SII-SWORD/CoKE huggingface dataset:
Pfam PF05213: Coronavirus NS2A protein (family)
This family contains a number of corona virus non-structural proteins of unknown function. The family also includes a polymerase protein fragment from Berne virus and does not seem to be related to the [pfam:PF04753] Coronavirus NS2 family. This family is part of the 2H phosphoesterase superfamily.
Pfam PF14123: Domain of unknown function (DUF4290) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 200 and 221 amino acids in length. There are two conserved sequence motifs: EYGR and KLWD.
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 PF10541: Nuclear envelope localisation domain (domain)
The KASH (for Klarsicht/ANC-1/Syne-1 homology) or KLS domain is a highly hydrophobic nuclear envelope localisation domain of approximately 60 amino acids comprising a 20-amino-acid transmembrane region and a 30-35-residue C-terminal region that lies between the inner and the outer nuclear membranes. During meiotic prophase, telomeres cluster to form a bouquet arrangement of chromosomes. SUN and KASH domain proteins form complexes that span both membranes of the nuclear envelope. The KASH domain links the dynein motor complex of the microtubules, through the outer nuclear membrane to the Sad1 domain in the inner nuclear membrane which then interacts with the bouquet proteins Bqt1 and Bqt2 that are complexed with Bqt4, Rap1 and Taz1 and attached to the telomere.  SUN domain-containing proteins are essential for recruiting KASH domain proteins at the outer nuclear membrane, and KASH domains provide a generic NE tethering device for functionally distinct proteins whose cytoplasmic domains mediate nuclear positioning, maintain physical connections with other cellular organelles, and possibly even influence chromosome dynamics.
Wikipedia: KASH domains are conserved C-terminal protein regions less than ~30 amino acids. KASH is an acronym for Klarsicht, ANC-1, Syne Homology. KASH domains always follow a transmembrane domain. Most proteins containing KASH domains are thought to be involved in the positioning of the nucleus in the cell. KASH domains interact with proteins containing SUN domains in the space between the outer and inner nuclear membranes to bridge the nuclear envelope, and may transfer force from the nucleoskeleton to the cytoplasmic cytoskeleton and enable mechanosensory roles in cells. KASH proteins are thought to largely localize to the outer nuclear membrane, although there are reports of inner nuclear membrane localization of some KASH protein isoforms.
Pfam PF24186: Domain of unknown function (DUF7414) (domain)
This entry represents an uncharacterised family of proteins. Structure prediction suggests these proteins form a four stranded beta sheet with a helix packed on one side. Structure prediction also suggests a confident dimer. The structure shows some weak similarity to large ribosomal subunit protein eL38.
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 PF03487: Interleukin-13 (domain)
This entry represents interleukin-13 (IL-13), it is a pleiotropic cytokine which may be important in the regulation of the inflammatory and immune responses . IL-13 inhibits inflammatory cytokine production and synergises with IL-2 in regulating interferon-gamma synthesis. The sequences of IL-4 and IL-13 are distantly related.
Wikipedia: Interleukins (ILs) are a group of cytokines that are expressed and secreted by white blood cells (leukocytes) as well as some other body cells. The human genome encodes more than 50 interleukins and related proteins.
Pfam PF16767: Sensor domain of alginate biosynthesis sensor protein KinB (family)
KinB_sensor is the N-terminal sensor domain of histidine kinase from Pseudomonas species. The domain is the extracellular sensing domain, and is four helical bundle. It recognises inorganic phosphate Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).
Pfam PF18570: NUP57/Nup54 C-terminal domain (coiled_coil)
The nuclear pore complex (NPC) constitutes the sole gateway for bidirectional nucleocytoplasmic transport. NPCs are formed by multiple copies of 34 distinct proteins, termed nucleoporins (nups). In yeast, the channel nups Nsp1, Nup49, and Nup57 constitute part of the central transport channel and form the diffusion barrier with their disordered phenylalanine-glycine (FG) repeats. Structural studies of yeast Nup57 indicate that it contains left-handed coiled-coil domains (CCD1-3). This entry represents the third CCD located at the C-terminal region of Nup57 which is composed of five heptad repeats. Nup57 in yeast is the equivalent to human Nup54 [pfam:PF13874].
Pfam PF13491: 4TM region of DNA translocase FtsK/SpoIIIE (domain)
4TM_FtsK is the integral membrane domain of the FtsK DNA tranlocases. During sporulation in Bacillus subtilis, the SpoIIIE protein is believed to form a translocation pore at the leading edge of the nearly closed septum. The E. coli FtsK protein is homologous to SpoIIIE, and can free chromosomes trapped in vegetative septa.
Pfam PF22386: Protease propeptides/inhibitors (domain)
This entry represents the propeptide domain found at the N-terminal of peptidases belonging to MEROPS family S8A, subtilisins. This propeptide is removed by proteolytic cleavage, which activates the enzyme.
Pfam PF06996: Type VI secretion, TssG (family)
This is a family of Gram-negative bacterial proteins that form part of the type VI pathogenicity secretion system (T6SS), including TssG. TssG is homologues to phage tail proteins and is required for proper assembly of the Hcp tube in bacteria.One other member in this family, SciB (Q93IT4) from Salmonella enterica, is thought to be involved in virulence.
Pfam PF12140: SLED domain (domain)
The SLED (Scm-Like Embedded Domain) domain is a double-stranded DNA binding domain found in Scml2 which is a member of the Polycomb  group of proteins involved in epigenetic gene silencing.
Pfam PF17061: PARM (family)
Human PARM-1 is a mucin-like, androgen-regulated transmembrane protein that is present in most tissues, with high levels in the heart, kidney and placenta. It has been shown to be induced and expressed in prostate after castration and may have a role in cell proliferation and immortalisation in prostate cancer.
Pfam PF09871: Uncharacterized protein conserved in archaea (DUF2098) (family)
This domain, found in various hypothetical prokaryotic 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 PF11774: Lsr2 dimerization domain (domain)
Lsr2 is a small, basic DNA-bridging protein present in Mycobacterium and related actinomycetes.  It is a functional homologue of the H-NS-like proteins.  H-NS proteins play a role in nucleoid organisation and also function as a pleiotropic regulator of gene expression. This entry represents the dimerization domain found at the N-terminal of Lsr2. Lsr2 dimers show a self-associative propensity allowing chromosome compaction and gene regulation in response to external stress.
Pfam PF06062: Uncharacterised protein family (UPF0231) (family)
Family of uncharacterised Proteobacteria proteins.
Pfam PF00230: Major intrinsic protein (family)
MIP (Major Intrinsic Protein) family proteins exhibit essentially two distinct types of channel properties: (1) specific water transport by the aquaporins, and (2) small neutral solutes transport, such as glycerol by the glycerol facilitators.
Wikipedia: Aquaporins, also called water channels, are channel proteins from a larger family of major intrinsic proteins that form pores in the membrane of biological cells, mainly facilitating transport of water between cells. The cell membranes of a variety of different bacteria, fungi, animal and plant cells contain aquaporins through which water can flow more rapidly into and out of the cell than by diffusing through the phospholipid bilayer. Aquaporins have six membrane-spanning alpha helical domains with both carboxylic and amino terminals on the cytoplasmic side. Two hydrophobic loops contain conserved asparagine–proline–alanine which form a barrel surrounding a central pore-like region that contains additional protein density. Because aquaporins are usually always open and are prevalent in just about every cell type, this leads to a misconception that water readily passes through the cell membrane down its concentration gradient. Water can pass through the cell membrane through simple diffusion because it is a small molecule, and through osmosis, in cases where the concentration of water outside of the cell is greater than that of the inside. However, because water is a polar molecule this process of simple diffusion is relatively slow, and in tissues with high water permeability the majority of water passes through aquaporin.
Pfam PF16511: N-terminal or F0 domain of Talin-head FERM (domain)
FERM_f0 forms a stable globular structure. The fold is an ubiquitin-like fold joined to the f1 domain in a novel fixed orientation by an extensive charged interface.  It is required for maximal integrin-activation, by interacting with other FA components, No binding partner has yet been found for it.
Pfam PF04824: Conserved region of Rad21 / Rec8 like protein (family)
This family represents a conserved region found in eukaryotic cohesins of the Rad21, Rec8 and Scc1 families.  Members of this family  mediate sister chromatid cohesion during mitosis and meiosis, as part of  the cohesin complex. Cohesion is necessary for homologous recombination (including double-strand break repair) and correct chromatid segregation.  These proteins may also be involved in chromosome condensation.  Dissociation at the metaphase to  anaphase transition causes loss of cohesion and chromatid segregation.
Pfam PF04677: Protein similar to CwfJ C-terminus 1 (family)
This region is found in the N terminus of Schizosaccharomyces pombe protein CwfJ ([swissprot:Q09909]).  CwfJ is part of the Cdc5p complex involved in mRNA splicing.
Pfam PF04839: Plastid and cyanobacterial ribosomal protein (PSRP-3 / Ycf65) (family)
This small acidic protein is found in 30S ribosomal subunit of cyanobacteria and plant plastids. In plants it has been named plastid-specific ribosomal protein 3 (PSRP-3), and in cyanobacteria it is named Ycf65. Plastid-specific ribosomal proteins may mediate the effects of nuclear factors on plastid translation.  The acidic PSRPs are thought to contribute to protein-protein interactions in the 30S subunit, and are not thought to bind RNA.
Pfam PF10200: NADH:ubiquinone oxidoreductase, NDUFS5-15kDa (family)
This is a family of short, approximately 105 amino acid residue, proteins which form part of NADH:ubiquinone oxidoreductase complex I. Complex I is the first multisubunit inner membrane protein complex of the mitochondrial electron transport chain and it transfers two electrons from NADH to ubiquinone. The protein carries four highly conserved cysteine residues but these do not appear to be in a configuration which would favour metal binding so the exact function of the protein is uncertain.
Wikipedia: Respiratory complex I, EC 7.1.1.2 is the first large protein complex of the respiratory chains of many organisms from bacteria to humans. It catalyzes the transfer of electrons from NADH to coenzyme Q10 (CoQ10) and translocates protons across the inner mitochondrial membrane in eukaryotes or the plasma membrane of bacteria.
Pfam PF04423: Rad50 zinc hook motif (conserved_site)
The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.
Pfam PF12190: Fungal protease inhibitor (family)
This entry represents fungal proteinase inhibitors from arthropods, including fungal protease inhibitor-1 from Antheraea mylitta (Tassar silkworm). FPI1 inhibits trypsin and chymotrypsin proteases from Aspergillus oryzae and Rhizopus oryzae. The crystal structure shows that it is a single domain protein with an unique fold consisting of three helices and five beta-strands stabilized by a network of six disulfide bonds. Members of this family belong to MEROPS inhibitor family I83, clan JH.
Pfam PF18067: Lipase C-terminal domain (domain)
This domain is found in Archaeoglobus fulgidus lipase (AFL). The domain consists of a layer of seven beta-sheet. When the domain is combined with the proximal domain, which is also a layer of seven beta-sheet, they form a beta sandwich. The combination of these two domains is known as the C-terminal domain. It is likely that the C-terminal domain plays an important role in substrate specificity, catalytic efficiency but also attributes partly to AFLs stability.
Pfam PF05714: Borrelia Bbcrasp-1 domain containing protein (domain)
This family contains lipoproteins from the Lyme disease spirochete Borrelia burgdorferi and related bacteria. This entry contains proteins from Paralogous family 54 (PFam54) and 60 and (PFam60). The first crystal structure of B. burgdorferi PFam54 member BBA68 revealed a previously unseen novel fold, which, according to the CATH protein domain classification, was named the Bbcrasp-1 fold because of the common name used for the protein BBA68.
Pfam PF20636: Survival Motor Neuron, Gemin2-binding domain (domain)
Survival Motor Neuron (SMN) protein forms the oligomeric core of a multi-protein complex that functions in spliceosomal snRNP biogenesis. It has three highly conserved domains: a short N-terminal segment responsible for binding with high affinity to Gemin2 (a protein involved in snRNP assembly), therefore, called Gemin2-binding domain (G2-BD), a central Tudor domain ([pfam:PF06003]) that recognises symmetric dimethylarginine (sDMA) modifications in proteins involved in RNA processing, and a C-terminal domain, referred to as the 'YG-box' domain ([pfam:PF20635]). This is the Gemin2-binding domain (G2-BD) of SMN proteins.
Pfam PF07122: Variable length PCR target protein (VLPT) (repeat)
This family consists of a number of 29 residue repeats which seem to be specific to the Ehrlichia chaffeensis variable length PCR target (VLPT) protein. Ehrlichia chaffeensis is a tick-transmitted rickettsial agent and is responsible for human monocytic ehrlichiosis (HME). The function of this family is unknown.
Pfam PF11050: Virus envelope protein E26 (family)
E26 is a multifunctional protein. One form of E26 associates with viral DNA or DNA binding proteins, while a second form associates with intracellular membranes.
Pfam PF01990: ATP synthase (F/14-kDa) subunit (family)
This family includes 14-kDa subunit from vATPases, which is in the peripheral catalytic part of the complex. The family also includes archaebacterial ATP synthase subunit F.
Wikipedia: V-type proton ATPase subunit F is an enzyme that in humans is encoded by the ATP6V1F gene.
Pfam PF00697: N-(5'phosphoribosyl)anthranilate (PRA) isomerase (domain)
N-(5'-phosphoribosyl) anthranilate isomerase (PRAI) is an enzyme that catalyses the third step of tryptophan biosynthesis. This domain can also be found at the C terminus of several multifunctional enzymes such as tryptophan biosynthesis protein TrpCF, TRP1 and TrpC.

Phosphoribosylanthranilate isomerase is monomeric and labile in most mesophilic microorganisms, but dimeric and stable in the hyperthermophile Thermotoga maritima (tPRAI) . The comparison to the known 2.0 A structure of PRAI from Escherichia coli (ePRAI) shows that tPRAI has the complete TIM- or (Î² Î±)8-barrel fold, whereas helix alpha5 in ePRAI is replaced by a loop. The subunits of tPRAI associate via the N-terminal faces of their central Î²-barrels. Two long, symmetry-related loops that protrude reciprocally into cavities of the other subunit provide for multiple hydrophobic interactions. Moreover, the side chains of the N-terminal methionines and the C-terminal leucines of both subunits are immobilized in a hydrophobic cluster, and the number of salt bridges is increased in tPRAI. These features appear to be mainly responsible for the high thermostability of tPRAI .
Wikipedia: In enzymology, a phosphoribosylanthranilate isomerase (PRAI) is an enzyme that catalyzes the third step of the synthesis of the amino acid tryptophan.
Pfam PF03226: Yippee zinc-binding/DNA-binding /Mis18, centromere assembly (domain)
This family includes both Yippee-type proteins and Mis18 kinetochore proteins.  Yippee are putative zinc-binding/DNA-binding proteins. Mis18 are proteins involved in the priming of centromeres for recruiting CENP-A. Mis18-alpha and beta form part of a small complex with Mis18-binding protein. Mis18-alpha is found to interact with DNA de-methylases through a Leu-rich region located at its carboxyl terminus. This entry also includes the CULT domain proteins such as Cereblon.
Pfam PF24294: Membrane-bound transcription factor PTM, chromo domain-like (domain)
This is the putative chromo domain-like domain found in the membrane-bound transcription factor PTM (also known as DDP1) and similar plant sequences. PTM is required for the plastid-to-nucleus retrograde signalling, which plays an important role in the coordinated expression of both nuclear- and chloroplast-localized genes that encode photosynthesis-related proteins.
Pfam PF00693: Thymidine kinase from herpesvirus (domain)
The thymidine kinase from Herpesviridae catalyses the reaction:

ATP + THYMIDINE = ADP + THYMIDINE 5'-PHOSPHATE.

The enzyme is not subject to feedback inhibition by its product and the crystal structure of the enzyme from Human herpesvirus 1 (HHV-1) has been reported .
Wikipedia: Thymidine kinase from herpesvirus is a sub-family of thymidine kinases that catalyses the transfer of phospho group of ATP to thymidine to generate thymidine monophosphate, which serves as a substrate during viral DNA replication.
Pfam PF03592: Terminase small subunit (family)
Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA.  This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology.  The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site.
Pfam PF10628: Outer spore coat protein E (CotE) (family)
CotE is a morphogenic protein that is required for the assembly of the outer coat of the endospore and spore resistance to lysozyme. CotE also regulates the expression of cotA, cotB, cotC and other genes encoding spore outer coat proteins. The timing of cotE expression has been shown in Bacillus subtilis to affect spore coat morphology but not lysozyme resistance. This protein consists of a SPOCS domain which may be determinant in recruiting proteins for coat assembly.
Pfam PF15659: JAB-like toxin 1 (family)
Structurally, the JAB domain is related to the nucleotide deaminase and binds a zinc-ion in a similar structural location . This entry represents a family of predicted JAB-like toxins .
Pfam PF03197: Bacteriophage FRD2 protein (family)
This is group of bacteriophage proteins has no known function.
Pfam PF00801: PKD domain (domain)
This domain was first identified in the Polycystic kidney disease protein PKD1. This domain has been predicted to contain an Ig-like fold.
Wikipedia: PKD  domain was first identified in the polycystic kidney disease protein, polycystin-1, and contains an Ig-like fold consisting of a beta-sandwich of seven strands in two sheets with a Greek key topology, although some members have additional strands. Polycystin-1 is a large cell-surface glycoprotein involved in adhesive protein–protein and protein–carbohydrate interactions; however it is not clear if the PKD domain mediates any of these interactions.
Pfam PF12823: Domain of unknown function (DUF3817) (domain)
This domain is of unknown function.  It is sometimes found adjacent to [pfam:PF07690] and [pfam:PF03176] which are both transporter domains.
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 PF18317: Shikimate 5'-dehydrogenase C-terminal domain (domain)
This domain is found in the C-terminal region of Shikimate 5'-dehydrogenase (SDH) present in Methanocaldococcus jannaschii. SDH catalyses the NADPH-dependent reduction of 3-dehydroshikimate to shikimate in the shikimate pathway. The domain is found just after the C-terminal domain ([pfam:PF01488]) which is responsible for NADP binding.
Pfam PF21929: Mu phage baseplate assembly protein GpP, fourth domain (domain)
This domain is found in Mu phage baseplate assembly protein GpP from Shewanella oneidensis ([swissprot:Q8EDP4]) and similar sequences found in tailed bacteriophages and prophages from proteobacteria. It is normally found associated with [pfam:PF21683].
Pfam PF05170: AsmA family (repeat)
The AsmA gene, whose product is involved in the assembly of outer membrane proteins in Escherichia coli. AsmA mutations were isolated as extragenic suppressors of an OmpF assembly mutant. AsmA may have a role in LPS biogenesis.
Pfam PF00207: Alpha-2-macroglobulin family (family)
This family includes the C-terminal region of the alpha-2-macroglobulin family.
Wikipedia: α2-Macroglobulin (α2M) or alpha-2-macroglobulin is a large plasma protein found in the blood. It is mainly produced by the liver, and also locally synthesized by macrophages, fibroblasts, and adrenocortical cells. In humans it is encoded by the A2M gene.
Pfam PF04403: Paraquat-inducible protein A (family)
Paraquat is a superoxide radical-generating agent.  The promoter for the  pqiA gene is also inducible by other known superoxide generators. This is predicted to be a family of integral membrane proteins, possibly  located in the inner membrane. This family is related to NADH dehydrogenase subunit 2 ([pfam:PF00361]).
Pfam PF24914: ACT domain-containing protein ACR10, N-terminal (domain)
This domain is found at the N-terminal end of ACT domain -containing protein ACR10 from Arabidopsis thaliana and similar plant proteins. ACR10 may bind amino acids.