-to-Golgi transport complex TRAPPIII.
Pfam PF03363: Herpesvirus leader protein (family)
This entry contains Epstein-Barr virus EBNA-LP protein. It is a protein involved in latency whose function is not fully understood. The protein contains three domains, each of which contains conserved serine residues within conserved regions (CR1 to CR3). These regions are essential for the EBNA2 cooperativity function. The domains have a bipartite nuclear localisation signal and nuclear localisation of EBNA-LP is essential for EBNA2 cooperativity function. .
Pfam PF22344: Regulatory protein SIR3, C-terminal domain (domain)
This domain is found at the C-terminal end of Regulatory protein SIR3 from Saccharomyces cerevisiae and similar fungal proteins. SIR3 is essential for gene silencing. It is organised into a highly conserved N-terminal BAH domain ([pfam:PF01426]), a C -terminal AAA+ ATPase-like domain ([pfam:PF17872]), plus an extreme C-terminal domain (this entry). This domain form a winged helix-turn-helix (HTH) variant with a strong homodimerisation function but without the ability to bind DNA.
Pfam PF12415: Poxvirus DNA dependent RNA polymerase (family)
This domain family is found in viruses, and is approximately 30 amino acids in length. The family is found in association with [pfam:PF04566], [pfam:PF00562], [pfam:PF04567], [pfam:PF04560], [pfam:PF04565]. This family is the second largest subunit of the poxvirus DNA dependent RNA polymerase. It has structural similarity to the second-largest RNA polymerase subunits of eubacteria, archaebacteria, and eukaryotes.
Pfam PF24306: THSD1 N-terminal domain (domain)
This domain is found N-terminal in human Thrombospondin type-1 domain-containing protein 1 (THSD1) and related proteins. THSD1 is involved in endothelial cell to extracellular matrix adhesion.  THSD1 forms a multimeric protein complex with FAK/talin/ vinculin, wherein THSD1 promotes talin binding to FAK but not to vinculin, a key step in nascent adhesion assembly. The domain represented by this entry is predicted to adopt Ig-like beta-sandwich.
Pfam PF14848: DNA-binding domain (domain)
This entry includes uncharacterised bacterial proteins, such as the hypothetical protein Bvu_2165 from Bacteroides vulgatus. These proteins consist of two domains, an N-terminal one similar to DNA sequence specific (integration host factor) IHF and non-specific (HU) domains which is represented in this entry, and a C-terminal Ig-like domain (IPR027824).
Pfam PF08454: RyR and IP3R Homology associated (repeat)
This eukaryotic domain is found in ryanodine receptors (RyR) and inositol 1,4,5-trisphosphate receptors (IP3R) which together form a superfamily of homotetrameric ligand-gated intracellular Ca2+ channels.  There seems to be no known function for this domain. Also see the IP3-binding domain [pfam:PF01365] and [pfam:PF02815].
Pfam PF04550: Phage holin family 2 (family)
Holins are a diverse family of proteins that cause bacterial membrane lysis during late-protein synthesis. It is thought that the temporal precision of holin-mediated lysis may occur through the buildup of a holin oligomer which causes the lysis.
Pfam PF08741: YwhD family (family)
This family of proteins are currently uncharacterised.  They are around 170 amino acids in length.
Pfam PF16370: C terminal of Calcineurin-like phosphoesterase (family)
This is the C-terminal of Calcineurin-like phosphoesterases. It is around 150 residues in length from various Bacteroides species. The function of this family is unknown.
Pfam PF04144: SCAMP family (family)
In vertebrates, secretory carrier membrane proteins (SCAMPs) 1-3 constitute a family of putative membrane-trafficking proteins composed of cytoplasmic N-terminal sequences with NPF repeats, four central transmembrane regions (TMRs), and a cytoplasmic tail. SCAMPs probably function in endocytosis by recruiting EH-domain proteins to the N-terminal NPF repeats but may have additional functions mediated by their other sequences.
Pfam PF07614: Protein of unknown function (DUF1577) (family)
A family of hypothetical proteins in Leptospira interrogans.
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 PF20006: YukD-like N-terminal domain (domain)
Uncharacterized domain found N-terminal to YukD-like Ubiquitin domain in FtsH ternary systems, a class of NTP-dependent biological conflict systems.
Pfam PF10829: Protein of unknown function (DUF2554) (family)
This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.
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 PF17881: Domain of unknown function (DUF5590) (domain)
This is a domain of unknown function found in bacterial 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 PF16454: Phosphatidylinositol 3-kinase regulatory subunit P85 inter-SH2 domain (domain)
This domain is found between the two SH2 domains in phosphatidylinositol 3-kinase regulatory subunit P85. It forms a complex with the adaptor-binding domain of phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha.
Pfam PF16135: Tify domain binding domain (domain)
This entry contains a C-terminal presumed zinc binding domain from the NINJA protein which interacts with the Tify domain of JAZ1.
Pfam PF16794: Fibronectin-III type domain (domain)
This entry represents the Fibronectin type III (Fn3) domain found in Activating transcription factor 7-interacting protein (MCAF) family of proteins.
Activating transcription factor 7-interacting protein (MCAF) family consists of MCAF1 and MCAF2 .

MCAF1 (also known as MBD1-containing chromatin-associated factor 1) is a recruiter that couples transcriptional factors to general transcription apparatus and thereby modulates transcription regulation and chromatin formation. It can both act as an activator or a repressor depending on the context .
Wikipedia: The Fibronectin type III domain  is an evolutionarily conserved protein domain that is widely found in animal proteins. The fibronectin protein in which this domain was first identified contains 16 copies of this domain. The domain is about 100 amino acids long and possesses a beta sandwich structure. Of the three fibronectin-type domains, type III is the only one without disulfide bonding present. Fibronectin domains are found in a wide variety of extracellular proteins. They are widely distributed in animal species, but also found sporadically in yeast, plant and bacterial proteins.
Pfam PF11800: Replication protein C C-terminal region (family)
Replication protein C is involved in the early stages of viral DNA replication.
Pfam PF13158: Protein of unknown function (DUF3993) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 160 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 PF16935: Putative Holin-like Toxin (Hol-Tox) (family)
Hol_Tox is a family of small proteins (34-48aas) with a single TM region. Members can exhibit antibacterial activity against Gram-positive bacteria but not against Gram-negative bacteria.
Pfam PF16209: Phospholipid-translocating ATPase N-terminal (family)
PhoLip_ATPase_N is found at the N-terminus of a number of phospholipid-translocating ATPases.  It is found in higher eukaryotes.