SII-SWORD/CoKE huggingface dataset:
Pfam PF19723: Family of unknown function (DUF6216) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001055) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide. It includes a member from the yersiniabactin  biosynthetic gene cluster from Escherichia coli. This family appears to be predominantly found in Proteobacteria.
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 PF21831: Domain of unknown function (DUF6891) (domain)
This entry represents a bacterial protein of unknown 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 PF12108: Splicing factor SF3a60 binding domain (domain)
This domain is found in eukaryotes. This domain is about 30 amino acids in length. This domain has a single completely conserved residue Y that may be functionally important. SF3a60 makes up the SF3a complex with SF3a66 and SF3a120. This domain is the binding site of SF3a60 for SF3a120. The SF3a complex is part of the spliceosome, a protein complex involved in splicing mRNA after transcription.
Pfam PF12911: N-terminal TM domain of oligopeptide transport permease C (domain)
Oligopeptide permeases (Opp) have been identified in numerous gram-negative and -positive bacteria. These transport systems belong to the superfamily of highly conserved ATP-binding cassette transporters. Typically, Opp importers comprise a complex of five proteins. The oligopeptide-binding protein OppA is responsible for the capture of peptides from the external medium. Two integral highly hydrophobic membrane spanning proteins, OppB and OppC, form a channel through the membrane used for peptide translocation.  This N-terminal domain appears to be the first TM domain of the molecule.
Pfam PF07782: DC-STAMP-like protein (family)
This is a family of sequences which are similar to a region of the dendritic cell-specific transmembrane protein (DC-STAMP, [swissprot:Q9H295]). This is thought to be a novel receptor protein that shares no identity with other multimembrane-spanning proteins. It is thought to have seven putative transmembrane regions, two of which are found in the region featured in this family. DC-STAMP is also described as having potential N-linked glycosylation sites and a potential phosphorylation site for PKC, but these are not conserved throughout the family.
Pfam PF16707: Cag pathogenicity island protein S of Helicobacter pylori (family)
CagS is a family of proteins from the pathogenicity island of Helicobacter pylori. The gene lies just downstream of the cluster whose protein-products resemble those of the Vibrio proteins that form the structural core of T4SS. The exact function of CagS is not known.
Pfam PF17661: Family of unknown function (DUF5523) (family)
This is a family of unknown function found in Eukaryotes. Family members such as the human CC1D2A protein [swissprot:Q9P2K1], carry the domain architecture where [pfam:PF15625] and [pfam:PF00168] are found at the C-terminal region of this family. However, other family members such as [swissprot:D6R9V3], do not carry either of the above mentioned Pfam families.
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 PF22414: Trimeric autotransporter adhesin, Trp ring domain (domain)
This domain is found in Adhesin from Haemophilus influenzae (Hia) and similar proteins predominantly from proteobacteria. Hia is a trimeric autotransporter that mediates bacterial adherence to the respiratory epithelium. This protein shows a modular architecture with repeats of structurally distinct domains. This entry represents one of the Trp-ring domains.
Pfam PF04499: SIT4 phosphatase-associated protein (family)
This family includes a conserved region from a group of yeast proteins that associate with the SIT4 phosphatase. This association is required for SIT4's role in G1 cyclin transcription and for bud formation. This family also includes homologous regions from other eukaryotes.
Pfam PF19890: Domain of unknown function (DUF6363) (domain)
This presumed domain is functionally uncharacterised. This domain is found at the C-terminal of patatin-like proteins from bacteria. There is a conserved tyrosine residue and a conserved FxxxPP sequence motif.
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 PF17952: Cas6 N-terminal domain (domain)
The CRISPR-Cas system is a prokaryotic defense mechanism against foreign genetic elements. The key elements of this defense system are the Cas proteins and the CRISPR RNA.Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes. CRISPRs appear to provide acquired resistance against mobile genetic elements (viruses, transposable elements and conjugative plasmids). CRISPR clusters contain sequences complementary to antecedent mobile elements and target invading nucleic acids. CRISPR clusters are transcribed and processed into CRISPR RNA (crRNA).The defense reaction is divided into three stages. In the adaptation stage, the invader DNA is cleaved, and a piece of it is selected to be integrated as a new spacer into the CRISPR locus, where it is stored as an identity tag for future attacks by this invader. During the second stage (the expression stage), the CRISPR RNA (pre-crRNA) is transcribed and subsequently processed into the mature crRNAs. In the third stage (the interference stage), Cas proteins, together with crRNAs, identify and degrade the invader.The CRISPR-Cas systems have been sorted into three major classes. In CRISPR-Cas types I and III, the mature crRNA is generally generated by a member of the Cas6 protein family. Whereas in system III the Cas6 protein acts alone, in some class I systems it is part of a complex of Cas proteins known as Cascade (CRISPR-associated complex for antiviral defense). This entry represents the N-terminal domain of Cas 6 proteins. The Cas6 protein is an endoribonuclease necessary for crRNA production whereas the additional Cas proteins that form the Cascade complex are needed for crRNA stability. Structural analysis of Sulfolobus sulfotaricus P2 Cas6 (SsCas6) proteins indicate that SsCas6 is able to bind and cleave the nonstructured RNA by stabilizing an otherwise unstable duplex of two base pairs near the cleavage site, leading to an inline conformation around the scissile phosphate necessary for its breakage.
Wikipedia: CRISPR is a family of DNA sequences found in the genomes of prokaryotic organisms such as bacteria and archaea. Each sequence within an individual prokaryotic cell is derived from a DNA fragment of a bacteriophage that had previously infected the prokaryote or one of its ancestors. These sequences are used to detect and destroy DNA from similar bacteriophages during subsequent infections. Hence these sequences play a key role in the antiviral defense system of prokaryotes and provide a form of heritable, acquired immunity. CRISPR is found in approximately 50% of sequenced bacterial genomes and nearly 90% of sequenced archaea.
Pfam PF23870: Domain of unknown function (DUF7225) (domain)
This domain is found in uncharacterised protein YnaC and related bacterial proteins. It is usually associated with ([pfam:PF22522]). This domain is a winged helix (WH) domain decorated at the C terminus with a small three stranded beta-sheet that packs on the WH domain to form a single globular structure.
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 PF22096: Teichoic acid transporter subunit TagH C-terminal domain (domain)
TagH is the ATPase subunit of the two-component transporter TagGH involved in the synthesis of bacterial polysaccharides-wall teichoic acids. This entry represents the C-terminal of TagH that adopts an alpha/beta structure consisting of a central antiparallel mixed beta-sheet packed on one side with helices. It is anticipated that this domain is involved in the binding to negatively charged polymer.
Pfam PF21569: Histone-lysine N-methyltransferase, RNA-binding domain (domain)
This domain is found in Histone-lysine N-methyltransferase, H3 lysine -4 specific from Saccharomyces cerevisiae (SET1) and similar proteins predominantly from yeast. SET1 is the methyltransferase subunit of the COMPASS (Set1C) complex that plays a role in telomere length maintenance and transcription elongation regulation. This entry represents the RNA-binding domain (RBD), which shows an alpha-beta structure.
Pfam PF20016: Thoeris protein ThsA, Macro domain (domain)
Thoeris is a bacterial antiphage defense system, which consists of two genes, thsA and thsB, via NAD+ degradation. ThsA has robust NAD+ cleavage activity and and a two-domain architecture containing a N-terminal NAD-binding domain (denoted as sirtuin-like or Macro) and C-terminal SLOG-like domain. In some instances, such as in B. amyloliquefaciens ThsA has an N-terminal transmembrane domain. ThsB (also referred to as TIR1 and TIR2) is structurally similar to TIR domain proteins but without enzymatic activity. This domain is found at the C-terminal of ThsA proteins which adopts a Rossmann-like fold that binds NAD+/NAD+derivatives. It has been characterised as the SLOG-like domain which binds NAD+ derivatives such as ADPR molecules produced by ThsB, which drives an oligomeric state change in ThsA and activates the NADase activity (represented in [pfam:PF18185]). This entry represents the NAD+-binding Macro domain from B. amyloliquefaciens.
Pfam PF06645: Microsomal signal peptidase 12 kDa subunit (SPC12) (family)
This family consists of several microsomal signal peptidase 12 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 12 kDa subunit (SPC12).
Pfam PF20012: GTPase-associated protein 1, N-terminal domain type 1 (domain)
One of two types of domain found at the N-terminus of the GTPase-associated protein 1 (GAP1) of the GTPase-centric ternary systems, a class of NTP-dependent biological conflict systems. This domain is predicted to mediate effector-GAP1 interactions.
Pfam PF06348: Protein of unknown function (DUF1059) (family)
This family consists of several short hypothetical archaeal proteins of unknown 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 PF11905: Domain of unknown function (DUF3425) (family)
This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 120 to 143 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 PF10329: Region of unknown function (DUF2417) (family)
This is a region of a family of proteins conserved in fungi some of whose members also have the Abhydrolase_1, [pfam:PF00561], domain in their sequence. The function of this region 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 PF09592: Protein of unknown function (DUF2031) (family)
This protein is expressed in Plasmodium; its function is unknown. It may be the product of gene family pyst-b.
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 PF13573: SprB repeat (domain)
This repeat occurs several times in SprB, a cell surface protein involved in gliding motility in the bacterium Flavobacterium johnsoniae.
Pfam PF16582: Middle domain of thiamine pyrophosphate (domain)
TPP_enzyme_M_2 is the middle domain of thiamine pyrophosphate in sequences not captured by [pfam:PF00205]. This enzyme is necessary for the first step of the biosynthesis of menaquinone, or vitamin K2, an important cofactor in electron transport in bacteria.
Pfam PF03086: Domain of unknown function (DUF240) (domain)
This is a domain of unknown function found in mycoplasma. It is found at the N-terminal region.
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 PF05431: Insecticidal Crystal Toxin, P42 (family)
Family of Bacillus insecticidal crystal toxins.  Strains of Bacillus that have this insecticidal activity use a binary toxin comprised of two proteins, P51 and P42 (this family).  Members of this family are highly conserved  between strains of different serotypes and phage groups.
Pfam PF14199: Domain of unknown function (DUF4317) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 225 and 451 amino acids in length. There is a single completely conserved residue P 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 PF14966: DNA repair REX1-B (family)
This family of proteins includes Chlamydomonas reinhardtii REX1-B (Required for Excision 1-B) which is involved in a light-independent DNA repair pathway.
Pfam PF13176: Tetratricopeptide repeat (repeat)
The tetratrico peptide repeat region (TPR) is a structural motif present in a wide range of proteins . It mediates protein-protein interactions and the assembly of multiprotein complexes . The TPR motif consists of 3-16 tandem-repeats of 34 amino acids residues, although individual TPR motifs can be dispersed in the protein sequence. Sequence alignment of the TPR domains reveals a consensus sequence defined by a pattern of small and large amino acids. TPR motifs have been identified in various different organisms, ranging from bacteria to humans. Proteins containing TPRs are involved in a variety of biological processes, such as cell cycle regulation, transcriptional control, mitochondrial and peroxisomal protein transport, neurogenesis and protein folding.

The X-ray structure of a domain containing three TPRs from protein phosphatase 5 revealed that TPR adopts a helix-turn-helix arrangement, with adjacent TPR motifs packing in a parallel fashion, resulting in a spiral of repeating anti-parallel Î±-helices . The two helices are denoted helix A and helix B. The packing angle between helix A and helix B is ~24 degrees within a single TPR and generates a right-handed superhelical shape. Helix A interacts with helix B and with helix A' of the next TPR. Two protein surfaces are generated: the inner concave surface is contributed to mainly by residue on helices A, and the other surface presents residues from both helices A and B.
Wikipedia: The tetratricopeptide repeat (TPR) is a structural motif. It consists of a degenerate 34 amino acid tandem repeat identified in a wide variety of proteins. It is found in tandem arrays of 3–16 motifs, which form scaffolds to mediate protein–protein interactions and often the assembly of multiprotein complexes. These alpha-helix pair repeats usually fold together to produce a single, linear solenoid domain called a TPR domain. Proteins with such domains include the anaphase-promoting complex (APC) subunits cdc16, cdc23 and cdc27, the NADPH oxidase subunit p67-phox, hsp90-binding immunophilins, transcription factors, the protein kinase R (PKR), the major receptor for peroxisomal matrix protein import PEX5, protein arginine methyltransferase 9 (PRMT9), and mitochondrial import proteins.
Pfam PF01062: Bestrophin, RFP-TM, chloride channel (family)
Bestrophin is a 68-kDa basolateral plasma membrane protein expressed in retinal pigment epithelial cells (RPE). It is encoded by the VMD2 gene, which is mutated in Best macular dystrophy, a disease characterised by a depressed light peak in the electrooculogram.  VMD2 encodes a 585-amino acid protein with an approximate mass of 68 kDa which has been designated bestrophin. Bestrophin shares homology with the Caenorhabditis elegans RFP gene family, named for the presence of a conserved arginine (R), phenylalanine (F), proline (P), amino acid sequence motif.  Bestrophin is a plasma membrane protein, localised to the basolateral surface of RPE cells consistent with a role for bestrophin in the generation or regulation of the EOG light peak. Bestrophin and other RFP family members represent a new class of chloride channels, indicating a direct role for bestrophin in generating the light peak. The VMD2 gene underlying Best disease was shown to represent the first human member of the RFP-TM protein family. More than 97% of the disease-causing mutations are located in the N-terminal RFP-TM domain implying important functional properties. The bestrophins are four-pass transmembrane chloride-channel proteins, and the RFP-TM or bestrophin domain extends from the N-terminus through approximately 350 amino acids and contains all of the TM domains as well as nearly all reported disease causing mutations. Interestingly, the RFP motif is not conserved evolutionarily back beyond Metazoa, neither is it in plant members.
Pfam PF11189: Protein of unknown function (DUF2973) (family)
Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently they 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 PF13911: AhpC/TSA antioxidant enzyme (domain)
This family contains proteins related to alkyl hydro-peroxide reductase (AhpC) and thiol specific antioxidant (TSA).
Pfam PF23619: VWA7 Ig-like domain (domain)
This domain id found in the human von Willebrand factor A domain-containing protein 7 (VWA7) and related proteins. It is predicted to fold into a beta-sandwich with an Ig-like topology.
Pfam PF17324: BLOC-1 interactor 1 (family)
In yeast BLOC-1 consists of six subunits localised to the endosomes. In the absence of BLOC-1 subunits, the balance between recycling and degradation of selected cargoes is impaired. This family contains BLI1 (BlOC-1 interactor 1) protein, a subunit of the BLOC-1 complex which mediates endosomal maturation.
Pfam PF06254: Bacterial toxin ydaT (family)
YdaT_toxin was first thought to be neutralised by the putative antitoxin YdaS ([pfam:PF15943]) but recent studies showed that both YdaS and YdaT can act independently as toxins and are regulated by RacR.
Pfam PF01947: Chorismate pyruvate-lyase Rv2949c-like (domain)
This domain is found in chorismate pyruvate-lyases ([ec:4.1.3.40], also known as 4-HB synthase and p-hydroxybenzoic acid synthase) such as those found in Mycobacterium tuberculosis where it removes the pyruvyl group from chorismate to provide 4-hydroxybenzoate (4HB). The chorismate pyruvate-lyase encoded by sll1797 in cyanobacteria Synechocystis sp. , has been shown to catalyse the initial and essential step in plastoquinone biosynthesis. In E. coli, the chorismate lyase (UbiC) catalyses the conversion of chorismate to p-hydroxybenzoate and pyruvate in the biosynthesis of ubiquinone as well.