SII-SWORD/CoKE huggingface dataset:
Pfam PF18073: Rubredoxin metal binding domain (domain)
This is the C-terminal rubredoxin metal binding domain found in Interest in lipopolysaccharide (LPS) assembly protein B (LapB) . Rubredoxin proteins form small non-heme iron binding sites that use four cysteine residues to coordinate a single metal ion in a tetrahedral environment. Rubredoxins are most commonly found in bacterial systems, but have also been found in eukaryotes. The key features of these rubredoxin-like domains are the extended loops or 'knuckles' and the tetracysteine mode of iron binding. Structural analysis of LapB from Escherichia coli show that the rubredoxin metal binding domain is intimately bound to the TPR motifs and that this association to the TPR motifs is essential to LPS regulation and growth in vivo. Other family members include RadA proteins which play a role in DNA damage repair. In E. coli, a protein known as RadA (or Sms) participates in the recombinational repair of radiation-damaged DNA in a process that uses an undamaged DNA strand in one DNA duplex to fill a DNA strand gap in a homologous sister DNA duplex. RadA carries a zinc finger at the N-terminal domain.
Pfam PF21369: STL11, N-terminal (domain)
This entry represents the N-terminal domain of STL11 from yeast and its homologues, such as RBM22 from human. This domain comprises a zinc finger, FYVE/PHD type. Members of this entry are involved in pre-mRNA splicing.
Pfam PF13299: Cleavage and polyadenylation factor 2 C-terminal (family)
This family lies at the C-terminus of many fungal and plant cleavage and polyadenylation specificity factor subunit 2 proteins. The exact function of the domain is not known, but is likely to function as a binding domain for the protein within the overall CPSF complex.
Pfam PF02007: Tetrahydromethanopterin S-methyltransferase MtrH subunit (family)
The enzyme tetrahydromethanopterin S-methyltransferase [ec:2.1.1.86] is composed of eight subunits. The enzyme is a membrane- associated enzyme complex which catalyses an energy-conserving, sodium-ion-translocating step in methanogenesis from hydrogen and carbon dioxide.
Pfam PF12084: Protein of unknown function (DUF3561) (family)
This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 110 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 PF24852: Domain of unknown function (DUF7726) (domain)
This domain is found in uncharacterised fungal proteins. It has detectable similarity to HTH domains and it is predicted to adopt similar 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 PF21484: Chromo domain-containing protein 1-like, PIN domain (domain)
This domain is found at the C-terminal end of Chromo domain- containing protein 1 from Schizosaccharomyces pombe (Chp1) and similar proteins predominantly found in yeast. Chp1 is a component of the RNA-induced initiation of Transcriptional Gene Silencing (RITS) complex, a central player RNA interference (RNAi) pathway which is important for heterochromatin formation and accurate chromosome segregation. This entry represents the PIN domain of Chp1, which shows an alpha-beta fold.
Pfam PF09416: RNA helicase (UPF2 interacting domain) (domain)
UPF1 is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation.  This domain contains 3 zinc binding motifs and forms interactions with another protein (UPF2) that is also involved nonsense-mediated mRNA decay (NMD).
Pfam PF13981: SopA-like central domain (domain)
This domain is found in the E. coli Type III secretion effector proteins SopA and NleL. These proteins have been shown to act as E3 ubiquitin ligase enzymes.
Pfam PF00589: Phage integrase family (family)
Members of this family cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment. The catalytic site residues in CRE recombinase  ([swissprot:P06956]) are Arg-173, His-289, Arg-292 and Tyr-324.
Pfam PF23348: RDM3 beta-solenoid (repeat)
This entry represents a beta-solenoid domain found at C-terminal region of Protein RNA-directed DNA methylation 3 (RDM3) from Arabidopsis thaliana and similar proteins from plants. RNA-directed DNA methylation (RdDM) initiates and re-establishes silencing of transposable elements through de novo methylation of cytosines.
Pfam PF22082: 2-thiouridine synthetase TtuA, N-terminal LIM domain (domain)
TtuA is an oxygen-labile iron-sulfur protein that is involved in a post-transcriptional thiolation of RNA. The iron-sulfur cluster of TtuA is required for sulfurtransferase activity. The enzyme structure consists of three domains: a central catalytic domain and two Zn-fingers. This entry represents the N-terminal Zn-finger domain that share a significant similarity to LIM domains.
Pfam PF16255: GDSL-like Lipase/Acylhydrolase (family)
This entry represents a group of putative GDSL-like Lipases/Acylhydrolases from bacteria.
Pfam PF14414: A nuclease of the HNH/ENDO VII superfamily with conserved WHH (family)
WHH is a predicted nuclease of the HNH/ENDO VII superfamily of the  treble clef fold. The name is derived from the conserved motif WHH. It is found in bacterial polymorphic toxin systems and functions as a toxin module. WHH is the shortest version of HNH nuclease families. Like AHH and LHH, the WHH nuclease contains 4 conserved histidines of which the first one is predicted to bind a metal-ion  and other three ones are involved in activation of water molecule for hydrolysis.
Pfam PF23377: IFT122 second beta-propeller (repeat)
IFT122 is one of the core components (together with WDR19/IFT144 and IFT140) 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. This entry represents the second beta-propeller of IFT122, which is a crucial subunit for IFT-A integrity.
Pfam PF18506: RelB Antitoxin (family)
RelE-RelB (RelBE) is a toxin-antitoxin (TA) protein complex. It is suggested that the toxic action of RelE is counteracted by antitoxin RelB, which wraps around RelE, blocks its active site and prevents sterically the binding to the ribosomal A-site. The long alpha-helix of the tightly bound RelB covers the presumed active site of the toxin RelE that is formed by a central beta-sheet. This entry represents RelB antitoxin from Methanocaldococcus jannaschii and similar prokaryotic proteins.
Pfam PF19764: Family of unknown function (DUF6251) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000700) is described by MIBiG as an example of the following biosynthetic class, saccharide. It includes a member from the istamycin biosynthetic gene cluster from Streptomyces  tenjimariensis.
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 PF15924: ALG11 mannosyltransferase N-terminus (family)
GDP-Man:Man(3)GlcNAc(2)-PP-Dol alpha-1,2-mannosyltransferase (ALG11) is involved in N-linked oligosaccharide synthesis . It is highly conserved, with homologues in fission yeast, worms, flies, and plants . It catalyses the sequential transfer of two alpha1,2-linked mannose residues from GDP-mannose to Man3GlcNAc2-PP-Dol forming the Man5GlcNAc2-PP-Dol intermediate at the cytosolic side of the ER before flipping to the luminal side. Alg11 contains three hydrophobic transmembrane-spanning helices found in the N-terminal domain .
Wikipedia: Asparagine-linked glycosylation protein 11  is an enzyme encoded by the ALG11 gene.
Pfam PF10496: SNARE-complex protein Syntaxin-18 N-terminus (domain)
This is the conserved N-terminal of Syntaxin-18. Syntaxin-18 is found in the SNARE complex of the endoplasmic reticulum and functions in the trafficking between the ER intermediate compartment and the cis-Golgi vesicle. In particular, the N-terminal region is important for the formation of ER aggregates. More specifically, syntaxin-18 is involved in endoplasmic reticulum-mediated phagocytosis, presumably by regulating the specific and direct fusion of the ER with the plasma or phagosomal membranes.
Pfam PF16675: KIX-binding domain of forkhead box O, CR2 (family)
FOXO_KIX_bd is the first part of the region of transcription factor forkhead box O family proteins that binds to the CREB-binding proteins via the KIX domain. Coactivator CBP/p300 is recruited by FOXO3 via the binding of this domain as well as the simultaneous binding of the more C-terminal TAD domain.
Pfam PF23838: Family of unknown function (DUF7208) (family)
This entry represents a domain of unknown function found in large phage virion structural proteins. The domain is approximately 290 to 330 amino acids in length. It is found in a variety of phage proteins infecting bacterial hosts such as Pseudomonas, Vibrio, Ralstonia, and Erwinia, among others.
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 PF06428: GDP/GTP exchange factor Sec2p (coiled_coil)
In Saccharomyces cerevisiae,  Sec2p is a GDP/GTP exchange factor for Sec4p, which is required for vesicular transport at the post-Golgi stage of yeast secretion.
Pfam PF10731: Thrombin inhibitor from mosquito (family)
Members of this family are all inhibitors of thrombin, the peptidase that is at the end of the blood coagulation cascade and which creates the clot by cleaving fibrinogen.  The interaction between thrombin and fibrinogen involves two different areas of contact - via the thrombin active site and via a second substrate-binding site known as an exosite.  The inhibitor acts by blocking the exosite, rather than by interacting with the active site.  The inhibitors are from mosquitoes that feed on human blood and which, by inhibiting thrombin, prevent the blood from clotting and keep it flowing.
Pfam PF19211: Coronavirus replicase NSP2, N-terminal (family)
This entry corresponds to the N-terminal region of coronavirus non-structural protein 2. NSP2 is encoded by ORF1a/1ab and proteolytically released from the pp1a/1ab polyprotein. Viral-host protein interaction studies in SARS-CoV and SARS_CoV-2 found that this protein could interact with several host proteins including prohibitin 1 (PHB1) and PHB2, which are implicated in a number of cellular functions, including cellular migration, differentiation and apoptosis. NSP2 structure from SARS-CoV-2 has been recently solved and revealed that it has three zinc fingers, covered in this entry, which may be involved in binding nucleic acids and regulating intracellular signalling pathways.
Pfam PF17050: Altered inheritance of mitochondria 5 (family)
AIM5 (also known as Mcs12 and Mic12) is a fungal mitochondrial inner membrane protein. It is a component of the mitochondrial inner membrane organising system (MINOS/MitOS), which promotes normal mitochondrial morphology.
Pfam PF04184: ST7 protein (repeat)
The ST7 (for suppression of tumorigenicity 7) protein is thought to be a tumour suppressor gene. The molecular function of this protein is uncertain.
Pfam PF13568: Outer membrane protein beta-barrel domain (domain)
This domain is found in a wide range of outer membrane proteins. This domain assumes a membrane bound beta-barrel fold.
Pfam PF08592: Anthrone oxygenase (family)
This family consists of anthrone oxygenases found in bacteria and fungi, and involved in the synthesis of different products. GedH from Aspergillus terreus is part of the gene cluster that mediates the biosynthesis of geodin, EncC from Neosartorya fumigata is involved in the biosynthesis of endocrocin, and MdpH from Aspergillus nidulans in the biosynthesis of monodictyphenone.
Pfam PF12952: Domain of unknown function (DUF3841) (domain)
This presumed domain is around 190 amino acids in length. As yet no function has been given to any member of the family.
Pfam PF12920: TcdA/TcdB pore forming domain (family)
This family represents the most conserved region within the C. difficile Toxin A and Toxin B pore forming region.
Wikipedia: Clostridioides difficile toxin B (TcdB) is a cytotoxin produced by the bacteria Clostridioides difficile. It is one of two major kinds of toxins produced by C. difficile, the other being a related enterotoxin. Both are very potent and lethal.
Pfam PF22611: Flattop (family)
This family represents the homologs of Flattop protein (also known as Cilia- and flagella-associated protein 126 CFAP126). This protein is microtubule inner protein (MIP) part of the doublet microtubules (DMTs) in cilia and sperm axoneme.
Pfam PF24444: Family of unknown function (DUF7563) (family)
This entry represents a small family of uncharacterised proteins found in archaea. They contain two pairs of conserved cysteines that are likely involved in metal coordination. These proteins are predicted to structurally resemble Zinc beta-ribbon domains.
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 PF15904: LKB1 serine/threonine kinase interacting protein 1 (family)
LIP1 is a protein found in eukaryotes. It represents the N-terminus of a leucine-rich-repeat protein that is implicated in Peutz-Jeghers syndrome. LIP1 interacts with the TGF-beta-regulated transcription factor SMAD4 to form a LKB1-LIP1-SMAD4 ternary complex. Mutations in SMAD4 lead to juvenile polyposis, suggesting a mechanistic link between these two diseases.
Pfam PF16086: Domain of unknown function (DUF4816) (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 178 and 456 amino acids in length. There is a conserved WKP sequence motif.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF24896: AHK4/CRE1/WOL receiver domain (domain)
This entry represents the receiver domain found in AHK4/CRE1/WOL from Arabidopsis thaliana, CRE1 from Medicago truncatula and homologues sequences from plants. AHK4/CRE1 is a cytokinin (CK) receptor. It functions as a histidine kinase and transmits the stress signal to a downstream MAPK cascade. This domain mediates dimerisation through 3D domain swapping, which suggests that a considerable change of conformation must occur upon the phosphorylation reaction to allow HPt binding.
Pfam PF14034: Sporulation protein YtrH (family)
This family of proteins is involved in sporulation. It may contribute to the formation and stability of the thick peptidoglycan layer between the two membranes of the spore, known as the cortex. In Bacillus subtilis its expression is regulated by sigma-E.
Pfam PF02075: Crossover junction endodeoxyribonuclease RuvC (domain)
This entry includes endodeoxyribonucleases found in bacteria, such as RuvC. RuvC is a small protein of about 20 kD. It requires and binds a magnesium ion. The structure of E. coli RuvC is a 3-layer alpha-beta sandwich containing a 5-stranded beta-sheet sandwiched between 5 alpha-helices. The Escherichia coli RuvC gene is involved in DNA repair and in the late step of RecE and RecF pathway recombination. RuvC protein ([ec:3.1.22.4]) cleaves cruciform junctions, which are formed by the extrusion of inverted repeat sequences from a super-coiled plasmid and which are structurally analogous to Holliday junctions, by introducing nicks into strands with the same polarity. The nicks leave a 5'terminal phosphate and a 3'terminal hydroxyl group which are ligated by E. coli or Bacteriophage T4 DNA ligases. Analysis of the cleavage sites suggests that DNA topology rather than a particular sequence determines the cleavage site. RuvC protein also cleaves Holliday junctions that are formed between gapped circular and linear duplex DNA by the function of RecA protein. The active form of RuvC protein is a dimer. This is mechanistically suited for an endonuclease involved in swapping DNA strands at the crossover junctions. It is inferred that RuvC protein is an endonuclease that resolves Holliday structures in vivo.
Pfam PF05769: SIKE family (family)
This family consists of several eukaryotic proteins. Suppressor of IKBKE 1 (SIKE) is a physiological suppressor of IKK-epsilon and TBK1, which are two IKK-related kinases involved in virus- and  TLR3-triggered activation of interferon regulatory factor 3 (IRF-3). Other members of this family are circulating cathodic antigen (CCA), found in Schistosoma mansoni (Blood fluke), and FGFR1 oncogene partner 2, which may be involved in wound healing pathway.
Pfam PF20191: Family of unknown function (DUF6554) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in Cyanobacteria. Proteins in this family are typically between 131 and 150 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 PF15827: UPF0730 unknown protein family (family)
UPF0730 is a family of proteins found in eukaryotes. Proteins in this family are typically between 51 and 156 amino acids in length.
Pfam PF20547: Family of unknown function (DUF6761) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in cyanobacteria. Proteins in this family are 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 PF23724: Caspase-8, second domain (domain)
This domain is found in Caspase-8 from Drosophila melanogaster (Dredd) and similar proteins mainly found in insects. Dredd is an effector of the programmed cell death (PCD) activators rpr, grim and hid. It plays a role in the innate immune response and may be involved in apoptosis in the germline as well as soma. This protein is predicted to be organised into three domains: an N-terminal, this entry, and a caspase domain ([pfam:PF00656]). This domain is predicted to adopt an all-alpha configuration.
Pfam PF14506: CppA N-terminal (family)
This is the N-terminal domain of the CppA protein found in species of Streptococcus. CppA is a putative C3-glycoprotein degrading proteinase, involved in pathogenicity. It is often found associated with [pfam:PF14507].
Pfam PF08239: Bacterial SH3 domain (domain)
SH3 domains are widespread among metazoan intracellular signalling proteins and typically bind proline-rich polypeptides. This SH3 domain is a prokaryotic homologue. It might have two possible functions: (1) promoting survival of a pathogen within the invaded cell by modulating pathways controlled by SH3 domains; or (2) promoting invasion by binding to receptors on eukaryotic cells .
SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues . They are found in a great variety of intracellular or membrane-associated proteins  for example, in a variety of proteins with enzymatic activity, in adaptor proteins, such as fodrin and yeast actin binding protein ABP-1.

The SH3 domain has a characteristic fold which consists of five or six Î²-strands arranged as two tightly packed anti-parallel Î²-sheets. The linker regions may contain short helices. The surface of the SH3-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes .
Pfam PF09113: Peptide-N-glycosidase F, C terminal (domain)
Members of this family adopt an eight-stranded antiparallel beta jelly roll configuration, with the beta strands arranged into two sheets. They are similar in topology to many viral capsid proteins, as well as lectins and several glucanases. The domain allows the protein to bind sugars and catalyses the complete removal of N-linked oligosaccharide chains from glycoproteins.
Pfam PF02513: Spin/Ssty Family (domain)
Spindlin (Spin) is a novel maternal transcript present in the unfertilised egg and early embryo. The Y-linked spermiogenesis -specific transcript (Ssty) is also expressed during gametogenesis  and forms part of this Pfam family. Members of this family contain three copies of this 50 residue repeat. The repeat is predicted to contain four beta strands.
Pfam PF06228: Haem utilisation ChuX/HutX (domain)
This family is found within haem utilisation operons. It has a similar structure to that of [pfam:PF05171]. [pfam:PF05171] usually occurs as a duplicated domain, but this domain occurs as a single domain and forms a dimer. The organisation of the dimer is very similar to that of the duplicated [pfam:PF05171] domains. It binds haem via conserved histidines.