SII-SWORD/CoKE huggingface dataset:
Pfam PF13194: Domain of unknown function (DUF4010) (domain)
This is a family of putative membrane proteins found in archaea and bacteria.    It is sometimes found C terminal to [pfam:PF02308].
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 PF09946: Predicted membrane protein (DUF2178) (family)
This domain, found in various hypothetical archaeal proteins, has no known function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF00438: S-adenosylmethionine synthetase, N-terminal domain (domain)
The three domains of S-adenosylmethionine synthetase have the same alpha+beta fold.
Wikipedia: S-Adenosylmethionine synthetase, also known as methionine adenosyltransferase (MAT), is an enzyme that creates S-adenosylmethionine by reacting methionine and ATP.
Pfam PF19188: Adhesion GPCR B N-terminal region (family)
This region is found at the N-terminus of various adhesion G-protein coupled receptor B proteins. This region contains 10 cysteine residues that probably form disulphide bonds.
Pfam PF19939: Family of unknown function (DUF6401) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001580) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the ebelactone biosynthetic gene cluster from Kitasatospora aburaviensis. This family appears to be predominantly found in actinobacteria.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF02516: Oligosaccharyl transferase STT3, N-terminal (domain)
This entry consists of the oligosaccharyl transferase STT3 subunit and related proteins.  The STT3 subunit is part of the oligosaccharyl transferase (OTase) complex of proteins and is required for its activity.  In eukaryotes, OTase transfers a lipid-linked core-oligosaccharide to selected asparagine residues in the ER. In the archaea STT3 occurs alone, rather than in an OTase complex, and is required for N-glycosylation of asparagines. This entry represents the N-terminal domain, consisting of transmembrane helices.
Wikipedia: Oligosaccharyltransferase or OST (EC 2.4.1.119) is a membrane protein complex that transfers a 14-sugar oligosaccharide from dolichol to nascent protein. It is a type of glycosyltransferase. The sugar Glc3Man9GlcNAc2 (where Glc=Glucose, Man=Mannose, and GlcNAc=N-acetylglucosamine) is attached to an asparagine (Asn) residue in the sequence Asn-X-Ser or Asn-X-Thr where X is any amino acid except proline. This sequence is called a glycosylation sequon. The reaction catalyzed by OST is the central step in the N-linked glycosylation pathway.
Pfam PF14667: Polysaccharide biosynthesis C-terminal domain (domain)
This domain is found at the C-terminal of proteins homologous to Staphylococcus aureus CapF (also known as WbjC in Pseudomonas aeruginosa and FnlB in Escherichia coli). CapF is a bifunctional metalloenzyme produced by certain pathogenic bacteria and is essential in the biosynthetic path of capsular polysaccharide (CP),  a mucous layer on the surface of bacterium that facilitates immune  evasion and infection. Thus, CapF is an antibacterial/therapeutic  target. In S. aureus, enzymes CapE, CapF and CapG catalyse the  sequential transformation of UDP-D-GlcNAc in the CP precursor  UDP-L-FucNAc via the intermediate compound UDP-N-acetyl-L-talosamine  (UDP-L-TalNAc). CapF consists of two domains; the C-terminal  cupin domain catalyses the epimerization of the compound produced by the upstream enzyme CapE, and the N-terminal short-chain dehydrogenase/reductase (SDR) domain catalyses the reduction of the  compound afforded by the cupin domain, requiring one equivalent of  NADPH. The cupin domain is crucial for catalysing the first chemical  reaction, and also important for the stability of the enzyme.  Similarly, in P. aeruginosa, WbjC, WbjB and WbjD enzymes  synthesise UDP-N-acetyl-L-reexamine, a precursor of the  lipopolysacharide component L-fucosamine. The N-terminal adopts a Rossmann fold and the cupin domain contains a conserved  "jelly roll-like" beta-barrel fold.
Pfam PF21830: Family of unknown function (DUF6890) (family)
This entry represents a family of small proteins composed largely of a single alpha helix. Some proteins in this family are annotated as from phage. The function of these proteins 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 PF04476: 4-HFC-P synthase (family)
(5-formylfuran-3-yl)methyl phosphate synthase, also known as 4-HFC-P synthase, is involved in the production of methanofuran. This family has a classical TIM-barrel structure whose biological unit is a homohexamer.
Pfam PF02763: Diphtheria toxin, C domain (domain)
N-terminal catalytic (C) domain - blocks protein synthesis by transfer of ADP-ribose from NAD to a diphthamide residue of EF-2.
Wikipedia: Diphtheria toxin is an exotoxin secreted mainly by Corynebacterium diphtheriae but also by Corynebacterium ulcerans and Corynebacterium pseudotuberculosis, the pathogenic bacterium that causes diphtheria. The toxin gene is encoded by a prophage called corynephage β.
The toxin causes the disease in humans by gaining entry into the cell cytoplasm and inhibiting protein synthesis.
Pfam PF24096: Domain of unknown function (DUF7379) (domain)
This entry represents a domain of unknown function found towards the N-terminal of CHAT domain-containing protein, such as SwissProt:A0A100JVW6, from Streptomyces scabiei. This domain may adopt a A/B hydrolase fold and is often found in association with TCAD7 ([pfam:PF19973]) and CHAT ([pfam:PF12770]) 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 PF12101: Protein of unknown function (DUF3577) (family)
This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 143 to 307 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 PF20386: Family of unknown function (DUF6681) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 258 and 288 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 PF12793: Sugar transport-related sRNA regulator N-term (family)
Small, non-coding RNA molecules play important regulatory roles in a variety of physiological processes in bacteria. SgrR_N is the N-terminus of a family of proteins which regulate the transcription of these sRNAs, in particular SgrS. SgrR_N contains a helix-turn-helix motif characteristic of winged-helix DNA-binding transcriptional regulators. SgrS is a small RNA required for recovery from glucose-phosphate stress in bacteria. In examining the regulation of sgrR expression it was found that SgrR negatively auto-regulates its own transcription in the presence and absence of stress, and thus SgrR coordinates the response to glucose-phosphate stress by binding specifically to sgrS promoter DNA.
Pfam PF01350: Flavivirus non-structural protein NS4A (family)
Flaviviruses encode a single polyprotein. This is cleaved into three structural and seven non-structural proteins. The NS4A protein is small and poorly conserved among the Flaviviruses. NS4A contains multiple hydrophobic potential membrane spanning regions.  NS4A has only been found in cells infected by Kunjin virus.
Pfam PF03127: GAT domain (domain)
The GAT domain is responsible for binding of GGA proteins to several members of the ARF family including ARF1 and ARF3. The GAT domain stabilises membrane bound ARF1 in its GTP bound state, by interfering with GAP proteins.
Pfam PF08467: Luteovirus RNA polymerase P1-P2/replicase (family)
This domain is found in RNA-dependent RNA polymerase P1-P2 fusion/replicase proteins in plant Luteoviruses.
Pfam PF06703: Microsomal signal peptidase 25 kDa subunit (SPC25) (family)
This family consists of several microsomal signal peptidase 25 kDa subunit proteins. Translocation of polypeptide chains across the endoplasmic reticulum (ER) membrane is triggered by signal sequences. Subsequently, signal recognition particle interacts with its membrane receptor and the ribosome-bound nascent chain is targeted to the ER where it is transferred into a protein-conducting channel. At some point, a second signal sequence recognition event takes place in the membrane and translocation of the nascent chain through the membrane occurs. The signal sequence of most secretory and membrane proteins is cleaved off at this stage. Cleavage occurs by the signal peptidase complex (SPC) as soon as the lumenal domain of the translocating polypeptide is large enough to expose its cleavage site to the enzyme. The signal peptidase complex is possibly also involved in proteolytic events in the ER membrane other than the processing of the signal sequence, for example the further digestion of the cleaved signal peptide or the degradation of membrane proteins. Mammalian signal peptidase is as a complex of five different polypeptide chains. This family represents the 25 kDa subunit (SPC25).
Pfam PF16921: Tex protein YqgF-like domain (domain)
This is the YqgF-like domain of the bacterial Tex protein, which is involved in transcriptional processes.
Pfam PF05476: PET122 (family)
The nuclear PET122 gene of S. cerevisiae encodes a mitochondrial-localised protein that activates initiation of translation of the mitochondrial mRNA from the COX3 gene, which encodes subunit III of cytochrome c oxidase.
Pfam PF17856: TIP49 AAA-lid domain (domain)
This family consists of the C-terminal region of several eukaryotic and archaeal RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin or TIP49b) proteins. The N-terminal domain contains the [pfam:PF00004] domain. In zebrafish, the liebeskummer (lik) mutation, causes development of hyperplastic embryonic hearts. lik encodes Reptin, a component of a DNA-stimulated ATPase complex. Beta-catenin and Pontin, a DNA-stimulated ATPase that is often part of complexes with Reptin, are in the same genetic pathways. The Reptin/Pontin ratio serves to regulate heart growth during development, at least in part via the beta-catenin pathway. TBP-interacting protein 49 (TIP49) was originally identified as a TBP-binding protein, and two related proteins are encoded by individual genes, tip49a and b. Although the function of this gene family has not been elucidated, they are supposed to play a critical role in nuclear events because they interact with various kinds of nuclear factors and have DNA helicase activities.TIP49a has been suggested to act as an autoantigen in some patients with autoimmune diseases.
Pfam PF11498: Transcriptional activator LAG-3 (family)
The C.elegans Notch pathway, involved in the control of growth, differentiation and patterning in animal development, relies on either of the receptors GLP-1 or LIN-12. Both these receptors promote signalling by the recruitment of LAG-3 to target promoters, where it then acts as a transcriptional activator. LAG-3 works as a ternary complex together with the DNA binding protein, LAG-1. Its N-terminal region adopts an elongated kinked helix that is required for complex assembly.
Wikipedia: In molecular biology, the transcriptional activator LAG-3 is a transcriptional activator protein. The C. elegans Notch pathway, involved in the control of growth, differentiation and patterning in animal development, relies on either of the receptors GLP-1 or LIN-12. Both these receptors promote signalling by the recruitment of LAG-3 to target promoters, where it then acts as a transcriptional activator. LAG-3 works as a ternary complex together with the DNA binding protein, LAG-1.
Pfam PF12333: Rix1 complex component involved in 60S ribosome maturation (repeat)
This domain family is found in eukaryotes, and is typically between 91 and 105 amino acids in length. This family is the N terminal of Ipi1, a component of the Rix1 complex which works in conjunction with Rea1 to mature the 60S ribosome.
Pfam PF00485: Phosphoribulokinase / Uridine kinase family (domain)
This family matches three types of P-loop containing kinases: phosphoribulokinases, uridine kinases and bacterial pantothenate kinases(CoaA).  Arabidopsis and other organisms have a dual uridine kinase/uracil phosphoribosyltransferase protein where the N-terminal region consists of a UK domain and the C-terminal region of a UPRT domain.
Pfam PF13724: DNA-binding domain (domain)
This domain, often found on ovate proteins, binds to single-stranded and double-stranded DNA. Binding to DNA is not sequence-specific.
Pfam PF18415: Histidine kinase receptor ArcB trans-membrane domain (domain)
Histidine kinase receptors (HKRs) are part of a two-component system, in which an HKR in the bacterial inner membrane transmits a signal to a response regulator located in the cytoplasm. This is a trans-membrane domain (TM) found in ArcB (class 2, aerobic respiratory control sensor). ArcB has two TM helices connected by a short periplasmic loop. TM domain structures suggests a loose helical packing which provides an inherent flexibility in the TM domains and that this is perhaps essential to the mechanism of signal transduction across the membrane.
Pfam PF16968: Pilus assembly protein TadZ N-terminal (family)
TadZ_N is the N-terminal region of the Flp pilus assembly protein TadZ, which carries an AAA, ATPase domain immediately downstream, AAA_31, [pfam:PF13614]. The domain is an example of a signal-transduction-response receiver. It is localised to the cytoplasmic side of the inner bacterial cell-membrane, contacting also with both tadA and RcpC.
Pfam PF24212: Family of unknown function (DUF7433) (family)
This entry represents a small region that is found in a variety of uncharacterised mycobacterial phage proteins.  Structure prediction suggests it adopts an alpha helix and beta hairpin structure that likely homodimerises.
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 PF17873: Replicase polyprotein 1ab regulatory domain (domain)
This entry relates to a regulatory domain found in replicase polyprotein 1ab found in Arterivirus. Structural studies of arterivirus helicase (nsp10), indicate that this domain undergoes conformational changes on substrate binding. Besides the large conformational change, it is suggested that the regions at the surface of domain 1B not directly involved in DNA binding may become flexible. For example, domain 1B residues Arg95, Gly125 and Ala131 become disordered after DNA binding. Together with domains 1A and 2A it forms a nucleic acid-binding channel where the single-stranded part of the DNA substrate is bound to.
Pfam PF02095: Extensin-like protein (disordered)
This entry represents extensin-like proteins.
Pfam PF09589: HrpA pilus formation protein (family)
HrpA is an essential component of the type III secretion system (TTSS) which pathogens use to inject virulence factors directly into their host cells, and to cause disease. The TTSS has an Hrp pilus appendage for channelling effector proteins through the plant cell wall and this pilus elongates by the addition of HrpA pilin subunits at the distal end.
Pfam PF09083: Domain of unknown function (DUF1923) (domain)
Members of this family are found in maltosyltransferases, and adopt a secondary structure consisting of eight antiparallel beta-strands, which form an open-sided 'jelly roll' Greek key beta-barrel. Their exact function is, as yet, 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 PF13610: DDE domain (domain)
This DDE domain is found in a wide variety of transposases including those found in IS240, IS26, IS6100 and IS26.
Pfam PF10650: Putative zinc-finger domain (domain)
This domain is conserved in fungi and might be a zinc-finger domain as it contains three conserved Cs and an H in the C-x8-C-x5-C-x3-H conformation typical of a zinc-finger.
Pfam PF23353: BBS2 hairpin (domain)
This entry represents the hairpin domain of BBS2. BBS2 is one of the BBS proteins that form the BBSome complex found in vertebrates and nematodes, including humans, mice, and Caenorhabditis elegans. BBSome complex is required for ciliogenesis and the assembly and movement of intraflagellar transport proteins along the ciliary membrane. This domain connects to the C-terminal region of BBS9.
Pfam PF22247: Catechol 2,3-dioxygenase-like N-terminal domain (domain)
This entry includes a group of bacterial proteins that function as 2,3-dioxigenases. This entry represents the N-terminal domain.
Pfam PF02151: UvrB/uvrC motif (family)
During the process of Escherichia coli nucleotide excision repair, DNA damage recognition and processing are achieved by the action of the uvrA, uvrB, and uvrC gene products . UvrB and UvrC share a common domain of around 35 amino acids, the so called UVR domain. This domain in UvrB can interact with the homologous domain in UvrC throughout a putative coiled coil structure. This interaction is important for the incision of the damaged strand .

A conserved region similar to the UVR domain is also found in the ATP-binding subunit of bacterial and chloroplastic Clp ATPases , which suggest that the UVR domain is not only involved in the interaction between uvrB and uvrC.
Pfam PF02179: BAG domain (family)
Domain present in Hsp70 regulators.
Wikipedia: In molecular biology, BAG domains are protein domains found in proteins which are modulators of chaperone activity, they bind to HSP70/HSC70 proteins and promote substrate release. The proteins have anti-apoptotic activity and increase the anti-cell death function of BCL-2 induced by various stimuli. BAG-1 binds to the serine/threonine kinase Raf-1 or Hsc70/Hsp70 in a mutually exclusive interaction. BAG-1 promotes cell growth by binding to and stimulating Raf-1 activity. The binding of Hsp70 to BAG-1 diminishes Raf-1 signalling and inhibits subsequent events, such as DNA synthesis, as well as arrests the cell cycle. BAG-1 has been suggested to function as a molecular switch that encourages cells to proliferate in normal conditions but become quiescent under a stressful environment.
Pfam PF19878: Tannase-like family of unknown function (DUF6351) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 717 and 769 amino acids in length. This family appears to be related to [pfam:PF07519].
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 PF25042: Domain of unknown function (DUF7787) (domain)
This domain is found in uncharacterised plant proteins. It contains the so-called HeH motif (helix-extended loop-helix). This motif is known to engage in protein-protein and/or nucleic acid interactions. Some proteins contain two copies of this 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 PF11055: Glucose signalling factor 2 (family)
Gsf2 is localised to the ER and functions to promote the secretion of certain hexose transporters.
Pfam PF18332: Exoribonuclease Xrn1 D1 domain (domain)
This domain can be found in 5' to 3' exoribonuclease 1 (XRN1) which belong to a family of conserved enzymes in eukaryotes and have important functions in transcription, RNA metabolism, and RNA interference. Xrn1 in fungi and animals is primarily cytosolic and is involved in degradation of decapped mRNAs, nonsense mediated decay, microRNA decay and is essential for proper development. The Xrn1 homolog in Drosophila, known as Pacman, is required for male fertility. This domain (D1) along with 3 other domains, make up a 510-residue segment following the conserved regions found in XRNs but they are only present in XRN1 and are absent in Rat1/XRN2. The amino acid sequences of these four domains contain an excess of basic residues, suggesting that these domains might help in binding the RNA substrate. Mutational studies carried out in D1 domain show that the mutant forms had dramatically reduced nuclease activity towards ssDNA substrate indicating that domain D1 is required for Xrn1 nuclease activity.