SII-SWORD/CoKE huggingface dataset:
Pfam PF15339: Acrosome formation-associated factor (family)
Afaf is a family of single pass type I membrane proteins. Afaf is a vesicle factor derived from the early endosome trafficking pathway that is involved in the biogenesis of the acrosome on the maturing spermatozoon head.
Pfam PF19804: Domain of unknown function (DUF6287) (domain)
This presumed domain, found in bacteria, is functionally uncharacterised. It is around 50 amino acids in length and contains a conserved GTW 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 PF08338: Domain of unknown function (DUF1731) (family)
This domain of unknown function appears towards the C-terminus of proteins of the NAD dependent epimerase/dehydratase family ([pfam:PF01370]) in bacteria, eukaryotes and archaea.  Many of the proteins in which it is found are involved in cell-division inhibition.
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 PF10199: Alpha and gamma adaptin binding protein p34 (family)
p34 is a protein involved in membrane trafficking.  It is known to interact with both alpha and gamma adaptin.  It has been speculated that p34 may play a chaperone role such as preventing the soluble adaptors from co-assembling with soluble clathrin, or helping to remove the adaptors from the coated vesicle. Another possible function is in aiding the recruitment of soluble adaptors onto the membrane.
Pfam PF15711: Interleukin-like EMT inducer (domain)
ILEI is a family of proteins found in vertebrates. It is heavily involved in the process of the transition from epithelial to mesenchymal tissue - EMT - during all of embryonic development, cancer progression, metastasis, and chronic inflammation/fibrosis. ILEI is upregulated exclusively at the level of translation, and abnormal ILEI expression, ie cytoplasmic over-expression instead of vesicular localisation, is associated with EMT in human cancerous tissue. In order to induce and maintain the EMT of hepatocytes in a TGF-beta-independent fashion ILEI needs the cooperation of oncogenic Ras.
Pfam PF03840: Preprotein translocase SecG subunit (family)
Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component . From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins. The translocase protein subunits are encoded on the bacterial chromosome.

The translocase itself comprises 7 proteins, including a chaperone protein (SecB), an ATPase (SecA), an integral membrane complex (SecCY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) . The chaperone protein SecB  is a highly acidic homotetrameric protein that exists as a "dimer of dimers" in the bacterial cytoplasm. SecB maintains preproteins in an unfolded state after translation, and targets these to the peripheral membrane protein ATPase SecA for secretion . Together with SecY and SecG, SecE forms a multimeric channel through which preproteins are translocated, using both proton motive forces and ATP-driven secretion. The latter is mediated by SecA.
Wikipedia: Sec61, termed SecYEG in prokaryotes, is a membrane protein complex found in all domains of life. As the core component of the translocon, it transports proteins to the endoplasmic reticulum in eukaryotes and out of the cell in prokaryotes. It is a doughnut-shaped pore through the membrane with 3 different subunits (heterotrimeric), SecY (α), SecE (γ), and SecG (β). It has a region called the plug that blocks transport into or out of the ER. This plug is displaced when the hydrophobic region of a nascent polypeptide interacts with another region of Sec61 called the seam, allowing translocation of the polypeptide into the ER lumen.
Pfam PF11470: TUG ubiquitin-like domain (family)
TUG is a GLUT4 regulating protein and functions to retain membrane vesicles containing GLUT4 intracellularly. TUG releases the GLUT4 containing vesicles to the cellular exocytic machinery in response to insulin stimulation which allows translocation to the plasma membrane. TUG has an N-terminal ubiquitin-like domain (UBL1) which in similar proteins appears to participate in protein-protein interactions. The region does have a area of negative electrostatic potential and increased backbone motility which leads to suggestions of a potential protein-protein interaction site. This domain is also found at the N-terminus of yeast UBX4.
Wikipedia: In molecular biology, TUG-UBL1 refers to a protein that regulates a glucose transporter called GLUT4. TUG-UBL1 is an acronym for Tether containing UBX domain for GLUT4-Ubiquitin Like 1, this is encoded for by the gene, ASPSCR1.
Pfam PF12266: Protein of unknown function (DUF3613) (family)
This family of proteins is found in bacteria. Proteins in this family are typically between 94 and 126 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 PF14675: FANCI solenoid 1 (repeat)
This is the solenoid 1 (S1) domain of the Fanconi anemia group I protein.
Pfam PF08565: Cdc37 Hsp90 binding domain (domain)
Cdc37 is a molecular chaperone required for the activity of numerous eukaryotic protein kinases.  This domains corresponds to the Hsp90 chaperone (Heat shocked protein 90) binding domain of Cdc37.  It is found between the N terminal Cdc37 domain [pfam:PF03234], which is predominantly involved in kinase binding, and the C terminal domain of Cdc37 [pfam:PF08564] whose function is unclear.
Wikipedia: Hsp90 co-chaperone Cdc37 is a protein that in humans is encoded by the CDC37 gene. This protein is highly similar to Cdc 37, a cell division cycle control protein of Saccharomyces cerevisiae. This protein is a HSP90 Co-chaperone with specific function in cell signal transduction. It has been shown to form complex with Hsp90 and a variety of protein kinases including CDK4, CDK6, SRC, RAF1, MOK, as well as eIF-2 alpha kinases. It is thought to play a critical role in directing Hsp90 to its target kinases.
Pfam PF02209: Villin headpiece domain (domain)
Villin is an F-actin bundling protein involved in the maintenance of the microvilli of the absorptive epithelia. The villin-type "headpiece" domain is a modular motif found at the extreme C terminus of larger "core" domains in over 25 cytoskeletal proteins in plants and animals, often in assocation with the Gelsolin repeat. Although the headpiece is classified as an F-actin-binding domain, it has been shown that not all headpiece domains are intrinsically F-actin-binding motifs, surface charge distribution may be an important element for F-actin recognition . An autonomously folding, 35 residue, thermostable subdomain (HP36) of the full-length 76 amino acid residue villin headpiece, is the smallest known example of a cooperatively folded domain of a naturally occurring protein. The structure of HP36, as determined by NMR spectroscopy, consists of three short helices surrounding a tightly packed hydrophobic core .
Wikipedia: Villin-1 is a 92.5 kDa tissue-specific actin-binding protein associated with the actin core bundle of the brush border. Villin-1 is encoded by the VIL1 gene. Villin-1 contains multiple gelsolin-like domains capped by a small "headpiece" at the C-terminus consisting of a fast and independently folding three-helix bundle that is stabilized by hydrophobic interactions. The headpiece domain is a commonly studied protein in molecular dynamics due to its small size and fast folding kinetics and short primary sequence.
Pfam PF24135: Domain of unknown function (DUF7402) (domain)
This entry represents the domain of unknown function found in bacterial and fungal sequences, including some F5/8 type C domain-containing proteins such as Swissprot:A0A4V0YDU8. This domain may adopt a galactose-binding domain-like fold. This domain is found in several copies, predominantly between two and six times, and it is found in association with PIG-L ([pfam:PF02585]) 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 PF12554: Mitotic-spindle organizing gamma-tubulin ring associated (family)
The name MOZART is derived from letters of 'mitotic-spindle organizing proteins associated with a ring of gamma-tubulin'. This family operates as part of the gamma-tubulin ring complex, gamma-TuRC, one of the complexes necessary for chromosome segregation. This complex is located at centrosomes and mediates the formation of bipolar spindles in mitosis; it consists of six subunits. However, unlike the other four known subunits, this family does not carry the conserved 'Spc97-Spc98' GCP domain, so the TUBCGP nomenclature cannot be used for it. MOZART1 is required for gamma-TuRC recruitment to centrosomes.
Pfam PF21960: RCF1/5-like, AAA+ ATPase lid domain (domain)
Sliding clamps are DNA-tracking platforms that are essential for processive DNA replication and it is carried out by a five-protein clamp loader complex, the replication factor-C (RFC) complex. RFC forms a stable ATP-dependent complex with the eukaryotic sliding clamp, PCNA, which binds specifically to primed DNA. These proteins share the same domain architecture consisting of a AAA+ ATPase, a lid domain and a C-terminal helical domain. This entry represents the AAA+ ATPase lid from RFC proteins, such as RFC5 from yeast.
Pfam PF18671: 4-Hydroxyphenylacetate decarboxylase subunit gamma N-terminal (domain)
4-Hydroxyphenylacetate decarboxylase (4-HPAD) is a heterotetramer consisting of catalytic beta-subunit harboring the putative glycyl/thiyl dyad and a distinct small gamma-subunit with two [4Fe-4S] clusters ([ec:4.1.1.83]). The gamma-subunit is proposed to be involved in the regulation of the oligomeric state and catalytic activity of the enzyme and it comprises two domains with some amino acid sequence identity that are structurally related by a pseudo-2-fold symmetry indicating a gene duplication origin. This entry represents the N-terminal domain which binds one [4Fe-4S] cluster through His3, Cys6, Cys19, and Cys36.
Wikipedia: High potential iron-sulfur proteins (HIPIP) are a class of iron-sulfur proteins. They are ferredoxins that participate in electron transfer in photosynthetic bacteria as well as in Paracoccus denitrificans.
Pfam PF23345: Nucleoporin NUP160, helical domain (domain)
This entry represents the central helical domain of NUP160, which is found in animals, including humans, mice, and Drosophila melanogaster. NUP160 is one of up to 60 proteins that constitute the Nuclear Pore Complex (NPC) as a component of the NUP107-160 subcomplex. NUP160, in conjunction with NUP133, interacts with NUP98 and NUP153, mediating mRNA export. NUP160 mutations have been associated with Steroid-Resistant Nephrotic Syndrome (SRNS). Silencing Drosophila NUP160 specifically in nephrocytes results in functional abnormalities, reduced cell size and nuclear volume, as well as a disorganised nuclear membrane structure.
Pfam PF23209: Increased DNA methylation 1, C-terminal (domain)
This domain is found at the C-terminal of Increased DNA methylation 1 (IDM1) from Arabidopsis thaliana and similar plant proteins. IDM1 is a histone H3 acetyltransferase that binds methylated DNA at chromatin sites lacking histone H3K4 di- or trimethylation and catalyses H3K18 and H3K23 acetylation.
Pfam PF09222: Fimbrial adhesin F17-AG, lectin domain (domain)
Members of this family are carbohydrate-specific lectin domains found in bacterial fimbrial adhesins. They adopt a compact, elongated structure consisting of a beta-sandwich with two major sheets: one consisting of five long strands in mixed orientations, and a front sheet with four antiparallel strands, forming an immunoglobin-like fold.
Pfam PF14285: Domain of unknown function (DUF4367) (domain)
This family of proteins is found in bacteria, archaea and eukaryotes. Proteins in this family are typically between 229 and 435 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 PF01883: Iron-sulfur cluster assembly protein (domain)
This family has an alpha/beta topology, with 13 conserved hydrophobic residues at its core and a putative active site containing a highly conserved cysteine. Members of this family are involved in a range of physiological functions. The family includes PaaJ (PhaH) [swissprot:O84984] from Pseudomonas putida. PaaJ forms a complex with PaaG (PhaF) [swissprot:O84982], PaaI (PhaG) [swissprot:O84983] and PaaK (PhaI) [swissprot:O84985], which hydroxylates phenylacetic acid to 2-hydroxyphenylacetic acid. It also includes PaaD [swissprot:P76080] from Escherichia coli, a member of a multicomponent oxygenase involved in phenylacetyl-CoA hydroxylation. Furthermore, several members of this family are shown to be involved in iron-sulfur (FeS) cluster assembly. Iron-sulfur (FeS) clusters are inorganic co-factors that are are able to transfer electrons and act as catalysts. They are involved in diverse cellular processes including cellular respiration, DNA replication and repair, antibiotic resistance, and dinitrogen fixation. The biogenesis of such clusters from elemental iron and sulfur is an enzymatic process that requires a set of specialised proteins. Proteins containing this domain include the chloroplast protein HCF101 (high chlorophyll fluorescence 101), [swissprot:Q6STH5], which has been described as an essential and specific factor for assembly of [4Fe-4S]-cluster-containing protein complexes such as the membrane complex Photosystem I (PSI) and the heterodimeric FTR (ferredoxin-thioredoxin reductase) complex and is involved in the assembly of [4Fe-4S] clusters and their transfer to apoproteins. The mature HCF101 protein contains this domain at the N-terminal as well as eight cysteine residues along the sequence.  All cysteine residues are conserved among higher plants, but of the two cysteine residues located in this domain only Cys128 is highly conserved and is present in the highly conserved P-loop domain of the plant HCF101 (CKGGVGKS). SufT protein from Staphylococcus aureus is composed of this domain solely and is shown to be involved in the maturation of FeS proteins. Given all this data, it is hypothesised that this domain might play a role in FeS cluster assembly.
Pfam PF00390: Malic enzyme, N-terminal domain (domain)
This entry represents the N-terminal domain of the NAD(P)-dependent malic enzyme and related proteins from bacteria, eukaryotes and archaea.
Malic enzymes (malate oxidoreductases) catalyse the oxidative decarboxylation of malate to form pyruvate, a reaction important in a number of metabolic pathways - e.g. carbon dioxide released from the reaction may be used in sugar production during the Calvin cycle of photosynthesis . There are 3 forms of the enzyme : an NAD-dependent form that decarboxylates oxaloacetate; an NAD-dependent form that does not decarboxylate oxalo-acetate; and an NADPH-dependent form . Other proteins known to be similar to malic enzymes are the Escherichia coli scfA protein; an enzyme from Zea mays (Maize), formerly thought to be cinnamyl-alcohol dehydrogenase ; and the hypothetical Saccharomyces cerevisiae protein YKL029c.

Studies on the duck liver malic enzyme reveals that it can be alkylated by bromopyruvate, resulting in the loss of oxidative decarboxylation and the subsequent enhancement of pyruvate reductase activity . The alkylated form is able to bind NADPH but not L-malate, indicating impaired substrate or divalent metal ion-binding in the active site . Sequence analysis has highlighted a cysteine residue as the point of alkylation, suggesting that it may play an important role in the activity of the enzyme , although it is absent in the sequences from some species.

Malic enzyme is a tetramer comprised of subunits with four domains each .
Pfam PF00131: Metallothionein (domain)
Metallothioneins (MT) are small proteins that bind heavy metals, such as zinc, copper, cadmium, nickel, etc. They have a high content of cysteine residues that bind the metal ions through clusters of thiolate bonds . An empirical classification into three classes has been proposed by Fowler and coworkers  and Kojima . Members of class I are defined to include polypeptides related in the positions of their cysteines to equine MT-1B, and include mammalian MTs as well as from crustaceans and molluscs. Class II groups MTs from a variety of species, including sea urchins, fungi, insects and cyanobacteria. Class III MTs are atypical polypeptides composed of gamma-glutamylcysteinyl units .

This original classification system has been found to be limited, in the sense that it does not allow clear differentiation of patterns of structural similarities, either between or within classes. Subsequently, a new classification was proposed on the basis of sequence similarity derived from phylogenetic relationships, which basically proposes an MT family for each main taxonomic group of organisms .
The members of family 1 are recognised by the sequence pattern K-x(1,2)-C-C-x-C-C-P-x(2)-C located at the beginning of the third exon. The taxonomic range of the members extends to vertebrates. Known characteristics: 60 to 68 AAs; 20 Cys (21 in one case), 19 of them are totally conserved; the protein sequence is divided into two structural domains, containing 9 and 11 Cys all binding 3 and 4 bivalent metal ions, respectively.
Wikipedia: Metallothionein (MT) is a family of cysteine-rich, low molecular weight proteins. They are localized to the membrane of the Golgi apparatus. MTs have the capacity to bind both physiological and xenobiotic heavy metals through the thiol group of its cysteine residues, which represent nearly 30% of its constituent amino acid residues.
Pfam PF06974: WS/DGAT C-terminal domain (domain)
This domain is found at the C-terminus of wax ester synthases (WS)/diacylglycerol O-acyltransferases (DGAT). These enzymes are utilised for the in vivo production of biodiesel and other wax esters.
Pfam PF10869: Domain of unknown function (DUF2666) (domain)
This domain found in archaeal proteins, including PF2050 from Pyrococcus furiosus ([swissprot:Q8TZE5]). PF2050, with an overall globular structure, contain this domain twice, each showing an antiparallel beta-sheet and an alpha-helical bundle, and shows a positively charged basic cleft on one side. This protein interacts with circular and linear dsDNA.
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 PF03213: Poxvirus P35 protein (family)
The Poxvirus P35 protein is an immunodominant envelope protein also known as Envelope protein OPG108. It binds to heparan sulphate on the cell surface to provide virion attachment to target cell .
Pfam PF21680: tRNA modifying enzyme MnmG/GidA C-terminal helical domain (domain)
The GidA associated domain is a domain that has been identified at the C-terminus of protein GidA. It consists of several helices, the last three being rather short and forming small bundle. GidA is an tRNA modification enzyme found in bacteria and mitochondrial. Based on mutational analysis this domain has been suggested to be implicated in binding of the D-stem of tRNA and, in particular the small bundle, to be responsible for the interaction with protein MnmE. Structures of GidA in complex with either tRNA or MnmE are missing. Reported to bind to Pfam family MnmE, [pfam:PF12631]. This entry represents the first helices of the GidA associated domain. The last three helices are covered in [pfam:PF13932].
Pfam PF20869: FAM186A, PQQAQ repeat (repeat)
This entry represents a short repeat found in protein FAM186A from human and related sequences from mammals. These repeats form a long alpha-solenoid structure, in which each repeat forms a single alpha- helix, characterised by PQQAQ sequence.
Pfam PF13427: Aminoglycoside adenylyltransferase, C-terminal domain (domain)
This domain is found at the C-terminal end of Aminoglycoside adenylyltransferase from Salmonella typhimurium (AadA) and other proteins associated with methicillin-resistant bacteria. AadA adenylates the 3''-hydroxyl group of the streptomycin glucosamine ring and the 9-hydroxyl group of the spectinomycin actinamine ring, mediating bacterial resistance to these antibiotics. This enzyme is organised into two domains: a N-terminal domain with a nucleotidyltransferase fold ([pfam:PF01909]) and a C-terminal domain (this entry) which consists of five alpha-helices forming an up-and-down alpha-helical bundle. This domain undergoes small conformational changes upon binding of ATP and magnesium that play a key role in the binding of the antibiotic compounds.
Pfam PF18481: Domain of unknown function (DUF5616) (domain)
This domain is found in a number of prokaryotic proteins. It is mostly found fused with the N-terminal domain [pfam:PF04256]. This C-terminal domain is suggested to be a PIN like 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 PF16141: Glycoside hydrolase family 18, BT1044-like (family)
This family of glycosyl hydrolases (GH) from CAZy family 18 is mainly found in Bacteroidetes, including the endoglycosidase BT1044 from Bacteroides thetaiotaomicron. This protein folds into the canonical (beta/alpha)8 barrel (TIM barrel) fold common to many GH structures.
Pfam PF00547: Urease, gamma subunit (domain)
Urease is a nickel-binding  enzyme that  catalyses the hydrolysis of  urea  to  carbon  dioxide and ammonia.