SII-SWORD/CoKE huggingface dataset:
Pfam PF08743: Nse4 C-terminal (domain)
Nse4 is the kleisin component of the Smc5/6 DNA repair complex. It bridges the heads of Smc5 and Smc6. This is the C-terminal domain of Nse4 that interacts with the head domain of Smc5.
Pfam PF09171: N-glycosylase/DNA lyase (domain)
This domain is predominantly found in the Archaeal protein N-glycosylase/DNA lyase.
Pfam PF18845: Bacterial archaeo-eukaryotic release factor family 3 (family)
Bacterial family of the archaeo-eukaryotic release factor superfamily. Likely to play roles in biological conflicts or regulation under stress conditions at the ribosome.
Pfam PF12502: Protein of unknown function (DUF3710) (family)
This family of proteins is found in bacteria. Proteins in this family are typically between 237 and 284 amino acids in length. There are two conserved sequence motifs: DLG and DGPRW.
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 PF05373: L-proline 3-hydroxylase, C-terminal (domain)
Iron (II)/2-oxoglutarate (2-OG)-dependent oxygenases catalyse oxidative reactions in a range of metabolic processes.  Proline 3-hydroxylase  hydroxylates proline at position 3, the first of a 2-OG oxygenase catalysing oxidation of a free alpha-amino acid. The structure contains conserved motifs present in other 2-OG oxygenases including a  jelly roll strand core and residues binding iron and 2-oxoglutarate,  consistent with divergent evolution within the extended family.  The structure differs significantly from many other 2-OG oxygenases in possessing a discrete C-terminal helical domain.
Pfam PF14730: Domain of unknown function (DUF4468) with TBP-like fold (domain)
A large family of (predicted) secreted proteins with unknown functions from human gut and oral cavity.  Typically forms a N-terminal domain with FMN binding  domain at the C-terminus. Experimentaly determined 3D structure of this domain shows a variant of a TATA box binding - like fold, but no detectable sequence similarity to other proteins with this fold
Pfam PF09286: Pro-kumamolisin, activation domain (domain)
Members of this family are found in various subtilase propeptides, and adopt a ferredoxin-like fold, with an alpha+beta sandwich. Cleavage of the domain results in activation of the peptide.
Pfam PF01373: Glycosyl hydrolase family 14 (domain)
This family are beta amylases.
Wikipedia: In molecular biology, Glycoside hydrolase family 14 is a family of glycoside hydrolases.
Pfam PF08459: UvrC RNAse H endonuclease domain (domain)
This domain is found in the C subunits of the bacterial and archaeal UvrABC system which catalyses nucleotide excision repair in a multi-step process.  UvrC catalyses the first incision on the fourth or fifth phosphodiester bond 3' and on the eighth phosphodiester bond 5' from the damage that is to be excised. The domain described here represents the RNAse H endonuclease domain, located at the C-terminal, between the UvrBC and the (HhH)2 domains, nearby the N-terminal of the HhH. Despite the lack of sequence homology, the endonuclease domain has an RNase H-like fold, which is characteristic of enzymes with nuclease or polynucleotide transferase activities. RNase H-related enzymes typically contain a highly conserved carboxylate triad, usually DDE, in their catalytic centre. However, instead of a third carboxylate, UvrC of Thermotoga maritima was found to contain a highly conserved histidine (H488) on helix-4 in close proximity to two aspartates.
Pfam PF02263: Guanylate-binding protein, N-terminal domain (domain)
Transcription of the anti-viral guanylate-binding protein (GBP) is induced by interferon-gamma during macrophage induction. This family contains GBP1 and GPB2, both GTPases capable of binding GTP, GDP and GMP.
Wikipedia: In molecular biology, the guanylate-binding proteins family is a family of GTPases that is induced by interferon (IFN)-gamma. GTPases induced by IFN-gamma are key to the protective immunity against microbial and viral pathogens. These GTPases are classified into three groups: the small 47-KD immunity-related GTPases (IRGs), the Mx proteins, and the large 65- to 67-kd GTPases. Guanylate-binding proteins (GBP) fall into the last class.
Pfam PF01822: WSC domain (domain)
This domain is involved in carbohydrate  binding.
Pfam PF15644: Papain fold toxin 1, glutamine deamidase (domain)
A papain fold toxin domain found in bacterial polymorphic toxin systems. In these systems they might function either as a releasing peptidase or toxin. In Shigella flexneri, UniProtKB:Q8VSD5, this protein is expressed from a plasmid, and delivered into the host via the type III secretion system where it deamidates the glutamine residue at position 100 in ubiquitin-activating enzyme E2, UBC13, to a glutamic acid residue. Invasion of host cells by pathogens normally invokes an acute inflammatory response through activating the TRAF6-mediated signalling pathway. UBC13 helps to activate TRAF6. Thus deamidation of UBC13 results in the dampening of the inflammatory response. The key glutaminase deamidase activity is mediated by a cys-his-glu triad, present in all members of the family.
Pfam PF12074: Generalcontrol nonderepressible 1 (Gcn1) N-terminal (repeat)
This entry represents a set of three HEAT repeats found towards the N-terminal region of Gcn1 protein, which acts as a translation activator that mediates translational control by regulating Gcn2 kinase activity. It is a ribosome collision sensor that activates a translation quality control pathway when a ribosome has stalled during translation.
Pfam PF06747: CHCH domain (domain)
we have identified a conserved motif in the LOC118487 protein that we have called the CHCH motif. Alignment of this protein with related members showed the presence of three subgroups of proteins, which are called the S (Small), N (N-terminal extended) and C (C-terminal extended) subgroups. All three sub-groups of proteins have in common that they contain a predicted conserved [coiled coil 1]-[helix 1]-[coiled coil 2]-[helix 2] domain (CHCH domain). Within each helix of the CHCH domain, there are two cysteines present in a C-X9-C motif. The N-group contains an additional double helix domain, and each helix contains the C-X9-C motif. This family contains a number of characterised proteins: Cox19 protein - a nuclear gene of Saccharomyces cerevisiae, codes for an 11-kDa protein (Cox19p) required for expression of cytochrome oxidase. Because cox19 mutants are able to synthesise the mitochondrial and nuclear gene products of cytochrome oxidase, Cox19p probably functions post-translationally during assembly of the enzyme. Cox19p is present in the cytoplasm and mitochondria, where it exists as a soluble intermembrane protein. This dual location is similar to what was previously reported for Cox17p, a low molecular weight copper protein thought to be required for maturation of the CuA centre of subunit 2 of cytochrome oxidase. Cox19p have four conserved potential metal ligands, these are three cysteines and one histidine. Mrp10 - belongs to the class of yeast mitochondrial ribosomal proteins that are essential for translation. Eukaryotic NADH-ubiquinone oxidoreductase 19 kDa (NDUFA8) subunit. The CHCH domain was previously called DUF657.
Wikipedia: The enzyme cytochrome c oxidase or Complex IV is a large transmembrane protein complex found in bacteria, archaea, and the mitochondria of eukaryotes.
Pfam PF14035: YlzJ-like protein (family)
The YlzJ-like protein family includes the B. subtilis YlzJ protein [swissprot:C0H413], which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 61 and 72 amino acids in length. There are two completely conserved residues (L and G) that may be functionally important.
Pfam PF10928: Protein of unknown function (DUF2810) (family)
This is a bacterial family of uncharacterised proteins.
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 PF09688: Protein of unknown function (Wx5_PLAF3D7) (family)
This set of protein sequences represent a family of at least four proteins in Plasmodium falciparum (isolate 3D7). An interesting feature is five perfectly conserved Trp residues.
Pfam PF08178: GnsA/GnsB toxin of bacterial toxin-antitoxin system (family)
This family consists of the GnsA/GnsB family. GnsA and GnsB are multicopy suppressors of the secG null mutation. These proteins participate in the synthesis of phospholipids, suggesting the functional relationship between SecG and membrane phospholipids. Over-expression of gnsA and gnsB causes a remarkable increase in the unsaturated fatty acid content.  However, the gnsA-gnsB double null mutant exhibits no effect.  Both proteins are predicted to possess a helix-turn-helix structure. GnsAB is a family of putative bacterial toxins (both GnsA and GnsB) that, are neutralised by the antitoxin YmcE, [pfam:PF15939].
Pfam PF03983: SLA1 homology domain 1, SHD1 (domain)
NPFXD peptides specifically interact with the SHD1 domain. NPFXD is a clathrin-facilitated endocytic targeting signal. NPFXD was originally discovered in the cytoplasmic  domain of the furin-like protease Kex2p. Sla1 is thought to function as an endocytic adaptor.
Pfam PF12448: Kinesin associated protein (family)
This domain family is found in eukaryotes, and is typically between 143 and 173 amino acids in length. The family is found in association with [pfam:PF04849]. This family is a region of the protein milton. Milton recruits the heavy chain of kinesin to mitochondria to allow the motor movement function of kinesin.
Pfam PF08331: Epoxyqueuosine reductase QueG, DUF1730 (family)
This domain of unknown function occurs in Epoxyqueuosine reductase QueG, an iron-sulfur cluster-binding protein, together with the 4Fe-4S binding domain ([pfam:PF00037]). QueG catalyses the conversion of epoxyqueuosine (oQ) to queuosine (Q), which is a hypermodified base found in the wobble positions of tRNA(Asp), tRNA(Asn), tRNA(His) and tRNA(Tyr).
Pfam PF19175: Family of unknown function (DUF5857) (family)
This is a family of uncharacterised proteins of unknown function predominantly found in viruses.
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 PF11117: Protein of unknown function (DUF2626) (family)
This family is conserved in the Bacillaceae family.  Several members are named as YqgY. The function 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 PF23927: Domain of unknown function (DUF7265) (domain)
This entry represents an C-terminal domain from a family of uncharacterised phage proteins. This domain has a beta sandwich 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 PF24695: PITM 1-3, beta-sandwich domain (domain)
This is a presumed beta-sandwich domain found towards the C-terminal of Membrane-associated phosphatidylinositol transfer proteins 1-3 (PITM1-3) and RDGB from Drosophila. These are class II phosphatidylinositol transfer proteins (PITPs) which can transfer phosphatidylinositol (PI) between membranes. RDGB can also transfer phosphatidic acid (PA) between membranes. PTIM1/2 bind PI, phosphatidylcholine (PC) and (PA) with the binding affinity order of PI > PA > PC.
Pfam PF16995: Transmembrane region of lysyl-tRNA synthetase (family)
tRNA-synt_2_TM is a family from the N-terminal region of tRNA-synthase-2, with 6xTMs. The presence of this region indicates that the protein is anchored in the membrane. The family is found in Actinobacteria.
Pfam PF07847: PCO_ADO (family)
This entry includes cysteine oxidases (PCOs) from plants and 2-aminoethanethiol dioxygenases (ADOs) from animals.
Pfam PF00144: Beta-lactamase (domain)
This family appears to be distantly related to [pfam:PF00905] and PF00768 D-alanyl-D-alanine carboxypeptidase.
Wikipedia: Beta-lactamases (β-lactamases) are enzymes produced by bacteria that provide multi-resistance to beta-lactam antibiotics such as penicillins, cephalosporins, cephamycins, monobactams and carbapenems (ertapenem), although carbapenems are relatively resistant to beta-lactamase. Beta-lactamase provides antibiotic resistance by breaking the antibiotics' structure. These antibiotics all have a common element in their molecular structure: a four-atom ring known as a beta-lactam (β-lactam) ring. Through hydrolysis, the enzyme lactamase breaks the β-lactam ring open, deactivating the molecule's antibacterial properties.
Pfam PF01628: HrcA protein C terminal domain (family)
HrcA is found to negatively regulate the transcription of heat shock genes. HrcA contains an amino terminal helix-turn-helix domain, however this corresponds to the carboxy terminal domain.
Pfam PF23750: Anti-sigma factor RsgI-like central domain (domain)
The heat shock genes in B. subtilis can be classified into several groups according to their regulation, and the sigma gene, sigI, of Bacillus subtilis belongs to the group IV heat-shock response genes and has many orthologues in the bacterial phylum Firmicutes. Regulation of sigma factor I is carried out by RsgI from the same operon, and this entry represents the central cytoplasmic portion of RsgI C-terminal to the single transmembrane helix.
Pfam PF12264: Waikavirus capsid protein 1 (family)
The rice tungro spherical waikavirus polyprotein is cleaved into 7 proteins, including three capsid proteins, by the tungro spherical virus-type peptidase [pfam:PF12381]. This family represents the capsid protein 1.
Pfam PF15000: Tumour suppressor candidate 2 (family)
This family of proteins are candidate tumour suppressors.
Wikipedia: Tumor suppressor candidate 2 is a protein that in humans is encoded by the TUSC2 gene.
Pfam PF14088: Domain of unknown function (DUF4268) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 151 and 387 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 PF11058: Antirestriction protein Ral (family)
Ral alleviates restriction and enhances modification by the E.Coli restriction and modification system.
Pfam PF21893: Family of unknown function (DUF6918) (family)
This is a family of uncharacterized bacterial proteins with a length of ~140-150 residues. They are predicted to adopt an alpha-helical structure consisting of two structural repeats.
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 PF00817: impB/mucB/samB family (family)
These proteins are involved in UV protection (Swiss).
Pfam PF00016: Ribulose bisphosphate carboxylase large chain, catalytic domain (domain)
The C-terminal domain of RuBisCO large chain is the catalytic domain adopting a TIM barrel fold.
Wikipedia: Ribulose-1,5-bisphosphate carboxylase/oxygenase, commonly known by the abbreviations RuBisCo, rubisco, RuBPCase, or RuBPco, is an enzyme involved in the light-independent part of photosynthesis, including the carbon fixation by which atmospheric carbon dioxide is converted by plants and other photosynthetic organisms to energy-rich molecules such as glucose. It emerged approximately four billion years ago in primordial metabolism prior to the presence of oxygen on Earth. It is probably the most abundant enzyme on Earth. In chemical terms, it catalyzes the carboxylation of ribulose-1,5-bisphosphate.
Pfam PF11571: Mediator complex subunit 27 (family)
Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species {1-2]. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function. Mediator exists in two major forms in human cells: a smaller form that interacts strongly with pol II and activates transcription, and a large form that does not interact strongly with pol II and does not directly activate transcription. The ubiquitous expression of Med27 mRNA suggests a universal requirement for Med27 in transcriptional initiation. Loss of Crsp34/Med27 decreases amacrine cell number, but increases the number of rod photoreceptor cells.
Wikipedia: Mediator of RNA polymerase II transcription subunit 27 is an enzyme that in humans is encoded by the MED27 gene. It forms part of the Mediator complex.
Pfam PF01059: NADH-ubiquinone oxidoreductase chain 4, amino terminus (domain)
This domain is found at the N-terminal end of NADH-ubiquinone oxidoreductase chain 4 and similar sequences from bacteria and eukaryotes. This domain is found upstream of [pfam:PF00361] and shows an all-alpha structure.
Wikipedia: Respiratory complex I, EC 7.1.1.2 is the first large protein complex of the respiratory chains of many organisms from bacteria to humans. It catalyzes the transfer of electrons from NADH to coenzyme Q10 (CoQ10) and translocates protons across the inner mitochondrial membrane in eukaryotes or the plasma membrane of bacteria.
Pfam PF18409: Polo-like Kinase 4 Polo Box 2 (domain)
This Polo box (PB) domain is found in Polo-like kinase 4 (Plk4) present in Drosophila melanogaster. Plk4 is a conserved component in the duplication pathway of centrioles which is needed to prevent chromosomal instability. Plk4 localizes to centrioles in M/G1. Structural analysis reveals two tandem, homodimerized polo boxes, PB1-PB2, that form a winged architecture. This domain is PB2, together with PB1 [pfam:PF18190] , they are required for binding the centriolar protein Asterless (Asl) as well as robust centriole targeting. In other words, PB1-PB2 cassette collectively binds Asl and affords robust centriole localization, optimally positioning the kinase domain for trans-autophosphorylation.
Pfam PF24416: Family of unknown function (DUF7548) (family)
This entry represents a group of uncharacterised archaeal proteins. They are predicted to fold into a four helical bundle.
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 PF06313: Drosophila ACP53EA protein (family)
This family consists of several Drosophila ACP53EA accessory gland (seminal) proteins.
Pfam PF08440: Potyviridae polyprotein (family)
This domain is found in polyproteins of the viral Potyviridae taxon.
Pfam PF00356: Bacterial regulatory proteins, lacI family (domain)
The lacI-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 residues present in the lacI/galR family of transcriptional regulators involved in metabolic regulation in prokaryotes. Most of these bacterial regulators recognize sugar-inducers. The family is named after the Escherichia coli lactose operon repressor lacI and galactose operon repressor galR. LacI-type regulators are present in diverse bacterial genera, in the cytoplasm. The 'helix-turn-helix' DNA-binding motif is located in the N-terminal extremity of these transcriptional regulators. The C-terminal part of lacI-type regulators contains several regions that can be involved in (1) binding of inducers, which are sugars and their analogues and (2) oligomerization. The lac repressor is a tetramer, whilst the gal and cyt repressors are dimers. LacI-type transcriptional regulators are important in the coordination of catabolic, metabolic and transport operons .

Several structures of lacI-type transcriptional regulators have been resolved and their DNA-binding domain encompasses a headpiece, formed by a fold of three helices, followed by a hinge region, which can form a fourth Î±-helix or hinge-helix. The helix-turn-helix motif comprises the first and second helices, the second being called the recognition helix. The HTH is involved in DNA-binding into the major groove, while the hinge-helix fits into the minor groove and the complete domain specifically recognizes the operator DNA .

Some proteins known to contain a lacI-type HTH domain:


 * Bacillus subtilis ccpA and ccpB, transcriptional regulators involved in the catabolic repression of several operons.
 * Salmonella typhimurium fruR, the fructose repressor, involved in the regulation of a large number of operons encoding enzymes which take part in central pathways of carbon metabolism.
 * Escherichia coli lacI, the lactose operon repressor, serving as a model for gene regulation.
 * Escherichia coli purF and purR, repressors involved in the regulation of enzymes for purine nucleotide synthesis.
 * Haemophilus influenzae galR, a repressor of the galactose operon.
Pfam PF18557: Anti-sigma factor NepR (domain)
The general stress response sigma factor in alphaproteobacteria, sigma EcfG is inactivated by the anti-sigma factor NepR, which is itself regulated by the response regulator PhyR. NepR forms two helices that extend over the surface of the PhyR subdomains. Homology modeling and comparative analysis of NepR, PhyR and sigmaEcfG mutants indicate that NepR contacts both proteins with the same determinants, showing sigma factor mimicry at the atomic level. This entry represents NepR domains found in alphaproteobacteria.