SII-SWORD/CoKE huggingface dataset:
Pfam PF25009: Domain of unknown function (DUF7785) (domain)
This is a presumed domain found in a group of uncharacterised fungal sequences.
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 PF12931: Sec16 Sec23-binding domain (repeat)
COPII coat assembly protein sec16 (Sec16) is a multi-domain vesicle coat protein that binds to COPII-coated vesicles, regulating the transport of secretory proteins from the endoplasmic reticulum. This entry represents the C-terminal domain of Sec16 from eukaryotes and related sequences such as Protein transport protein Sec16A-B and Sec31A-B. This domain adopts a TPR-like fold and has been shown to act as a protein-protein interaction platform that binds Sec23. This interaction is regulated by alternative splicing upon T-cell activation to control protein secretion. Sec16 has also been shown to respond to nutrient signalling, coupling environmental stimuli to secretory capacity.
Pfam PF06037: Bacterial protein of unknown function (DUF922) (family)
This family of proteins has a conserved HEXXH motif, suggesting they are putative peptidases of zincin 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 PF00053: Laminin EGF domain (domain)
This family is like [pfam:PF00008] but has 8 conserved  cysteines instead of six.
Wikipedia: Laminins are a family of glycoproteins of the extracellular matrix of all animals. They are major constituents of the basement membrane, namely the basal lamina. Laminins are vital to biological activity, influencing cell differentiation, migration, and adhesion.
Pfam PF02447: GntP family permease (family)
This is a family of integral membrane permeases that are involved in gluconate uptake. E. coli contains several members of this family including GntU [swissprot:P46858] a low affinity transporter and GntT [swissprot:P39835] a high affinity transporter.
Wikipedia: The gluconate:H+ symporter (GntP) family (TC# 2.A.8) is a family of transport proteins belonging to the ion transporter (IT) superfamily. Members of the GntP family include known gluconate permeases of E. coli and Bacillus species such as the D-Gluconate:H+ symporter of Bacillus subtillus (GntP; TC# 2.A.8.1.1) and the D-fructuronate/D-gluconate:H+ symporter of E. coli (GntP; TC# 2.A.8.1.3). A representative list of proteins belonging to the GntP family can be found in the Transporter Classification Database.
Pfam PF24192: Domain of unknown function (DUF7417) (domain)
This entry represents an uncharacterized protein domain found in various phage and bacterial proteins. The domain is approximately 60-80 amino acids in length. The domain is composed of four alpha helices that form a small bundle. The surface of the domain is negatively charged.
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 PF13094: CENP-Q, a CENPA-CAD centromere complex subunit (family)
CENP-Q is one of the components that assembles onto the CENPA-nucleosome distal (CAD) centromere. The centromere, which is the basic element of chromosome inheritance, is epigenetically determined in mammals. CENP-A, the centromere-specific histone H3 variant, assembles an array of nucleosomes and it is this that seems to be the prime candidate for specifying centromere identity. CENPA nucleosomes directly recruit a proximal CENPA-nucleosome-associated complex (NAC) comprised of CENP-M, CENP-N and CENP-T, CENP-U(50), CENP-C and CENP-H. Assembly of the CENPA NAC at centromeres is dependent on CENP-M, CENP-N and CENP-T. Additionally, there are seven other subunits which make up the CENPA-nucleosome distal (CAD) centromere, CENP-K, CENP-L, CENP-O, CENP-P, CENP-Q, CENP-R and CENP-S, also assembling on the CENP-A NAC. Fta7 is the equivalent component of the fission yeast Sim4 complex.
Pfam PF21952: PRKCH upstream open reading frame 2 (family)
This protein family represents human PRKCH upstream open reading frame 2 (PRKCH_uORF2), also known as Protein uPEP2, the product of an upstream open reading frame (uORF). PRKCH_uORF2 exhibits kinase inhibitory functions. It possesses the typical PKC pseudosubstrate motif present in all PKCs that autoinhibits their kinase activity.
Pfam PF22910: Enhanced disease resistance 4-like, N-terminal domain (domain)
This domain is found at the N-terminal end of Protein Enhanced disease resistance 4 from Arabidopsis thaliana (EDR4), which plays a negative role in salicylic acid (SA)-mediated resistance to powdery mildew. It is predicted to adopt an all-beta structure.
Pfam PF15997: Domain of unknown function (DUF4772) (family)
This presumed domain is functionally uncharacterised. This domain family is found in eukaryotes, and is typically between 107 and 124 amino acids in length. There is a single completely conserved residue V that may be functionally important.
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 PF05733: Tenuivirus/Phlebovirus nucleocapsid protein (family)
This family consists of several Tenuivirus and Phlebovirus nucleocapsid proteins. These are ssRNA viruses. In crystal structures the nucleocapsid protein from the Rift Valley fever virus (RVFV) displays a ring-shaped oligomeric assembly. Electron microscopy (EM) also demonstrates that, in complex with  RNA, the RVFV nucleocapsid protein forms rings in solution.
Pfam PF01715: IPP transferase (domain)
This is a family of IPP transferases [ec:2.5.1.8] also known as tRNA delta(2)-isopentenylpyrophosphate transferase. These enzymes modify both cytoplasmic and mitochondrial tRNAs  at A(37) to give isopentenyl A(37).
Pfam PF09103: BRCA2, oligonucleotide/oligosaccharide-binding, domain 1 (domain)
Members of this family assume an OB fold, which consists of a highly curved five-stranded beta-sheet that closes on itself to form a beta-barrel. OB1 has a shallow groove formed by one face of the curved sheet and is demarcated by two loops, one between beta 1 and beta 2 and another between beta 4 and beta 5, which allows for weak single strand DNA binding. The domain also binds the 70-amino acid DSS1 (deleted in split-hand/split foot syndrome) protein, which was originally identified as one of three genes that map to a 1.5-Mb locus deleted in an inherited developmental malformation syndrome.
Wikipedia: BRCA2 and BRCA2 are human genes and their protein products, respectively. The official symbol and the official name are maintained by the HUGO Gene Nomenclature Committee. One alternative symbol, FANCD1, recognizes its association with the FANC protein complex. Orthologs, styled Brca2 and Brca2, are common in other vertebrate species. BRCA2 is a human tumor suppressor gene, found in all humans; its protein, also called by the synonym breast cancer type 2 susceptibility protein, is responsible for repairing DNA.
Pfam PF01943: Polysaccharide biosynthesis protein (family)
Members of this family are integral membrane proteins. Many members of the family are implicated in production of polysaccharide. The family includes RfbX part of the O antigen biosynthesis operon. The family includes SpoVB from Bacillus subtilis [swissprot:Q00758], which is involved in spore cortex biosynthesis.
Pfam PF01076: Plasmid recombination enzyme (family)
With some plasmids, recombination can occur in a site specific manner that is independent of RecA. In such cases, the recombination event requires another protein called Pre. Pre is a plasmid recombination enzyme. This protein is also known as Mob (conjugative mobilisation). This family is also known as Mob-V. One of the family members, MobM, is encoded by a promiscuous plasmid actively involved in the spread of antibiotic resistance. Homologs of MobM are found in many plasmids and other mobile genetic elements of pathogenic bacteria, including S. aureus. MobM is a metal-dependent nuclease that uses histidine nitrogen for the nucleophilic attack on the scissile phosphate. Furthermore, in contrast to other DNA-processing enzymes, MobM is a histidine relaxase, a DNA-breaking and -joining enzyme, that operates through a phosphorus-nitrogen protein-DNA adduct for cell-to-cell DNA transfer. Mutational analysis indicate that the H(N/D)(Q/E)R N-terminal motif of MobM plays a crucial role in the cleavage and generation of stable DNA-protein adducts.
Pfam PF18630: Peptidase M60 C-terminal domain (domain)
This is C-terminal domain (CTD) of M60-peptidases [pfam:PF13402].  It Can also be found at the C-terminal region of gingipain B (RgpB) from P. gingivalis. It was found to possess a typical Ig-like fold encompassing seven antiparallel beta-strands organized in two beta-sheets, packed into a beta-sandwich structure that can spontaneously dimerise through C-terminal strand swapping. Translocation of gingipains from the periplasm across the OM is dependent on the conserved CTD, which appears to be important for secretion of the proteins and in particular, truncation of the last few C-terminal residues of this domain leads to accumulation of gingipains in the periplasm. Subsequently, the T9SS targeting signal was demonstrated to reside within the last 22 residues at the C-terminus of the CTD. During gingipain translocation across the OM, the CTD is cleaved off by PorU.
Pfam PF10652: Protein of unknown function (DUF2480) (family)
All the members of this family are uncharacterised proteins, but the environment in which they are found on the bacterial genome suggests a function as a glucose-6-phosphate isomerase (EC 5.3.1.9).  This could not, however, be confirmed.
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 PF06906: Protein of unknown function (DUF1272) (family)
This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its 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 PF02823: ATP synthase, Delta/Epsilon chain, beta-sandwich domain (domain)
Part of the ATP synthase CF(1). These subunits are part of the head unit of the ATP synthase. The subunit is called epsilon in bacteria and delta in mitochondria.  In bacteria the delta (D) subunit is equivalent to the mitochondrial Oligomycin sensitive subunit, OSCP ([pfam:PF00213]).
Pfam PF23069: Domain of unknown function (DUF7042) (domain)
This domain is found in a group of uncharacterised metazoan proteins. It is predicted to adopt a globular structure with lipocalin fold. It also contains several highly conserved cysteine residues that are likely involved in the formation of intra-domain disulfide bridges.
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 PF12085: Protein of unknown function (DUF3562) (family)
This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 62 to 84 amino acids in length. This protein has two completely conserved residues (A and Y) that may be functionally important.
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 PF21582: Carbohydrate binding domain 30 (domain)
This carbohydrate binding domain is found at the N-terminal end of Glycoside hydrolase family 9 (GH9) from Acetivibrio thermocellus ([swissprot:A3DD30]). This protein contains GH9 and GH44 as catalytic modules ([pfam:PF00759] and [pfam:PF12891]). It also presents a family 30 carbohydrate binding domain (CBM30), which displays affinity for beta-1,4-glucopolymers and plays a pivotal role in the function of of GH9, a typical processive endoglucanase. This domain adopts a beta-sandwich fold with two five-stranded beta-sheets.
Pfam PF13327: Type III secretion system subunit (family)
This is a family of bacterial putative type III secretion apparatus proteins associated with the locus of enterocyte effacement (LEE).
Pfam PF14944: Tongue Cancer Chemotherapy Resistant Protein 1 (family)
This family of proteins are found in eukaryotes. Tongue Cancer Chemotherapy Resistant-associated Protein 1 (TCRP1) is resistant to the chemotherapy drug, cisplatin, which induces apoptosis in tumour cells. There is suggestion that TCRP1 can be targeted to reverse chemotherapy resistance. The precise mechanism of TCRP1 inducing resistance against chemotherapy is still not clear, but it is thought that TCRP1 alters cell signalling pathways affecting apoptosis or DNA repair capacity. Proteins in this family are typically between 194 and 235 amino acids in length.
Pfam PF11855: Protein of unknown function (DUF3375) (family)
This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 479 to 499 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 PF09590: Lentivirus surface glycoprotein (family)
This protein is found in feline immunodeficiency retrovirus. It represents the surface glycoprotein which is found in the polyprotein C-terminal to the Env protein.
Pfam PF10238: E2F-associated phosphoprotein (family)
This entry represents the conserved C-terminal portion of an E2F binding protein. E2F transcription factors play an essential role in cell proliferation and apoptosis and their activity is frequently deregulated in human cancers. E2F activity is regulated by a variety of mechanisms, frequently mediated by proteins binding to individual members or a subgroup of the family. EAPP interacts with a subset of E2F factors and influences E2F-dependent promoter activity. EAPP is present throughout the cell cycle but disappears during mitosis.
Pfam PF02249: Methyl-coenzyme M reductase alpha subunit, C-terminal domain (domain)
Methyl-coenzyme M reductase (MCR) is the enzyme responsible for microbial formation of methane. It is a hexamer composed of 2 alpha (this family), 2 beta ([pfam:PF02241]), and 2 gamma ([pfam:PF02240]) subunits with two identical nickel porphinoid active sites. The C-terminal domain is comprised of an all-alpha multi-helical bundle.
Pfam PF07209: Protein of unknown function (DUF1415) (family)
This family consists of several hypothetical bacterial proteins of around 180 residues in length. 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 PF23577: LysM domain (domain)
This entry represents a set of LysM domains found in the LysM domain receptor-like kinase family is involved in innate immunity and symbiotic interactions in plants. Members of this family function as cell surface receptors that recognize specific molecular patterns associated with microbial activity, such as chitin oligosaccharides and peptidoglycans. These receptors play crucial roles in plant defense by detecting pathogen-associated molecular patterns (PAMPs) and microbe-associated molecular patterns (MAMPs), leading to the activation of defense genes. They are also involved in symbiotic relationships, such as the nitrogen-fixing root nodule symbiosis with rhizobia, by recognizing Nod factor signals. The family includes kinases that phosphorylate downstream partners in response to elicitation, mediating signal transduction from the extracellular to intracellular spaces and contributing to resistance against pathogenic fungi and bacteria.
Pfam PF02979: Nitrile hydratase, alpha chain (domain)
Nitrile hydratases (4.2.1.84) are bacterial enzymes that catalyse the hydration of nitrile compounds to the corresponding amides. They are used as biocatalysts in acrylamide production, one of the few commercial scale bioprocesses, as well as in environmental remediation for the removal of nitriles from waste streams. Nitrile hydratases are composed of two subunits, alpha and beta, and are normally active as a tetramer, Î±(2)Î²(2). Nitrile hydratases contain either a non-haem iron or a non-corrinoid cobalt centre, both types sharing a highly conserved peptide sequence in the alpha subunit (CXLCSC) that provides all the residues involved in coordinating the metal ion. Each type of nitrile hydratase specifically incorporated its metal with the help of activator proteins encoded by flanking regions of the nitrile hydratase genes that are necessary for metal insertion. The Fe-containing enzyme is photo-regulated: in the dark the enzyme is inactivated due to the association of nitric oxide (NO) to the iron, while in the light the enzyme is active by photo-dissociation of NO. The NO is held in place by a claw setting formed through specific oxygen atoms in two modified cysteines and a serine residue in the active site . The cobalt-containing enzyme is unaffected by NO, but was shown to undergo a similar effect with carbon monoxide . Fe-and cobalt-containing enzymes also display different inhibition patterns with nitrophenols.

Thiocyanate hydrolase (SCNase) is a cobalt-containing metalloenzyme with a cysteine-sulphinic acid ligand that hydrolyses thiocyanate to carbonyl sulphide and ammonia .

The two enzymes, nitrile hydratase and SCNase, are homologous over regions corresponding to almost the entire coding regions of the genes: the beta and alpha subunits of thiocyanate hydrolase were homologous to the amino-and carboxyl-terminal halves of the beta subunit of nitrile hydratase, and the gamma subunit of thiocyanate hydrolase was homologous to the alpha subunit of nitrile hydratase .
This entry represents the structural domain of the alpha subunit of both iron- and cobalt-containing nitrile hydratases; the alpha subunit is a duplication of two structural repeats, each consisting of 4 layers, Î±/Î²/Î²/Î± . This structure is also found in the related protein, the gamma subunit of thiocyanate hydrolase (SCNase).
Wikipedia: Nitrile hydratases are mononuclear iron or non-corrinoid cobalt enzymes that catalyse the hydration of diverse nitriles to their corresponding amides:R-C≡N + H2O → R-C(O)NH2
Pfam PF06338: ComK protein (family)
This family consists of several bacterial ComK proteins. The ComK protein of Bacillus subtilis positively regulates the transcription of several late competence genes as well as comK itself. It has been found that ClpX plays an important role in the regulation of ComK at the post-transcriptional level.
Pfam PF16026: Mitochondria-eating protein (family)
This domain is found at the C-terminus of mitochondria-eating proteins. This family of proteins regulate mitochondrial quality. They have a role in the degradation of damaged mitochondrial proteins and in the degradation of damaged mitochondria.
Pfam PF21364: Fibrillin, first EGF domain (domain)
Fibrillins are the primary constituents of the microfibrills in the extracellular matrix of many elastic and non-elastic connective tissues. They consists of an N-terminal fibrillin unique domain (FUN) ([pfam:PF18193]) and several calcium-binding epidermal growth factor-like (cbEGF-like) domains. This entry represents the first EGF-like domain which together with FUN, contributes to the binding to cbEGFs.
Pfam PF15756: Small Novel Rich in Cartilage (family)
This family of proteins is found in eukaryotes and include SNORC, a cartilage specific small membrane proteoglycan that plays a role in the regulation of chondrocyte maturation and postnatal endochondral ossification. There are two conserved sequence motifs: LGPGAI and LRKF.
Pfam PF15064: CATSPERG beta-propeller domain (repeat)
The CATSPER (cation channel of sperm) complex is a tetrameric complex consisting of CATSPER1, CATSPER2, CATSPER3 and CATSPER4, it functions as an alkalinisation-activated calcium channel. This complex is involved in sperm cell hyperactivation, a process needed for sperm motility, which is essential late in the preparation of sperm for fertilisation. This complex requires four auxiliary subunits (beta, gamma, delta and epsilon), which play a role in channel assembly. These are multidomain proteins which share a similar domain organisation. This entry represents the beta-propeller domain of the gamma subunit (CATSPERG).
Wikipedia: The cation channels of sperm also known as Catsper channels or CatSper, are ion channels that are related to the two-pore channels and distantly related to TRP channels. The four members of this family form voltage-gated Ca2+ channels that seem to be specific to sperm. As sperm encounter the more alkaline environment of the female reproductive tract, CatSper channels become activated by the altered ion concentration. These channels are required for proper fertilization. The study of these channels has been slow because they do not traffic to the cell membrane in many heterologous systems.