SII-SWORD/CoKE huggingface dataset:
Pfam PF16955: Ferrous iron uptake permease, iron-lead transporter (family)
OFeT_1 is a family of conserved archaeal membrane proteins that are putative oxidase-dependent Fe2+ transporters.
Pfam PF23180: Receptor-like PK ALE2 N-terminal domain (domain)
This domain is found toward N terminus of the Receptor-like serine/threonine-protein kinase ALE2 and related proteins found mainly in plants. ALE2 is required during the differentiation of the protoderm into shoots epidermis and cuticle. This domain is predicted to adopt a globular alpha/beta structure that has some structural similarity to Notch domain.
Pfam PF24863: Mcm10, CCCH-type zinc motif (domain)
This is the CCCH-type zinc motif of Mcm10, a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha. This motif is found immediately N-terminal to [pfam:PF09332].
Pfam PF25051: MCM8 winged helix domain (domain)
Minichromosome maintenance 8 (MCM8) is a member of the minichromosome maintenance family, which possesses helicase and ATPase activity. It interacts with MCM9 and participates in homologous recombination repair. The domain represented by this entry is located at the C terminus of MCM8. It adopts a winged helix fold and it has a DNA binding activity.
Pfam PF19957: Effector-associated domain 5 (domain)
Effector-associated domains (EADs) are predicted to function as adaptor domains mediating protein-protein interactions. The EADs show a characteristic architectural pattern. One copy is always fused, typically to the N- or C-terminus, of a core component of a biological conflict system; examples include VMAP, iSTAND, or GAP1. Further copies of the same EAD are fused to either effector or signal-transducing domains, or additional EADs. EAD pairs are frequently observed together on the genome in conserved gene neighborhoods, but can also be severed from such neighborhoods and located in distant regions, indicating the EAD-EAD coupling approximates the advantages of collinear transcription. Profile-profile searches unify EAD5 with the Death superfamily of domains.
Pfam PF05123: S-layer like family, central region (family)
This entry represents the central region of one of the archaeal S-layer protein families.
Pfam PF03126: Plus-3 domain (domain)
This domain is about 90 residues in length and is often found associated with the [pfam:PF02213] domain.  The function of this domain is uncertain. It is possible that this domain is involved in DNA binding as it has three conserved positively charged residues, hence this domain has been named the plus-3 domain. It is found in yeast Rtf1 which may be a transcription elongation factor.
Pfam PF09644: Mg296 protein (domain)
This protein of 129 residues is expressed in bacteria. It consists of three identical chains of five alpha helices.  Two copies of each chain associate into a complex of six units of possible biological significance but of unknown function.
Pfam PF14986: Domain of unknown function (DUF4514) (family)
This family of uncharacterised proteins are found in mammals.
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 PF13790: SR1 protein (family)
This family of proteins is encoded by the dual function SR1 RNA. SR1 is a sRNA which regulates arginine metabolism, it also encodes a short protein that binds to glyceraldehyde-3-phosphate dehydrogenase (GapA) and stabilises the gapA operon mRNAs.
Wikipedia: In molecular biology, the SR1 RNA is a small RNA (sRNA) produced by species of Bacillus and closely related bacteria. It is a dual-function RNA which acts both as a protein-coding RNA and as a regulatory sRNA.
Pfam PF23324: Domain of unknown function (DUF7086) (domain)
This domain is found in a group of uncharacterised plant proteins. It is predicted to adopt a globular structure consisting of a rubredoxin-like zinc finger capped with an elaborated alpha-helical subdomain. This arrangement is similar to the zinc finger domain found in hypA ([pfam:PF01155]).
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 PF08036: Diapausin family of antimicrobial peptide (family)
This family consists of diapausin-related antimicrobial peptides. Diapause during periods of environmental adversity is an essential part of the life cycle of many organisms with the molecular basis being different among animals. Diapause-specific peptides provide anti-fungal activity and act as N-type voltage-gated calcium channel blocker.
Pfam PF12389: Camelysin metallo-endopeptidase (family)
Camelysin is a novel surface metallopeptidase from Bacillus cereus . Camelysin prefers cleavage sites in front of aliphatic and hydrophilic amino acid residues (-OH, -SO3H, amido group), and requires zinc for activity .

This entry also includes TasA, a major biofilm matrix component from Bacillus subtilis .
Pfam PF17165: Domain of unknown function (DUF5121) (family)
This domain 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 PF08451: Adenosine/AMP deaminase N-terminal (family)
This domain is found to the N-terminus of the Adenosine/AMP deaminase domain ([pfam:PF00962]) in metazoan proteins such as the Cat eye syndrome critical region protein 1 and its homologues.
Wikipedia: Adenosine deaminase is an enzyme involved in purine metabolism. It is needed for the breakdown of adenosine from food and for the turnover of nucleic acids in tissues.
Pfam PF10309: Nuclear cap-binding protein subunit 3 (family)
NCBP3 and NCBP1 form an alternative cap-binding complex in higher  eukaryotes. NCBP3 binds mRNA, associates with components of the  mRNA processing machinery and contributes to polyA RNA export.
Pfam PF25079: COBRA family C-terminal domain (domain)
This entry represents a domain found C-terminal in the COBRA family of proteins from Arabidopsis thaliana and related species. COBRA family members are all extracellular glycosyl-phosphatidyl inositol-anchored proteins (GPI-linked). COBRA is involved in determining the orientation of cell expansion, probably by playing an important role in cellulose deposition. The domain represented by this entry is predicted to adopt a beta-sandwich
Pfam PF01530: Zinc finger, C2HC type (family)
This is a DNA binding zinc finger domain.
Wikipedia: A zinc finger is a small protein structural motif that is characterized by the coordination of one or more zinc ions (Zn2+) which stabilizes the fold. It was originally coined to describe the finger-like appearance of a hypothesized structure from the African clawed frog (Xenopus laevis) transcription factor IIIA. However, it has been found to encompass a wide variety of differing protein structures in eukaryotic cells. Xenopus laevis TFIIIA was originally demonstrated to contain zinc and require the metal for function in 1983, the first such reported zinc requirement for a gene regulatory protein followed soon thereafter by the Krüppel factor in Drosophila. It often appears as a metal-binding domain in multi-domain proteins.
Pfam PF22101: Homoserine dehydrogenase C-terminal domain (domain)
Homoserine dehydrogenase (HSD) coordinates a critical branch point of the metabolic pathway that leads to the synthesis of bacterial cell-wall components such as L-lysine and m-DAP in addition to other amino acids such as L-threonine, L-methionine and L-isoleucine. The enzyme structure consists of three domains. This entry represents the C-terminal domain that folds into a four-stranded antiparallel beta-sheet with two alpha-helices packed on one side.
Pfam PF21531: DNA-binding protein Rv2175c, wHTH domain (domain)
This entry represents the N-terminal wHTH domain of Rv2175c from Mycobacterium tuberculosis, which has been shown to bind DNA. The C-terminal domain ([pfam:PF18367]) may play a regulatory role.
Pfam PF09671: Spore coat protein (Spore_GerQ) (family)
Members of this protein family are the spore coat protein GerQ of endospore-forming Firmicutes (low GC Gram-positive bacteria). This protein is cross-linked by a spore coat-associated transglutaminase.
Pfam PF21605: Cytokine receptor-like factor 2-like, D2 domain (domain)
CRLF2 is a receptor for thymic stromal lymphopoietin (TSLP). It forms a functional complex with TSLP and IL7R which is capable of stimulating cell proliferation through activation of STAT3 and STAT5. CRFL2 is implicated in the development of the hematopoietic system. It consists of two FnIII-like domains, D1 and D2. This entry represents the membrane-proximal D2 domain, which displays a an ABE/C'CFG topology with two disulfide bridges. This domain interacts with IL7R D2 domain and forms a compact network of interactions. This domain is also found in the cytokine receptor common subunit gamma (IL2RG), a common subunit for the receptors for a variety of interleukins.
Pfam PF09765: FANCL UBC-like domain 1 (domain)
This entry represents the first of three UBC-like domain found in the FANCL protein, which is the catalytic E3 ubiquitin ligase subunit of the FA complex (Fanconi anaemia). Eight subunits of the Fanconi anaemia gene products form a multisubunit nuclear complex which is required for mono-ubiquitination of a downstream FA protein, FANCD2.
Pfam PF18348: Bacterial dipeptidyl-peptidase Sh3 domain (domain)
This is the first of two N-terminal bacterial SH3 (SH3b) domains found in bacterial dipeptidyl-peptidases VI such as gamma-D-glutamyl-L-diamino acid endopeptidases. The first SH3b domain plays an important role in defining substrate specificity by contributing to the formation of the active site, such that only murein peptides with a free N-terminal alanine are allowed.
Pfam PF10785: NADH-ubiquinone oxidoreductase complex I, 21 kDa subunit (domain)
This family is the N-terminal domain of NADH-ubiquinone oxidoreductase 21 kDa subunits from fungi, lower metazoa and plants.
Pfam PF01504: Phosphatidylinositol-4-phosphate 5-Kinase (family)
This family contains a region from the common kinase core found in the type I phosphatidylinositol-4-phosphate 5-kinase (PIP5K) family as described in. The family consists of various type I, II and III PIP5K enzymes. PIP5K catalyses the formation of phosphoinositol-4,5-bisphosphate via the  phosphorylation of phosphatidylinositol-4-phosphate a precursor in the phosphinositide signaling pathway.
Pfam PF21314: Epidermal growth factor receptor transmembrane-juxtamembrane segment (domain)
Epidermal growth factor receptor (ErbB) family is a class of receptor tyrosine kinases (RTKs) that have a pivotal role in the processes of cell growth, proliferation, and differentiation. They exist on the cell surface as dimers in both active and inactive states, which switch between them through conformational changes upon ligand binding. They suffer a strong lateral dimerization that leads to proper assembly of their extracellular ligand-binding, single-span transmembrane, and cytoplasmic kinase domains which is key for ErbB activation. The transmembrane (TM) and juxtamembrane region of these receptors are essential for dimerization and activation. This entry represents the TM and juxtamembrane segment of EGFR, ErbB2 and ErbB4.
Pfam PF01316: Arginine repressor, DNA binding domain (domain)
The arginine dihydrolase (AD) pathway is found in many prokaryotes and some primitive eukaryotes, an example of the latter being Giardia lamblia (Giardia intestinalis) . The three-enzyme anaerobic pathway breaks down L-arginine to form 1 mol of ATP, carbon dioxide and ammonia. In simpler bacteria, the first enzyme, arginine deiminase, can account for up to 10% of total cell protein .

Most prokaryotic arginine deiminase pathways are under the control of a repressor gene, termed ArgR . This is a negative regulator, and will only release the arginine deiminase operon for expression in the presence of arginine . The crystal structure of apo-ArgR from Bacillus stearothermophilus has been determined to 2.5A by means of X-ray crystallography . The protein exists as a hexamer of identical subunits, and is shown to have six DNA-binding domains, clustered around a central oligomeric core when bound to arginine. It predominantly interacts with A.T residues in ARG boxes. This hexameric protein binds DNA at its N terminus to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbour-joining tree, some of these paralogous sequences show long branches and differ significantly from the well-conserved C-terminal region.
Wikipedia: In molecular biology, the arginine repressor (ArgR) is a repressor of prokaryotic arginine deiminase pathways.
Pfam PF17118: Domain of unknown function (DUF5105) (family)
This is a family of Firmicutes proteins of unknown function. There is one structure, PDB:4r4g, a lipoprotein, whose N-terminus is represented by DUF4352, [pfam:PF11611].
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 PF07055: Enoyl reductase FAD binding domain (family)
This family carries the region of the enzyme trans-2-enoyl-CoA reductase, at the very C-terminus, that binds to FAD. The activity was characterised in Euglena where an unusual fatty acid synthesis path-way in mitochondria performs a malonyl-CoA independent synthesis of fatty acids leading to accumulation of wax esters, which serve as the sink for electrons stemming from glycolytic ATP synthesis and pyruvate oxidation. The full enzyme catalyses the reduction of enoyl-CoA to acyl-CoA. The conserved region is seen as the motif FGFxxxxxDY.
Pfam PF07485: Domain of Unknown Function (DUF1259) (family)
This family is the lppY/lpqO homologue family.
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 PF01644: Chitin synthase (family)
This region is found commonly in chitin synthases classes I, II and III. Chitin a linear homopolymer of GlcNAc residues, it is an important component of the cell wall of fungi and is synthesised on the cytoplasmic surface of the cell membrane by membrane bound chitin synthases.
Wikipedia: In enzymology, a chitin synthase is an enzyme that catalyzes the chemical reactionUDP-N-acetyl-D-glucosamine + [1,4-(N-acetyl-beta-D-glucosaminyl)]n  UDP + [1,4-(N-acetyl-beta-D-glucosaminyl)]n+1
Pfam PF08767: CRM1 C terminal (repeat)
CRM1 (also known as Exportin1) mediates the nuclear export of proteins bearing a leucine-rich nuclear export signal (NES). CRM1 forms a complex with the NES containing protein and the small GTPase Ran.  This region forms an alpha helical structure formed by six helical hairpin motifs that are structurally similar to the HEAT repeat, but share little sequence similarity to the HEAT repeat.
Pfam PF07927: HicA toxin of bacterial toxin-antitoxin, (family)
HicA_toxin is a bacterial family of toxins that act as mRNA interferases. The antitoxin that neutralises this is family HicB, [pfam:PF15919].
Wikipedia: A toxin-antitoxin system consists of a "toxin" and a corresponding "antitoxin", usually encoded by closely linked genes. The toxin is usually a protein while the antitoxin can be a protein or an RNA. Toxin-antitoxin systems are widely distributed in prokaryotes, and organisms often have them in multiple copies. When these systems are contained on plasmids – transferable genetic elements – they ensure that only the daughter cells that inherit the plasmid survive after cell division. If the plasmid is absent in a daughter cell, the unstable antitoxin is degraded and the stable toxic protein kills the new cell; this is known as 'post-segregational killing' (PSK).
Pfam PF16587: 17 kDa common-antigen outer membrane protein (family)
This is a family of bacterial lipoproteins related to the 17 kDa common-antigen proteins.
Pfam PF19871: Family of unknown function (DUF6344) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000843) is described by MIBiG as an example of the following biosynthetic class, other (unspecified), in particular the alanylclavam biosynthetic gene cluster from Streptomyces clavuligerus ATCC 27064. 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 PF11543: Nuclear pore localisation protein NPL4 (family)
Npl4 is part of the heterodimer UN along with Ufd1 which is involved in the recruitment of p97, an AAA ATPase, for tasks involving the ubiquitin pathway. Npl4 has a ubiquitin-like domain which has within its structure a beta-grasp fold with a helical insert.
Pfam PF10442: FIST C domain (domain)
The FIST C domain is a novel sensory domain, which is present in signal transduction proteins from Bacteria, Archaea and Eukarya. Chromosomal proximity of FIST-encoding genes to those coding for proteins involved in amino acid metabolism and transport suggest that FIST domains bind small ligands, such as amino acids.
Pfam PF05770: Inositol 1,3,4-trisphosphate 5/6-kinase ATP-grasp domain (domain)
This family consists of several inositol 1, 3, 4-trisphosphate 5/6-kinase proteins. Inositol 1,3,4-trisphosphate is at a branch point in inositol phosphate metabolism. It is dephosphorylated by specific phosphatases to either inositol 3,4-bisphosphate or inositol 1,3-bisphosphate. Alternatively, it is phosphorylated to inositol 1,3,4,6-tetrakisphosphate or inositol 1,3,4,5-tetrakisphosphate by inositol trisphosphate 5/6-kinase. This entry represents the ATP-grasp domain.
Pfam PF21490: Polymerase basic protein 2, cap-binding domain (domain)
Polymerase basic protein 2 (PB2) is a subunit of the RNA-dependent RNA polymerase of Orthomyxovirus Influenza A virus (IAV) which performs transcription of viral mRNAs by cap-snatching, a processes that generated capped primers by host pre-mRNA binding, mediated by PB2. This protein has two domains, the cap-binding and the so-called '627-domain'. This entry represents the cap-binding domain and includes PB2 from Thogoto (THOV) virus, which is similar to IAV.
Pfam PF19831: Family of unknown function (DUF6312) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001772) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the  scytophycin biosynthetic gene cluster from Anabaena sp. UHCC 0451.
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 PF08796: Protein of unknown function (DUF1797) (family)
This is a domain of unknown function.  It forms a central anti-parallel beta sheet with flanking alpha helical regions.
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 PF09203: MspA (domain)
MspA is a membrane porin produced by Mycobacteria, allowing hydrophilic nutrients to enter the bacterium. The protein forms a tightly interconnected octamer with eightfold rotation symmetry that resembles a goblet and contains a central channel. Each subunit fold contains a beta-sandwich of Ig-like topology and a beta-ribbon arm that forms an oligomeric transmembrane barrel.
Wikipedia: Mycobacterial porins are a group of transmembrane beta-barrel proteins produced by mycobacteria, which allow hydrophilic nutrients to enter the bacterium. They are located in the impermeable mycobacterial outer membrane, or mycomembrane of fast-growing mycobacteria. The mycomembrane is unique and composed of very-long chain fatty acids, mycolic acids. These proteins are structurally different from the typical porins located in the outer membrane of Gram-negative bacteria. For example, the MspA protein forms a tightly interconnected octamer with eight-fold rotation symmetry that resembles a goblet and contains a central channel. Each protein subunit contains a beta-sandwich of immunoglobulin-like topology and a beta-ribbon arm that forms an oligomeric transmembrane beta-barrel.
Pfam PF01077: Nitrite and sulphite reductase 4Fe-4S domain (family)
Sulphite and nitrite reductases are vital in the biosynthetic assimilation of sulphur and nitrogen, respectfully.  They are also both important for the dissimilation of oxidised anions for energy transduction.
Pfam PF19978: Tail virion protein G7P (family)
Tail virion protein 7P is a viral transmembrane protein that interacts with the packaging signal of the viral genome leading to the initiation the virion concomitant assembly-budding process in the host inner membrane.
Pfam PF03762: Vitelline membrane outer layer protein I (VOMI) (repeat)
VOMI binds tightly to ovomucin fibrils of the egg yolk membrane. The structure that consists of three beta-sheets forming Greek  key motifs, which are related by an internal pseudo three-fold  symmetry. Furthermore, the structure of VOMI has strong similarity  to the structure of the delta-endotoxin, as well as a  carbohydrate-binding site in the top region of the common fold.
Wikipedia: In molecular biology, this entry refers to a protein domain called, the Vitelline membrane outer layer protein I (VMO-I). It is a structure found on the outside of an egg, in the vitelline membrane.
Pfam PF17585: Accessory recombination function protein (family)
Family members are found in Caudovirales such as Salmonella virus P22. Family members have a recombination accessory function.