SII-SWORD/CoKE huggingface dataset:
Pfam PF22994: RSC4 Ig-like domain (domain)
The RSC4 family includes components of the RSC chromatin remodeling complex, which plays a crucial role in the regulation of transcription and the positioning of nucleosomes. Members of the RSC4 family are particularly important for the control of genes associated with membrane and organelle development, thereby influencing cellular structure and function. This protein contains two N-terminal bromodomains followed by this C-terminal Ig-like domain.
Pfam PF00447: HSF-type DNA-binding (domain)
Heat shock factor (HSF) is a transcriptional activator of heat shock genes : it binds specifically to heat shock promoter elements, which are palindromic sequences rich with repetitive purine and pyrimidine motifs . Under normal conditions, HSF is a homo-trimeric cytoplasmic protein, but heat shock activation results in relocalisation to the nucleus . Each HSF monomer contains one C-terminal and three N-terminal leucine zipper repeats . Point mutations in these regions result in disruption of cellular localisation, rendering the protein constitutively nuclear . Two sequences flanking the N-terminal zippers fit the consensus of a bi- partite nuclear localisation signal (NLS). Interaction between the N- and C-terminal zippers may result in a structure that masks the NLS sequences: following activation of HSF, these may then be unmasked, resulting in relocalisation of the protein to the nucleus . The DNA-binding component of HSF lies to the N terminus of the first NLS region, and is referred to as the HSF domain.
Wikipedia: In molecular biology, heat shock factors (HSF), are the transcription factors that regulate the expression of the heat shock proteins. A typical example is the heat shock factor of Drosophila melanogaster.
Pfam PF13436: Glycine-zipper domain (family)
This entry represents a glycine-zipper-containing OmpA-like membrane domain. The domain is found in a number of experimentally uncharacterised transmembrane proteins.
Pfam PF22388: Domain of unknown function (DUF6974) (domain)
This entry represents a dimeric alpha/beta barrel domain from an uncultured marine organism (PDB:2op5). 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 PF11274: Protein of unknown function (DUF3074) (domain)
This eukaryotic family of proteins has no known function but appears to be part of the START superfamily.
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 PF20409: SnoaL-like domain (domain)
This family contains a large number of proteins that share the SnoaL fold.
Pfam PF11172: Protein of unknown function (DUF2959) (family)
This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
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 PF02985: HEAT repeat (repeat)
The HEAT repeat family is related to armadillo/beta-catenin-like repeats (see [pfam:PF00514]).
Wikipedia: A HEAT repeat is a protein tandem repeat structural motif composed of two alpha helices linked by a short loop. HEAT repeats can form alpha solenoids, a type of solenoid protein domain found in a number of cytoplasmic proteins. The name "HEAT" is an acronym for four proteins in which this repeat structure is found: Huntingtin, elongation factor 3 (EF3), protein phosphatase 2A (PP2A), and the yeast kinase TOR1. HEAT repeats form extended superhelical structures which are often involved in intracellular transport; they are structurally related to armadillo repeats. The nuclear transport protein importin beta contains 19 HEAT repeats.
Pfam PF01382: Avidin family (domain)
This entry includes avidin and streptavidin, and their homologs such as afifavidin , hoefavidin  and fibropellin .
Avidin  is a minor constituent of egg white in several groups of oviparous vertebrates. Avidin, which was discovered in the 1920's, takes its name from the avidity with which it binds biotin. These two molecules bind so strongly that is extremely difficult to separate them. Streptavidin is a protein produced by Streptomyces avidinii which also binds biotin and whose sequence is evolutionary related to that of avidin.

Avidin and streptavidin both form homotetrameric complexes of noncovalently associated chains. Each chain forms a very strong and specific non-covalent complex with one molecule of biotin. The three-dimensional structures of both streptavidin  and avidin  have been determined and revealed them to share a common fold: an eight stranded anti-parallel Î²-barrel with a repeated +1 topology enclosing an internal ligand binding site.

Fibropellins I and III  are proteins that form the apical lamina of the sea urchin embryo, a component of the extracellular matrix. These two proteins have a modular structure composed of a CUB domain (see[prositedoc:PDOC00908]), followed by a variable number of EGF repeats and a C-terminal avidin-like domain.
Wikipedia: Avidin is a tetrameric biotin-binding protein produced in the oviducts of birds, reptiles and amphibians and deposited in the whites of their eggs. Dimeric members of the avidin family are also found in some bacteria. In chicken egg white, avidin makes up approximately 0.05% of total protein (approximately 1800 μg per egg). The tetrameric protein contains four identical subunits (homotetramer), each of which can bind to biotin (Vitamin B7, vitamin H) with a high degree of affinity and specificity. The dissociation constant of the avidin-biotin complex is measured to be KD ≈ 10−15 M, making it one of the strongest known non-covalent bonds.
Pfam PF11093: Mitochondrial export protein Som1 (family)
Som1 is a component of the mitochondrial protein export system. The various Som1 proteins exhibit a highly conserved region and a pattern of cysteine residues. Stabilisation of Som1 occurs through an interaction between Som1 and Imp1, a peptidase required for proteolytic processing of certain proteins during their transport across the mitochondrial membrane. This suggests that Som1 represents a third subunit of the Imp1 peptidase complex
Pfam PF21439: Protein MxiC, C-terminal (domain)
This is a domain found at the C-terminal of Shigella flexneri type III secretion protein MxiC. It is composed of three domains, each possessing a four-helix X-bundle fold.
Pfam PF09202: Rio2, N-terminal (domain)
Members of this family are found in Rio2, and are structurally homologous to the winged helix (wHTH) domain. They adopt a structure consisting of four alpha helices followed by two beta strands and a fifth alpha helix. The domain confers DNA binding properties to the protein, as per other winged helix domains.
Pfam PF23910: Domain of unknown function (DUF7252) (domain)
This entry represents a domain of unknown function found in bacteriophage proteins. The domain is around 115-125 residues long composed of a four stranded beta sheet with helices packed on one side. There is evidence for a confident dimer from structure prediction. In addition the dimer shows a strong electrostatic polarity possibly suggesting a nucleic acid binding 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 PF22066: Cep192 domain 8 (domain)
Cep192 is a centrosomal protein with key roles in centriole duplication and pericentriolar material recruitment, organisation and regulation. Most of the metazoan Cep192 homologs consist of eight ASH/PapD-like domains. These are located at the C-terminal part of the proteins and are likely arranged in a beads-on-string fashion. This entry represents the eighth domain found in the metazoan Cep192 homologs.
Pfam PF09143: AvrPphF-ORF-2 (domain)
Members of this family of plant pathogenic proteins adopt an elongated structure somewhat reminiscent of a mushroom that can be divided into 'stalk' and 'head' subdomains. The stalk subdomain is composed of the N-terminal helix (alpha1) and beta strands beta3-beta4. An antiparallel beta sheet (beta5, beta7-beta8) forms the base of the head subdomain that interacts with the stalk. A pair of twisted antiparallel beta sheets (beta1 and beta6; beta2 and beta9/9') supported by alpha2 form the dome of the head. The head subdomain possesses weak structural similarity with the catalytic portion of a number of ADP-ribosyltransferase toxins.
Pfam PF23037: Transcription elongation factor SPT5, KOWx domain (domain)
This domain is found in human Transcription elongation factor SPT5 and related proteins from eukaryotes. SPT5 is a component of the elongation factor DRB-sensitivity inducing factor (DSIF) that plays multiple roles during transcription. SPT5 is a multidomain protein consisting of an N-terminal NusG domain, a tandem of KOW domains and and a mobile C-terminal-repeat region. This entry represents the KOWx domain that is located between domains KOW3 and KOW4. The KOWx domain along with KOW4 and KOW5 forms an RNA clamp. The tandem KOWx-4 contacts the wall, stalk, and dock domains of Pol II.
Pfam PF00080: Copper/zinc superoxide dismutase (SODC) (domain)
superoxide dismutases (SODs) catalyse the conversion of superoxide radicals to hydrogen peroxide and molecular oxygen. Three evolutionarily distinct families of SODs are known, of which the copper/zinc-binding  family is one. Defects in the human SOD1 gene cause familial amyotrophic lateral sclerosis (Lou Gehrig's disease). Structure is an eight-stranded beta sandwich, similar to the immunoglobulin fold.
Wikipedia: Superoxide dismutase (SOD, EC 1.15.1.1) is an enzyme that alternately catalyzes the dismutation (or partitioning) of the superoxide (O−2) anion radical into normal molecular oxygen (O2) and hydrogen peroxide (H2O2). Superoxide is produced as a by-product of oxygen metabolism and, if not regulated, causes many types of cell damage. Hydrogen peroxide is also damaging and is degraded by other enzymes such as catalase. Thus, SOD is an important antioxidant defense in nearly all living cells exposed to oxygen. One exception is Lactobacillus plantarum and related lactobacilli, which use intracellular manganese to prevent damage from reactive O−2.
Pfam PF15045: Clathrin-binding box of Aftiphilin, vesicle trafficking (family)
Aftiphilin forms a stable complex with p200 and gamma-synergin. This family contains a clathrin box, with two identified clathrin-binding motifs.  This family of proteins is found in eukaryotes.
Wikipedia: Aftiphilin is a protein that in humans is encoded by the AFTPH gene. It forms a stable complex with p200 and synergin gamma. It contains a clathrin box with two known clathrin-binding sequence motifs, is involved in vesicle trafficking and is found in many eukaryotes.
Pfam PF06113: Brain and reproductive organ-expressed protein (BRE) (family)
This family consists of several eukaryotic brain and reproductive organ-expressed (BRE) proteins. BRE is a putative stress-modulating gene, found able to down-regulate TNF-alpha-induced-NF-kappaB activation upon over expression. A total of six isoforms are produced by alternative splicing predominantly at either end of the gene.Compared to normal cells, immortalised human cell lines uniformly express higher levels of BRE. Peripheral blood monocytes respond to LPS by down-regulating the expression of all the BRE isoforms.It is thought that the function of BRE and its isoforms is to regulate peroxisomal activities.
Pfam PF01510: N-acetylmuramoyl-L-alanine amidase (domain)
This family includes zinc amidases that have N-acetylmuramoyl-L-alanine amidase activity [ec:3.5.1.28]. This enzyme domain cleaves the amide bond between N-acetylmuramoyl and L-amino acids in bacterial cell walls (preferentially: D-lactyl-L-Ala).  The structure is known for the bacteriophage T7 structure and shows that two of the conserved histidines are zinc binding.
Wikipedia: In enzymology, a N-acetylmuramoyl-L-alanine amidase is an enzyme that catalyzes a chemical reaction that cleaves the link between N-acetylmuramoyl residues and L-amino acid residues in certain cell-wall glycopeptides.
Pfam PF17319: Family of unknown function (DUF5362) (family)
This is a family of unknown function found in Bacteria. Most of the family members are predicted to have 2 trans-membrane regions.
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 PF19989: Family of unknown function (DUF6425) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001281) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the  ustilagic acid biosynthetic gene cluster from Ustilago maydis 521. This family appears to be predominantly found in fungi.
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 PF17759: Phenylalanyl tRNA synthetase beta chain CLM domain (domain)
This domain corresponds to the catalytic like domain (CLM) in the beta chain of phe tRNA synthetase.
Pfam PF06532: Negative regulator of sigma F (family)
This family includes CC3252 (NrsF- Negative regulator of sigma F) from Caulobacter crescentus, which is proposed to be an anti-sigma factor. In particular, overexpression of NrsF prevents the induction of the sigF regulon after dichromate stress. Family members also include the anti-sigma factor OsrA (blr3039) from Bradyrhizobium japonicum, which is involved in sensing reactive oxygen species. There is evidence that OsrA binds an ECF-type sigma factor (EcfF) in vivo. Furthermore, the conserved cysteine residues 129 and 179 of OsrA are shown to be required for normal function. Family members have 6 predicted transmembrane regions.
Pfam PF21472: Baseplate structural protein gp6, C-terminal domain II (domain)
This entry represents domain II found in the C-terminal of gp6 from bacteriophage T4, which adopts a beta-barrel fold. This protein is involved in tail assembly. It forms the gp25-(gp6)2-gp7 module, involved in sheath contraction.
Pfam PF18178: ATP nucleosidase Cap17-like, N-terminal (domain)
This entry represents the N-terminal domain of ATP nucleosidase Cap17 from E.coli and related sequences. Cap17 is likely an effector protein with (d)ATP degrading activity of a CBASS (cyclic oligonucleotide-based antiphage signaling system) antivirus system which provides immunity against bacteriophages. Members of this entry often co-occur genomically with the bacterial HORMA and Pch2/TRIP13 domains.
Pfam PF01729: Quinolinate phosphoribosyl transferase, C-terminal domain (domain)
Quinolinate phosphoribosyl transferase (QPRTase) or nicotinate-nucleotide pyrophosphorylase [ec:2.4.2.19] is involved in the de novo synthesis of NAD in both prokaryotes and eukaryotes. It catalyses the reaction of quinolinic acid with 5-phosphoribosyl-1-pyrophosphate (PRPP) in the presence of Mg2+ to give rise to nicotinic acid mononucleotide (NaMN), pyrophosphate and carbon dioxide. The QA substrate is bound between the C-terminal domain of one subunit, and the N-terminal domain of the other.  The C-terminal domain has a 7 beta-stranded TIM barrel-like fold.
Pfam PF10164: Brain protein I3 (family)
This is a highly conserved family of proteins which contains three pairs of cysteine residues within a length of 42 amino acids and is rich in proline residues towards the N-terminus. It includes a membrane protein that has been found to be highly expressed in the mouse brain and consequently, several members have been assigned as brain protein I3 (Bri3). Their function is unknown but they appear to play a role in TNF-induced cell death.
Pfam PF23829: Family of unknown function (DUF7199) (family)
This family consists of several mycobacteriophage putative membrane proteins of around 99 amino acids in length. These proteins are characterized by an N-terminal transmembrane helix, a small central putative zinc binding domain containing 2 conserved cysteine and 2 histidine residues and disordered C-terminal region rich in basic and acidic 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 PF16213: Mon2/Sec7/BIG1-like, dimerisation and cyclophilin-binding domain (repeat)
DCB domain is found at the N-terminal of Mon2 and BIG1-like proteins from metazoa, and in fungal homologues like Sec7 and Gea1/2. Mon2 and BIG1 like proteins play an important role in the cytoplasm-to-vacuole transport pathway and are required for Golgi homeostasis. This domain is sufficient for targeting BIG1 to the Golgi.
Pfam PF20305: prokaryotic YEATS domain (family)
This entry represents a prokaryotic YEATS domain. pYEATS is fused to diverse effector domains, suggesting that the binding to a ligand activates an effector-based response against an invasive threat. It has been predicted to specifically recognise invader-induced modifications of macromolecules by acyl moieties (e.g. phage-encoded acylations of surface polysaccharides) to unleash the fused effectors through a conformational change.
Pfam PF09715: Plasmodium protein of unknown function (Plasmod_dom_1) (family)
These sequences represent an uncharacterised family consisting of a small number of hypothetical proteins of the malaria parasite Plasmodium falciparum (isolate 3D7).
Pfam PF11338: Protein of unknown function (DUF3140) (family)
Some members in this family of proteins are annotated as DNA binding proteins. No function is currently 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 PF23677: Protein YnaL-like (family)
This protein family includes Protein YnaL from Escherichia coli, a 57-residues long protein encoded by a small open reading frame (smORF).
Pfam PF11605: Vacuolar protein sorting protein 36 Vps36 (domain)
Vps36 is a subunit of ESCRT-II, a protein involved in driving protein sorting from endosomes to lysosomes. The GLUE domain of Vps36 allows for a tight interaction to occur between the protein and Vps28, a subunit of ESCRT-I. This interaction is critical for ubiquitinated cargo progression from early to late endosomes.
Pfam PF19708: Family of unknown function (DUF6205) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000078) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from the incednine biosynthetic gene cluster from Streptomyces sp.  ML694-90F3.
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 PF12267: Protein of unknown function (DUF3614) (family)
This family of proteins is found in viruses. Proteins in this family are typically between 162 and 495 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 PF12372: Huntingtin, N-terminal HEAT (repeat)
This entry represents HEAT repeats from Huntingtin (HTT), which are part of the N-terminal HEAT domain. These are a second set, separated from N-HEAT_1 ([pfam:PF20926]) by an unstructured region. HTT is expressed in many tissues with various expression levels and is involved in a number of cellular functions. However, its exact function is not yet clear. An abnormal polyglutamine (polyQ) expansion in this protein causes Huntington's disease (HD) a progressive autosomal-dominant neurodegenerative disease characterised by an uncontrolled motor movement known as chorea, cognitive disorder and depression. HTT consists of multiple HEAT repeats organised in N-terminal, bridge and C-terminal domains, which function as a scaffold that mediated interactions with binding partners.
Pfam PF00825: Ribonuclease P (family)
Ribonuclease P (3.1.26.5) (RNase P)  is a site specific endonuclease that generates mature tRNAs by catalysing the removal of the 5'-leader sequence from pre-tRNA to produce the mature 5'-terminus. It can also cleave other RNA substrates such as 4.5S RNA. In bacteria RNase P is known to be composed of two components: a large RNA (about 400 base pairs) encoded by rnpB, and a small protein (119 to 133 amino acids) encoded by rnpA. The RNA moiety of RNase P carries the catalytic activity; the protein component plays an auxiliary, but essential, role in vivo by binding to the 5'-leader sequence and broadening the substrate specificity of the ribozyme. The sequence of rnpA is not highly conserved, however there is, in the central part of the protein, a conserved basic region.