SII-SWORD/CoKE huggingface dataset:
Pfam PF06586: TraK N-terminal domain (domain)
This entry represents the N-terminal domain from the TraK protein. The TraK N-terminal domain is a structural motif identified in bacterial type IV secretion systems (T4SSs), which play a crucial role in the proliferation of multi-drug resistance. This domain is involved in the formation of the outer-membrane core complex (OMCCF) of T4SS encoded by conjugative F plasmids. The structure of the TraK N-terminal domain shows a a beta-sandwich fold composed of five-stranded and four-stranded beta sheets. TraK assembles as a dimer within the complex, with the TraK N-terminal domains situated side by side. The TraK N-terminal domain plays a critical role in stabilizing the OMCCF structure, facilitating the assembly of the outer ring complex (ORC) of the T4SS. This domain interacts with other components of the OMCCF, including TraV and TraK C-terminal domains, contributing to the overall stability and function of the T4SS.
Pfam PF15196: Activator of apoptosis harakiri (family)
Apoptosis, or programmed cell death (PCD), is a common and evolutionarily conserved property of all metazoans . In many biological processes, apoptosis is required to eliminate supernumerary or dangerous (such as pre-cancerous) cells and to promote normal development. Dysregulation of apoptosis can, therefore, contribute to the development of many major diseases including cancer, autoimmunity and neurodegenerative disorders. In most cases, proteins of the caspase family execute the genetic programme that leads to cell death.
The protein harakiri (Hrk, also called death protein 5, DP5) is a pro-apoptotic Bcl-2 homology domain 3-only (BH3-only) member protein, which belongs to the Bcl-2 family. Hrk is associated to the mitochondrial outer membrane via a putative trans-membrane domain at the C-terminal, which adopts a predominantly Î±-helical structure. This domain is able to insert itself into membranes where it perturbs the physical properties of the membrane considerably .

It can be activated by a diverse array of developmental cues or experimentally applied stress stimuli. Hrk contributes to apoptosis signalling elicited by trophic factor withdrawal in certain neuronal cells but is not critical for apoptosis of haematopoietic cells . DP5 is important in neuronal cell death that can be induced by axotomy and neuronal growth factor (NGF) deprivation. It acts by regulating the mitochondrial function and caspase-3 activation .
Wikipedia: Activator of apoptosis harakiri is a protein that in humans is encoded by the HRK gene.
Pfam PF16573: N-terminal beta-sandwich domain of polyadenylation factor (family)
This family is the short N-terminal domain of the pre-mRNA cleavage complex II protein Clp1. Clp1 function involves some degree of adenine or guanine nucleotide-binding and participates in the 3'-end-processing of mRNAs in eukaryotes.
Pfam PF03835: Rad4 transglutaminase-like domain (domain)
RAD4/Xp-C proteins contain an ancient transglutaminase fold that is also found in peptide-N-glycanases (PNGases), which remove glycans from glycoproteins during their degradation. The PNGases retain the catalytic triad that is typical of this fold and are predicted to have a reaction mechanism similar to that involved in transglutamination. In contrast, the RAD4/Xp-C proteins are predicted to be inactive and are likely to only possess the interaction function in DNA repair .
Pfam PF13496: Domain of unknown function (DUF4120) (family)
Based on Bacteroides thetaiotaomicron gene BT_2585, a putative uncharacterised protein.  As seen in gene expression experiments (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE2231), it appears to be upregulated in the presence of host or vs when in culture.
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 PF21097: Spectrin repeat (domain)
This entry represents a spectrin repeat found in a variety of plectin and related proteins.
Pfam PF16857: RNA polymerase inhibitor (domain)
This bacteriophage protein inhibits the bacterial host RNA polymerase by interacting with the RpoC subunit and inhibiting the formation of a promoter complex.
Pfam PF22288: Domain of unknown function (DUF6963) (domain)
This domain is found N-terminal in uncharacterised bacterial proteins. It is distantly related to class-II glutamine amidotransferase domains [pfam:PF13522].
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 PF09427: Domain of unknown function (DUF2014) (domain)
This domain is found at the C terminal of a family of ER membrane bound transcription factors called sterol regulatory element binding proteins (SREBP).
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 PF07229: VirE2 (family)
This family consists of several VirE2 proteins which seem to be specific to Agrobacterium tumefaciens and Rhizobium etli. VirE2 is known to interact, via its C terminus, with VirD4. Agrobacterium tumefaciens transfers oncogenic DNA and effector proteins to plant cells during the course of infection. Substrate translocation across the bacterial cell envelope is mediated by a type IV secretion (TFS) system composed of the VirB proteins, as well as VirD4, a member of a large family of inner membrane proteins implicated in the coupling of DNA transfer intermediates to the secretion machine. VirE2 is therefore thought to be a protein substrate of a type IV secretion system which is recruited to a member of the coupling protein superfamily.
Pfam PF01845: CcdB protein (domain)
CcdB protein is a topoisomerase poison from Escherichia coli . It is responsible for killing plasmid-free segregants, and interferes with the activity of DNA gyrase. It acts to inhibit partitioning of the chromosomal DNA.
Wikipedia: The CcdA/CcdB Type II Toxin-antitoxin system is one example of the bacterial toxin-antitoxin (TA) systems that encode two proteins, one a potent inhibitor of cell proliferation (toxin) and the other its specific antidote (antitoxin). These systems preferentially guarantee growth of plasmid-carrying daughter cells in a bacterial population by killing newborn bacteria that have not inherited a plasmid copy at cell division.
Pfam PF23676: Protein YnaM-like (family)
This protein family includes Protein YnaM, a 37-residues long protein encoded by a small open reading frame (smORF) in the Rac prophage from Escherichia coli.
Pfam PF09839: Uncharacterized protein conserved in bacteria (DUF2066) (family)
This domain, found in various 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 PF13984: MsyB protein (family)
The MsyB protein has been found to be able to restore protein export defects caused by a temperature-sensitive secY or secA mutation. However, its exact molecular function is still unknown, but it may play a role in protein export. Proteins in this family are approximately 120 amino acids in length. This family of proteins is found in bacteria.
Pfam PF21182: Zinc finger protein ZFPM1-like, PR domain (domain)
This domain is found in Zinc finger protein ZFPM1 from humans (FOG1) and similar proteins from animals. FOG1 is a transcriptional regulator involved in the coordination of the differentiation of platelets and erythrocytes. This domain shares close structural similarity with SET domains, showing substantial beta-sheet secondary structure. Its specific function remains unknown.
Pfam PF14110: Domain of unknown function (DUF4282) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and eukaryotes. Proteins in this family are typically between 93 and 155 amino acids in length. There is a single completely conserved residue E 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 PF09327: Bacteriophage tail tip fiber protein (family)
The Tail Tip Fiber Protein family includes proteins involved in the attachment and penetration of bacteriophages into host cells. Members of this family are responsible for recognizing and irreversibly binding to specific host receptors, which triggers structural changes in the viral tail necessary for the injection of viral DNA into the host. This process is critical for the successful infection and propagation of the virus. The family includes proteins that initiate distal tail tip assembly during phage tail assembly and play a key role in the virus entry by mediating the attachment to the host receptor and inducing DNA ejection through the receptor's pore. This entry represents the beta prism domain which is formed from a homotrimeric complex of members of this family.
Pfam PF23314: TASOR alpha/beta domain (domain)
This is a domain found in TASOR proteins, a key component of the HUSH complex, a vertebrate-specific multiprotein complex that mediates epigenetic repression of both exogenous and endogenous genetic elements. The HUSH complex regulates H3K9me3 deposition by promoting recruitment of SETDB1 and also recruits MORC2 to compact chromatin. TASOR is crucial in early embryonic development and contains a catalytically-inactive PARP domain, necessary for epigenetic regulation of target elements. This entry represents an alpha/beta domain found towards the C-terminal of TASOR and TASOR2 which consist of four beta-sheets and short alpha-helices.
Pfam PF09406: Protein of unknown function (DUF2004) (family)
This is a family of proteins with unknown function.  The structure of one of the proteins in this family has revealed a novel alpha-beta 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 PF12712: Domain of unknown function (DUF3805) (domain)
This family represent the N-terminal domain of the structure. In two related Bacteroides species the gene lies immediately upstream from a putative ATP binding component of an ATP transporter and a putative histidinol phosphatase. The structure of this domain is strikingly similar to the N-terminal structure of 1tui, also of unknown function. The domain carries four conserved tryptophan residues.
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 PF10163: Transcription factor e(y)2 (family)
EnY2 is a small transcription factor which is combined in a complex with the TAFII40 protein. The protein is conserved from paramecium to humans.
Pfam PF24367: Family of unknown function (DUF7523) (family)
This family includes a group of proteins from archaea. Members are predicted to be organised into two domains, an N-terminal with an all-alpha configuration and a C-terminal with an alpha-beta 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 PF08745: PINc domain ribonuclease (family)
This is a family of bacterial and archaeal PINc domains. PIN domains are characterised by the conservation of three acidic residues, possibly four, an Asp at residue 13, a Glu at 63, and then Asps at 172 and 194 in UniProtKB:Q58360. Family members include Homologs of Aquifex RNase P (HARP) proteins.
Pfam PF10028: Predicted integral membrane protein (DUF2270) (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 PF17376: Family of unknown function (DUF5398) (family)
This is a family of unknown function found in Chlamydiales.
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 PF12436: ICP0-binding domain of Ubiquitin-specific protease 7 (family)
This domain is one of two C-terminal domains on the much longer ubiquitin-specific proteases. This particular one is found to interact with the herpesvirus 1 trans-acting transcriptional protein ICP0/VMW110.
Pfam PF15099: Phosphoinositide-interacting protein family (family)
The function of this family, PIRT, is not known, however it is predicted to be a multi-pass membrane protein. This family of proteins is thought to have a role in positively regulating TRPV1 channel activity via phosphatidylinositol 4,5-bisphosphate (PIP2). This family of proteins is found in eukaryotes. Proteins in this family are located in the cell membrane. Proteins in this family are approximately 140 amino acids in length.
Pfam PF08478: POTRA domain, FtsQ-type (domain)
FtsQ/DivIB bacterial division proteins ([pfam:PF03799]) contain an N-terminal POTRA domain (for polypeptide-transport-associated domain). This is found in different types of proteins, usually associated with a transmembrane beta-barrel. FtsQ/DivIB may have chaperone-like roles, which has also been postulated for the POTRA domain in other contexts.
Pfam PF07126: Cell-division protein ZapC, C-terminal (domain)
ZapC is one of four FtsZ-binding components of the Z ring in bacteria. Formation of the Z ring on the cytoplasmic surface of the membrane is the starting process for assembly of the cell-division apparatus. It binds directly to the Z ring, and although it is not essential for absolute cell division it contributes to it by enhancing the interactions between the FtsZ protofilaments (or polymers) which aggregate to form the ring conformation in the Z ring. This is the C-terminal domain which contains a pocket with a hydrophobic centre surrounded by conserved basic residues, critical for FtsZ binding.
Pfam PF10061: Uncharacterized conserved protein (DUF2299) (family)
Members of this family of hypothetical bacterial proteins 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 PF11978: Shoulder domain (domain)
This domain is found in the Major Vault Protein and has been called the shoulder domain. This family includes two bacterial proteins [swissprot:A6FXE2] and [swissprot:A1ZGE7]. This suggests that some bacteria may possess vault particles.
Pfam PF05806: Noggin (family)
This family consists of the eukaryotic Noggin proteins. Noggin is a glycoprotein that binds bone morphogenetic proteins (BMPs) selectively and, when added to osteoblasts, it opposes the effects of BMPs. It has been found that noggin arrests the differentiation of stromal cells, preventing cellular maturation.
Pfam PF09573: TaqI restriction endonuclease (family)
This family includes the TaqI (recognises and cleaves T^CGA) restriction endonuclease.
Pfam PF20294: KTSC and Metallopeptidase N-terminal fusion domain (family)
Uncharacterized alpha/beta domain N-terminally fused to diverse Metallopeptidase (MPTase) and the lysyl tRNA synthetase KTSC RNA-binding domain protein. Currently observed in only the jumbo phages.
Pfam PF13834: Domain of unknown function (DUF4193) (family)
This domain of unknown function contains four conserved cysteines and a conserved histidine, including a CXXXXH 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 PF08750: CNP1-like family (family)
This family of proteins are likely to be lipoproteins. CNP1 (cryptic neisserial protein) has been expressed in E. coli and shown to be localised periplasmicly.
Pfam PF24039: Domain of unknown function (DUF7348) (domain)
This domain is found N-terminal in a group of uncharacterised archaeal proteins. In some proteins, this domain precedes [[pfam:PF18069]] and [[pfam:PF18009]]. It is predicted to fold into a globular alpha/beta 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 PF13468: Glyoxalase-like domain (domain)
This domain is related to the Glyoxalase domain [pfam:PF00903].
Pfam PF12702: Lipocalin-like (domain)
This is a family of proteins of 115 residues on average.  The family has two highly conserved tryptophan residues. The fold is very similar to the lipocalin-like fold from several comparable structures.
Wikipedia: The lipocalins are a family of proteins which transport small hydrophobic molecules such as steroids, bilins, retinoids, and lipids, and most lipocalins are also able to bind to complexed iron as well as heme. They share limited regions of sequence homology and a common tertiary structure architecture. This is an eight stranded antiparallel beta barrel with a repeated + 1 topology enclosing an internal ligand binding site.
Pfam PF13780: Domain of unknown function (DUF4176) (family)
The function of these proteins 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 PF22908: Histone-lysine N-methyltransferase NSD-like, PHD zinc finger (domain)
This domain is found in the NSD (nuclear receptor SET domain- containing) family of histone-lysine N-methyltransferase such as NSD1, NSD2, NSD3 and other related proteins. It adopts a classical PHD finger fold and is frequently found in tandem with an atypical (C5HCH) plant homeo-domain (PHD) finger. Both domains form an integral unit that plays an important role by engaging in multiple protein-protein interactions. This domain determines the differences in the histone binding specificity of the NSD family members.
Pfam PF01109: Granulocyte-macrophage colony-stimulating factor (domain)
Granulocyte-macrophage colony-stimulating factor (GMCSF) is a cytokine that acts in hematopoiesis to stimulate growth and differentiation of hematopoietic precursor cells from various lineages including granulocytes, macrophages, eosinophils and erythrocytes . GMCSF is a glycoprotein of ~120 residues that contains 4 conserved cysteines that participate in disulphide bond formation. The crystal structure of recombinant human GMCSF has been determined . There are two molecules in the asymmetric unit, which are related by an approximate non-crystallographic 2-fold axis. The overall structure, which is highly compact and globular with a predominantly hydrophobic core, is characterised by a 4-Î±-helix bundle. The helices are arranged in a left-handed anti-parallel fashion, with two overhand connections. Within the connections is a two-stranded anti-parallel Î²-sheet. The tertiary structure has a topology similar to that of Sus scrofa (pig) growth factor and interferon-beta. Most of the proposed critical regions for receptor binding are located on a continuous surface at one end of the molecule that includes the C terminus .
Wikipedia: Granulocyte-macrophage colony-stimulating factor (GM-CSF), also known as colony-stimulating factor 2 (CSF2), is a monomeric glycoprotein secreted by macrophages, T cells, mast cells, natural killer cells, endothelial cells and fibroblasts that functions as a cytokine. The pharmaceutical analogs of naturally occurring GM-CSF are called sargramostim and molgramostim.
Pfam PF23057: ZCCHC3, first RNA-binding domain (domain)
This entry represents the first RNA-binding domain (RBD) found in the Zinc finger CCHC domain-containing protein 3 (ZCCHC3). ZCCHC3 is a nucleic acid-binding protein crucial for the innate immune response to DNA and RNA viruses. It functions in the cytoplasm by binding to viral DNA and RNA, facilitating the recognition of these nucleic acids by key virus sensors like RIGI, IFIH1/MDA5, and CGAS.