SII-SWORD/CoKE huggingface dataset:
Pfam PF02437: SKI/SNO/DAC Dachshund homology domain (domain)
This entry represents a domain known as the Dachshund homology domain (DHD) that is about 100 amino acids long and found in members of Ski/Sno family. This domain contains a conserved CLPQ motif. The c-ski proto-oncogene has been shown to influence proliferation, morphological transformation and myogenic differentiation. Sno, a Ski proto-oncogene homologue, is expressed in two isoforms and plays a role in the response to proliferation stimuli. Dachshund also contains this domain.  It is involved in various aspects of development. The SKI-DHD adopts a mixed alpha/beta structure which includes features found in the forkhead/winged-helix family of DNA binding proteins, although SKI-DHD is not a DNA binding domain.
Pfam PF04767: DNA-binding 11 kDa phosphoprotein (family)
Family of poxvirus proteins required for virus morphogenesis. Protein function necessary for proteolytic processing of the major viral structural proteins, P4a and P4b.
Pfam PF12100: Domain of unknown function (DUF3576) (family)
This presumed domain is functionally uncharacterised. This domain is found in bacteria. This domain is about 100 amino acids in length. This domain has a single completely conserved residue G 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 PF08615: Ribonuclease H2 non-catalytic subunit (Ylr154p-like) (family)
This entry represents the non-catalytic subunit of RNase H2, which in S. cerevisiae is Ylr154p/Rnh203p [swissprot:Q12338] (. Whereas bacterial and archaeal RNases H2 are active as single polypeptides, the Saccharomyces cerevisiae homologue, Rnh2Ap, when expressed in Escherichia coli, fails to produce an active RNase H2. For RNase H2 activity three proteins are required [Rnh2Ap (Rnh201p), Ydr279p (Rnh202p) and Ylr154p (Rnh203p)]. Deletion of any one of the proteins or mutations in the catalytic site in Rnh2A leads to loss of RNase H2 activity. RNase H2 ia an endonuclease that specifically degrades the RNA of RNA:DNA hybrids. It participates in DNA replication, possibly by mediating the removal of lagging-strand Okazaki fragment RNA primers during DNA replication.
Pfam PF09145: Ubiquitin-associated (domain)
Ubiquitin associated domains contain approximately 40 residues and bind ubiquitin non-covalently. They adopt a secondary structure consisting of three alpha-helices, and have been identified in various modular proteins involved in protein trafficking, clathrin assembly/disassembly, DNA repair, proteasomal degradation, and cell cycle regulation.
Pfam PF07072: Cell division protein (family)
Cell division protein ZapD enhances FtsZ-ring assembly. It directly interacts with FtsZ and promotes bundling of FtsZ protofilaments, with a reduction in FtsZ GTPase activity.
Pfam PF23781: Phage tail assembly chaperone protein (domain)
This family represents a phage tail assembly chaperone protein.
Pfam PF05934: Mid-1-related chloride channel (MCLC) (family)
This family consists of several mid-1-related chloride channels. mid-1-related chloride channel (MCLC) proteins function as a chloride channel when incorporated in the planar lipid bilayer.
Pfam PF22879: Abortive infection phage resistance protein N-terminal domain (domain)
This entry represents a N-terminal domain found in an abortive infection phage resistance protein often found in restriction modification system operons.
Pfam PF23390: WDR35 second beta-propeller (repeat)
WDR35 (also known as IFT121) is a component of the IFT-A complex, which is required for retrograde ciliary transport and entry into cilia of G protein-coupled receptors (GPCRs), being involved in cilia function and/or assembly. IFT-A polymerises interacts with IFT-B, and uses an array of beta-propeller and TPR domains to create 'carriages' of the IFT train that engage TULP adaptor proteins. Proteins in this entry are part of the non-core subcomplex, together with IFT43 and IFT139. This entry represents the second beta-propeller of WDR35. Knock-out WDR35 cells showed defective retrograde trafficking within cilia.
Pfam PF18134: Adenylyl/Guanylyl and SMODS C-terminal sensor domain (domain)
This entry represents a sensor domain found in cytidylate cyclase (PycC, clade E) and cyclic GMP-AMP synthase (CdnB) from E.coli, which are involved in immunity against bacteriophage. PycC and CdnB are part of the Pycsar (pyrimidine cyclase system for antiphage resistance) and CBASS respectively, which are closely related; both of these proteins synthesise cyclic nucleotides in response to infection which serve as specific second messenger signals that activate the adjacent effectors. This domain (AGS-C) adopts an Ig-like fold and it has been suggested to mediate phage detection.
Pfam PF06952: PsiA protein (family)
This family consists of several Enterobacterial PsiA proteins. The function of PsiA is unknown although it is thought that it may affect the generation of an SOS signal in Escherichia coli.
Pfam PF02764: Diphtheria toxin, T domain (domain)
Central domain of diphtheria toxin is the translocation (T) domain.   pH induced conformational change in this domain triggers insertion  into the endosomal membrane and facilitates the transfer of the  catalytic domain into the cytoplasm.
Wikipedia: Diphtheria toxin is an exotoxin secreted mainly by Corynebacterium diphtheriae but also by Corynebacterium ulcerans and Corynebacterium pseudotuberculosis, the pathogenic bacterium that causes diphtheria. The toxin gene is encoded by a prophage called corynephage β.
The toxin causes the disease in humans by gaining entry into the cell cytoplasm and inhibiting protein synthesis.
Pfam PF03369: Herpesvirus UL3 protein (family)
Herpes simplex viruses are large DNA viruses, the genome of which encode approximately 80 genes. The UL3 gene of Human herpesvirus 2 (HHV-2) is predicted to encode a 233 amino acid protein with a molecular mass of 26kDa. Homologues of the UL3 protein are encoded only among alphaherpesviruses. The function of the UL3 protein of Herpes simplex viruses remains unknown but it is known to localize to the nucleus and is a phosphoprotein .
Pfam PF06021: Aralkyl acyl-CoA:amino acid N-acyltransferase (domain)
This family consists of several mammalian specific aralkyl acyl-CoA:amino acid N-acyltransferase (glycine N-acyltransferase) proteins [ec:2.3.1.13]. this entry represents the N-terminal domain in Glycine N-acyltransferases.
Pfam PF13807: G-rich domain on putative tyrosine kinase (family)
This domain is found between two families, Wzz, [pfam:PF02706] and CbiA [pfam:PF01656]. There is a highly conserved GNVR sequence motif which characterises this domain. The function is not known.
Pfam PF07371: Protein of unknown function (DUF1490) (family)
This family consists of several hypothetical bacterial proteins of around 90 residues in length. Members of the family seem to be found exclusively in Mycobacterium species. 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 PF17474: Tegument protein UL11 homolog (family)
Human herpesvirus 6A (HHV-6A) and HHV-6B are classified as roseoloviruses and are highly prevalent in the human population. Roseolovirus reactivation in an immunocompromised host can cause severe pathologies. During their productive cycle, herpesviruses have a regulated temporal cascade of gene expression that can be divided into three general stages: immediate-early (IE), early (E), and late (L). Following viral DNA replication, late viral genes that mainly encode structural proteins start to be transcribed, ultimately leading to the assembly and release of infectious particles. This domain family is found in tegument protein UL11 homolog (U71) in HHV-6A/B. It is a myristylated virion protein which is expressed at the early stage of the lytic cycle.
Pfam PF14278: Transcriptional regulator C-terminal region (domain)
This domain is a tetracycline repressor, domain 2, or C-terminus.
Pfam PF03220: Tombusvirus P19 core protein (family)
This family represents the Tombusvirus P19 core protein.
Wikipedia: RNA silencing suppressor p19 is a protein expressed from the ORF4 gene in the genome of tombusviruses. These viruses are positive-sense single-stranded RNA viruses that infect plant cells, in which RNA silencing forms a widespread and robust antiviral defense system. The p19 protein serves as a counter-defense strategy, specifically binding the 19- to 21-nucleotide double-stranded RNAs that function as small interfering RNA (siRNA) in the RNA silencing system. By sequestering siRNA, p19 suppresses RNA silencing and promotes viral proliferation. The p19 protein is considered a significant virulence factor and a component of an evolutionary arms race between plants and their pathogens.
Pfam PF12327: FtsZ family, C-terminal domain (domain)
This family includes the bacterial FtsZ family of proteins. Members of this family are involved in polymer formation. FtsZ is the polymer-forming protein of bacterial cell division. It is part of a ring in the middle of the dividing cell that is required for constriction of cell membrane and cell envelope to yield two daughter cells. FtsZ is a GTPase, like tubulin. FtsZ can polymerise into tubes, sheets, and rings in vitro and is ubiquitous in eubacteria and archaea.
Wikipedia: FtsZ is a protein encoded by the ftsZ gene that assembles into a ring at the future site of bacterial cell division. FtsZ is a prokaryotic homologue of the eukaryotic protein tubulin. The initials FtsZ mean "Filamenting temperature-sensitive mutant Z." The hypothesis was that cell division mutants of E. coli would grow as filaments due to the inability of the daughter cells to separate from one another. FtsZ is found in almost all bacteria, many archaea, all chloroplasts and some mitochondria, where it is essential for cell division. FtsZ assembles the cytoskeletal scaffold of the Z ring that, along with additional proteins, constricts to divide the cell in two.
Pfam PF22020: RlmL ferredoxin-like domain (domain)
This entry represents the ferredoxin-like domain found at the N-terminal of RmlL, referred to as NFLD domain usually fused to the THUMP domain. Ribosomal RNA large subunit methyltransferase K/L from E.coli (also known as YcbY) specifically methylates the guanine in positions 2445 and 2069 of 23S rRNA before its assembly into 50S subunits.
Pfam PF20003: FtsH ternary system domain X5 (domain)
Uncharacterized domain found in the FtsH ternary system, a class of NTP-dependent biological conflict systems.
Pfam PF09133: SANTA (SANT Associated) (domain)
The SANTA domain (SANT Associated domain) is approximately 90 amino acids in length and is conserved in Eukaryota.  It is sometimes found in association with the SANT domain ([pfam:PF00249], also known as Myb-like DNA-binding domain) implying a putative function in regulating chromatin remodelling.  Sequence analysis has showed that the SANTA domain is likely to form four central beta-sheets with three flanking alpha- helixes.  Many conserved hydrophobic residues are present which implying a possible role in protein-protein interactions.
Pfam PF04567: RNA polymerase Rpb2, domain 5 (domain)
RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial. and chloroplast polymerases). Domain 5, is also known as the external 2 domain.
Pfam PF21132: MFD, D3 domain (domain)
The transcription-repair coupling factor (TRCF, also known as MFD) couples transcription and DNA repair in bacteria. MFD removes transcription elongation complexes stalled at DNA lesions and recruits the nucleotide excision repair (NER) machinery to the site. This protein consists of eight domains, of which D3 is represented in this entry and its function is unknown. This domain plays a critical role in unmasking of the UvrA binding site.
Pfam PF15605: Bacterial toxin 28 (family)
This entry represents the C-terminal RNase toxin domain found in bacterial polymorphic toxin systems. The toxin possesses an all alpha-helical fold and conserved aspartate and glutamate residues, and K[DE] and [DN]HxxE motifs. In bacterial polymorphic toxin systems, the toxin is exported by the type 2, type 5 or type 7 secretion system. This C-terminal domain cleaves within tRNA anticodon loops, tRNase activity that is stimulated by CysK which stabilises this domain and allows its binding to the tRNA substrate.
Pfam PF13506: Glycosyl transferase family 21 (domain)
This is a family of ceramide beta-glucosyltransferases - [ec:2.4.1.80].
Pfam PF00391: PEP-utilising enzyme, mobile domain (domain)
This domain is a "swivelling" beta/beta/alpha domain which is thought to be mobile in all proteins known to contain it.
Wikipedia: Pyruvate, phosphate dikinase, or PPDK is an enzyme in the family of transferases that catalyzes the chemical reactionATP + pyruvate + phosphate  AMP + phosphoenolpyruvate + diphosphate
Pfam PF14080: Domain of unknown function (DUF4261) (family)
This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 80 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 PF24403: Inactive Sirtuin (domain)
This entry represents and inactive sirtuin domain.
Pfam PF03010: GP4 (family)
GP4 is a minor membrane-associated glycoproteins. This family contains envelope protein GP4 from equine arteritis virus.
Pfam PF03543: Yersinia/Haemophilus virulence surface antigen (family)
This group of sequences are characterised by a cysteine protease domain, corresponding to MEROPS peptidase family C58 (clan CA), found in proteins of bacteria that include plant pathogens (Pseudomonas syringae), root nodule bacteria, and intracellular pathogens (e.g. Yersinia pestis, Haemophilus ducreyi, Pasteurella multocida, Chlamydia trachomatis) of animal hosts. The domain features a catalytic triad of Cys, His, and Asp. Sequences can be extremely divergent outside of a few well-conserved motifs. YopT, a virulence effector protein of Y. pestis, cleaves and releases host cell Rho GTPases from the membrane, thereby disrupting the actin cytoskeleton. Members of the family from pathogenic bacteria are likely to be pathogenesis factors .
Pfam PF16911: Phthiocerol/phthiodiolone dimycocerosyl transferase C-terminus (family)
This entry represents the C-terminal domain of phthiocerol/phthiodiolone dimycocerosyl transferase. Proteins containing this domain include papA5 from Mycobacterium tuberculosis. PapA5 catalyses diesterification of phthiocerol and phthiodiolone with mycocerosic acids, the final step in the phthiocerol and phthiodiolone dimycocerosate esters (PDIM) synthesis.
Pfam PF23735: Kinesin-like protein KIF9 domain (domain)
This domain is found in mouse Kinesin-like protein KIF9 and similar animal proteins. KIF9 is essential for normal male fertility and for progressive motility of spermatozoa. This domain, which is predicted to form two long alpha-helices, is often found associated with [pfam:PF00225].
Pfam PF00772: DnaB-like helicase N terminal domain (domain)
The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerisation of the N-terminal domain has been observed and may occur during the enzymatic cycle. This N-terminal domain is required both for interaction with other proteins in the primosome and for DnaB helicase activity.
Wikipedia: DnaB helicase is an enzyme in bacteria which opens the replication fork during DNA replication. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerisation of the N-terminal domain has been observed and may occur during the enzymatic cycle. Initially when DnaB binds to dnaA, it is associated with dnaC, a negative regulator. After DnaC dissociates, DnaB binds dnaG.
Pfam PF00162: Phosphoglycerate kinase (domain)
Phosphoglycerate kinase (2.7.2.3) (PGK) is an enzyme that catalyses the formation of ATP to ADP and vice versa. In the second step of the second phase in glycolysis, 1,3-diphosphoglycerate is converted to 3-phosphoglycerate, forming one molecule of ATP. If the reverse were to occur, one molecule of ADP would be formed. This reaction is essential in most cells for the generation of ATP in aerobes, for fermentation in anaerobes and for carbon fixation in plants.

PGK is found in all living organisms and its sequence has been highly conserved throughout evolution. The enzyme exists as a monomer containing two nearly equal-sized domains that correspond to the N-and C-termini of the protein (the last 15 C-terminal residues loop back into the N-terminal domain). 3-phosphoglycerate (3-PG) binds to the N-terminal, while the nucleotide substrates, MgATP or MgADP, bind to the C-terminal domain of the enzyme. This extended two-domain structure is associated with large-scale 'hinge-bending' conformational changes, similar to those found in hexokinase . At the core of each domain is a 6-stranded parallel Î²-sheet surrounded by Î± helices. Domain 1 has a parallel Î²-sheet of six strands with an order of 342156, while domain 2 has a parallel Î²-sheet of six strands with an order of 321456. Analysis of the reversible unfolding of yeast phosphoglycerate kinase leads to the conclusion that the two lobes are capable of folding independently, consistent with the presence of intermediates on the folding pathway with a single domain folded .
Wikipedia: Phosphoglycerate kinase is an enzyme that catalyzes the reversible transfer of a phosphate group from 1,3-bisphosphoglycerate (1,3-BPG) to ADP producing 3-phosphoglycerate (3-PG) and ATP :1,3-bisphosphoglycerate + ADP ⇌ glycerate 3-phosphate + ATP
Pfam PF15873: Domain of unknown function (DUF4730) (family)
This family of proteins is found in eukaryotes. Proteins in this family are approximately 60 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 PF14825: Cilia- and flagella-associated protein 77 (family)
This family of proteins is found in flagella. Proteins in this family are typically between 203 and 326 amino acids in length. There is a single completely conserved residue N that may be functionally important.
Pfam PF08680: TATA-box binding (family)
TATA-box_bdg is a family of bacterial proteins. YwmB from Bacillus subtilis contains a circularly permuted TATA-box binding protein-like fold. Jian-Xiang Liu, Qi Xie, Jun Lin. Protein Structural Data Mining and Evolutionary Bioinformatic Analysis on Domains of TATA-box Binding Protein-like Fold. Life Science Journal 2014; 11(2): 298-302 (not yet in PubMed 27-02-2014).
Pfam PF04606: Ogr/Delta-like zinc finger (family)
This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F. This family also includes zinc fingers in recombinase proteins.
Pfam PF11240: Protein of unknown function (DUF3042) (family)
This family of proteins with unknown function appears to be restricted to Firmicutes.
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 PF24406: Novel STAND NTPase 4 (domain)
This entry represents a novel domain of the STAND-superfamily of AAA+ ATPases found in bacterial conflict systems.
Pfam PF06179: Surfeit locus protein 5 subunit 22 of Mediator complex (family)
This family consists of several eukaryotic Surfeit locus protein 5 (SURF5) sequences. The human Surfeit locus has been mapped on chromosome 9q34.1.  The locus includes six tightly clustered housekeeping genes (Surf1-6), and the gene organisation is similar in human, mouse and chicken Surfeit locus.  The Med22 subunit of Mediator complex is part of the essential core head region.
Wikipedia: Mediator of RNA polymerase II transcription subunit 22 is an enzyme that in humans is encoded by the MED22 gene.
Pfam PF08557: Sphingolipid Delta4-desaturase (DES) (domain)
Sphingolipids are important membrane signalling molecules involved in many different cellular functions in eukaryotes. Sphingolipid delta 4-desaturase catalyses the formation of (E)-sphing-4-enine.  Some proteins in this family have bifunctional delta 4-desaturase/C-4-hydroxylase activity.  Delta 4-desaturated sphingolipids may play a role in early signalling required for entry into meiotic and spermatid differentiation pathways during Drosophila spermatogenesis.  This small domain associates with FA_desaturase [pfam:PF00487] and appears to be specific to sphingolipid delta 4-desaturase.
Pfam PF13210: Domain of unknown function (DUF4018) (family)
This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 190 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 PF03303: WTF protein (family)
This is a family of hypothetical Schizosaccharomyces pombe proteins. Their function is unknown.
Pfam PF08383: Maf N-terminal region (family)
This region is found in various leucine zipper transcription factors of the Maf family. These are implicated in the regulation of insulin gene expression, in erythroid differentiation, and in differentiation of the neuroretina.
Pfam PF13804: Retro-transcribing viruses envelope glycoprotein (domain)
This family comes from human endogenous retrovirus K envelope glycoproteins.