SII-SWORD/CoKE huggingface dataset:
Pfam PF07420: Protein of unknown function (DUF1509) (family)
This family consists of several uncharacterised viral proteins from the Marek's disease-like viruses. Members of this family are typically around 400 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 PF23468: Plastid division regulator alpha solenoid domain (repeat)
This entry represents the alpha helical solenoid domain of the Plastid Division Regulators family that is involved in the coordination and regulation of plastid division in plants. Members of this family function as key components of the plastid division machinery, which is responsible for the constriction and division of plastids, including chloroplasts and non-green plastids. They play roles in the placement of division sites, formation of FtsZ rings, and regulation of FtsZ assembly dynamics. The family includes proteins that act as antagonistic regulators, influencing the interaction between FtsZ proteins and other division components, such as ARC3 and ARC6. They are also involved in stromule biogenesis and may contribute to plant gravitropism.
Pfam PF23816: Family of unknown function (DUF7187) (family)
This entry represents a family of small proteins of around 60 residues found in Omarvirus and related bacteriophages that infect Streptomyces species. The function of this protein family is currently unknown.  Homologous proteins are also found in a small number of Streptomyces genomes.  The AlphaFold model of A0A7G7BJ30 shows a pair of alpha helices at the C-terminus of the protein.
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 PF11783: Cytochrome c bacterial (family)
This is a family of long bacterial cytochrome c proteins, found in Proteobacteria and Chlorobi families.
Pfam PF08139: Prokaryotic membrane lipoprotein lipid attachment site (conserved_site)
In prokaryotes, membrane lipoproteins are synthesized with a precursor signal peptide, which is cleaved by a specific lipoprotein signal peptidase (signal peptidase II). The peptidase recognizes a conserved sequence and cuts upstream of a cysteine residue to which a glyceride-fatty acid lipid is attached. Analysis of lipoprotein and non-lipoprotein signal peptides reveals that the two classes differ significantly only in the region close to the signal peptidase cleavage site. This region is apolar and has the consensus sequence LA(G,A) 1C in the lipoproteins, but is polar and has small, uncharged residues in positions - 3 and - 1 in the non-lipoproteins. Specialised signal peptide containing a lipobox motif in the carboxyl region of the signal peptide carries a cysteine residue which is the invariable target for lipidation by lipoprotein diacylglyceryl transferase (Lgt). Lipidation at this residue serves to anchor the lipoprotein to the membrane. Lipidation has been considered to be a prerequisite for the action of lipoprotein signal peptidase (Lsp), which removes the signal peptide and leaves the cysteine of the lipobox as the new amino-terminal residue of the mature lipoprotein.
Pfam PF14925: Domain of unknown function (family)
Members of this family carry two distinct, highly conserved sequence motifs, CPPPLYYTHL and HPHLAWLY. The family is found in eukaryotes, and the function is not known. This family lies at the C-terminus of members.
Pfam PF10629: Ciliary microtubule inner protein 2B-like (domain)
This family represents a domain found in human Ciliary microtubule inner protein 2B (CMI2B) and similar proteins from eukaryotes. CMI2B is a microtubule inner proteins (MIP) that form part of the dynein-decorated doublet microtubules (DMTs) in cilia axoneme, which is required for motile cilia beating. This domain is a tubulin-binding domain. Some proteins contain multiple copies of this domain.
Pfam PF01730: UreF (family)
This family consists of the Urease accessory protein  UreF. The urease enzyme (urea amidohydrolase) hydrolyses urea into ammonia and carbamic acid.  UreF is proposed to modulate the activation process of urease by eliminating the binding of nickel irons to  noncarbamylated protein.
Pfam PF15107: FAM216B protein family (family)
The function of this family of proteins, FAM216B, has not, as yet, been determined. Members of this family are as yet uncharacterised. This family of proteins are found in eukaryotes. Proteins in this family are approximately 150 amino acids in length. In humans, the gene encoding this protein is located in the position, C13orf30.
Pfam PF03918: Cytochrome C biogenesis protein (family)
Members of this family include NrfF, CcmH, CycL, Ccl2.
Pfam PF05159: Capsule polysaccharide biosynthesis protein (family)
This family includes export proteins involved in capsule polysaccharide biosynthesis, such as KpsS [swissprot:P42218] and LipB [swissprot:P57038].
Pfam PF16888: YwqH-like (family)
This entry represents a family of proteins from firmicutes, including Protein YwqH from Bacillus subtilis, an homologue of the polymorphic LXG toxin.
Pfam PF05558: DREPP plasma membrane polypeptide (family)
This family contains several plant plasma membrane proteins termed DREPPs as they are developmentally regulated plasma membrane polypeptides.
Pfam PF10832: YhfG (family)
This protein family includes proteins predominantly found in Gammaproteobacteria, such as YhfG from Escherichia coli. YhfG is a FicA antitoxin homologue (also known as antitoxin EcFicA) that interacts with EcFiT and forms a complex with it. YhfG shows a unique conformation, forming two parallel alpha- helices linked by a 10-residues loop. The structure of the complex shows a highly conserved extended ligand-binding pocket.
Pfam PF02445: Quinolinate synthetase A protein (family)
Quinolinate synthetase catalyses the second step of the de novo biosynthetic pathway of pyridine nucleotide formation. In particular, quinolinate synthetase is involved in the condensation of dihydroxyacetone phosphate and iminoaspartate to form quinolinic acid. This synthesis requires two enzymes, a FAD-containing "B protein" and an "A protein".
Pfam PF05505: Ebola nucleoprotein (family)
This family consists of Ebola and Marburg virus nucleoproteins. These proteins are responsible for encapsidation of genomic RNA. It has been found that nucleoprotein DNA vaccines can offer protection from the virus.
Pfam PF17369: Family of unknown function (DUF5391) (family)
This is a family of unknown function found in Bacilli. Family members are predicted to have 4 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 PF13728: F plasmid transfer operon protein (family)
TraF protein undergoes proteolytic processing associated with export. The 19 amino acids at the amino terminus of the polypeptides appear to constitute a typical membrane leader peptide - not included in this family, while the remainder of the molecule is predicted to be primarily hydrophilic in character. F plasmid TraF and TraH are required for F pilus assembly and F plasmid transfer, and they are both localised to the outer membrane in the presence of the complete F transfer region, especially TraV, the putative anchor.
Pfam PF19058: Family of unknown function (DUF5754) (family)
This is a family of uncharacterised proteins of unknown function found in viruses.
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 PF03684: Uncharacterised protein family (UPF0179) (family)
The function of this family is unknown, however the proteins contain two cysteine clusters that may be iron sulphur redox centres.
Pfam PF16742: N-terminus of interleukin 17 receptor D (family)
IL17R_D_N is found in higher eukaryotes. The function of this N-terminal domain is not known.
Pfam PF12397: U3 small nucleolar RNA-associated protein 10 (family)
This domain family is found in eukaryotes, and is approximately 120 amino acids in length. The family is found in association with [pfam:PF08146]. This family is the protein associated with U3 snoRNA which is involved in the processing of pre-rRNA.
Pfam PF01754: A20-like zinc finger (family)
The A20 Zn-finger of bovine/human Rabex5/rabGEF1 is a Ubiquitin Binding Domain. The zinc finger mediates self-association in A20. These fingers also mediate IL-1-induced NF-kappa B activation.
Pfam PF10904: Protein of unknown function (DUF2694) (family)
This family of proteins with unknown function appears to be restricted to Mycobacterium spp.
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 PF17215: S1 domain (domain)
This domain corresponds to the S1 domain found at the C-terminus of ribonucleases such as yeast Rrp44.
Wikipedia: The S1 domain is a protein domain that was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site.
Pfam PF17114: Gef2-related medial cortical node protein Nod1 (family)
This is a small family of fungal proteins that are involved in cytokinesis, the last stage of the cell-division cycle. Nod1 co-localises with Gef2 - RhoGEF - in the contractile ring and its precursor cortical nodes. Nod1 and Gef2 interact through this C-terminal region of each, this interaction being important for their localisation.
Pfam PF01289: Thiol-activated cytolysin (family)
Thiol-activated cytolysins  are toxins produced by a variety of Gram-positive bacteria and are characterised by their ability to lyse cholesterol-containing membranes, their reversible inactivation by oxidation and their capacity to bind to cholesterol. All these proteins contain a single cysteine residue, located in their C-terminal section, which has been shown  to be essential for the binding to cholesterol.
Wikipedia: The thiol-activated Cholesterol-dependent Cytolysin (CDC) family is a member of the MACPF superfamily. Cholesterol dependent cytolysins are a family of β-barrel pore-forming exotoxins that are secreted by gram-positive bacteria. CDCs are secreted as water-soluble monomers of 50-70 kDa, that when bound to the target cell, form a circular homo-oligomeric complex containing as many as 40 monomers. Through multiple conformational changes, the β-barrel transmembrane structure is formed and inserted into the target cell membrane. The presence of cholesterol in the target membrane is required for pore formation, though the presence of cholesterol is not required by all CDCs for binding. For example, intermedilysin secreted by Streptococcus intermedius will bind only to target membranes containing a specific protein receptor, independent of the presence of cholesterol, but cholesterol is required by intermedilysin for pore formation. While the lipid environment of cholesterol in the membrane can affect toxin binding, the exact molecular mechanism that cholesterol regulates the cytolytic activity of the CDC is not fully understood.
Pfam PF03709: Orn/Lys/Arg decarboxylase, N-terminal domain (domain)
This domain has a flavodoxin-like fold, and is termed the "wing" domain because of its position in the overall 3D  structure.
Wikipedia: In molecular biology, group III pyridoxal-dependent decarboxylases are a family of bacterial enzymes comprising ornithine decarboxylase EC 4.1.1.17, lysine decarboxylase EC 4.1.1.18 and arginine decarboxylase EC 4.1.1.19.
Pfam PF23251: PARP14, fourth type I KH domain (domain)
This domain is found in human Protein mono-ADP-ribosyltransferase PARP14 and related proteins. PARP14 is a large multidomain protein which in the N-terminal half contains a series of consecutive RRM and KH domains that are known to be nucleic acid-binding. PARP14 is involved in multiple signaling pathways linked to cancer, inflammation, and infection. PARP14 is an ADP-ribosyltransferase that mediates mono-ADP-ribosylation of glutamate residues on target proteins. In contrast to PARP1 and PARP2, it is not able to mediate poly-ADP-ribosylation. The domain represented by this entry is a KH domain found fourth in the human PARP14.
Pfam PF20842: Rax2 second domain (domain)
Diploid yeast cells repeatedly polarise and bud from their poles, due probably to the presence of highly stable membrane markers, and Rax2 is one such marker. It is inherited immutably at the cell cortex for multiple generations, and has a half-life exceeding several generations. The persistent inheritance of cortical protein markers would provide a means of coupling a cell's history with the future development of a precise morphogenetic form. Both Rax1 and Rax2 localise to the distal pole as well as to the division site and they interact both with each other and with Bud8p and Bud9p in the establishment and/or maintenance of the cortical markers for bipolar budding. Thus Rax2 is likely to control cell polarity during vegetative growth, and in fission yeast this is done by regulating the localisation of for3p. This entry represents the second domain of Rax2 that is inserted within a beta propeller domain.
Pfam PF19590: TrbL/VirB6 plasmid conjugal transfer like protein (family)
This family of proteins are related to the Type IV secretion system protein TrbL. This family of proteins is found in archaea. Proteins in this family are typically between 353 and 403 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 PF02093: Gag P30 core shell protein (family)
According to Swiss-Prot annotation this protein is the viral core shell protein. P30 is essential for viral assembly.
Pfam PF00590: Tetrapyrrole (Corrin/Porphyrin) Methylases (domain)
This family uses S-AdoMet in the methylation of diverse substrates.  This family includes a related group of bacterial proteins of unknown function, including [swissprot:P45528]. This family includes the methylase Dipthine synthase.
Pfam PF00239: Resolvase, N terminal domain (domain)
The N-terminal domain of the resolvase family (this family) contains the active site and the dimer interface.  The extended arm at the C-terminus of this domain connects to the C-terminal helix-turn-helix domain of resolvase - see [pfam:PF02796].
Pfam PF22758: Structural cement protein (E217 gp24/Pam3 gp6) (family)
E217 is a Pseudomonas phage used in an experimental cocktail to eradicate cystic fibrosis-associated Pseudomonas aeruginosa. Gp24 is a trimeric structural protein and component of the E217 icosahedral head.Gp24 adopts a beta-tulip fold similar to the gp87 protein found in the thermophilic phage P74-26. Each gp24 subunit consists of two anti-parallel beta-sheets, that form a tulip-like structure. Gp24 structural protein probably stabilises the E217 capsid.  This entry includes the cement protein gp6 of cyanophage Pam3. It consists of an N-terminal beta-tulip domain followed by a C-terminal domain of seven antiparallel beta-strands. Gp6 trimers sit at the icosahedral threefold and quasi-threefold axes, stabilizing the capsid shell.
Pfam PF10533: Plant zinc cluster domain (domain)
This zinc binding domain was identified by Babu and colleagues and found associated with the WRKY domain [pfam:PF03106].
Pfam PF22902: BOS complex subunit NOMO1-like, beta sandwich domain (domain)
This domain is found in human BOS complex subunit NOMO1 and similar sequences mainly from animals and plants. NOMO1 is a component of the multi-pass translocon (MPT) complex that mediates insertion of multi-pass membrane proteins into the lipid bilayer of membranes. This domain is predicted to adopt a seven stranded beta sandwich fold.
Pfam PF08558: Telomere repeat binding factor (TRF) (repeat)
Telomere repeat binding factor (TRF) family proteins are important for the regulation of telomere stability. The two related human TRF proteins hTRF1 and hTRF2 form homodimers and bind directly to telomeric TTAGGG repeats via the myb DNA binding domain [pfam:PF00249] at the carboxy terminus. TRF1 is implicated in telomere length regulation and TRF2 in telomere protection. Other telomere complex associated proteins are recruited through their interaction with either TRF1 or TRF2. The fission yeast protein Taz1p (telomere-associated in Schizosaccharomyces pombe) has similarity to both hTRF1 and hTRF2 and may perform the dual functions of TRF1 and TRF2 at fission yeast telomeres. This domain is composed of multiple alpha helices arranged in a solenoid conformation similar to TPR repeats. The fungal members have now also been found to carry two double strand telomeric repeat binding factors.
Pfam PF02879: Phosphoglucomutase/phosphomannomutase, alpha/beta/alpha domain II (domain)
This entry represents domain II found in alpha-D-phosphohexomutase enzymes. This domain has a 3-layer Î±/Î²/Î± topology.
The alpha-D-phosphohexomutase superfamily is composed of four related enzymes, each of which catalyses a phosphoryl transfer on their sugar substrates: phosphoglucomutase (PGM), phosphoglucomutase/phosphomannomutase (PGM/PMM), phosphoglucosamine mutase (PNGM), and phosphoacetylglucosamine mutase (PAGM) . PGM (5.4.2.2) converts D-glucose 1-phosphate into D-glucose 6-phosphate, and participates in both the breakdown and synthesis of glucose . PGM/PMM (5.4.2.2; 5.4.2.8) are primarily bacterial enzymes that use either glucose or mannose as substrate, participating in the biosynthesis of a variety of carbohydrates such as lipopolysaccharides and alginate . Both PNGM (5.4.2.3) and PAGM (5.4.2.10) are involved in the biosynthesis of UDP-N-acetylglucosamine .
Pfam PF15749: MRN-interacting protein (family)
This family is found in eukaryotes. Family members include MRN complex-interacting protein (MRNIP), which plays a role in preventing the accumulation of damaged DNA in cells. It associates with the MRE11-RAD50-NBS1 (MRN) damage-sensing complex and is rapidly recruited to sites of DNA damage. Phosphorylation of a serine promotes nuclear localization of MRNIP.
Pfam PF18364: Molybdopterin oxidoreductase N-terminal domain (domain)
This is the N-terminal domain of [pfam:PF00384] found in a number of molybdopterin-containing oxidoreductases such as dimethyl sulfoxide/trimethylamine N-oxide reductase, also known as DMSO reductase ([ec:1.7.2.3], [ec:1.8.5.3]).
Pfam PF13313: Domain of unknown function (DUF4082) (domain)
This domain is distantly related to the PHR domain [pfam:PF08005]. This domain is often found between successive bacterial Ig domains, [pfam:PF13205].
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 PF11577: NF-kappa-B essential modulator NEMO (family)
NEMO is a regulatory protein which is part of the IKK complex along with the catalytic IKKalpha and beta kinases. The IKK complex phosphorylates IkappaB targeting it for degradation which results in the release of NF-kappaB which initiates the inflammatory response, cell proliferation or cell differentiation. NEMO activates the IKK complex's activity by associating with the unphosphorylated IKK kinase C termini.The core domain of NEMO is a dimer which binds to two fragments of IKK.
Pfam PF22106: NGO1945 C-terminal domain (domain)
This domain represents the C-terminal part of a Neisseria protein, [swissprot:Q5F5I0], PDB:3dee. It runs from residues 135-220 including a beta sheet containing three antiparallel beta strands and three alpha helices. From genomic context and the fold of the C-terminal part, it is suggested that this protein is involved in transcriptional regulation. The N-terminal domain found in PDB:3dee is represented in [pfam:PF09836].
Pfam PF11123: DNA packaging protein (family)
This DNA packaging protein is also referred to as gene 18 product (gp18). This protein is required for DNA packaging and functions in a complex with gp19.
Pfam PF00865: Osteopontin (family)
The major event of endochondrial ossification is the proteolytic degradation of calcified cartilage and the extracellular matrix, and their substitution with bone-specific extracellular matrix produced and organised by osteoblasts . One of the most abundant products of osteoblasts is osteopontin, a glycosylated phosphoprotein with a high acidic amino acid content and one copy of the cell attachment sequence RGD . It is thought that osteopontin may act as a bridge between osteoblasts and the apatite mineral of the bone . Osteopontin-K is a kidney protein, similar to osteopontin and probably also involved in cell adhesion .
Wikipedia: Osteopontin (OPN), also known as bone /sialoprotein I, early T-lymphocyte activation (ETA-1), secreted phosphoprotein 1 (SPP1), 2ar and Rickettsia resistance (Ric), is a protein that in humans is encoded by the SPP1 gene. The murine ortholog is Spp1. Osteopontin is a SIBLING (glycoprotein) that was first identified in 1986 in osteoblasts.
Pfam PF04582: Reovirus sigma C capsid protein C-terminal domain (domain)
Protein sigmaC in its native state was shown to be a homotrimer. It was demonstrated that the sigmaC subunits are not covalently bound via disulphide linkages and the formation of an intrachain disulphide bond between the two cysteine residues of the sigmaC polypeptide may have a negative effect on oligomer stability. The susceptibility of the trimer to pH, temperature, ionic strength, chemical denaturants and detergents indicates that hydrophobic interactions contribute much more to oligomer stability than do ionic interactions and hydrogen bonding .