SII-SWORD/CoKE huggingface dataset:
Pfam PF22782: Splicing regulator SDE2, SDE2 domain (domain)
Sde2 (silencing defective 2) is a ubiquitin-fold-containing splicing regulator that supports splicing of selected pre-mRNAs in an intron-specific manner in Schizosaccharomyces pombe. This splicing regulator is conserved among intron-rich eukaryotes up to humans but is absent in intron-poor organisms such as S. cerevisiae. SDE2 is important in pre-mRNA splicing in mammalian cells. Human SDE2 is a regulatory component of the fork protection complex (FPC) at active and stalled replication forks. This protein is translated as an inactive precursor protein harbouring an ubiquitin-fold at its N-terminal that is processed by deubiquitinating enzymes (DUBs, Ubp5 and Ubp15 in S.pombe) in a conserved GG-K motif to form activated K-Sde2-C, which is necessary to get incorporated into the spliceosome. This entry represents the SDE2 domain, a coiled-coil domain required for the interaction of SDE2 with TIMELESS (TIM), which promotes stable association of the FPC at active replication forks.
Pfam PF01888: CbiD (family)
CbiD is essential for cobalamin biosynthesis in both S. typhimurium and B. megaterium, no functional role has been ascribed to the protein. The CbiD protein has a putative S-AdoMet binding site. It is possible that CbiD might have the same role as CobF in undertaking the C-1 methylation and deacylation reactions required during the ring contraction process.
Wikipedia: Cobalamin biosynthesis is the process by which bacteria and archea make cobalamin, vitamin B12. Many steps are involved in converting aminolevulinic acid via uroporphyrinogen III and adenosylcobyric acid to the final forms in which it is used by enzymes in both the producing organisms and other species, including humans who acquire it through their diet.
Pfam PF04303: PrpF protein (family)
PrpF is a protein found in the 2-methylcitrate pathway. It is structurally similar to DAP epimerase and proline racemase. This protein is likely to acts to isomerise trans-aconitate to cis-aconitate.
Pfam PF07878: CopG-like RHH_1 or ribbon-helix-helix domain, RHH_5 (domain)
This family contains bacterial proteins that form a ribbon-helix-helix fold. This fold occurs in many examples of bacterial antitoxins.
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 PF02313: Fumarate reductase subunit D (domain)
Fumarate reductase is a membrane-bound flavoenzyme consisting of four subunits, A-B. A and B comprise the membrane-extrinsic catalytic domain and C and D link the catalytic centres to the electron-transport chain. This family consists of the 13kD hydrophobic subunit D.
Pfam PF22582: Amylosucrase, C-terminal domain (domain)
This entry represents a domain found C-terminal in amylosucrase and related proteins. This domain follows the catalytic beta/alpha barrel domain. It folds into a beta-sandwich with a greek-key topology.
Pfam PF17312: Bacteriocin helveticin-J (repeat)
Bacteriocins are biologically active proteins or protein complexes that display a bactericidal mode of action towards closely related species. Bacteriocins produced by lactic acid bacteria are grouped into different classes. Class III of bacteriocins includes large heat liable proteins. Lactobacillus helveticus 481 produces a 37-kDa bacteriocin called helveticin J which is a representative for Class III bacteriocins.
Wikipedia: Bacteriocins are proteinaceous or peptidic toxins produced by bacteria to inhibit the growth of similar or closely related bacterial strain(s). They are similar to yeast and paramecium killing factors, and are structurally, functionally, and ecologically diverse. Applications of bacteriocins are being tested to assess their application as narrow-spectrum antibiotics.
Pfam PF16293: C2H2 type zinc-finger (1 copy) (domain)
This entry represents a C2H2 type zinc-finger domain found in a group of uncharacterised proteins known as UCP032676.
Pfam PF00445: Ribonuclease T2 family (domain)
Ribonuclease T2 (RNase T2) is a widespread family of secreted RNases found in every organism examined thus far. This family includes RNase Rh, RNase MC1, RNase LE, and self-incompatibility RNases (S-RNases) . Plant T2 RNases are expressed during leaf senescence in order to scavenge phosphate from ribonucleotides. They are also expressed in response to wounding or pathogen invasion. S-RNases are thought to prevent self-fertilization by acting as selective cytotoxins of "self" pollen. Generally, RNases have two distinct binding sites: the primary site (B1 site) and the subsite (B2 site), for nucleotides located at the 5'- and 3'- terminal ends of the sissile bond, respectively.
The fungal ribonucleases T2 from Aspergillus oryzae, M from Aspergillus saitoi and Rh from Rhizopus niveus are structurally and functionally related 30 Kd glycoproteins  that cleave the 3'-5' internucleotide linkage of RNA via a nucleotide 2',3'-cyclic phosphate intermediate (3.1.27.1). Two histidines residues have been shown  to be involved in the catalytic mechanism of RNase T2 and Rh. These residues and the region around them are highly conserved in a number of other RNAses that have been found to be evolutionary related to these fungal enzymes.
Pfam PF15006: Domain of unknown function (DUF4517) (family)
The function of this protein remains unknown. This family of proteins is found in eukaryotes and are typically between 160 and 182 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 PF01891: Cobalt uptake substrate-specific transmembrane region (family)
This family of proteins forms part of the cobalt-transport complex in prokaryotes, CbiMNQO. CbiMNQO and NikMNQO are the most widespread groups of microbial transporters for cobalt and nickel ions and are unusual uptake systems as they consist of eg two transmembrane components (CbiM and CbiQ), a small membrane-bound component (CbiN) and an ATP-binding protein (CbiO) but no extracytoplasmic solute-binding protein. Similar components constitute the nickel transporters with some variability in the small membrane-bound component, either NikN or NikL, which are not similar to CbiN at the sequence level. CbiM is the substrate-specific component of the complex and is a seven-transmembrane protein. The CbiMNQO and NikMNQO systems form part of the coenzyme B12 biosynthesis pathway. The NikM protein is [pfam:PF10670].
Wikipedia: Cobalamin biosynthesis is the process by which bacteria and archea make cobalamin, vitamin B12. Many steps are involved in converting aminolevulinic acid via uroporphyrinogen III and adenosylcobyric acid to the final forms in which it is used by enzymes in both the producing organisms and other species, including humans who acquire it through their diet.
Pfam PF08476: Viral D10 N-terminal (family)
This domain is found on the N-terminus of the viral protein D10 (VD10) and the related MutT motif proteins.  The VD10 protein is probably essential for virus replication and is often found to the N-terminus of a [pfam:PF00293] domain.
Pfam PF19284: Arc MA domain (domain)
This is the N-terminal matrix-like domain (MA) of Activity-Regulated Cytoskeleton-Associated protein (Arc). This domain might be involved in stabilising the relative domain orientations of the capside-like domain (CA) upon capsid assembly. Arc is a regulator of synaptic scaling and dendrite remodelling.
Pfam PF03622: IBV 3B protein (family)
Product of ORF 3B from Avian infectious bronchitis virus (IBV). Currently, the function of this protein remains unknown.
Pfam PF06502: Equine infectious anaemia virus S2 protein (family)
This family consists of several equine infectious anaemia virus S2 proteins. The function of this family is unknown.
Pfam PF14870: Photosynthesis system II assembly factor YCF48 (repeat)
YCF48 is one of several assembly factors of the photosynthesis system II. The photosynthesis system II occurs in Cyanobacteria that are Gram-negative bacteria performing oxygenic photosynthesis. One of the three membranes surrounding these bacteria is the inner thylakoid membrane (TM) system that is localised within the cell and houses the large pigment-protein complexes of the photosynthetic electron transfer chain, i.e. Photosystem (PS) II, PSI, the cytochrome b6f complex, and the ATP synthase. YCF48 is necessary for efficient assembly and repair of the PSII. YCF48 is found predominantly in the thykaloid membrane. It is a BNR repeat protein.
Pfam PF06415: BPG-independent PGAM N-terminus (iPGM_N) (domain)
This family represents the N-terminal region of the 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (or phosphoglyceromutase or BPG-independent PGAM) protein ([ec:5.4.2.1]). The family is found in conjunction with [pfam:PF01676] (located in the C-terminal region of the protein).
Pfam PF16738: Starch-binding module 26 (domain)
CBM26 is a carbohydrate-binding module that binds starch.
Pfam PF07348: Syd protein (SUKH-2) (family)
This family contains a number of bacterial Syd proteins approximately 180 residues long. It has been suggested that Syd is loosely associated with the cytoplasmic surface of the cytoplasmic membrane, and that interaction with SecY may be involved in this membrane association. Operon analysis showed that Syd protein may function as immunity protein in bacterial toxin systems.
Pfam PF19559: Family of unknown function (DUF6081) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001964) is described by MIBiG as an example of the following biosynthetic class, polyketide. This family includes a  protein from the alkylpyrone-407 biosynthetic gene cluster from  Cystobacterineae bacterium.
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 PF00565: Staphylococcal nuclease homologue (domain)
Present in all three domains of cellular life. Four copies in the transcriptional coactivator p100: these, however, appear to lack the active site residues of Staphylococcal nuclease. Positions 14 (Asp-21), 34 (Arg-35), 39 (Asp-40), 42 (Glu-43) and 110 (Arg-87) [SNase numbering in parentheses] are thought to be involved in substrate-binding and catalysis.
Wikipedia: Micrococcal nuclease is an endo-exonuclease that preferentially digests single-stranded nucleic acids. The rate of cleavage is 30 times greater at the 5' side of A or T than at G or C and results in the production of mononucleotides and oligonucleotides with terminal 3'-phosphates. The enzyme is also active against double-stranded DNA and RNA and all sequences will be ultimately cleaved.
Pfam PF09168: X-Prolyl dipeptidyl aminopeptidase PepX, N-terminal (domain)
Members of this family adopt a secondary structure consisting of a helical bundle of eight alpha helices and three beta strands, the last alpha helix connecting to the first strand of the catalytic domain. The first strand of the N-terminus also forms a small parallel beta sheet with strand 5' of catalytic domain. The domain mediates dimerisation of the protein, with two proline residues present in the domain being critical for interaction.
Pfam PF15759: TMEM108 family (family)
This family of proteins is found in eukaryotes. Proteins in this family are typically between 258 and 575 amino acids in length.
Pfam PF17237: ERMES regulator 1 (family)
The endoplasmic reticulum-mitochondria encounter structure (ERMES) complex creates contact sites between the endoplasmic reticulum and mitochondria, playing crucial roles in interorganelle communication, mitochondrial fission, mtDNA inheritance, lipid transfer, and autophagy. Emr1, also known as Mco6 in budding yeasts, mediates the formation ERMES foci, thereby contributing to the formation of ER-mitochondrial contact sites.
Pfam PF16559: GIT coiled-coil Rho guanine nucleotide exchange factor (coiled_coil)
GIT-CC is the coiled-coil region of GIT (G protein-coupled receptor kinase-interacting) proteins. This coiled-coil region is the surface that associates with the equivalent binding-region on beta-PIX, or p21-activated kinase-interacting exchange factor proteins.  Both GIT and PIX complex together to form a scaffold for the formation of multi-protein assemblies. On its own the GIT-CC region assembles into a parallel two-stranded CC in the asymmetric unit. Similarly the PIX coiled-coil region assembles into a trimer. At least in vitro the two regions associate together into a stable heteropentameric complex that consists of one PIX trimer and one GIT dimer.
Pfam PF17191: RecG wedge domain (domain)
This DNA-binding domain has an OB-fold with large elaborations.
Pfam PF09270: Beta-trefoil DNA-binding domain (domain)
Members of this family of DNA binding domains adopt a beta-trefoil fold, that is, a capped beta-barrel with internal pseudo threefold symmetry. In the DNA-binding protein LAG-1, it also is the site of mutually exclusive interactions with NotchIC (and the viral protein EBNA2) and co-repressors (SMRT/N-Cor and CIR).
Pfam PF23382: Family of unknown function (DUF7097) (family)
This protein family includes a group of proteins from halobacteria. It shows several conserved motifs DCPH, RGCL and RPLL/VEEHHLSxY. Members are predicted to show an alpha-beta configuration.
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 PF11340: Protein of unknown function (DUF3142) (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 PF14750: Integrator complex subunit 2 (family)
This family of proteins are subunits of the integrator complex involved in snRNA transcription and processing.
Pfam PF16083: LydA holin phage, holin superfamily III (family)
Phage_holin_3_3 is a family of small hydrophobic holin proteins with one or more transmembrane domains. Holins are encoded within the genomes of Gram-positive and Gram-negative bacteria as well as those of the bacteriophages of these organisms. Their primary function appears to be transport of murein hydrolases across the cytoplasmic membrane to the cell wall where these enzymes hydrolyse the cell wall polymer as a prelude to cell lysis. When chromosomally encoded, these enzymes are therefore autolysins. Holins may also facilitate leakage of electrolytes and nutrients from the cell cytoplasm, thereby promoting cell death. Some may catalyse export of nucleases. LydA and lydB are encoded on the dar operon.  The phenotype of a rapid lysis in the absence of active LydB suggests that this protein might be an antagonist of the holin LydA.
Pfam PF17577: ECORI-T site (family)
This is a family of unknown function found in Alphabaculovirus.
Pfam PF03901: Alg9-like mannosyltransferase family (family)
Members of this family are mannosyltransferase enzymes. At least some members are localised in endoplasmic reticulum and involved in GPI anchor biosynthesis.
Pfam PF20988: Phosphoinositide phosphatase (family)
Legionella pneumophila modulates the host metabolism of phosphoinositides (PIs) to impair membrane trafficking and establish the Legionella-containing vacuole (LCV) for its own replication. The virulence factor SidF is a unique PI phosphatase that specifically hydrolyses PI(3,4)P2 and PI(3,4,5)P3. This protein shows a large single domain that resembles a cowboy hat, which consists of 19 alpha-helices located around a 10-pleated beta-sheet core.
Pfam PF07353: Uroplakin II (family)
This family contains uroplakin II, which is approximately 180 residues long and seems to be restricted to mammals. Uroplakin II is an integral membrane protein, and is one of the components of the apical plaques of mammalian urothelium formed by the asymmetric unit membrane - this is believed to play a role in strengthening the urothelial apical surface to prevent the cells from rupturing during bladder distension.
Pfam PF04705: Thiostrepton-resistance methylase, N terminus (family)
This region is found in some members of the SpoU-type rRNA methylase family ([pfam:PF00588]).
Pfam PF01751: Toprim domain (family)
This is a conserved region from DNA primase. This corresponds to the Toprim domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR proteins. Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely  abolish DnaG type primase activity. DNA primase [ec:2.7.7.6] is a nucleotidyltransferase it synthesises the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the leading stand and has been implicated in cell division. This family also includes the atypical archaeal A subunit from type II DNA topoisomerases. Type II DNA topoisomerases catalyse the relaxation of DNA supercoiling by causing transient double strand breaks.
Wikipedia: DNA primase is an enzyme involved in the replication of DNA and is a type of RNA polymerase. Primase catalyzes the synthesis of a short RNA segment called a primer complementary to a ssDNA template. After this elongation, the RNA piece is removed by a 5' to 3' exonuclease and refilled with DNA.
Pfam PF11716: Mycothiol maleylpyruvate isomerase N-terminal domain (domain)
This entry represents the N-terminal metal-binding domain in mycothiol-dependent maleylpyruvate isomerases .
Pfam PF02096: 60Kd inner membrane protein (family)
This entry represents the C-terminal domain of YidC/Oxa1/ALB proteins from some species and full length protein from other species. Members of this group of proteins are found in bacteria and eukaryotes.

YidC is a bacterial membrane protein which is required for the insertion and assembly of inner membrane proteins . The well-characterised YidC protein from Escherichia coli and its close homologues contain a large N-terminal periplasmic domain (IPR028053).

COX18 is a mitochondrial membrane insertase required for the translocation of the C terminus of cytochrome c oxidase subunit II (MT-CO2/COX2) across the mitochondrial inner membrane. It plays a role in MT-CO2/COX2 maturation following the COX20-mediated stabilization of newly synthesized MT-CO2/COX2 protein and before the action of the metallochaperones SCO1/2 .

OXA1 is a mitochondrial inner membrane insertase that mediates the insertion of both mitochondrion-encoded precursors and nuclear-encoded proteins from the matrix into the inner membrane. It links mitoribosomes with the inner membrane .

Plant ALBINO3-like proteins are required for the insertion of some light harvesting chlorophyll-binding proteins (LHCP) into the chloroplast thylakoid membrane .
Wikipedia: The enzyme cytochrome c oxidase or Complex IV is a large transmembrane protein complex found in bacteria, archaea, and the mitochondria of eukaryotes.
Pfam PF24627: PUMA coiled-coil (coiled_coil)
This entry represents a coiled-coil region found in PUMA from Parascaris univalens and similar sequences from nematodes. PUMA may play a role in the organization of the spindle apparatus and its interaction with the centromeres.
Pfam PF15447: N-terminal segments of PfEMP1 (domain)
This family, the N-terminal segment, is the most variable part of the variant surface antigen family of Plasmodium falciparum, the erythrocyte membrane protein-1 (PfEMP1) proteins. PfEMP1 is an important target for protective immunity and is implicated in the pathology of malaria through its ability to adhere to host endothelial receptors. A structural and functional study of the N-terminal domain of PfEMP1 from the VarO variant comprising the N-terminal segment (NTS) and the first DBL domain (DBL1alpha1), shows this region is directly implicated in rosetting.  NTS, previously thought to be a structurally independent component of PfEMP1, forms an integral part of the DBL1alpha domain that is found to be the important heparin-binding site.  This family is closely associated with PFEMP, [pfam:PF03011], and Duffy_binding, [pfam:PF05424].
Wikipedia: Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) is a family of proteins present on the membrane surface of red blood cells that are infected by the malarial parasite Plasmodium falciparum. PfEMP1 is synthesized during the parasite's blood stage inside the RBC, during which the clinical symptoms of falciparum malaria are manifested. Acting as both an antigen and adhesion protein, it is thought to play a key role in the high level of virulence associated with P. falciparum. It was discovered in 1984 when it was reported that infected RBCs had unusually large-sized cell membrane proteins, and these proteins had antibody-binding (antigenic) properties. An elusive protein, its chemical structure and molecular properties were revealed only after a decade, in 1995. It is now established that there is not one but a large family of PfEMP1 proteins, genetically regulated (encoded) by a group of about 60 genes called var. Each P. falciparum is able to switch on and off specific var genes to produce a functionally different protein, thereby evading the host's immune system. RBCs carrying PfEMP1 on their surface stick to endothelial cells, which facilitates further binding with uninfected RBCs, ultimately helping the parasite to both spread to other RBCs as well as bringing about the fatal symptoms of P. falciparum malaria.
Pfam PF10239: Protein of unknown function (DUF2465) (family)
FAM98A and B proteins are found from worms to humans but their function is unknown. This entry is of a family of proteins that is rich in glycines.
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.