SII-SWORD/CoKE huggingface dataset:
Pfam PF15775: Domain of unknown function (DUF4703) (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 149 and 210 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 PF21018: TypA/BipA C-terminal domain (domain)
This entry represents the C-terminal domain of the TypA/BipA protein. The C-terminal domain of BipA, consisting of residues, forms a unique motif with two crossed beta sheets (comprising of two and four beta-strands, respectively) wrapped by three short alpha helices forming a nearly equilateral triangle.
Pfam PF05698: Bacterial trigger factor protein (TF) C-terminus (family)
In the E. coli cytosol, a fraction of the newly synthesised proteins requires the activity of molecular chaperones for folding to the native state. The major chaperones implicated in this folding process are the ribosome-associated Trigger Factor (TF), and the DnaK and GroEL chaperones with their respective co-chaperones. Trigger Factor is an ATP-independent chaperone and displays chaperone and peptidyl-prolyl-cis-trans-isomerase (PPIase) activities in vitro. It is composed of three domains, an N-terminal domain which mediates association with the large ribosomal subunit (ribosome-binding domain, RBD), a central PPIase domain with homology to FKBP proteins, and a C-terminal substrate-binding domain (SBD) which forms the central body of the protein and has two helical arms that create a cavity. The association between its N-terminal domain with the ribosomal protein L23 located next to the peptide tunnel exit is essential for the interaction with nascent polypeptides and its in vivo function. This entry represents the C-terminal region of TF which has a multi-helical structure consisting of an irregular array of long and short helices structurally similar to the peptide-binding domain of the bacterial porin chaperone SurA.
Pfam PF14005: YpjP-like protein (family)
The YpjP-like protein family includes the B. subtilis YpjP protein [swissprot:P54172] which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 200 amino acids in length.
Pfam PF02703: Early E1A protein (family)
This is a family of adenovirus early E1A proteins.  The E1A protein is  32 kDa it can however be cleaved to yield the 28 kDa protein.  The E1A protein is responsible for the transcriptional activation of the early genes with in the viral genome at the start of the infection process as  well as some cellular genes.
Pfam PF13848: Thioredoxin-like domain (domain)
Wikipedia: The thioredoxin fold is a protein fold common to enzymes that catalyze disulfide bond formation and isomerization. The fold is named for the canonical example thioredoxin and is found in both prokaryotic and eukaryotic proteins. It is an example of an alpha/beta protein fold that has oxidoreductase activity. The fold's spatial topology consists of a four-stranded antiparallel beta sheet sandwiched between three alpha helices. The strand topology is 2134 with 3 antiparallel to the rest.
Pfam PF06309: Torsin (family)
This family consists of several eukaryotic torsin proteins. Torsion dystonia is an autosomal dominant movement disorder characterised by involuntary, repetitive muscle contractions and twisted postures. The most severe early-onset form of dystonia has been linked to mutations in the human DYT1 (TOR1A) gene encoding a protein termed torsinA. While causative genetic alterations have been identified, the function of torsin proteins and the molecular mechanism underlying dystonia remain unknown. Phylogenetic analysis of the torsin protein family indicates these proteins share distant sequence similarity with the large and diverse family of ([pfam:PF00004]) proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia.
Pfam PF23532: Apicomplexa microprotein (family)
This protein family includes uncharacterised microproteins encoded by small open reading frames (smORFs) from apicomplexa, including [swissprot:A7AVD2] from the parasite Babesia bovis.
Pfam PF14540: Nucleotidyltransferase-like (domain)
Structural comparisons with PDB:1kny indicate that this N-terminal domain resembles a nucleotidyltransferase fold.
Pfam PF10245: Mitochondrial 28S ribosomal protein S22 (family)
This is the conserved N-terminus and central portion of the mitochondrial small subunit 28S ribosomal protein S22. Mammalian mitochondria carry out the synthesis of 13 polypeptides that are essential for oxidative phosphorylation and, hence, for the synthesis of the majority of the ATP used by eukaryotic organisms. The number of proteins produced by prokaryotes is smaller, reflected in the lower number of ribosomal proteins present in them.
Pfam PF13787: Protein of unknown function with HXXEE motif (family)
This domain contains an HXXEE motif, another conserved histidine and a YXPG motif. Its function is unknown.
Pfam PF01921: tRNA synthetases class I (K) (family)
This family includes only lysyl tRNA synthetases from prokaryotes.
Pfam PF14243: ATP-grasp domain, R2K clade family 3 (domain)
Family of ATP-grasp enzymes belonging to the R2K clade, wherein one of the absolutely-conserved lysine residues has migrated to the RAGYNA domain which is a part of the core ATP-grasp module. This family is predicted to catalyze peptide ligation reactions on protein substrates in biological conflict contexts, probably between bacteriophages and their hosts.
Pfam PF17833: NIP7/UPF0113, pre-PUA domain (domain)
This entry represents the N-terminal, pre-PUA domain of yeast 60S ribosome subunit biogenesis protein NIP7 and homologues, some uncharacterised proteins from the UPF0113 family and similar sequences from eukaryotes and some archaeal species. NIP7 is required for proper 27S pre-rRNA processing and 60S ribosome subunit assembly. This domain is found associated with [pfam:PF03657].
Pfam PF13648: Lipocalin-like domain (domain)
The lipocalin fold is dominated by eight Î²-strands which together form a cup-shaped antiparallel Î²-barrel that encloses an internal ligand-binding site . This entry represents domains with a fold that is related to the to the lipocalin fold.
Wikipedia: The lipocalins are a family of proteins which transport small hydrophobic molecules such as steroids, bilins, retinoids, and lipids, and most lipocalins are also able to bind to complexed iron as well as heme. They share limited regions of sequence homology and a common tertiary structure architecture. This is an eight stranded antiparallel beta barrel with a repeated + 1 topology enclosing an internal ligand binding site.
Pfam PF08212: Lipocalin-like domain (domain)
Lipocalins are transporters for small hydrophobic molecules, such as lipids, steroid hormones, bilins, and retinoids. The structure is an eight-stranded beta barrel.
Wikipedia: The lipocalins are a family of proteins which transport small hydrophobic molecules such as steroids, bilins, retinoids, and lipids, and most lipocalins are also able to bind to complexed iron as well as heme. They share limited regions of sequence homology and a common tertiary structure architecture. This is an eight stranded antiparallel beta barrel with a repeated + 1 topology enclosing an internal ligand binding site.
Pfam PF19877: Family of unknown function (DUF6350) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 414 and 529 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 PF05029: Timeless PAB domain (domain)
The timeless (tim) gene is essential for circadian function in Drosophila. Putative homologues of Drosophila tim have been identified in both mice and humans (mTim and hTIM, respectively). Mammalian TIM is not the true orthologue of Drosophila TIM, but is the likely orthologue of a fly gene, timeout (also called tim-2). mTim has been shown to be essential for  embryonic development, but does not have substantiated circadian  function. This entry corresponds to the PAB (PARP-1-binding domain).
Wikipedia: Timeless (tim) is a gene in multiple species but is most notable for its role in Drosophila for encoding TIM, an essential protein that regulates circadian rhythm. Timeless mRNA and protein oscillate rhythmically with time as part of a transcription-translation negative feedback loop involving the period (per) gene and its protein.
Pfam PF02704: Gibberellin regulated protein (family)
This is the GASA gibberellin regulated cysteine rich protein family.  The expression of these proteins is up-regulated by the plant hormone gibberellin, most of these proteins have some role in plant development. There are 12 cysteine residues conserved within the alignment giving the potential for these proteins to posses 6 disulphide bonds.
Pfam PF01414: Delta serrate ligand (domain)
This family has been redefined to correspond to the EGF-like domain defined by structure.
Wikipedia: Notch proteins are a family of type 1 transmembrane proteins that form a core component of the Notch signaling pathway, which is highly conserved in animals. The Notch extracellular domain mediates interactions with DSL family ligands, allowing it to participate in juxtacrine signaling. The Notch intracellular domain acts as a transcriptional activator when in complex with CSL family transcription factors. Members of this type 1 transmembrane protein family share several core structures, including an extracellular domain consisting of multiple epidermal growth factor (EGF)-like repeats and an intracellular domain transcriptional activation domain (TAD). Notch family members operate in a variety of different tissues and play a role in a variety of developmental processes by controlling cell fate decisions. Much of what is known about Notch function comes from studies done in Caenorhabditis elegans (C.elegans) and Drosophila melanogaster. Human homologs have also been identified, but details of Notch function and interactions with its ligands are not well known in this context.
Pfam PF21923: BON-like domain (domain)
This entry represents BON-like domain that appears to lack the first alpha helix of the classical BON domain structure.
Pfam PF08049: IlvB leader peptide (family)
This family consists of the leader peptides of the ilvB operon. This region encodes a potential leader polypeptide containing 32 amino acids, 12 of which are the regulatory amino acids valine and leucine. A model for the multivalent regulation of this operon by valyl- and leucyl-tRNA is proposed on the basis of the mutually exclusive formation of five strong stem-and-loop structures in the leader mRNA.
Pfam PF00481: Protein phosphatase 2C (family)
Protein phosphatase 2C is a Mn++ or Mg++ dependent protein serine/threonine phosphatase.
Pfam PF03965: Penicillinase repressor (family)
The penicillinase repressor negatively regulates  expression of the penicillinase gene. The N-terminal region of this protein is involved in operator recognition, while the C-terminal is responsible for dimerisation of the  protein.
Pfam PF08392: FAE1/Type III polyketide synthase-like protein (family)
The members of this family are described as 3-ketoacyl-CoA synthases, type III polyketide synthases, fatty acid elongases and fatty acid condensing enzymes, and are found in both prokaryotic and eukaryotic (mainly plant) species. The region featured in this family contains the active site residues, as well as motifs involved in substrate binding.
Pfam PF24494: Domain of unknown function (DUF7587) (domain)
This domain is found in a group of uncharacterised proteins predominantly from fungi. It has a detectable similarity to ADP ribosyltransferase domains and it is predicted to adopt a similar 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 PF16249: Domain of unknown function (DUF4906) (family)
A family of uncharacterised proteins around 300 residues in length and found in various Bacteroides species. The function of this family is unknown.
Pfam PF10401: Interferon-regulatory factor 3 (family)
This is the interferon-regulatory factor 3 chain of the hetero-dimeric structure which also contains the shorter chain CREB-binding protein.  These two subunits make up the DRAF1 (double-stranded RNA-activated factor 1).          Viral dsRNA produced during viral transcription or replication leads to the activation of DRAF1. The DNA-binding specificity of DRAF1 correlates with transcriptional induction of ISG (interferon-alpha,beta-stimulated gene). IRF-3 preexists in the cytoplasm of uninfected cells and translocates to the nucleus following viral infection. Translocation of IRF-3 is accompanied by an increase in serine and threonine phosphorylation, and association with the CREB coactivator occurs only after infection.
Pfam PF04901: Receptor activity modifying family (family)
The calcitonin-receptor-like receptor can function as either a calcitonin-gene-related peptide or an adrenomedullin receptor. The receptors function is modified by receptor-activity-modifying  protein or RAMP. RAMPs are single-transmembrane-domain proteins.
Wikipedia: Receptor activity-modifying proteins (RAMPs) are a class of protein that interact with and modulate the activities of several Class B G protein-coupled receptors including the receptors for secretin, calcitonin (CT), glucagon, and vasoactive intestinal peptide (VIP). There are three distinct types of RAMPs in mammals, designated RAMP1, RAMP2, and RAMP3, each encoded by a separate gene.
Pfam PF16560: Putative mobile pathogenicity island (family)
SAPI is a family of putative Gram-positive mobile pathogenicity island proteins. SAPIs are responsible for many superantigen-related diseases in humans as they carry two or more superantigens.
Pfam PF20190: Family of unknown function (DUF6553) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, mainly Firmicutes and Actinobacteria. Proteins in this family are approximately 200 amino acids in length and contain the conserved motifs RY and DxF/Y
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 PF06478: Coronavirus RNA-dependent RNA polymerase, N-terminal (domain)
This domain covers the N-terminal region of the coronavirus RNA-directed RNA Polymerase which corresponds to the nonstructural protein 12 (NSP12) produced by cleavage of ORF1b. NSP12 contains a polymerase domain that assumes a structure resembling a cupped 'right hand', similar to other polymerases, containing a fingers domain, a palm domain and a thumb domain. Coronavirus NSP12 also contains a nidovirus-unique N-terminal extension (nidovirus RdRp-associated nucleotidyltransferase (NiRAN) that possesses a kinase-like fold allowing the binding of NSP12 to NSP7 and NSP8. NSP12 possesses some minimal activity on its own, but the addition of the NSP7 and NSP8 co-factors greatly stimulates polymerase activity. This domain represents the N-terminal region of the coronavirus RNA-directed RNA Polymerase, which includes the NiRAN and interface domains. The function of the NiRAN domain is not clear and its target is yet unknown, but it has enzymatic activity that is essential for viral propagation. Structure from SARS-CoV-2 revealed that this domain binds ADP-Mg+2, which may constitute a new pocket for anti-viral treatment development.
Pfam PF07066: Lactococcus phage M3 protein (family)
This family consists of several Lactococcus phage middle-3 (M3) proteins of around 160 residues in length. The function of this family is unknown.
Pfam PF23004: Histone-lysine N-methyltransferase NSD-like, variant PHD zinc finger (domain)
This domain is found in the NSD (nuclear receptor SET domain- containing) family of histone-lysine N-methyltransferase such as NSD1, NSD2, NSD3 and other related proteins. It is a variant of the classical PHD zinc finger containing a C4HC2H zinc finger-like motif which is distinct from the typical C4HC3 motif.
Pfam PF02664: S-Ribosylhomocysteinase (LuxS) (family)
This family consists of the LuxS protein involved in autoinducer AI2  synthesis and its hypothetical relatives. S-ribosylhomocysteinase (LuxS) catalyses the cleavage of the thioether bond in S-ribosylhomocysteine (SRH) to produce homocysteine and 4,5-dihydroxy-2,3-pentanedione (DPD), the precursor of type II bacterial quorum sensing molecule.
Wikipedia: The enzyme S-ribosylhomocysteine lyase catalyzes the reactionS-(5-deoxy-D-ribos-5-yl)-L-homocysteine = L-homocysteine + (4S)-4,5-dihydroxypentan-2,3-dione
Pfam PF09344: CT1975-like protein (family)
CRISPR is a term for Clustered, Regularly Interspaced Short Palidromic Repeats. A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins. This family is represented by CT1975 of Chlorobium tepidum.
Pfam PF17980: DNMT3, cysteine rich ADD domain, GATA1-like zinc finger (domain)
This is a C4-type GATA1-like zinc finger of a cysteine-rich domain termed ADD (ATRX-DNMT3-DNMT3L, AD-DATRX) found in animal DNMT3A proteins. The ADD domains of the DNMT3 family have a decisive role in blocking DNMT activity in the areas of the genome with chromatin containing methylated H3K4. This domain contains two parts, a GATA1-like and a PHD-like ([pfam:PF21255]) zinc fingers. The DNA methyltransferase (DNMT) 3 family members DNMT3A and the DNMT3-like non-enzymatic regulatory factor DNMT3L, are involved in de-novo establishment of DNA methylation patterns in early mammalian development.
Wikipedia: The PHD finger was discovered in 1993 as a Cys4-His-Cys3 motif in the plant homeodomain proteins HAT3.1 in Arabidopsis and maize ZmHox1a. 
The PHD zinc finger motif resembles the metal binding RING domain (Cys3-His-Cys4) and FYVE domain. It occurs as a single finger, but often in clusters of two or three, and it also occurs together with other domains, such as the chromodomain and the bromodomain.
Pfam PF13970: Domain of unknown function (DUF4221) (repeat)
This family of bacterial lipoproteins contain a beta propeller 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 PF00267: Gram-negative porin (domain)
Porins are found in the outer membranes of Gram-negative bacteria, mitochondria and chloroplasts, where they form ion-selective channels for small hydrophilic molecules (up to ~600 D) . X-ray structure analyses of several bacterial porins  have revealed a large 16-stranded anti-parallel Î²-barrel structure enclosing the transmembrane pore, by contrast with all other integral membrane proteins described to date, which are Î±-helical. Three subunits form a trimer; the 3-fold axis is approximately parallel to the barrel axes and is assumed to be perpendicular to the membrane plane.

From the range of porins now known, similarities have been observed between porins from different species, and between porins of different specificity within the same species. But most porins cannot be related to each other on the basis of sequence alone, and this is reflected in the lengths of the known porin sequences, which range from 282-483 residues/monomer.
This entry represents porins from Gram-negative bacteria.
Wikipedia: General bacterial porins are a family of porin proteins from the outer membranes of Gram-negative bacteria. The porins act as molecular filters for hydrophilic compounds. They are responsible for the 'molecular sieve' properties of the outer membrane. Porins form large water-filled channels which allow the diffusion of hydrophilic molecules into the periplasmic space. Some porins form general diffusion channels that allow any solute up to a certain size to cross the membrane, while other porins are specific for one particular solute and contain a binding site for that solute inside the pores. As porins are the major outer membrane proteins, they also serve as receptor sites for the binding of phages and bacteriocins.
Pfam PF18811: Dipeptidyl peptidase IV (DPP IV) low complexity region (repeat)
Dipeptidyl peptidase IV includes an helical N-terminal region, the [pfam:PF00930] domain and the [pfam:PF00326] domain, comprising the  active site. This Pfam entry represents a sequence that can be  repeated in the low complexity region between the helical N-terminus and the DPPIV_N domain.
Pfam PF05209: Septum formation inhibitor MinC, N-terminal domain (domain)
In Escherichia coli [swissprot:P06138] assembles into a Z ring at midcell while assembly at polar sites is prevented by the min system. MinC [swissprot:P18196] a component of this system, is an inhibitor of FtsZ assembly that is positioned within the cell by interaction with MinDE. MinC is an oligomer, probably a dimer. The C terminal half of MinC is the most conserved and interacts with MinD.  The N terminal half is thought to interact with FtsZ.
Pfam PF12999: Glucosidase II beta subunit-like (family)
The sequences found in this family are similar to a region found in the beta-subunit of glucosidase II ([swissprot:P14314]), which is also known as protein kinase C substrate 80K-H (PRKCSH). The enzyme catalyses the sequential removal of two alpha-1,3-linked glucose residues in the second step of N-linked oligosaccharide processing. The beta subunit is required for the solubility and stability of the heterodimeric enzyme, and is involved in retaining the enzyme within the endoplasmic reticulum.
Pfam PF01307: Plant viral movement protein (family)
This family includes several known plant viral movement proteins (e.g. [swissprot:Q85292]) from a number of different ssRNA plant virus families including potexviruses, hordeiviruses and carlaviruses.