SII-SWORD/CoKE huggingface dataset:
Pfam PF09923: Uncharacterized protein conserved in bacteria (DUF2155) (family)
This domain, found in various hypothetical prokaryotic 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 PF21207: Glyoxalase domain-containing protein 4, N-terminal (domain)
This domain is found at the N-terminal end of Glyoxalase domain- containing protein 4 from humans (GLOD4) and similar proteins from vertebrates. This protein seem to be involved in metabolic detoxification. The specific function of this domain is still unknown.
Pfam PF22623: KIAA1064-like, CCCH zinc finger (domain)
This domain is found in human KIAA1064 (also known as Zinc finger CCCH domain-containing protein 4, a RNA-binding protein that suppresses transcription of long non-coding RNAs (lncRNAs).
Pfam PF04952: AstE/AspA barrel-sandwich hybrid domain (domain)
This entry represents the barrel-sandwich hybrid domain found in Succinylglutamate desuccinylase (AstE), aspartoacylase (AspA) and related enzymes. AstE catalyses the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway whereas AspA cleaves acylaspartate into a fatty acid and aspartate. Mutations in human AspA lead to Canavan disease disease. The domain represented by this entry has similarity to known barrel-sandwich domains that are defined by sandwich of half-barrel shaped beta-sheets. This domain is also described as shielding domain as it was found to cover the enzyme active site and thus limiting its accessibility.
Pfam PF04708: Poxvirus F16 protein (family)
This entry represents the Poxvirus F16 proteins, also known as Protein OPG061. This protein is expressed in the early phase of the viral replicative cycle .
Pfam PF21571: Arginine dihydrolase ArgZ-like, C-terminal, first region (domain)
This domain is found at the C-terminal end of Arginine dihydrolase ArgZ from Synechocystis sp (also known as Sll1336 protein) and similar prokaryotic sequences. ArgZ is involved in an ornithine- ammonia cycle (OAC) in cyanobacteria, which confers substantial adaptability under environmental nitrogen fluctuations. This protein is organised into three domains: a N-terminal domain belonging to the guanidino group-modifying enzyme (GME) family, a middle oxoglutarate reductase/saccharopine dehydrogenase bifunctional enzyme ([pfam:PF04455]) and a C-terminal uncharacterized region that can be divided in two subdomains. This entry represents the small first region of the C-terminal domain, which folds into beta-strands. Its specific function is unknown.
Pfam PF18476: PIN like domain (domain)
This is a domain of unknown function, suggested to be a member of PIN like domains clan.
Pfam PF13725: Possible tRNA binding domain (family)
This domain, found at the C-terminus of tRNA(Met) cytidine acetyltransferase, may be involved in tRNA-binding.
Pfam PF17903: Krr1 KH1 domain (domain)
This entry represents the first KH domain in the KRR1 protein. Krr1 is a ribosomal assembly factor. The KH1 domain is a divergent KH domain that lacks the RNA-binding GXXG motif and is involved in binding another assembly factor, Kri1.
Pfam PF21411: S. pombe DNA-binding protein Rap1, C-terminal (domain)
DNA-binding protein Rap1 is involved in protecting chromosome ends in fission yeast and its C-terminal domain (RCT) structurally resembles the first 3-helix bundle found in yeast and human RAP1 RCT. S. pombe RAP1 lacks direct DNA-binding activity and is localised to telomeres via Taz1. This entry represents the C-terminal domain of Rap1 from S. pombe.
Pfam PF24281: HVO_2928, N-terminal (domain)
This domain is found at the N-terminal of the predicted transcription regulator HVO_2928 from Haloferax volcanii and similar archaeal proteins. This domain is predicted to adopt an alpha-beta structure. It is often found associated with [pfam:PF04967].
Pfam PF23006: Tyrosine-protein kinase receptor torso, first FN3 domain (domain)
This domain is found in the Tyrosine-protein kinase receptor torso from Bombyx mori (Tor), which is involved in the initiation of metamorphosis during postembryonic development. This protein is organised into three consecutive fibronectin type III (FN3) domains and a C-terminal Kinase domain. This entry represents the first FN3 domain. This domain has an N-terminal alpha-helical extension.
Pfam PF15389: Domain of unknown function (DUF4612) (family)
This protein family is a domain of unknown function, which is found in eukaryotes. Proteins in this family are typically between 109 and 323 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 PF12609: Wound-induced protein (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 81 and 97 amino acids in length. The proteins in the family are often annotated as wound-induced proteins however there is little accompanying literature to confirm this.
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 PF14108: ABA DEFICIENT 4-like (family)
This family of proteins is found in bacteria and plants. It includes abscisic acid (ABA)-deficient 4 protein (ABA4) from Arabidopsis thaliana, which has a role in neoxanthin synthesis and may be important for the de novo ABA synthesis specifically during dehydration.
Pfam PF25103: Domain of unknown function (DUF7811) (domain)
This domain is found in uncharacterised plant proteins. It is predicted to fold into a five-stranded antiparallel beta-sheet and two alpha-helices packed on it.
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 PF18109: Ferredoxin I 4Fe-4S cluster domain (domain)
This is domain is found in Ferredoxin I (FdI), an Iron-sulfur ([Fe-S]) cluster-containing protein, present in species such as Azotobacter vinelandii. [Fe-S] proteins participate in electron transfer, catalytic, regulatory, and structural function. The FdI cluster exhibits a pH-dependent reduction potential and reversible protonation in the reduced state.
Pfam PF21417: Tyrosine 3-monooxygenase-like, ACT domain (domain)
This domain is found in Tyrosine 3-monooxygenase from Rattus norvegicus (TH) and similar proteins from vertebrates. TH catalyses the hydroxylation of tyrosine to form 3,4-dihydroxyphenylalanine in the biosynthesis of the catecholamine neurotransmitters. This entry represents the regulatory domain, which is centrally located (C- terminal to [pfam:PF12549] and N-terminal to [pfam:PF00351]). It is an ACT domain that shows a four stranded antiparallel beta-sheet and two alpha-helices connected by four loops. It adopts a dimeric configuration. In humans, TH is associated with several disorders.
Pfam PF06105: Aph-1 protein (family)
This family consists of several eukaryotic Aph-1 proteins.Gamma-secretase catalyses the intramembrane proteolysis of Notch, beta-amyloid precursor protein, and other substrates as part of a new signaling paradigm and as a key step in the pathogenesis of Alzheimer's disease. It is thought that the presenilin heterodimer comprises the catalytic site and that a highly glycosylated form of nicastrin associates with it. Aph-1 and Pen-2, two membrane proteins genetically linked to gamma-secretase, associate directly with presenilin and nicastrin in the active protease complex.  Co-expression of all four proteins leads to marked increases in presenilin heterodimers, full glycosylation of nicastrin, and enhanced gamma-secretase activity. APH-1 proteins have a similar but different set of motifs as compared to other families. Their four motifs are: QExxR, Fxxxx, Hxxxs and Hxxxs respectively. Given the inferred homology between APH-1 and other membrane proteases such as type II CAAX proteases and PrsW proteases, it is speculated that APH-1 may possess protease activity.
Pfam PF12709: Fungal Transforming acidic coiled-coil (TACC) proteins (coiled_coil)
TACC proteins are present in different organisms, ranging from yeasts to mammals. Schizosaccharomyces pombe has one TACC protein, known as Alp7 or Mia1p. Alp7/TACC consists of two domains: the N-terminal half that contains the nuclear localization signal (NLS) and has no homology to the other TACC members, and the C-terminal half, which consists of the conserved coiled-coil TACC domain. Alp7/TACC forms a complex with Alp14/TOG and localizes to microtubules, SPBs and kinetochores. This complex is necessary for mitotic and meiotic spindle assembly and proper chromosome segregation. The homologue from S. cerevisiae, Slk19, also has a role in spindle assembly and stability, and it is required for proper chromosome segregation.
Pfam PF17491: Spider Toxins mu-diguetoxin-1 a, b and c (family)
This family has members that are 56-59 residue mu-diguetoxin-1 toxins, which have been isolated from the weaving spider, Diguetia canities. These toxins were isolated as a result of their potent insect paralytic activities, designated mu-DGTX-Dc1a to -Dc1c (formerly DTX9.2, DTX11 and DTX12). Family members such as beta-Diguetoxin-Dc1a (Dc1a) has been structurally characterized and shown to have disulfide bonds which form a classical inhibitor cysteine knot (ICK) motif in which the Cys13-Cys26 and Cys20-Cys40 disulfide bonds and the intervening sections of the polypeptide backbone forming a 23-residue ring that is pierced by the Cys25-Cys54 disulfide bond. This ICK motif is commonly found in spider toxins, and this particular scaffold provides these peptides (so-called knottins) with an unusually high degree of chemical, thermal and biological stability. Dc1a contains an additional disulfide bond (Cys42-Cys52) that appears to serve as a molecular staple which limits the flexibility of a disordered serine-rich hairpin loop. The extended N-terminus of Dc1a along with an unusually large loop between Cys26 and Cys40 enables the formation of an N-terminal three-stranded antiparallel beta-sheet that is not found in any other knottin.The molecular surface of Dc1a contains a relatively uniform distribution of charged residues; moreover, there are no distinct clusters of hydrophobic residues that might mediate an interaction with lipid bilayers.
Pfam PF16133: Domain of unknown function (DUF4844) (family)
this family consists of short uncharacterized proteins found mostly in different strains of Acinetobacter bumanii, but also in several Shewanella species and in some bacteria from the CFB group. Solved structure of ABAYE3784 protein from Acinetobacter baumannii AYE shows a five helical bundle with a very strong structural similarity to a bromodomain domain. However, the specific function of proteins from the DUF4844 family is unknown
Pfam PF23574: Zinc finger protein 142 C2H2 domain (domain)
This C2H2 domain is found in the human Zinc finger protein 142 (ZNF142) and related proteins. ZNF142 plays a role in nervous system development. It is thought to be involved in transcriptional regulation.
Pfam PF13389: Protein of unknown function (DUF4107) (family)
This family of putative proteins are found in Trichomonas vaginalis in large numbers.        The function of this protein is unknown.
Pfam PF00301: Rubredoxin (domain)
Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer , sometimes replacing ferredoxin as an electron carrier . Rubredoxins possess a 45- to 55-residue domain containing one iron atom tetrahedrally coordinated to four cysteinyl residues. Structural analysis of the domains have shown them to be folded into a short three-stranded antiparallel Î²-sheet and a number of loops .
This entry represents the rubredoxin domain.
Wikipedia: Rubredoxins are a class of low-molecular-weight iron-containing proteins found in sulfur-metabolizing bacteria and archaea. Sometimes rubredoxins are classified as iron-sulfur proteins; however, in contrast to iron-sulfur proteins, rubredoxins do not contain inorganic sulfide. Like cytochromes, ferredoxins and Rieske proteins, rubredoxins are thought to participate in electron transfer in biological systems. Recent work in bacteria and algae have led to the hypothesis that some rubredoxins may instead have a role in delivering iron to metalloproteins.
Pfam PF08496: Peptidase family S49 N-terminal (family)
This domain is found to the N-terminus of bacterial signal peptidases of the S49 family ([pfam:PF01343]).
Pfam PF05915: Transmembrane proteins 230/134 (family)
This family consists of the eukaryotic transmembrane proteins 230 and 134 (TMEM230 and 134). TMEM134 function is unknown, but it has been shown to interact with E virus ORF2. TMEM 230 is involved in trafficking and recycling of synaptic vesicles.
Pfam PF11823: Putative Se/S carrier protein-like (family)
This family of proteins are functionally uncharacterised. This protein is found in bacteria and archaea. Proteins in this family are typically between 78 to 102 amino acids in length. It has been suggested that this family of proteins may be chaperones involved in Se or S trafficking in the cell.
Pfam PF16138: Domain of unknown function (4846) (family)
This family consists of uncharacterized proteins around 260 residues in length and is mainly found in various Bacteroides species. The function of this family is unknown.
Pfam PF01725: Ham1 family (domain)
This family consists of the HAM1 protein [swissprot:P47119] and hypothetical archaeal bacterial and C. elegans proteins. HAM1 controls 6-N-hydroxylaminopurine (HAP) sensitivity and mutagenesis in S. cerevisiae [swissprot:P47119]. The HAM1 protein protects the cell from HAP, either on the level of deoxynucleoside triphosphate or the DNA level by a yet unidentified set of reactions.
Pfam PF02680: Uncharacterized ArCR, COG1888 (family)
This entry represents a group of prokaryotic proteins of unknown function that includes Uncharacterized protein MJ0319 from Methanocaldococcus jannaschii (Q57767).
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 PF17580: Group B Rotavirus Non-structural protein 5 (family)
Family members such as non-structural protein 5 (NSP5), are found in Group B rotaviruses (GBR). Group B rotavirus (GBR) is genetically and antigenically distinct from Group A rotavirus (GAR). Hence phylogneetic studies have been carried out and show that the C-terminal region of NSP5, which is conserved among GAR and critical for its function for viroplasm-like structure formation in cells, was also conserved in GBR NSP5.
Wikipedia: NSP5 encoded by genome segment 11 of group A rotaviruses. In virus-infected cells NSP5 accumulates in the viroplasms. NSP5 has been shown to be autophosphorylated.
Interaction of NSP5 with NSP2 was also demonstrated. In rotavirus-infected cells, the non-structural proteins NSP5 and NSP2 localize in complexes called viroplasms, where replication and assembly occur and they can drive the formation of viroplasm-like structures in the absence of other rotaviral proteins and rotavirus replication.
Pfam PF17904: FMRP KH0 domain (domain)
This entry corresponds to the KH0 domain from the FMRP protein. This is a divergent KH domain that was discovered through solving the structure of an N-terminal fragment of the FMRP protein. KH0 does not have the canonical G-X-X-G motif between helices A and B. It has been suggested that this domain may be involved in RNA binding.
Pfam PF24520: KNTC1 first ARM-repeats domain (repeat)
This entry represents the first segment of ARM repeats present in KNTC1 (also known as ROD), following the beta-propeller domain. KNTC1 is a crucial component of the mitotic checkpoint, ensuring cells do not exit mitosis prematurely. KNTC1 is required for the assembly of essential complexes onto kinetochores, such as dynein-dynactin and MAD1-MAD2. KNTC1 is the major subunit of the RZZ (ROD-Zwilch-ZW10) complex, which plays a significant role in spindle assembly, kinetochore-microtubule attachment, and spindle pole separation.
Pfam PF20655: Vps52, C-terminal (repeat)
Vps52 complexes with Vps53 and Vps54 to form the Golgi-associated retrograde protein (GARP) complex that is involved in retrograde transport from early and late endosomes to the trans-Golgi network, regulating membrane trafficking events. It is also part of EARP (Endosome-Associated Recycling Protein) complex, involved in endocytic recycling. This entry represents the C-terminal domain of Vps52, which consists of alpha-helical bundles, conserved among subunits of other multisubunit tethering complexes (MTC) such as conserved oligomeric Golgi (COG), Dsl1 and the exocyst, all belong to a family of evolutionarily conserved complexes associated with tethering containing helical rods (CATCHR). This domain may interact with the small GTPase Ypt6p/Rab6.
Pfam PF06807: Pre-mRNA cleavage complex II protein Clp1 (family)
This family consists of several pre-mRNA cleavage complex II Clp1 (or HeaB) proteins. Six different protein factors are required in vitro for 3' end formation of mammalian pre-mRNAs by endonucleolytic cleavage and polyadenylation. Clp1 is a subunit of cleavage complex IIA, which is required for cleavage, but not for polyadenylation of pre-mRNA.
Pfam PF01214: Casein kinase II regulatory subunit (domain)
Casein kinase, a ubiquitous well-conserved protein kinase involved in cell metabolism and differentiation, is characterised by its preference for Ser or Thr in acidic stretches of amino acids. The enzyme is a tetramer of 2 alpha-and 2 beta-subunits . However, some species (e.g., mammals) possess 2 related forms of the alpha-subunit (alpha and alpha'), while others (e.g., fungi) possess 2 related beta-subunits (beta and beta') .
Wikipedia: Casein kinase II subunit beta is a protein that in humans is encoded by the CSNK2B gene. It is a ubiquitous protein kinase which regulates metabolic pathways, signal transduction, transcription, translation, and replication. The enzyme localizes to the endoplasmic reticulum and the Golgi apparatus.
Pfam PF03591: AzlC protein (family)
This entry includes some uncharacterised bacterial proteins and the branched-chain amino acid transport protein AzlC encoded by azlC gene, which is part of the azl operon, involved in branched-chain amino acid transport . AzlCD is a bipartite histidine exporter consisting of AzlC and AzlD subunits . Overexpression of this gene results in resistance to a leucine analogue, 4-azaleucine.
Pfam PF16807: Putative tail termination protein (domain)
This entry likely represents a family of phage tail termination proteins. This protein likely forms a hexameric complex that binds to the tail tube complex of phage.
Pfam PF07155: ECF-type riboflavin transporter, S component (family)
This family is the substrate-binding component (S component) of the energy coupling-factor (ECF)-type riboflavin transporter. It is a transmembrane protein which binds riboflavin, and is responsible for riboflavin-uptake by cells.
Pfam PF10088: Uncharacterised protein conserved in bacteria (DUF2326) (family)
This domain, found in various hypothetical bacterial 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 PF04107: Glutamate-cysteine ligase family 2(GCS2) (family)
Also known as gamma-glutamylcysteine synthetase and gamma-ECS ([ec:6.3.2.2]). This enzyme catalyses the first and rate limiting step in de novo glutathione biosynthesis. Members of this family are found in archaea, bacteria and plants. May and Leaver discuss the possible evolutionary origins of glutamate-cysteine ligase enzymes in different organisms and suggest that it evolved independently in different eukaryotes, from an ancestral bacterial enzyme. They also state that Arabidopsis thaliana gamma-glutamylcysteine synthetase is structurally unrelated to mammalian, yeast and Escherichia coli homologues. In plants, there are separate cytosolic and chloroplast forms of the enzyme.
Pfam PF22937: PDXDC1-like second central domain (domain)
This entry represents a domain found in Pyridoxal-dependent decarboxylase domain-containing protein 1 (PDXDC1) and related proteins. PDXDC1 has been associated with the modulation of prepulse inhibition of acoustic startle, perhaps through the metabolism of catecholamine neurotransmitters. The function of this domain is unknown.
Pfam PF12742: Gryzun, putative Golgi trafficking (domain)
Members of this family are involved in Golgi trafficking.
Pfam PF05993: Reovirus major virion structural protein Mu-1/Mu-1C (M2) (family)
This family consists of several Reovirus major virion structural protein Mu-1/Mu-1C (M2) sequences. This family is family is thought to play a role in host cell membrane penetration.
Pfam PF09775: Keratinocyte-associated protein 2 (family)
Members of this family comprise various keratinocyte-associated proteins. Their exact function has not, as yet, been determined.
Pfam PF00903: Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily (domain)
Glyoxalase I (4.4.1.5) (lactoylglutathione lyase) catalyzes the first step of the glyoxal pathway. S-lactoylglutathione is then converted by glyoxalase II to lactic acid . Glyoxalase I is an ubiquitous enzyme which binds one mole of zinc per subunit. The bacterial and yeast enzymes are monomeric while the mammalian one is homodimeric. The sequence of glyoxalase I is well conserved.

The domain represented by this entry is found in glyoxalase I and in other related proteins, including fosfomycin resistance proteins FosB , FosA , FosX  and dioxygenases (eg. 4-hydroxyphenylpyruvate dioxygenase).
Pfam PF21964: NSF, AAA+ ATPase lid domain (domain)
This entry represents the ATPase lid domain of the second AAA+ ATP-binding domain (also known as D2) of NSF proteins, found at the C-terminal. NFS proteins are essential membrane fusion events. They play the role of a chaperone by activating SNAP receptor proteins (SNAREs) so that they can participate in membrane fusion.