SII-SWORD/CoKE huggingface dataset:
Pfam PF01244: Membrane dipeptidase (Peptidase family M19) (domain)
This group of peptidases belong to the MEROPS peptidase family M19 (membrane dipeptidase family, clan MJ). The protein fold of the peptidase domain for members of this family resembles that of Klebsiella urease, the type example for clan MJ .

Renal dipeptidase (3.4.13.19), also known as microsomal dipeptidase or membrane-bound dipeptidase, is a zinc-dependent metalloenzyme that hydrolyses a wide range of dipeptides. It is involved in renal metabolism of glutathione and its conjugates. It is a homodimeric disulphide-linked glycoprotein attached to the renal brush border microvilli membrane by a GPI-anchor. A glutamate residue has recently been shown  to be important for the catalytic activity of renal dipeptidase. Renal dipeptidase seems to be evolutionary related to hypothetical proteins in the PQQ biosynthesis operons of Acinetobacter calcoaceticus and Klebsiella pneumoniae .
Pfam PF15227: zinc finger of C3HC4-type, RING (domain)
This is a family of primate-specific Ret finger protein-like (RFPL) zinc-fingers of the C3HC4 type. Ret finger protein-like proteins are primate-specific target genes of Pax6, a key transcription factor for pancreas, eye and neocortex development. This domain is likely to be DNA-binding. This zinc-finger domain together with the RDM domain, [pfam:PF11002], forms a large zinc-finger structure of the RING/U-Box superfamily. RING-containing proteins are known to exert an E3 ubiquitin protein ligase activity with the zinc-finger structure being mandatory for binding to the E2 ubiquitin-conjugating enzyme.
Pfam PF12478: UBAP2/protein lingerer (family)
This entry includes ubiquitin-associated protein 2 (UBAP2) from humans and protein lingerer (lig) from Drosophila melanogaster. Lig  is a cytoplasmic protein involved in initiation and termination of copulation. Lig can act as a growth suppressor that associates with the RNA-binding proteins Fragile X messenger ribonucleoprotein 1 (FMR1) and Caprin (Capr) and directly interacts with and regulates the RNA-binding protein Rasputin (Rin).
Pfam PF03623: Focal adhesion targeting region (domain)
Focal adhesion kinase (FAK) is a tyrosine kinase found in focal adhesions, intracellular signaling complexes that are formed following engagement of the extracellular matrix by integrins. The C-terminal 'focal adhesion targeting' (FAT) region is necessary and sufficient for localising FAK to focal adhesions. The crystal structure of FAT shows it forms a four-helix bundle that resembles those found in two other proteins involved in cell adhesion, alpha-catenin and vinculin. The binding of FAT to the focal adhesion protein, paxillin, requires the integrity of the helical bundle, whereas binding to another focal adhesion protein, talin, does not.
Wikipedia: In structural and cell biology, the focal adhesion targeting domain is a conserved protein domain that was first identified in focal adhesion kinase (FAK), also known as PTK2 protein tyrosine kinase 2 (PTK2).
Pfam PF16657: Maltogenic Amylase, C-terminal domain (family)
This is the C-terminal domain of Maltogenic amylase, an enzyme that hydrolyses starch material.  Maltogenic amylases are central to carbohydrate metabolism.
Pfam PF24929: Domain of unknown function (DUF7749) (domain)
This domain is found in uncharacterised proteins from eukaryotes. It is predicted to adopt a globular a/b 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 PF10036: RNA transcription, translation and transport factor protein (family)
This entry represents RNA transcription, translation and transport factor protein (RTRAF, also known as hCLE/C14orf166) from eukaryotes. It is part of the DDX1-HSPC117-FAM98B complex that shuttles between the nucleus and the cytoplasm transporting RNAs. It is also a component of the tRNA-splicing ligase complex and is required for tRNA ligation. Human RTRAF works as a positive modulator of the RNA polymerase II activity. It also interacts with influenza virus polymerase subunit PA and plays an important role in influenza virus replication. Family members carry a characteristic RLL sequence-motif.
Pfam PF20192: Family of unknown function (DUF6555) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in Proteobacteria. Proteins in this family are typically between 76 and 94 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 PF17142: Outer membrane protein SusF, N-terminal domain (domain)
This domain is N-terminal in outer membrane protein SusF from Bacteroides thetaiotaomicron and similar sequences from bacteroidetes. SusF is a starch-binding protein organised into three tandem domains packed against each other: N-terminal (this entry), middle, and C-terminal. The last two, represented by [pfam:PF16411], are common to SusE and SusF. This domain forms a beta-barrel that is similar in overall-fold and topology to several immunoglobulin superfamily domains found in cell adhesion proteins.
Pfam PF23702: ECM29, ARM-like repeats (repeat)
This is a region of armadillo-like repeats found in human Proteasome adapter and scaffold protein ECM29 and similar protein sequences predominantly found in vertebrates. ECM29 binds to the 26S proteasome, motor proteins and other compartment specific proteins. This entry is often found C-terminal to [pfam:PF13001].
Pfam PF16826: Domain of unknown function (DUF5076) (family)
This entry represents a group of uncharacterised bacterial 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 PF07370: Protein of unknown function (DUF1489) (family)
This family consists of several hypothetical bacterial proteins of around 150 residues in length. Members of this family seem to be founds exclusively in the Class Alphaproteobacteria. 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 PF19489: Transglycosylase SLT domain (domain)
This entry represents a set of SLT like domains found in proteobacteria. SLT domains are enzymes that degrade murein.
Pfam PF05542: Protein of unknown function (DUF760) (family)
This family contains several uncharacterised plant 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 PF20693: YobI-like P-loop NTPase (domain)
This is a P-loop NTPase involved in antiviral immunity in bacteria. Members of this entry have a pair of transmembrane helices inserted into the P-loop NTPase domain.
Pfam PF23675: YciZ-like (family)
This protein family includes YciZ from Escherichia coli and similar short sequences encoded by small open reading frames (smORFs) from gammaproteobacteria.
Pfam PF18575: HAMP N-terminal domain 3 (domain)
Aer2 soluble receptor from Pseudomonas aeruginosa contains three successive HAMP domains in the N-terminal region. HAMP domains are widespread prokaryotic signaling modules. This entry is the third N-terminal HAMP domain (HAMP3). HAMP3 adopt a conformation resembling Af1503, with only minor differences in helical tilt and orientation. The basic construction of each HAMP domain consists of a monomeric unit of two parallel alpha helices (AS1 and AS2) joined by an elongated connector of 12-14 residues form a parallel four-helix bundle.
Wikipedia: In molecular biology, the HAMP domain is an approximately 50-amino acid alpha-helical region that forms a dimeric, four-helical coiled coil. It is found in bacterial sensor and chemotaxis proteins and in eukaryotic histidine kinases. The bacterial proteins are usually integral membrane proteins and part of a two-component signal transduction pathway. One or several copies of the HAMP domain can be found in association with other domains, such as the histidine kinase domain, the bacterial chemotaxis sensory transducer domain, the PAS repeat, the EAL domain, the GGDEF domain, the protein phosphatase 2C-like domain, the guanylate cyclase domain, or the response regulatory domain. In its most common setting, the HAMP domain transmits conformational changes in periplasmic ligand-binding domains to cytoplasmic signalling kinase and methyl-acceptor domains and thus regulates the phosphorylation or methylation activity of homodimeric receptors.
Pfam PF23589: AprA winged helix domain (family)
This entry represents a domain found in the homologues of AprA Methyltransferase 1. AprA is an S-adenosylmethionine and Fe3+-dependent dimethyltransferase that acts in the initiation steps of apratoxin A biosynthesis. This domain has similarity to winged helix domains.
Pfam PF05843: Suppressor of forked protein (Suf) (repeat)
This family consists of several eukaryotic suppressor of forked (Suf) like proteins. The Drosophila melanogaster Suppressor of forked [Su(f)] protein shares homology with the yeast RNA14 protein and the 77-kDa subunit of human cleavage stimulation factor, which are proteins involved in mRNA 3' end formation. This suggests a role for Su(f) in mRNA 3' end formation in Drosophila. The su(f) gene produces three transcripts; two of them are polyadenylated at the end of the transcription unit, and one is a truncated transcript, polyadenylated in intron 4. It is thought that su(f) plays a role in the regulation of poly(A) site utilisation and an important role of the GU-rich sequence for this regulation to occur.
Pfam PF19195: Family of unknown function (DUF5870) (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 PF03513: Cloacin immunity protein (family)
The cloacin immunity protein complexes with cloacin in equimolar quantities and inhibits it by binding with high affinity to the cloacin C-terminal catalytic domain. The immunity protein is relatively small, containing 85 amino acids.

An extra ribosome binding site has been found to precede the immunity gene on the polycistronic Clo DF13 mRNA , which perhaps accounts for the fact that, in cloacinogenic cells, more immunity protein than cloacin is synthesised . Comparison of the complete amino acid sequence of the Clo DF13 immunity protein with that of the Col E3 and Col E6 immunity proteins reveals extensive similarities in primary structure, although Col E3 and Clo DF13 immunity proteins are exchangeable only to a low extentin vivoandin vitro.
Wikipedia: In molecular biology, the cloacin immunity protein is produced by bacteria if they contain a certain plasmid. It inhibits the polypeptide bacterial toxin, cloacin, which is produced by the same or other bacteria. It complexes with cloacin in equimolar quantities and inhibits it by binding with high affinity to the cloacin C-terminal catalytic domain.
Pfam PF14463: E1 N-terminal domain (family)
An uncharacterised alpha/beta domain fused to E1 proteins. This protein is usually present in gene neighbourhoods with genes encoding a JAB protein and a predicted metal-binding protein. In related E1 proteins, the E1-N domain is replaced by an E2/UBC superfamily domain.
Pfam PF04012: PspA/IM30 family (family)
This family includes PspA a protein that suppresses sigma54-dependent transcription. The PspA protein, a negative regulator of the Escherichia coli phage shock psp operon, is produced when virulence factors are exported through secretins in many Gram-negative pathogenic bacteria and its homologue in plants, VIPP1, plays a critical role in thylakoid biogenesis, essential for photosynthesis. Activation of transcription by the enhancer-dependent bacterial sigma(54) containing RNA polymerase occurs through ATP hydrolysis-driven protein conformational changes enabled by activator proteins that belong to the large AAA(+) mechanochemical protein family. It has been shown that PspA directly and specifically acts upon and binds to the AAA(+) domain of the PspF transcription activator.
Pfam PF14544: Domain of unknown function (DUF4443) (domain)
This is a family of archaeal proteins. The domain is a putative gyrase domain.
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 PF24720: Family of unknown function (DUF7673) (domain)
This entry represents an uncharacterised family of proteins, which are typically between 100 and 122 amino acids in length. This protein is often found to be plasmid borne and in a few cases is associated with ParBc domains that are critical for plasmid segregation. This suggests that this domain may play a role in chromosome segregation or plasmid partitioning. Structural modelling suggests this domain will form a homodimeric complex.
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 PF16899: Cyclin C-terminal domain (domain)
Cyclins contain two domains of similar all-alpha fold, this family corresponds with the C-terminal domain of some cyclins including cyclin C and cyclin H.
Pfam PF10198: Histone acetyltransferases subunit 3 (family)
Ada3 is a family of proteins conserved from yeasts to humans. It is an essential component of the Ada transcriptional coactivator (alteration/deficiency in activation) complex. Ada3 plays a key role in linking histone acetyltransferase-containing complexes to p53 (tumour suppressor protein) thereby regulating p53 acetylation, stability and transcriptional activation following DNA damage.
Pfam PF04484: QWRF family (family)
AUG8 belongs to the plant QWRF motif-containing protein family, which also includes microtubule-associated protein ENDOSPERM DEFECTIVE 1 and SNOWY COTYLEDON 3. AUG8 binds the microtubule plus-end and participates in the reorientation of microtubules in hypocotyls (the stem of a germinating seedling).
Pfam PF21177: Leukemia inhibitory factor receptor, Ig-like domain (domain)
This domain is found in Leukemia inhibitory factor receptor from mouse (LIF-R) and similar proteins from animals. LIF-R binds a cytokine that acts on many cell types including embryonic stem cells, megakaryocytes, osteoblasts, and neuronal cells. The extracellular region of this protein shows a modular structure with two cytokine-binding modules (CBM, with [pfam:PF17971] representing the second subdomain of CBM1, D2) separated by an Ig-like domain (this entry) and followed by three membrane- proximal fibronectin type-III (FNIII) domains ([pfam:PF00041]) This domain interacts directly with site 3 of Cilliary Neutrophic Factor (CNTF).
Pfam PF23438: Domain of unknown function (DUF7123) (domain)
This domain is found in a group of proteins mainly from halobacteria. It is predicted to show an HTH 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 PF09078: CheY binding (domain)
Members of this family adopt a secondary structure consisting of an open-face beta/alpha sandwich, with four antiparallel beta-strands and two alpha-helices. They bind to a corresponding domain on CheY, with subsequent phosphorylation of the CheY Asp57 residue, and activation of CheY, which then affects flagellar rotation.
Pfam PF03843: Outer membrane lipoprotein Slp family (family)
Slp superfamily members are present in the Gram-negative gammaproteobacteria Escherichia coli (which also contains a close paralog), Haemophilus influenzae and Pasteurella multocida and Vibrio cholerae. The known members of the family to date share a motif LX[GA]C near the N terminus, which is compatible with the possibility that the protein is modified into a lipoprotein with Cys as the new N terminus. Slp from E. coli is known to be a lipoprotein of the outer membrane and to be expressed in response to carbon starvation .
Pfam PF16846: Centromere DNA-binding protein complex CBF3 subunit B (family)
Cep3 is one of the major components of the CBF3. It dimerises and in so doing forms a large central channel that is large enough to accommodate duplex B-form DNA. The dimerisation region is followed by a linker to the zinc-finger domain at the C-terminus. The CBF3 complex is an essential core component of the budding yeast kinetochore and is required for the centromeric localisation of all other kinetochore proteins. Cep3 is the only component with DNA-binding properties.
Pfam PF04417: Protein of unknown function (DUF501) (family)
Family of uncharacterised bacterial 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 PF12756: C2H2 type zinc-finger (2 copies) (family)
This family contains two copies of a C2H2-like zinc finger domain.
Pfam PF00111: 2Fe-2S iron-sulfur cluster binding domain (domain)
Ferredoxins are small, acidic, electron transfer proteins that are ubiquitous in biological redox systems. They have either 4Fe-4S, 3Fe-4S, or 2Fe-2S cluster. Among them, ferredoxin with one 2Fe-2S cluster per molecule are present in plants, animals, and bacteria, and form a distinct Ferredoxin family . They are proteins of around one hundred amino acids with four conserved cysteine residues to which the 2Fe-2S cluster is ligated. This conserved region is also found as a domain in various metabolic enzymes.

Several structures of the 2Fe-2S ferredoxin-type domain have been determined . The domain is classified as a Î²-grasp, which is characterised as having a Î²-sheet comprised of four Î²-strands and one Î±-helix flanking the sheet. The two Fe atoms are coordinated tetrahedrally by the two inorganic S atoms and four cysteinyl S atoms.
Wikipedia: 
Ferredoxins are iron–sulfur proteins that mediate electron transfer in a range of metabolic reactions. The term "ferredoxin" was coined by D.C. Wharton of the DuPont Co. and applied to the "iron protein" first purified in 1962 by Mortenson, Valentine, and Carnahan from the anaerobic bacterium Clostridium pasteurianum.
Pfam PF11348: Protein of unknown function (DUF3150) (family)
This bacterial family of proteins with unknown function appears to be restricted to Proteobacteria.
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 PF24275: T2SS substrate NttA (domain)
This entry represents the type II secretion system substrate NttA from Legionella pneumophila and related proteins found mainly in Legionellales species. Homologues of NttA are also found outside Legionella genus. NttA contains and N-terminal disordered region followed by a globular all-alpha helical domain consisting of four alpha-helices. NttA was shown to interact with phosphoinositides with a clear preference for phosphatidylinositol -3,5-biphosphate [PtdIns(3,5)P2]. NttA is likely targeted to host organelles, such as the Legionella containing vacuole, during intracellular infection.
Pfam PF11520: Chromatin protein Cren7 (family)
Cren7 is a chromatin protein found in Crenarchaeota and has a higher affinity for double-stranded DNA than for single-stranded DNA. The protein contains negative DNA supercoils and is associated with genomic DNA in vivo.Cren7 interacts with duplex DNA through a beta-sheet and a long flexible loop. The function has not been completely determined but it is thought that the protein may have a role similar to that of archaeal proteins in Euryarchaea.