SII-SWORD/CoKE huggingface dataset:
Pfam PF00263: Bacterial type II and III secretion system protein (family)
This family includes: protein D that is involved in the general (type II) secretion pathway (GSP) within Gram-negative bacteria, a signal sequence-dependent process responsible for protein export  and protein G from the type III secretion system.

A number of proteins are involved in the GSP; one of these is known as protein D (GSPD protein), the most probable location of which is the outer membrane . This suggests that protein D constitutes the apparatus of the accessory mechanism, and is thus involved in transporting exoproteins from the periplasm, across the outer membrane, to the extracellular environment.

The type III secretion system is of great interest, as it is used to transport virulence factors from the pathogen directly into the host cell and is only triggered when the bacterium comes into close contact with the host. The protein subunits of the system are very similar to those of bacterial flagellar biosynthesis. However, while the latter forms a ring structure to allow secretion of flagellin and is an integral part of the flagellum itself , type III subunits in the outer membrane translocate secreted proteins through a channel-like structure. Protein G aids in the structural assembly of the invasion complex .
Wikipedia: The type 2 secretion system is a type of protein secretion machinery found in various species of Gram-negative bacteria, including many human pathogens such as Pseudomonas aeruginosa and Vibrio cholerae. The type II secretion system is one of six protein secretory systems commonly found in Gram-negative bacteria, along with the type I, type III, and type IV secretion systems, as well as the chaperone/usher pathway, the autotransporter pathway/type V secretion system, and the type VI secretion system. Like these other systems, the type II secretion system enables the transport of cytoplasmic proteins across the lipid bilayers that make up the cell membranes of Gram-negative bacteria. Secretion of proteins and effector molecules out of the cell plays a critical role in signaling other cells and in the invasion and parasitism of host cells.
Pfam PF18807: Tripartite Tc toxins repeat (family)
Tripartite Tc toxin complexes of bacterial pathogens perforate the  host membrane and translocate toxic enzymes into the host cell. These structures undergo a transition between a prepore to a pore state  and they are mainly constituted by closed beta-layer repeats. This  Pfam entry includes a single repeat unit.
Pfam PF04876: Tenuivirus major non-capsid protein (family)
This protein of unknown function accumulates in large amounts in tenuivirus infected cells.  It is found in all forms of the inclusion bodies that are formed after infection.
Pfam PF07312: Protein of unknown function (DUF1459) (family)
This family consists of several hypothetical Caenorhabditis elegans proteins of around 85 residues in length. The function of this family is 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 PF12458: ATPase involved in DNA repair (family)
This domain family is found in bacteria, and is approximately 450 amino acids in length. There are two conserved sequence motifs: DVF and SPNGED.
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 PF20010: Collagen trimerization domain (domain)
This small domain mediate trimerization in various collagen proteins.
Pfam PF22322: Domain of unknown function (DUF6973) (domain)
This domain is found in uncharacterised proteins. It is predicted to adopt a globular structure consisting of five alpha-helices. It is probably distantly related to Wnt 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 PF04865: Baseplate J-like protein (family)
The P2 bacteriophage J protein lies at the edge of the baseplate. This family also includes a number of bacterial homologues, which are thought to have been horizontally transferred.
Pfam PF13634: Nucleoporin FG repeat region (family)
This family includes a number of FG repeats that are found in nucleoporin proteins. This family includes the yeast nucleoporins Nup116, Nup100, Nup49, Nup57 and Nup 145.
Wikipedia: Nucleoporins are a family of proteins which are the constituent building blocks of the nuclear pore complex (NPC). The nuclear pore complex is a massive structure embedded in the nuclear envelope at sites where the inner and outer nuclear membranes fuse, forming a gateway that regulates the flow of macromolecules between the cell nucleus and the cytoplasm. Nuclear pores enable the passive and facilitated transport of molecules across the nuclear envelope. Nucleoporins, a family of around 30 proteins, are the main components of the nuclear pore complex in eukaryotic cells. Nucleoporin 62 is the most abundant member of this family. Nucleoporins are able to transport molecules across the nuclear envelope at a very high rate. A single NPC is able to transport 60,000 protein molecules across the nuclear envelope every minute.
Pfam PF07323: Protein of unknown function (DUF1465) (family)
This family consists of several hypothetical bacterial proteins of around 180 residues in length. The function of this family is 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 PF23159: Repressor Rok winged helix domain (domain)
This entry represents the C-terminal domain of repressor Rok from Bacillus subtilis, a repressor of comK, the master regulator of competence development. It is a xenogeneic silencer that binds the DNA minor groove, with preference towards DNA sequences harbouring AACTA, TACTA, and flexible multiple TpA steps. This is a typical winged helix fold, with a novel DNA recognition mechanism different from other winged helix proteins or xenogeneic silencers.
Pfam PF06618: Protein of unknown function (DUF1148) (family)
This family consists of several Maize streak virus proteins of unknown 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 PF04684: BAF1 / ABF1 chromatin reorganising factor (family)
ABF1 is a sequence-specific DNA binding protein involved in transcription  activation, gene silencing and initiation of DNA replication. ABF1 is known to remodel chromatin, and it is proposed that it mediates its effects on  transcription and gene expression by modifying local chromatin architecture. These functions require a conserved stretch of 20 amino acids in the C-terminal region of ABF1 (amino acids 639 to 662 S. cerevisiae ([swissprot:P14164])).  The N-terminal two thirds of the protein are  necessary for DNA binding, and the N-terminus (amino acids 9 to 91 in S.  cerevisiae) is thought to contain a novel zinc-finger motif which may  stabilise the protein structure.
Pfam PF11903: ParD-like antitoxin of type II bacterial toxin-antitoxin system (domain)
ParD-like antitoxin is a family of archaeal and bacterial proteins of a type II bacterial toxin-antitoxin system.  Many of the cognate toxins for these molecules fall into family ParE-like_toxin, [pfam:PF15781]. Gene-pairs are expressed from the same operon, the toxin of the pair being expressed first, eg, for UniProtKB:Q3AQ93 and UniProtKB:Q3AQ94.
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 PF02080: TrkA-C domain (domain)
This domain is often found next to the [pfam:PF02254] domain.  The exact function of this domain is unknown. It has been suggested that it may bind an unidentified ligand.  The domain is predicted to adopt an all beta structure.
Pfam PF11683: Protein of unknown function (DUF3278) (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 PF17927: Inositol 1,3,4-trisphosphate 5/6-kinase pre-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 N-terminal pre-ATP-grasp domain.
Pfam PF19499: Family of unknown function (DUF6034) (family)
This family of proteins is functionally uncharacterised. This family of proteins is mainly found in Clostridia. Proteins in this family are typically between 466 and 533 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 PF11302: Protein of unknown function (DUF3104) (family)
This family of proteins with unknown function appears to be restricted to Cyanobacteria.
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 PF12729: Four helix bundle sensory module for signal transduction (family)
This family is a four helix bundle that operates as a ubiquitous sensory module in prokaryotic signal-transduction. The 4HB_MCP is always found between two predicted transmembrane helices indicating that it detects only extracellular signals. In many cases the domain is associated with a cytoplasmic HAMP domain suggesting that most proteins carrying the bundle might share the mechanism of transmembrane signalling which is well-characterised in E coli chemoreceptors. This domain recognises citrate and TCA cycle intermediates, cis-aconitate, boric acid, Phenanthrene, pyrene and benzopyrene (Matilla et el., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).
Pfam PF16395: Domain of unknown function (DUF5004) (domain)
This small family of proteins is functionally uncharacterized. This family is found in bacteroides. Proteins in this family are typically around 150 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 PF17347: Family of unknown function (DUF5377) (family)
This is a family of unknown function found in Pasteurellaceae.
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 PF22510: Flagellar biosynthesis protein FlhF, N domain (domain)
This domain is found in Flagellar biosynthesis protein FlhF from Bacillus subtilis, a protein that is necessary for flagellar biosynthesis. FlhF contains a basic N-terminal domain followed by the conserved NG domain, which can be divided into two segments: the N domain (this entry) and the G domain ([pfam:PF00448]).
Pfam PF20965: DZF C-terminal domain (domain)
The function of this domain is unknown. It is usually found in combination with [pfam:PF07528].
Pfam PF01116: Fructose-bisphosphate aldolase class-II (domain)
Class-II aldolases , mainly found in prokaryotes and fungi, are homodimeric enzymes, which require a divalent metal ion, generally zinc, for their activity. They include fructose-bisphosphate aldolase , a glycolytic enzyme that catalyses the reversible aldol cleavage or condensation of fructose-1,6-bisphosphate into dihydroxyacetone-phosphate and glyceraldehyde 3-phosphate. The family also includes the Escherichia coli galactitol operon protein, gatY, which catalyses the transformation of tagatose 1,6-bisphosphate into glycerone phosphate and D-glyceraldehyde 3-phosphate; and E. coli N-acetyl galactosamine operon protein, agaY, which catalyses the same reaction. There are two histidine residues in the first half of the sequence of these enzymes that have been shown to be involved in binding a zinc ion .
Wikipedia: Fructose-bisphosphate aldolase, often just aldolase, is an enzyme catalyzing a reversible reaction that splits the aldol, fructose 1,6-bisphosphate, into the triose phosphates dihydroxyacetone phosphate (DHAP) and glyceraldehyde 3-phosphate (G3P). Aldolase can also produce DHAP from other (3S,4R)-ketose 1-phosphates such as fructose 1-phosphate and sedoheptulose 1,7-bisphosphate. Gluconeogenesis and the Calvin cycle, which are anabolic pathways, use the reverse reaction. Glycolysis, a catabolic pathway, uses the forward reaction. Aldolase is divided into two classes by mechanism.
Pfam PF18061: CRISPR-Cas9 WED domain (domain)
This domain, known as the wedge (WED) domain, is found in Cas9 proteins which are present in Staphylococcus aureus. Cas9 cleaves double-stranded DNA targets with a protospacer adjacent motif (PAM) and complementarity to the guide RNA. The Cas9 WED domain has a fold comprising a twisted five-stranded beta sheet flanked by four alpha helices, and is responsible for the recognition of the distorted repeat: anti-repeat duplex. WED domains are responsible for the recognition of single-guide RNA scaffolds.
Pfam PF07635: Planctomycete cytochrome C (family)
These proteins share a region of homology at their N-terminus that contains the C-{CPWHF}-{CPWR}-C-H-{CFYW} motif typical of cytochromes C, or CxxCH.
Pfam PF24883: Nephrocystin 3, N-terminal (domain)
This entry represents a P-loop like domain found at the N-terminal of nephrocystin-3, 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. This entry represents the N-terminal domain of nephrocystin-3 (NPHP3) which belongs to NACHT NTPases clade defined by a residue (glycine, alanine or serine) directly C-terminal  of the Mg2+-coordinating aspartate, and two additional acidic residues one position downstream, with a consensus sequence hhhhD[GAS]hDE. This domain is also found in Ankyrin repeat domain-containing protein 50 from human.
Pfam PF04813: Hepatocyte nuclear factor 1 (HNF-1), alpha isoform C terminus (family)
This family consists of an alternative C terminus of homeobox-containing transcription factor HNF-1, found in the HNF-1A isoform.  Different isoforms of HNF-1 are generated by the differential use of polyadenylation sites and by alternative splicing.                      The C-terminal region of HNF-1 is responsible for the activation of transcription, and HNF-1A, which has this C-terminal extension, transactivates less well than the B and C isoforms. Mutations and polymorphisms in HNF-1 cause the type 3 form of maturity-onset diabetes of the young (MODY3).
Pfam PF12812: PDZ-like domain (domain)
PDZ domains are found in diverse signalling proteins in bacteria, yeasts, plants, insects and vertebrates. this is a family of PDZ-like domains from bacteria, plants and fungi.
Pfam PF22730: NACHT C-terminal Cysteine and Histidine-containing (domain)
This is a domain discovered C-terminal to HEAT repeat modules, observed in some bacterial NACHT conflict systems. These domains feature highly conserved cysteine and histidine residues.
Pfam PF00401: ATP synthase, Delta/Epsilon chain, long alpha-helix domain (domain)
Part of the ATP synthase CF(1). These subunits are part of the head unit of the ATP synthase. This subunit is called epsilon in bacteria and delta in  mitochondria.  In bacteria the delta (D) subunit is equivalent to the mitochondrial Oligomycin sensitive subunit, OSCP ([pfam:PF00213]). This entry includes the epsilon subunit from bacteria and plants.
Pfam PF00856: SET domain (family)
SET domains are protein lysine methyltransferase enzymes. SET domains appear to be protein-protein interaction domains. It has been demonstrated that SET domains mediate interactions with a family of proteins that display similarity with dual-specificity phosphatases (dsPTPases).  A subset of SET domains have been called PR domains.  These domains are divergent in sequence from other SET domains, but also appear to mediate protein-protein interaction.  The SET domain consists of two regions known as SET-N and SET-C.  SET-C forms an unusual and conserved knot-like structure of probably functional importance. Additionally to SET-N and SET-C, an insert region (SET-I) and flanking regions of high structural variability form part of the overall structure.
Wikipedia: The SET domain is a protein domain that typically has methyltransferase activity. It was originally identified as part of a larger conserved region present in the Drosophila Trithorax protein and was subsequently identified in the Drosophila Su(var)3-9 and 'Enhancer of zeste' proteins, from which the acronym SET is derived [Su(var)3-9, Enhancer-of-zeste and Trithorax].
Pfam PF14869: Domain of unknown function (DUF4488) (domain)
In most members this domain covers almost the whole sequence, but a few member-sequences also carry a TonB_C domain, PF03544. This domain has a lipocalin fold.
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 PF04697: pinin/SDK conserved region (family)
SDK2/3 is localised in nuclear speckles where as pinin is known to localise at the desmosomes where it is thought to be involved in anchoring intermediate filaments to the desmosomal plaque. The role of SDK2/3 in the nucleus is thought to be concerned with modulation of alternative pre-mRNA splicing. pinin has also been implicated as a tumour suppressor.  The conserved region is found at the N-terminus of the member proteins.
Pfam PF14812: Transmembrane domain of transglycosylase PBP1 at N-terminal (family)
This is the N-terminal, transmembrane, domain of the transglycosylases ()penicillin-binding proteins), the multi-domain membrane proteins essential for cell wall synthesis that are targeted by penicillin antibiotics. The TM domain is a single helix, several of whose residues lie in close proximity to hydrophobic residues in the TGT domain. The TM helix seems to be necessary for stabilizing the protein-membrane interaction, and the resulting orientation limits the interaction between PBPb1 and lipid II in the membrane in a 2D lateral diffusion fashion.
Pfam PF03733: Inner membrane component domain (domain)
Domain occurs as one or more copies in bacterial and eukaryotic proteins.  These are membrane proteins of four TM regions, two appearing in each of the two copies when both are present. Many of the latter members also carry the sodium/calcium exchanger protein family [pfam:PF01699], which have multipass membrane regions.
Pfam PF19837: Domain of unknown function (DUF6316) (domain)
This domain is found in bacterial proteins, functionally uncharacterised. It is approximately 50-70 amino acids in length and it has the conserved sequence TRExxxxGPF/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.