SII-SWORD/CoKE huggingface dataset:
Pfam PF07221: N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase) (repeat)
This family contains a number of eukaryotic and bacterial N-acylglucosamine 2-epimerase (GlcNAc 2-epimerase) enzymes ([ec:5.1.3.8]) approximately 500 residues long. This converts N-acyl-D-glucosamine to N-acyl-D-mannosamine.
Wikipedia: In enzymology, a N-acylglucosamine 2-epimerase is an enzyme that catalyzes the chemical reactionN-acyl-D-glucosamine  N-acyl-D-mannosamine
Pfam PF05348: Proteasome maturation factor UMP1 (family)
UMP1 is a short-lived chaperone present in the precursor form of the 20S proteasome and absent in the mature complex. UMP1 is required for the correct assembly and enzymatic activation of the proteasome. UMP1 seems to be degraded by the proteasome upon its formation
Pfam PF00500: L1 (late) protein (domain)
This entry represents the major late capsid protein L1 from Papillomaviruses, such as Human papillomavirus (HPV) . Papillomaviruses are members of the papovavirus superfamily. More than 70 different types of papillomavirus have been discovered in humans, some of which have been shown to cause genital carcinomas and cutaneous warts . The viruses contain a circular dsDNA genome surrounded by an icosahedral capsid (non-enveloped). Two proteins are involved in capsid formation: a major (L1) and a minor (L2) protein, in the approximate proportion 95:5%. L1 forms a pentameric assembly unit of the viral shell in a manner that closely resembles VP1 from polyomaviruses. Intermolecular disulphide bonding holds the L1 capsid proteins together . L1 capsid proteins can bind via its nuclear localisation signal (NLS) to karyopherins Kapbeta(2) and Kapbeta(3) and inhibit the Kapbeta(2) and Kapbeta(3) nuclear import pathways during the productive phase of the viral life cycle . Surface loops on L1 pentamers contain sites of sequence variation between HPV types.
Wikipedia: A late protein is a viral protein that is formed after replication of the virus. One example is VP4 from simian virus 40 (SV40).
Pfam PF03845: Spore germination protein (family)
Amino acid permeases are integral membrane proteins involved in the transport of amino acids into the cell. A number of such proteins have been found to be evolutionary related . These proteins seem to contain up to 12 transmembrane segments. The best conserved region in this family is located in the second transmembrane segment.

Spore germination protein (amino acid permease) is involved in the response to the germinative mixture of L-asparagine, glucose, fructose and potassium ions (AFFK). These proteins could be amino acid transporters.
Pfam PF22799: Cell wall mannoprotein PIR1-like, C-terminal domain (domain)
This entry represents a presumed domain found at the C-terminal of fungal Cell wall mannoproteins, including PIR1, CIS3 and PIR5 from S.  cerevisiae. These proteins are part of the outer cell wall layer, required for stability of the cell wall and for optimal growth. This domain has a beta trefoil fold and may suggest these domains have a sugar binding lectin function.
Pfam PF12680: SnoaL-like domain (domain)
This family contains a large number of proteins that share the SnoaL fold.
Pfam PF11501: Betacoronavirus replicase NSP1 (family)
This entry represents the non structural protein NSP1 from Betacoronavirus NSP1 is the N-terminal cleavage product from the viral replicase that mediates RNA replication and processing. Structurally, the protein consists of a mixed parallel/antiparallel 6-stranded beta barrel with an alpha helix covering one end of the barrel and another helix alongside the barrel. NSP1 binds to the 40S ribosomal subunit and inhibits translation, and it also induces a template-dependent endonucleolytic cleavage of host mRNAs. NSP1 also suppresses the host innate immune functions by inhibiting type I interferon expression and host antiviral signalling pathways.
Pfam PF17630: Family of unknown function (DUF5511) (family)
This is a family of unknown function found in Bacillus.
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 PF07824: Type III secretion chaperone domain (domain)
Type III secretion chaperones are involved in delivering virulence effector proteins from  bacterial pathogens directly into eukaryotic cells. The chaperones may prevent aggregation and degradation of their substrates, may target the effector to the  secretion apparatus, and may ensure a secretion-component unfolded confirmation of their specific substrate. One member of this family, SigE ([swissprot:O30917]) forms  homodimers in crystal. The monomers have a novel fold  with an alpha-beta(3)-alpha-beta(2)-alpha topology.
Pfam PF05685: Putative restriction endonuclease (family)
This entry includes a group of putative nuclease, including hypothetical protein TT1808 (also known as Uma2 or TTHA1514), an AT-rich DNA-binding protein from Thermus thermophilus. This domain has a 3-layer alpha/beta/alpha topology similar to that found in restriction endonucleases. The nuclease domain is ubiquitously found in enzymes involved in metabolism of nucleic acids, mostly in nucleases with diverse biological functions.
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 PF06307: Herpesvirus IR6 protein (family)
This family consists of several Herpesvirus IR6 proteins. The equine herpesvirus 1 (EHV-1) IR6 protein forms typical rod-like structures in infected cells, influences virus growth at elevated temperatures, and determines the virulence of EHV-1 Rac strains.
Pfam PF20338: Family of unknown function (DUF6633) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 148 and 213 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 PF10156: Subunit 17 of Mediator complex (family)
This Mediator complex subunit was formerly known as Srb4 in yeasts or Trap80 in Drosophila and human. The Med17 subunit is located within the head domain and is essential for cell viability to the extent that a mutant strain of cerevisiae lacking it shows all RNA polymerase II-dependent transcription ceasing at non-permissive temperatures.
Wikipedia: Mediator of RNA polymerase II transcription subunit 17 is an enzyme that in humans is encoded by the MED17 gene.
Pfam PF09411: Lipid A 3-O-deacylase (PagL) (family)
PagL is an outer membrane protein with lipid A 3-O-deacylase activity. It forms an 8 stranded beta barrel structure.
Wikipedia: Lipid A deacylase (PagL)  is an outer membrane protein with lipid A 3-O-deacylase activity. It forms an 8 stranded beta barrel structure.
Pfam PF19816: Family of unknown function (DUF6299) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000376) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide), in  particular JBIR-34 biosynthetic gene cluster from Streptomyces  sp. Sp080513GE-23. 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 PF25143: IFT122, C-terminal zinc ribbon domain (domain)
This zinc ribbon domain is found C-terminal in the Intraflagellar transport protein 122 and related proteins. IFT122 is one of the core components (together with WDR19/IFT144 and IFT140) of the IFT-A complex which is required for retrograde ciliary transport and entry into cilia of G protein-coupled receptors (GPCRs), being involved in cilia function and/or assembly. IFT-A polymerises interacts with IFT-B, and uses an array of beta-propeller and TPR domains to create 'carriages' of the IFT train that engage TULP adaptor proteins. IFT122 contains to zinc ribbon domains toward the C-terminus. This one is the second of the pair.
Pfam PF23828: Family of unknown function (DUF7198) (family)
This entry represents a family of putative phage membrane proteins. It is characterized by a single transmembrane helix at the N-terminus that likely serves to anchor these proteins to the membrane. The exact functions of the proteins containing this domain remain 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 PF14558: ML-like domain (domain)
This domain is distantly similar to [pfam:PF02221] and conserves its pattern of conserved cysteines. This suggests that this domain may be involved in lipid binding.
Pfam PF24492: Proteasome adapter and scaffold protein ECM29, HEAT-repeat domain (repeat)
This entry represents a HEAT-repeat domain found in ECM29, an adapter/scaffolding protein that binds to the 26S proteasome, motor proteins and other compartment specific proteins. This domain is found in the C-terminal half of ECM29, which binds kinesin and myosin.
Pfam PF15325: Modulator of retrovirus infection (family)
MRI, or modulator of retrovirus infection, is a family of eukaryotic proteins that regulate the activity of the proteasome in the uncoating of retroviruses.
Pfam PF15142: INCA1 (family)
This family of proteins inhibits cyclin-dependent kinase activity.
Pfam PF03468: XS domain (domain)
The XS (rice gene X and SGS3) domain is found in a family of plant proteins including gene X [swissprot:Q9SBW2] and SGS3 [swissprot:Q9LDX1].  SGS3 is thought to be involved in post-transcriptional gene silencing (PTGS). This domain contains a conserved aspartate residue that may be functionally important. The XS domain has recently been predicted to possess an RRM-like RNA-binding domain by fold recognition.
Pfam PF21699: Iron-only hydrogenase system regulator, putative (family)
This protein family includes Iron-only hydrogenase system regulator, putative from Thermotoga maritima (TM1266) and similar bacterial proteins. Members of this family are thought to play a role as a transcription factor.
Pfam PF00566: Rab-GTPase-TBC domain (family)
Identification of a TBC domain in GYP6_YEAST and GYP7_YEAST, which are GTPase activator proteins of yeast Ypt6 and Ypt7, implies that these domains are GTPase activator proteins of Rab-like small GTPases.
Wikipedia: The TBC domain is an evolutionarily conserved protein domain found in all eukaryotes. It is approximately 180 to 200 amino acids long. The domain is named for its initial discovery in the proteins Tre-2, Bub2, and Cdc16.
Pfam PF24442: Family of unknown function (DUF7561) (family)
This entry represents a small family of uncharacterised proteins found in archaea. They contain two pairs of conserved cysteines that are likely involved in metal coordination. These proteins are predicted to structurally resemble treble-clef zinc fingers.
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 PF12829: Transcriptional regulation of mitochondrial recombination (family)
This family is involved in the transcriptional regulation of recombination in the mitochondria,
Pfam PF11185: Protein of unknown function (DUF2971) (family)
This bacterial family of proteins has no known function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF00812: Ephrin (domain)
Ephrins are a family of proteins  that are ligands of class V (EPH-related) receptor protein-tyrosine kinases. Initially identified as regulators of axon pathfinding and neuronal cell migration, the Eph receptors and their ephrin ligands are now known to have roles in many other cell-cell interactions, including those of vascular endothelial cells and specialised epithelia .

Ephrins are membrane-attached proteins of 205 to 340 residues. Attachment appears to be crucial for their normal function. Type-A ephrins are linked to the membrane via a GPI linkage, while type-B ephrins are type-I membrane proteins.

The globular ephrin receptor-binding domain (ephrin RBD) is a Î² barrel composed of eight strands arranged in two sheets around a hydrophobic core. Interspersed between Î² strands are two Î± helices and one 3(10) helix. The sheets are composed of mixed parallel and antiparallel Î² strands arranged in a Greek key topology. Like other cell-surface proteins, ephrins contain disulfide bonds to enhance stability. Two buried disulfide bonds are present: one pair holds together Î² strands C and F, and the other pair anchors two small helices, E and I, at the top of the barrel .
Wikipedia: Ephrins are a family of proteins that serve as the ligands of the Eph receptor. Eph receptors in turn compose the largest known subfamily of receptor protein-tyrosine kinases (RTKs).
Pfam PF15297: Cytoskeleton-associated protein 2 C-terminus (family)
This family includes the C-terminus of CKAP2 and CKAP2L. CKAP2 is a microtubule associated protein which stabilises microtubules.
Pfam PF10022: Uncharacterized protein conserved in bacteria (DUF2264) (repeat)
Members of this family of hypothetical bacterial proteins have no known function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF15908: Hyaluronan mediated motility receptor C-terminal (coiled_coil)
HMMR_C is the C-terminal region of eukaryotic hyaluronan-mediated motility receptor proteins. The protein is functionally associated with BRCA1 and thus predicted to be a common, low-penetrance breast cancer candidate.
Pfam PF12798: 4Fe-4S binding domain (domain)
This superfamily includes proteins containing domains which bind to iron-sulfur clusters. Members include bacterial ferredoxins, various dehydrogenases, and various reductases.  Structure of the domain is an alpha-antiparallel beta sandwich.
Pfam PF10005: zinc-ribbon domain (domain)
This family appears to be a true zinc-ribbon, with two sets of putative zinc-binding domains in tandem.
Pfam PF23228: PCFS4 zinc finger domain (domain)
This zinc finger domain is found in the homologues of Polyadenylation and cleavage factor homolog 4 (PCFS4) including PCFS1 and PCFS5. PCFS4 is known to promote flowering suppressing FLC-mediated inhibition of flowering through the regulation of FCA pre-mRNA alternative processing. This protein regulates mRNA maturation including alternative polyadenylation, splicing or transcription initiation of stress-associated genes. This domain contains three highly conserved cysteine residues and histidine. Its structure is predicted to be similar to known Treble clef zinc finger domains.
Pfam PF23957: Family of unknown function (DUF7286) (family)
This entry represents uncharacterised proteins found in Euryarchaeota.
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 PF24884: Nephrocystin 3, helical domain (domain)
This entry represents a mostly helical domain found in nephrocystin-3 (NPHP3), a protein required for normal ciliary development and function. It inhibits disheveled-1-induced canonical Wnt-signaling activity and may also play a role in the control of non-canonical Wnt signaling which regulates planar cell polarity.
Pfam PF16332: Domain of unknown function (DUF4962) (repeat)
This family consists of uncharacterized proteins around 870 residues in length and is mainly found in various Bacteroides species. The function of this protein is unknown.
Pfam PF00993: Class II histocompatibility antigen, alpha domain (domain)
This entry represents the N-terminal domain (also called alpha-1 domain) of the alpha chain of class II MHC glycoproteins from vertebrates.
Major Histocompatibility Complex (MHC) glycoproteins are heterodimeric cell surface receptors that function to present antigen peptide fragments to T cells responsible for cell-mediated immune responses. MHC molecules can be subdivided into two groups on the basis of structure and function: class I molecules present intracellular antigen peptide fragments (~10 amino acids) on the surface of the host cells to cytotoxic T cells; class II molecules present exogenously derived antigenic peptides (~15 amino acids) to helper T cells. MHC class I and II molecules are assembled and loaded with their peptide ligands via different mechanisms. However, both present peptide fragments rather than entire proteins to T cells, and are required to mount an immune response.
Class II MHC glycoproteins are expressed on the surface of antigen-presenting cells (APC), including macrophages, dendritic cells and B cells. MHC II proteins present peptide antigens that originate extracellularly from foreign bodies such as bacteria. Proteins from the pathogen are degraded into peptide fragments within the APC, which sequesters these fragments into the endosome so they can bind to MHC class II proteins, before being transported to the cell surface. MHC class II receptors display antigens for recognition by helper T cells (stimulate development of B cell clones) and inflammatory T cells (cause the release of lymphokines that attract other cells to site of infection) .

MHC class II molecules are comprised of two membrane-spanning chains, alpha and beta, of similar size. Both chains consist of two globular domains (N-and C-terminal), and a transmembrane segment to anchor them to the membrane . A groove in the structure acts as the peptide-binding site.
Pfam PF22161: Mre11 C-terminal domain, bacteria (domain)
This entry represents the helix-turn-helix domain of Mre11 from Thermotoga maritima and similar proteins. It binds Rad50 and attaches flexibly to the nuclease domain which allows large conformational changes.
Pfam PF14085: Domain of unknown function (DUF4265) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 139 and 168 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 PF08972: Domain of unknown function (DUF1902) (domain)
Members of this family of prokaryotic proteins adopt a fold consisting of one alpha-helix and four beta-strands. Their function has not, as yet, been elucidated.
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 PF04397: LytTr DNA-binding domain (domain)
This domain is found in a variety of bacterial transcriptional regulators. The domain binds to a specific DNA sequence pattern (see).
Pfam PF18353: Phosphoglucose isomerase N-terminal domain (domain)
This domain is found in the N-terminal region of glucose-6-phosphate isomerase-like protein, just before the phospho-glucose isomerase C-terminal SIS domain ([pfam:PF10432]).
Pfam PF20220: ABC toxin N-terminal region (family)
This entry represents the region found N-terminal to the neuraminidase domain in the pore forming ABC toxins.
Pfam PF23282: Disease resistance protein Roq1-like, winged-helix domain (domain)
This is the winged-helix domain (WHD) of Disease resistance protein Roq1 from Nicotiana benthamiana, which specifically recognises the Xanthomonas and Pseudomonas effector proteins XopQ and HopQ1, and triggers cell death. Members of this family are found in plants.
Pfam PF02973: Sialidase, N-terminal domain (domain)
O-Glycosyl hydrolases (3.2.1.) are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families . This classification is available on the CAZy (CArbohydrate-Active EnZymes) website.
Sialidases (GH33) hydrolyse alpha-(2->3)-, alpha-(2->6)-, alpha-(2->8)-glycosidic linkages of terminal sialic residues in oligosaccharides, glycoproteins, glycolipids, colominic acid and synthetic substrates. Sialidases may act as pathogenic factors in microbial infections .

The 1.8 A structure of trans-sialidase from leech (Macrobdella decora, Q27701) in complex with 2-deoxy-2, 3-didehydro-NeuAc was solved. The refined model comprising residues 81-769 has a catalytic Î²-propeller domain, a N-terminal lectin-like domain and an irregular Î²-stranded domain inserted into the catalytic domain .
Wikipedia: In molecular biology, glycoside hydrolase family 33 is a family of glycoside hydrolases.