SII-SWORD/CoKE huggingface dataset:
Pfam PF23871: Domain of unknown function (DUF7226) (domain)
This domain is found in uncharacterised proteins. It is usually found in combination with [[pfam:PF22515]] and [[pfam:PF22518]]. It is predicted to contain a winged helix (WH) domain that is flanked at the C terminus with a small helical subdomain. The latter packs on the WH domain to form a compact 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 PF23666: Host specificity protein-like, C-terminal (domain)
This domain is found in Host specificity protein from Rhodobacter capsulatus (rcc01698) and similar proteins found in proteobacteria and some viral species.
Pfam PF24808: Domain of unknown function (DUF7707) (domain)
This domain is found in uncharacterised fungal proteins. It contains a set of highly conserved cysteine residues that are predicted to form disulfide bonds. It is likely that proteins containing this domain are secreted.
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 PF10791: Mitochondrial F1-F0 ATP synthase subunit F of fungi (family)
The membrane bound F1-FO-type H+ ATP synthase of mitochondria catalyses the terminal step in oxidative respiration converting the generation of the electrochemical gradient into ATP for cellular biosynthesis. The general structure and the core subunits of the enzyme are highly conserved in both prokaryotic and eukaryotic organisms.
Pfam PF24085: Family of unknown function (DUF7370) (family)
This entry represents a family of uncharacterised phage proteins. Many of these proteins are annotated as gp11, but the origin of this annotation is unclear.  Structure prediction shows this protein adopts an alpha helical 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 PF17616: Viral unique short region 6 (family)
This family has members such as US6 [swissprot:Q6SW00] found in HCMV (Human cytomegalovirus). US6 is a unique short region glycoprotein found in the ER. It blocks the binding of ATP by TAP1 (Transporter associated with Antigen Processing 1) through a conformational change and subsequently inhibits TAP-mediated peptide translocation to the ER. It also down regulates only MHC class I. Inhibition of US6 of TAP has been shown to require residues 89 to 108 of the HCMV US6 luminal domain, whereas sequences that flank this region stabilize the binding of the viral protein to TAP. Residues 81 to 90 and the C-terminal 39 residues of HCMV US6 may also contribute to the stabilization of the interaction between US6 and TAP.
Pfam PF03929: PepSY-associated TM region (family)
The PepSY_TM family is so named because it is an alignment of up to five transmembranes helices found in bacterial species some of which carry a nested PepSY domain, [pfam:PF03413].
Pfam PF14928: Short tail fibre protein receptor-binding domain (domain)
This domain is a receptor binding domain found on bacteriophage short tail fibre proteins. It contains a zinc-binding site and a potential lipopolysaccharide-binding site.
Pfam PF18153: Cap15, cyclic dinucleotide receptor domain (domain)
This entry represents the cyclic dinucleotide receptor domain of CD-NTase-associated protein 15 (Cap15), an effector protein of a CBASS antivirus system. These proteins occur in conserved genome contexts with the SMODS nucleotide synthetase. Cap15 consists of two transmembrane segments (TM) at the N-terminal and an eight-stranded beta-barrel scaffold that forms a cyclic dinucleotide receptor domain, which oligomerises upon activation. Activated Cap15 binds the cyclic nucleotide second messenger 3',3'-cGAMP, re-localizes throughout the cell and specifically induces rupture of the inner membrane. This domain exhibits more distantly related structural homology to streptavidin proteins.
Pfam PF04889: Cwf15/Cwc15 cell cycle control protein (family)
This family represents Cwf15/Cwc15 (from Schizosaccharomyces pombe and Saccharomyces cerevisiae respectively) and their homologues. The function of these proteins is unknown, but they form part of the spliceosome and are thus thought to be involved in mRNA splicing.
Pfam PF23231: Pre-mRNA-splicing factor Syf1/CRNKL1 C-terminal HAT repeat (repeat)
This entry includes a group of pre-mRNA-processing factors that are components of the spliceosome, involved in pre-RNA splicing, including Syf1 from human and its homologues from fungi, crooked neck from Drosophila and its homologues from human and fungi Crooked neck-like protein 1 (CRNKL1/SYF-3) and CFL1, respectively. These proteins contain HAT (Half A TPR) repeats which have a repetitive pattern characterised by three aromatic residues with a conserved spacing. They are structurally and sequentially similar to TPRs. The HAT repeats in these proteins can be divided in three segments, N-terminal, central and C-terminal. This entry represents the C-terminal HAT repeats of these proteins. The C-terminal HAT repeats make contacts with other proteins in the complex, to stabilise it.
Pfam PF11472: Protein of unknown function (DUF3206) (family)
This bacterial family of proteins has no known function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF15919: HicB_like antitoxin of bacterial toxin-antitoxin system (domain)
This is a family of HicB-like antitoxins.
Wikipedia: A toxin-antitoxin system consists of a "toxin" and a corresponding "antitoxin", usually encoded by closely linked genes. The toxin is usually a protein while the antitoxin can be a protein or an RNA. Toxin-antitoxin systems are widely distributed in prokaryotes, and organisms often have them in multiple copies. When these systems are contained on plasmids – transferable genetic elements – they ensure that only the daughter cells that inherit the plasmid survive after cell division. If the plasmid is absent in a daughter cell, the unstable antitoxin is degraded and the stable toxic protein kills the new cell; this is known as 'post-segregational killing' (PSK).
Pfam PF07043: Protein of unknown function (DUF1328) (family)
This family consists of several hypothetical bacterial proteins of around 50 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 PF05575: Vibrio cholerae RfbT protein (family)
This family consists of several RfbT proteins from Vibrio cholerae. It has been found that genetic alteration of the rfbT gene is responsible for serotype conversion of Vibrio cholerae O1 and determines the difference between the Ogawa and Inaba serotypes, in that the presence of rfbT is sufficient for Inaba-to-Ogawa serotype conversion.
Pfam PF20081: Domain of unknown function (DUF6475) (domain)
This presumed domain is functionally uncharacterised. This domain family is found in Proteobacteria and viruses, and is approximately 90 amino acids in length. It contains the conserved motifs FDD and MGGW.
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 PF03423: Carbohydrate binding domain (family 25) (domain)
This entry represents CBM25, which has been shown to bind starch .
A carbohydrate-binding module (CBM) is defined as a contiguous amino acid sequence within a carbohydrate-active enzyme with a discreet fold having carbohydrate-binding activity. A few exceptions are CBMs in cellulosomal scaffolding proteins and rare instances of independent putative CBMs. The requirement of CBMs existing as modules within larger enzymes sets this class of carbohydrate-binding protein apart from other non-catalytic sugar binding proteins such as lectins and sugar transport proteins.

CBMs were previously classified as cellulose-binding domains (CBDs) based on the initial discovery of several modules that bound cellulose . However, additional modules in carbohydrate-active enzymes are continually being found that bind carbohydrates other than cellulose yet otherwise meet the CBM criteria, hence the need to reclassify these polypeptides using more inclusive terminology.

Previous classification of cellulose-binding domains were based on amino acid similarity. Groupings of CBDs were called "Types" and numbered with roman numerals (e.g. Type I or Type II CBDs). In keeping with the glycoside hydrolase classification, these groupings are now called families and numbered with Arabic numerals. Families 1 to 13 are the same as Types I to XIII. For a detailed review on the structure and binding modes of CBMs see .
Wikipedia: In molecular biology, a carbohydrate-binding module (CBM) is a protein domain found in carbohydrate-active enzymes. The majority of these domains have carbohydrate-binding activity. Some of these domains are found on cellulosomal scaffoldin proteins. CBMs were previously known as cellulose-binding domains. CBMs are classified into numerous families, based on amino acid sequence similarity. There are currently 64 families of CBM in the CAZy database.
Pfam PF03828: Cid1 family poly A polymerase (family)
This domain is found in poly(A) polymerases and has been shown to have polynucleotide adenylyltransferase activity. Proteins in this family have been located to both the nucleus and the cytoplasm.
Pfam PF17381: Seminal vesicle secretory proteins 4/5/6 (family)
There are seven major proteins involved in murine seminal vesicle secretion (SVS1-7). Mouse Svs2-Svs6 genes evolved by gene duplication and belong to the same gene family. This domain family is found in SVS4/5 and 6. SVS4 is a basic, thermostable, secretory protein synthesized by rat seminal vesicle epithelium under strict androgen transcriptional control. This protein has potent nonspecies-specific immunomodulatory, anti-inflammatory, and pro-coagulant activities that have been shown to be located in the N-terminal region of Svs4 (fragment 1-70). The N-terminal segment has a high amino-acid sequence similarity with the C-terminal segment 34-66 of uteroglobin, a rabbit steroid-inducible, cytokine-like, multifunctional, secreted protein. Furthermore, SVS4 acts as a sperm capacitation inhibitor, by interacting with SVS3 and SVS2.
Pfam PF17512: Metapneumovirus Small hydrophobic protein (family)
This family is found in SH (small hydrophobic) proteins present in Metapneumovirus such as the Avian metapneumovirus (AMPV), a paramyxovirus that has three membrane proteins (G, F, and SH). Among them, the SH protein is a small type II integral membrane protein. It is located in both the plasma membrane as well as within intracellular compartments. AMPV type C- SH protein localizes in the endoplasmic reticulum (ER), Golgi, and cell surface, and is transported through ER-Golgi secretory pathway. AMPV SH protein is modified by N-linked glycans and can be released into the extracellular environment. Furthermore, it has been shown that glycosylated AMPV SH proteins form homodimers through cysteine-mediated disulfide bonds.
Pfam PF13500: AAA domain (domain)
This domain is found in a number of proteins involved in cofactor biosynthesis such as dethiobiotin synthase and cobyric acid synthase. This domain contains a P-loop motif.
Wikipedia: AAA proteins are a large group of protein family sharing a common conserved module of approximately 230 amino acid residues. This is a large, functionally diverse protein family belonging to the AAA+ protein superfamily of ring-shaped P-loop NTPases, which exert their activity through the energy-dependent remodeling or translocation of macromolecules.
Pfam PF17107: N-terminal domain on NACHT_NTPase and P-loop NTPases (family)
This is a family of fungal N-terminal domains that appear at the N-terminus of P-loop NTPases, NACHT-NTPases and Ankyrin or WD repeat proteins.  The exact function is not known.
Pfam PF10127: RNA repair pathway DNA polymerase beta family (family)
Family of the DNA polymerase beta superfamily, with closest affinities to the Minimal Nucleotide Transferase clade (MNT). Observed in diverse RNA repair genome contexts centered on both RtcB and Rnl-type (ATP-grasp fold) repair ligases. Members of this family of bacterial proteins catalyze the transfer of nucleotide residues from nucleoside diphosphates or triphosphates into dimer or polymer forms.
Pfam PF01390: SEA domain (domain)
Domain found in Sea urchin sperm protein, Enterokinase, Agrin (SEA). Proposed function of regulating or binding carbohydrate side chains. Recently a proteolytic activity has been shown for a SEA domain.
Pfam PF14793: Pyrimidine/purine nucleotide 5'-monophosphate nucleosidases (domain)
This is an N-terminal domain found in pyrimidine/purine nucleotide 5'-monophosphate nucleosidases (PpnN) in bacteria. PpnN catalyzes the hydrolysis of the N-glycosidic bond of diverse pyrimidine and purine nucleotide 5'-monophosphates, to form ribose 5-phosphate and the corresponding free base. It can use AMP, GMP, IMP, CMP, dTMP and UMP as substrates. It is found in association with [pfam:PF03641] and [pfam:PF11892].
Pfam PF13580: SIS domain (domain)
SIS (Sugar ISomerase) domains are found in many phosphosugar isomerases and phosphosugar binding proteins. SIS domains are also found in proteins that regulate the expression of genes involved in synthesis of phosphosugars.
Pfam PF24570: BPM/SPOP, BACK domain (domain)
This entry represent the BACK domain present in BPM proteins from plants, SPOP from animals and related sequences. BPM proteins are part of the Cullin E3 ubiquitin ligase complexes playing a role as substrate-specific adaptors of CUL3-based E3 ligases in the ubiquitin-proteasome pathway. They bind at least three families of transcription factors: ERF/AP2 class I, homeobox-leucine zipper and R2R3 MYB, playing an important role in plant flowering, seed development and abiotic stress response. SPOP, also known as HIB homologue 1 or Roadkill homologue 1 in humans, is an adaptor protein that forms a complex with Cul3, cullin-RING-based BCR (BTB-CUL3-RBX1) E3 ubiquitin-protein ligase complex, and is involved in ubiquitination of BMI1, H2AFY, and the death-associated protein 6 (DAXX). This domain is involved in dimerization together with the BTB domain ([pfam:PF00651]), resulting in linear higher-order oligomers.
Pfam PF24487: Kinetochore protein NDC80 loop region (coiled_coil)
This entry represents the loop region found at the C-terminal of Kinetochore protein NDC80, a component of the mitotic spindle and it is required for kinetochore integrity and the organization of stable microtubule binding sites in the outer plate of the kinetochore.
Pfam PF21914: Domain of unknown function (DUF6921) (domain)
This family of proteins is based on the known structure of a protein from Ruminococcus gnavus PDB:3noh. The structure shows similarity to solute binding proteins. The exact function of these proteins is not yet 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 PF09612: Bacterial protein of unknown function (HtrL_YibB) (family)
The protein from this rare, uncharacterized protein family is designated HtrL or YibB in E. coli, where its gene is found in a region of LPS core biosynthesis genes. Homologues are found in Shigella flexneri, Campylobacter jejuni, and Caenorhabditis elegans only. The htrL gene may represent an insertion to the LPS core biosynthesis region, rather than an LPS biosynthetic protein.
Pfam PF24254: Domain of unknown function (DUF7455) (domain)
This entry represents a family of uncharacterised actinobacterial zinc binding domains. The proteins contain a characteristic CXHH motif. Only the second of those two histidines acts as the zinc ligand according to structure prediction (ipTM = 0.94).
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 PF16803: Fe-S cluster assembly protein DRE2 N-terminus (domain)
This is the N-terminal domain of the fungal Fe-S cluster assembly protein DRE2.
Pfam PF12957: Domain of unknown function (DUF3846) (domain)
A family of uncharacterized proteins found by clustering human gut metagenomic sequences. This domain is found associated with an [pfam:PF07275] like domain. This suggests that this family may also be involved in evading host restriction.
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 PF11767: Histone lysine methyltransferase SET associated (domain)
SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. A subset of SET domains have been called PR domains. The SET domain consists of two regions known as N-SET and SET-C. SET-C forms an unusual and conserved knot-like structure of probably functional importance.  Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure. This domain is found in fungi associated with SET and N-SET domains.
Pfam PF09895: RecB-family nuclease (DUF2122) (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 PF08369: Proto-chlorophyllide reductase 57 kD subunit (family)
This domain is found in bacteria and plant chloroplast proteins. It often appears at the C-terminal of Nitrogenase component 1 type Oxidoreductases ([pfam:PF00148]) and sometimes independently in bacterial proteins such as the Proto-chlorophyllide reductase 57 kD subunit of the Cyanobacterium Synechocystis.
Pfam PF20400: BAR-like domain (domain)
This entry represents a BAR-like domain found in a variety of fungal proteins.
Pfam PF18028: Zmiz1 N-terminal tetratricopeptide repeat domain (repeat)
This is the N-terminal domain found in Zmiz1 proteins (Zinc finger MIZ domain-containing protein 1). Zmiz1 is a direct Notch1 cofactor that heterogeneously regulates Notch target genes. Zmiz1 directly interacts with the RAM1 domain of Notch1 through this N-terminal tetratricopeptide repeat (TPR) domain. Furthermore, it has been shown that Zmiz1 and Notch1 cooperatively recruit each other to chromatin through direct interaction via the N-terminal TPR domain resulting in a slight increase in activating histone marks and decrease of repressive histone marks. Functional analysis indicate that the N-Terminal Domain of Zmiz1 is important for driving Myc transcription and proliferation indirectly.
Pfam PF22985: Protein bicaudal C homolog 1, KH-like domain (domain)
This domain is found in the homologues of human Protein bicaudal C homolog 1 (Bicc1). Bicc1 is an RNA-binding protein composed of three KH and two KH-like domains that are linked by an intervening sequence to a C-terminal SAM domain. Bicc1 acts as a negative regulator of Wnt signaling. It is also involved in regulating gene expression during embryonic development. Bicc1 binds the 3' UTRs of the target mRNAs via KH domains, whereas self-polymerization of its SAM domain mediates recruitment to large cytoplasmic foci for translational silencing. This entry represents the Bicc1 KH-like domains.
Pfam PF04378: Ribosomal RNA large subunit methyltransferase D, RlmJ (domain)
RlmJ is ribosomal RNA large subunit methyltransferase J is required for full methylation of 23S ribosomal RNA (rRNA) during ribosome biogenesis. The ribosomal RNA of E. coli carries 24 residues that require methylation, and this methyltransferase is the last to be described, that modifies A2030. RlmJ displays a variant of the Rossmann-like methyltransferase (MTase) fold with an inserted helical subdomain. On binding cofactor and substrate a large shift of the N-terminal motif X tail is induced in order to make it cover the cofactor-binding site and to trigger active-site changes in motifs IV and VIII.