SII-SWORD/CoKE huggingface dataset:
Pfam PF01809: Putative membrane protein insertion efficiency factor (family)
This family consists of membrane insertion efficiency factor proteins. They contain three conserved cysteine residues. Family members such as YidD may be involved in insertion of integral membrane proteins into the membrane by assisting YidC (membrane protein insertase). Some members of the yidD family have been previously thought to posses alpha-hemolysin activity, however no sufficient evidence was found to corroborate this idea. Secondary structure prediction indicated the presence of three alpha-helices in YidD. None of the three alpha-helices appeared sufficiently hydrophobic to serve as a transmembrane, suggesting a cytoplasmic localization for YidD. However, a closer examination of the alpha-helical wheel projection of the predicted first alpha-helix in YidD suggested an amphipathic structure in its N-terminal region which might be involved in membrane targeting.
Pfam PF16004: 116 kDa U5 small nuclear ribonucleoprotein component N-terminus (family)
This entry represents the N-terminal domain of U5 small nuclear ribonucleoprotein (snRNP) protein (U5-116kDa). It is also found in Snu114p, a 114kDa protein homologous to U5-116kDa that has been identified in Saccharomyces cerevisiae . Both proteins seem to have a role in pre-mRNA splicing process.
Wikipedia: 116 kDa U5 small nuclear ribonucleoprotein component is a protein that in humans is encoded by the EFTUD2 gene.
Pfam PF13351: Protein of unknown function (DUF4099) (family)
A family of uncharacterized proteins found by clustering human gut metagenomic sequences. The C-terminal repeat region of this family is DUF4098, [pfam:PF13345].
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 PF19749: Family of unknown function (DUF6236) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001432) is described by MIBiG as an example of the following biosynthetic classes, NRP (non-ribosomal peptide) and polyketide. It includes a member from the myxochromide D  biosynthetic gene cluster from Stigmatella erecta.
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 PF06150: ChaB (domain)
This family of proteins contain a conserved 60 residue region. This protein is known as ChaB in E. coli and is found next to ChaA which is a cation transporter protein.  ChaB may be regulate ChaA function in some way.
Pfam PF04577: Glycosyltransferase 61 (family)
This family represents the Glycosyltransferase Family 61. Members in this family are further processed into a mature form. It includes O-linked-mannose beta-1,4-N-acetylglucosaminyltransferase 2 (POMGnT2, also known as AGO61 or EOGLT) and EGF domain-specific O-linked N-acetylglucosamine transferase (EOGT). This family also includes plant beta-1,2-xylosyltransferases.
Pfam PF07259: ProSAAS precursor (family)
This family consists of several mammalian proSAAS precursor proteins. ProSAAS mRNA is expressed primarily in brain and other neuroendocrine tissues (pituitary, adrenal, pancreas); within brain, the mRNA is broadly distributed among neurons. ProSAAS is thought to be an endogenous inhibitor of prohormone convertase 1 and may function as a neuropeptide. N-terminal fragments of ProSAAS in intracellular Pick Bodies (PBs) may cause a functional disturbance of neurons in Pick's disease. This protein is also associated with Alzheimer's and Parkinson's disease.
Wikipedia: Proprotein convertase subtilisin/kexin type 1 inhibitor is a protein by the name of proSAAS that in humans is encoded by the PCSK1N gene.
Pfam PF01548: Transposase (domain)
Transposase proteins are necessary for efficient DNA transposition.  This family includes an amino-terminal region of the pilin gene inverting protein (PIVML) and of members of the IS111A/IS1328/IS1533 family of transposases. The C-terminus is represented by family [pfam:PF02371].
Pfam PF13547: GTA TIM-barrel-like domain (domain)
This domain is found in the gene transfer agent protein.  An unusual system of genetic exchange exists in the purple nonsulfur bacterium Rhodobacter capsulatus. DNA transmission is mediated by a small bacteriophage-like particle called the gene transfer agent (GTA) that transfers random 4.5-kb segments of the producing cell's genome to recipient cells, where allelic replacement occurs. The genes involved in this process appear to be found widely in bacteria. According to the SUPERFAMILY database this domain has a TIM barrel fold.
Pfam PF07931: Chloramphenicol phosphotransferase-like protein (domain)
The members of this family are all similar to chloramphenicol 3-O phosphotransferase (CPT, [swissprot:Q56148]) expressed by Streptomyces venezuelae. Chloramphenicol (Cm) is a metabolite produced by this bacterium that can inhibit ribosomal peptidyl transferase activity and therefore protein production. By transferring a phosphate group  to the C-3 hydroxyl group of Cm, CPT inactivates this potentially  lethal metabolite.
Wikipedia: In molecular biology, the chloramphenicol phosphotransferase-like protein family includes the chloramphenicol 3-O phosphotransferase (CPT) expressed by Streptomyces venezuelae. Chloramphenicol (Cm) is a metabolite produced by this bacterium that can inhibit ribosomal peptidyl transferase activity and therefore protein production. By transferring a phosphate group to the C-3 hydroxyl group of Cm, CPT inactivates this potentially lethal metabolite.
Pfam PF00156: Phosphoribosyl transferase domain (domain)
This family includes a range of diverse phosphoribosyl transferase enzymes.  This family includes: Adenine phosphoribosyl-transferase [ec:2.4.2.7], [swissprot:P07672]. Hypoxanthine-guanine-xanthine phosphoribosyl-transferase [swissprot:P51900]. Hypoxanthine phosphoribosyl-transferase [ec:2.4.2.8] [swissprot:P36766]. Ribose-phosphate pyrophosphokinase i [ec:2.7.6.1] [swissprot:P09329]. Amidophosphoribosyltransferase [ec:2.4.2.14] [swissprot:P00496]. Orotate phosphoribosyl-transferase [ec:2.4.2.10] [swissprot:P11172]. Uracil phosphoribosyl-transferase [ec:2.4.2.9] [swissprot:P25532]. Xanthine-guanine phosphoribosyl-transferase [ec:2.4.2.22] [swissprot:P00501].  In Arabidopsis, At the very N-terminus of this domain is the P-Loop NTPase domain.
Pfam PF04625: DEC-1 protein, N-terminal region (family)
The defective chorion-1 gene (dec-1) in Drosophila encodes follicle cell proteins necessary for proper eggshell assembly. Multiple products of the dec-1 gene are formed by alternative RNA splicing and proteolytic processing.  Cleavage products include S80 (80 kDa) which is incorporated into the eggshell, and further proteolysis of S80 gives S60 (60 kDa).
Pfam PF08430: Forkhead N-terminal region (family)
The region described in this family is found towards the N-terminus of various eukaryotic forkhead/HNF-3-related transcription factors (which contain the [pfam:PF00250] domain). These proteins play key roles in embryogenesis, maintenance of differentiated cell states, and tumourigenesis.
Pfam PF15260: Protein family FAM219A (family)
This protein family, FAM219A is a domain of unknown function. This protein family has been found in eukaryotes. Proteins in this family are typically between 144 and 191 amino acids in length. There are two conserved sequence motifs: QLL and LDE.
Pfam PF14104: Domain of unknown function (DUF4277) (family)
This presumed domain is functionally uncharacterised. This domain family is found in bacteria and archaea, and is approximately 110 amino acids in length. There is a conserved NGLGF 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 PF07425: Pardaxin (family)
This family consists of several Pardaxin proteins. Pardaxin, a 33-amino-acid pore-forming polypeptide toxin isolated from the Red Sea Moses sole Pardachirus marmoratus, has a helix-hinge-helix structure. This is a common structural motif found both in antibacterial peptides that can act selectively on bacterial membranes (e.g., cecropin), and in cytotoxic peptides that can lyse both mammalian and bacterial cells (e.g., melittin). Pardaxin possesses a high antibacterial activity with a significantly reduced haemolytic activity towards human red blood cells compared with melittin. Pardaxin has also been found to have a shark repellent action.
Pfam PF23626: aECM cysteine-cradle domain (domain)
This domain is found in nematode proteins that are known to be aECM (apical ExtraCellular Matrice) components. It is predicted to adopt a globular alpha-helical structure with a cradle-like shape. This domain contains four invariant cysteines which are probably involved in forming two disulfide bonds. The latter likely contribute to the maintenance of the cradle-like shape.
Pfam PF17286: PRMT5 oligomerisation domain (domain)
This entry represents the C-terminal oligomerisation domain of PRMT5.
Proteins containing this domain includes Skb1 from S. pombe , Hsl7 from S. cerevisiae  and their homologues PRMT5 from animals  and plants . Skb1 is a mediator of hyperosmotic stress response in Schizosaccharomyces pombe . Plant PMRT15 is involved in the post-transcriptional regulation of the circadian clock . Human PRMT5 is a component of multiple protein complexes and contributes to essential cellular processes, such as RNA transport and splicing, cell cycle regulation, tumour growth, and chromatin remodelling, leading to either gene silencing or activation .
Pfam PF08247: ENOD40 protein (family)
Rohrig et al. reported the in vitro translation of two peptides of 12 and 24 amino acids from the short, overlapping ORFs of soybean ENOD40 mRNA. The putative role of the enod40 genes has been in favour of organogenesis, such as induction of the cortical cell divisions that lead to initiation of nodule primordia, in developing lateral roots and embryonic tissues. This supports the hypothesis for a role of enod40 in lateral organ development.
Wikipedia: enod40, also known as early nodulin 40, is a gene found in flowering plants. The gene has characteristics of both protein and Non-coding RNA genes. There is
some evidence that the non-coding characteristics of this gene are more widely conserved than the
protein coding sequences.
In soyabeans enod40 was found to be expressed during
early stages of formation of nitrogen-fixing root nodules that are associated with symbiotic soil rhizobial bacteria.
The gene is also active in roots containing fungi forming phosphate-acquiring arbuscular mycorrhiza.

An interaction with a novel RNA-binding protein MtRBP1 investigated in the development of Root nodule suggests ENOD40 has a function of cytoplasmic relocalization of nuclear proteins.
In the study of non-legume plants, the over-expression of ENOD40 in transgenic Arabidopsis lines was observed a reduction of cell expansion.
Pfam PF22309: HK/GC/Chemotaxis protein-like, sensor domain (domain)
This entry represents a sensor domain found in methyl-accepting chemotaxis proteins, diguanylate-cyclase and histidine kinase receptors. Signals detected by the sensor domain are transmitted to the effector domain, implying a combinatorial molecular evolution.
Pfam PF05111: Ameloblastin precursor (Amelin) (family)
This family consists of several mammalian Ameloblastin precursor (Amelin) proteins. Matrix proteins of tooth enamel consist mainly of amelogenin but also of non-amelogenin proteins, which, although their volumetric percentage is low, have an important role in enamel mineralisation. One of the non-amelogenin proteins is ameloblastin, also known as amelin and  sheathlin. Ameloblastin (AMBN) is one of the enamel sheath proteins which is though to have a role in determining the prismatic structure of growing enamel crystals.
Pfam PF20503: Family of unknown function (DUF6730) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 105 and 155 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 PF16402: Domain of unknown function (DUF5010) (family)
This small family of proteins is functionally uncharacterised. This family is found in bacteroides. Proteins in this family are around 600 amino acids in length. This family is related to glycosyl hydrolase family 99.
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 PF08471: Class II vitamin B12-dependent ribonucleotide reductase (family)
This domain is found to the N-terminus of the ribonucleotide reductase barrel domain ([pfam:PF02867]).  It occurs in bacterial class II ribonucleotide reductase proteins which depend upon coenzyme B12 (deoxyadenosylcobalamine).
Pfam PF14007: YtpI-like protein (family)
The YtpI-like protein family includes the B. subtilis YtpI protein [swissprot:O34922] which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 73 and 101 amino acids in length.
Pfam PF05818: Enterobacterial TraT complement resistance protein (family)
The traT gene is one of the F factor transfer genes and encodes an outer membrane protein which is involved in interactions between an Escherichia coli and its surroundings.
Pfam PF18381: YcaO cyclodehydratase C-terminal domain (repeat)
This is the proline-rich C-terminal domain found in ribosomal protein S12 methylthiotransferase accessory factor YcaO. It has been shown to be involved in both C protein recognition and cyclodehydration. The C-terminal domain resembles a tetratricopeptide repeat that mediates dimerization.
Pfam PF03616: Sodium/glutamate symporter (family)
This entry represents a membrane protein, GltS, which is a glutamate carrier of an Na+-dependent, binding protein-independent, and glutamate-specific transport system .
Wikipedia: The sodium/glutamate symporter, also known as glutamate permease, is a transmembrane protein family found in bacteria and archaea. These proteins are symporters that are responsible for the sodium-dependent uptake of extracellular glutamate into the cell. They are integral membrane proteins located in the bacterial inner membrane. The best-studied member of the family is GltS from Escherichia coli. GltS contains ten transmembrane helices arranged in two antiparallel 5-helix domains and functions as a homodimer. Substrates for GltS include L- and D-glutamate, as well as toxic analogs α-methylglutamate, and homocysteate. In studies of E. coli growth, bacteria without GltS were unable to grow in a medium where glutamate is the only source of carbon.
Pfam PF21032: PROPPIN (repeat)
This entry includes PROPPIN family members, which are beta-propellers that bind polyphosphoinositides, conserved from yeast to human. These are PI(3)P sensors that share a beta-propeller fold and the presence of an FRRG motif required for phosphoinositide binding and autophagy, playing a key role in autophagosome biogenesis. Four PROPPINs are known in human (WIPI1-4) and three in yeast (Atg18, Atg21 and Hvs2). EPG6 from C. elegans is an homologue of human WIPI4.
Pfam PF23464: WWE domain (domain)
This entry represents a WWE domain found in the PA-PLA1 family of proteins. The PA-PLA1 family is involved in various cellular processes related to membrane lipid metabolism and organelle structure maintenance. Members of the family exhibit phospholipase activity, preferentially hydrolyzing phosphatidic acid and phosphatidylethanolamine. They also have specific lipid-binding capabilities, interacting with phosphatidylinositol phosphates such as PI(3)P, PI(4)P, and PI(5)P. This binding is crucial for their role in organizing endoplasmic reticulum exit sites and may influence the transport between the Golgi apparatus and plasma membrane. The family's function is essential for maintaining the integrity of the endoplasmic reticulum and Golgi structures, which are critical for proper cellular function.
Pfam PF17510: Gene product 44 (family)
This is a family with unknown function. Family members are hypothetical proteins found in Mycobacterium phages.
Pfam PF13994: PgaD-like protein (family)
This family includes the PgaD protein from E. coli [swissprot:P69432]. The homopolymer poly-beta-1,6-N-acetyl-D-glucosamine (beta-1,6-GlcNAc; PGA) serves as an adhesin for the maintenance of biofilm structural stability in eubacteria. The pgaABCD operon is required for its synthesis and export. It has been shown that PgaD is essential for this process.
Pfam PF11264: Thylakoid formation protein (family)
THF1 is localised to the outer plastid membrane and the stroma. THF1 has a role in sugar signalling. THF1 is also thought to have a role in chloroplast and leaf development. THF1 has been shown to play a crucial role in vesicle-mediated thylakoid membrane biogenesis.
Pfam PF16000: CARMIL C-terminus (family)
This domain is found near to the C-terminus of leucine-rich repeat-containing proteins in the CARMIL family. In leucine-rich repeat-containing protein 16A (LRRC16A) it includes the region responsible for interaction with F-actin-capping protein subunit alpha-2 (CAPZA2).
Pfam PF12629: Poxvirus poly(A) polymerase C-terminal domain (domain)
This domain is found at the C-terminus of the pox virus PolyA polymerase protein.
Pfam PF02679: (2R)-phospho-3-sulfolactate synthase (ComA) (family)
In methanobacteria (2R)-phospho-3-sulfolactate synthase (ComA) catalyses the first step of the biosynthesis of coenzyme M from phosphoenolpyruvate (P-enolpyruvate). This novel enzyme catalyses the stereospecific Michael addition of sulfite to P-enolpyruvate, forming L-2-phospho-3-sulfolactate (PSL). It is suggested that the ComA-catalysed reaction is analogous to those reactions catalysed by beta-elimination enzymes that proceed through an enolate intermediate.
Pfam PF07539: U3 small nucleolar RNA-associated protein 20, N-terminal (repeat)
This domain is found towards the N-terminal of eukaryotic proteins including U3 small nucleolar RNA-associated protein 20 (UTP20) from yeast and the homologue from human, also known as DRIM (Down-Regulated In Metastasis) ([swissprot:O75691]), which is differentially expressed in metastatic and non-metastatic human breast carcinoma cells.  Proteins of this entry are involved in processing of non-coding RNA as components of of the small-subunit (SSU) processome; SSU processome is involved in the biogenesis of the 18S rRNA. UTP20 is a huge alpha-solenoid structure that functions as a scaffold.
Pfam PF20889: Antitoxin TsiV3 (family)
Antitoxin TsiV3, also known as TsaB, is a immmunity protein from Vibrio cholerae that inhibits the activity of toxin VgrG3, a protein found in the spike of the type VI secretion system (T6SS) syringe- like complex. TsiV3 folds into a three-helix bundle and adopts a dimeric assembly to bind the deep active-site groove of the catalytic domain in the C-terminal region of VgrG3, modifying the conformation and preventing substrate binding.
Pfam PF19747: Family of unknown function (DUF6234) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000709) is described by MIBiG as an example of the following biosynthetic class, saccharide. It includes a member from the neomycin biosynthetic gene cluster from Streptomyces fradiae  ATCC 10745 = DSM 40063. This family appears to be predominantly found in Actinobacteria.
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 PF07681: DoxX (family)
These proteins appear to have some sequence similarity with [pfam:PF04173] but their function is unknown.
Pfam PF00965: Tissue inhibitor of metalloproteinase (domain)
Members of this family are common in extracellular regions of vertebrate species
Pfam PF02005: N2,N2-dimethylguanosine tRNA methyltransferase (family)
This enzyme [ec:2.1.1.32] used S-AdoMet to methylate tRNA. The TRM1 gene of Saccharomyces cerevisiae is necessary for the N2,N2-dimethylguanosine modification of both mitochondrial and cytoplasmic tRNAs. The enzyme is found in both eukaryotes and archaebacteria
Pfam PF01435: Peptidase family M48 (domain)
Peptidase_M48 is the largely extracellular catalytic region of CAAX prenyl protease homologues such as Human FACE-1 protease. These are metallopeptidases, with the characteristic HExxH motif giving the two histidine-zinc-ligands and an adjacent glutamate on the next helix being the third. The whole molecule folds to form a deep groove/cleft into which the substrate can fit.
Wikipedia: A metalloproteinase, or metalloprotease, is any protease enzyme whose catalytic mechanism involves a metal. An example is ADAM12 which plays a significant role in the fusion of muscle cells during embryo development, in a process known as myogenesis.
Pfam PF02732: ERCC4 domain (domain)
This domain is a family of nucleases. The family includes EME1 which is an essential component of a Holliday junction resolvase.  EME1 interacts with MUS81 to form a DNA structure-specific endonuclease.
Pfam PF08714: Formaldehyde-activating enzyme (Fae) (family)
Formaldehyde-activating enzyme is an enzyme required for energy metabolism and formaldehyde detoxification.  It catalyses the condensation of formaldehyde and tetrahydromethanopterin to methylene tetrahydromethanopterin.
Pfam PF23115: STOP2-like, C2H2-type zinc finger (domain)
This domain is found in Protein SENSITIVE TO PROTON RHIZOTOXICITY 2 from Arabidopsis thaliana (STOP2) and similar sequences from plants. STOP2 is a probable transcription factor. It plays an important role in tolerance to major stress factors in acid soils such as proton H+ and aluminum ion Al3+. This entry represents one of its C2H2 or beta-beta -alpha zinc finger DNA-binding domain.
Pfam PF02497: Arterivirus glycoprotein (family)
This is a family of structural glycoproteins from arterivirus that corresponds to open reading frame 4 (ORF4) of the virus.
Pfam PF09363: XFP C-terminal domain (family)
Bacterial enzyme splits fructose-6-P and/or xylulose-5-P with the aid of inorganic phosphate into either acetyl-P and erythrose-4-P and/or acetyl-P and glyeraldehyde-3-P [ec:4.1.2.9], [ec:4.1.2.22].