SII-SWORD/CoKE huggingface dataset:
Pfam PF01823: MAC/Perforin domain (domain)
The membrane-attack complex (MAC) of the complement system forms transmembrane channels. These channels disrupt the phospholipid bilayer of target cells, leading to cell lysis and death. A number of proteins participate in the assembly of the MAC. Freshly activated C5b binds to C6 to form a C5b-6 complex, then to C7 forming the C5b-7 complex. The C5b-7 complex binds to C8, which is composed of three chains (alpha, beta, and gamma), thus forming the C5b-8 complex. C5b-8 subsequently binds to C9 and acts as a catalyst in the polymerisation of C9. Active MAC has a subunit composition of C5b-C6-C7-C8-C9{n}. Perforin is a protein found in cytolytic T-cell and killer cells. In the presence of calcium, perforin polymerises into transmembrane tubules and is capable of lysing, non-specifically, a variety of target cells. There are a number of regions of similarity in the sequences of complement components C6, C7, C8-alpha, C8-beta, C9 and perforin.  The X-ray crystal structure of a MACPF domain reveals that it shares a common fold with bacterial cholesterol dependent cytolysins ([pfam:PF01289]) such as perfringolysin O. Three key pieces of evidence suggests that MACPF domains and CDCs are homologous: Functional similarity (pore formation), conservation of three glycine residues at a hinge in both families and conservation of a complex core fold.
Wikipedia: The Membrane Attack Complex/Perforin (MACPF) superfamily, sometimes referred to as the MACPF/CDC superfamily, is named after a domain that is common to the membrane attack complex (MAC) proteins of the complement system and perforin (PF). Members of this protein family are pore-forming toxins (PFTs). In eukaryotes, MACPF proteins play a role in immunity and development.
Pfam PF20983: ExoU toxin, C-terminal domain (domain)
This domain is found in the toxin ExoU from Pseudomonas aeruginosa, an effector of the type III secretion system of the bacteria. ExoU is a patatin-like phospholipase that binds to the host membranes and induces cytotoxic effects leading to rapid necrotic cell death. This protein shows four domains: a putative chaperone binding domain. a patatin-like domain ([pfam:PF01734]), and two domains that form the membrane localization domain (MLD). This entry represents the C-terminal domain, which folds into a four-helical bundle with a conserved arginine exposed. This residue seems to be essential for localization.
Pfam PF21864: Multiple organellar RNA editing factor 1, MORF domain (domain)
This domain is found in Multiple organellar RNA editing factor 1 from Arabidopsis thaliana (MORF1) and similar proteins from plants involved in organellar RNA editing in mitochondria. This conserved domain, termed MORF domain, plays a role in the multimerisation of MORF proteins. It adopts a globular fold with seven beta-strands and three alpha-helices combined with four major loops.
Pfam PF02006: Phosphopantothenate/pantothenate synthetase (family)
This family of archaeal proteins includes pantothenate synthetase from Methanosarcina mazei and 4-phosphopantoate--beta-alanine ligase (phosphopantothenate synthetase) from Pyrococcus kodakaraensis. Pantothenate synthetase catalyses the condensation of pantoate with beta-alanine in an ATP-dependent and ADP-producing reaction. 4-phosphopantoate--beta-alanine ligase catalyses the conversion of (R)-4-phosphopantoate and beta-alanine to 4'-phosphopantothenate in the CoA biosynthesis pathway. It cannot use (R)-pantoate as substrate and thus does not display pantothenate synthetase activity.
Pfam PF05094: Late expression factor 9 (LEF-9) (family)
Late expression factor 9 (LEF-9) is one of the primary components of RNA polymerase produced by baculoviruses. LEF-9 is homologous to the largest beta-subunit of prokaryotic DNA-directed RNA polymerase.
Pfam PF16285: Domain of unknown function (DUF4931) N-terminal domain (domain)
This family consists of uncharacterized proteins around 270 residues in length and is mainly found in various Bacillus cereus species. Some members of this family are annotated as Galactose-1-phosphate uridylyltransferases, but the specific function of this family is unknown.
Pfam PF09563: LlaJI restriction endonuclease (family)
This family includes the LlaJI (recognises GACGC) restriction endonucleases.
Pfam PF10049: Protein of unknown function (DUF2283) (family)
Members of this family of hypothetical bacterial proteins have no known function.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF15043: CB1 cannabinoid receptor-interacting protein 1 (family)
This family of proteins interacts with cannabinoid receptor 1 (CNR1) and attenuates CNR1-mediated tonic inhibition of voltage-gated calcium channels.
Pfam PF15812: Melanoregulin (family)
Melanoregulin is a family of proteins found in eukaryotes. It is a putative membrane fusion regulator. MREG forms a complex with peripherin-2. It is required for lysosome maturation and plays a role in intracellular trafficking. It is a negative regulator of melanosome intercellular transfer and it regulates intercellular melanosome transfer through palmitoylation.
Pfam PF05053: Menin (family)
MEN1, the gene responsible for multiple endocrine neoplasia type 1, is a tumour suppressor gene that encodes a protein called Menin which may be an atypical GTPase stimulated by nm23.
Pfam PF14626: Zc3h12a-like Ribonuclease NYN domain (family)
This family is found to be a divergent form of the NYN-domain- containing RNAse family.
Pfam PF18221: Mutator 2 Fork head associated domain (domain)
This is the N-terminal forkhead-associated (FHA) domain found in Drosophila mutator 2 (MU2) protein. FHA domains are generally phosphothreonine (pThr) specific-binding domains and are present in DNA repair and checkpoint proteins. However, phosphothreonine binding is not conserved in the MU2 active site pocket due to the absence of three key residues needed for pThr binding. Dimerization, is conserved between FHA domains of Drosophila MU2 and human MDC1 albeit through different interfaces. The MU2 FHA domain dimerizes via the beta-sheet 2, the MDC1 FHA domain dimerizes via the opposite beta-sheet 1.
Pfam PF07906: ShET2 enterotoxin, N-terminal region (family)
The members of this family are are sequences that are similar to the N-terminal half of the ShET2 enterotoxin produced by Shigella flexneri ([swissprot:Q47635]) and Escherichia coli ([swissprot:Q47634]). This protein was found to confer toxigenicity in the Ussing chamber, and the N-terminal region was found to be important for the protein's enterotoxic effect. It is thought to be a hydrophobic protein that forms inclusion bodies within the bacterial cell, and may be secreted by the Mxi system. Most members of this family are annotated as putative enterotoxins, but one member ([swissprot:Q8X606]) is a regulator of acetyl CoA synthetase, and another two members ([swissprot:P76205] and [swissprot:P23325]) are annotated as ankyrin-like regulatory proteins and contain Ank repeats ([pfam:PF00023]).
Pfam PF17001: Type III secretion basal body protein I, YscI, HrpB, PscI (family)
T3SS_basalb_I represents a family of Gram-negative type III secretion basal body proteins I. It is the inner rod protein of the secreted needle. YscI is suggested to form a rod that allows substrate passage across the inner membrane of the needle protein YscF through it.
Pfam PF03416: Peptidase C54 catalytic domain (domain)
This is the catalytic domain of of cysteine peptidases from  C54 family, which includes cysteine protease ATG4 from human and its homologues from fungi and plants. ATG4 plays a key role in cytoplasm to vacuole transport (Cvt) and autophagy by mediating both proteolytic activation and delipidation of ATG8.
Pfam PF03315: Serine dehydratase beta chain (domain)
L-serine dehydratase ([ec:4.2.1.13]) is a found as a heterodimer of alpha and beta chain or as a fusion of the two chains in a single protein. This enzyme catalyses the deamination of serine to form pyruvate. This enzyme is part of the gluconeogenesis pathway.
Pfam PF07418: Acidic phosphoprotein precursor PCEMA1 (family)
This family consists of several acidic phosphoprotein precursor PCEMA1 sequences which appear to be found exclusively in Plasmodium chabaudi. PCEMA1 is an antigen that is associated with the membrane of the infected erythrocyte throughout the entire intraerythrocytic cycle. The exact function of this family is unclear.
Pfam PF25114: AtTam38 family (family)
This entry represents the AtTam38 protein from Arabidopsis thaliana and related plant proteins. AtTam38 is a component of the AtYcf2-FtsHi complex. AtTam38 serves as an anchor of the stromal motor module to the IEM (inner envelope membrane of the chloroplast). It plays a key role in AtYcf2-FtsHi assembly and maintenance of the tilted posture of the motor module.
Pfam PF09466: Hypothetical protein Yqai (domain)
This hypothetical protein is expressed in bacteria, particularly Bacillus subtilis. It forms a homo-dimer, with each monomer containing an alpha helix and four beta strands.
Pfam PF23106: Teneurin-like EGF domain (domain)
This entry contains EGF domains that are commonly found in the tenascin and teneurin-like proteins.
Pfam PF10254: PACS-1 cytosolic sorting protein (family)
PACS-1 is a cytosolic sorting protein that directs the localisation of membrane proteins in the trans-Golgi network (TGN)/endosomal system. PACS-1 connects the clathrin adaptor AP-1 to acidic cluster sorting motifs contained in the cytoplasmic domain of cargo proteins such as furin, the cation-independent mannose-6-phosphate receptor and in viral proteins such as human immunodeficiency virus type 1 Nef.
Pfam PF24082: SPEF2 C-terminal domain (domain)
This domain is found in the axoneme central apparatus (CA) associated proteins such as Chlamydomonas Central pair complex 1 (CPC1) and its mammalian orthologues Sperm flagellar protein 2 (SPEF2). CPC1 is located at C1 microtubule. Most of the distal components of the C1b projection bind CPC1 and its correct recruitment and positioning is critical to the formation of the C1b projection, and ciliary motility in Chlamydomonas and humans. CPC1 serves as the rachis of the entire C1b arm. This domain is predicted to fold into two EF-hand pairs that seem to lack the Ca2+-coordinating residues.
Pfam PF08157: NUC129 domain (domain)
This C terminal domain is found in a novel family of hypothetical nucleolar proteins.
Pfam PF00463: Isocitrate lyase family (domain)
Isocitrate lyase (4.1.3.1)  is an enzyme that catalyzes the conversion of isocitrate to succinate and glyoxylate. This is the first step in the glyoxylate bypass, an alternative to the tricarboxylic acid cycle (also known as the TCA cycle) in bacteria, fungi and plants. A cysteine, a histidine and a glutamate or aspartate have been found to be important for the enzyme's catalytic activity. Only one cysteine residue is conserved between the sequences of the fungal, plant and bacterial enzymes; it is located in the middle of a conserved hexapeptide.

Mitochondrial 2-methylisocitrate lyase ICL2 from the yeast Saccharomyces cerevisiae does not act on isocitrate but on 2-methylisocitrate. It catalyses the formation of pyruvate and succinate during the metabolism of endogenous propionyl-CoA . Methylisocitrate lyase, mitochondrial from the filamentous fungus Aspergillus nidulans is responsible for the same reaction .
Wikipedia: Isocitrate lyase, or ICL, is an enzyme in the glyoxylate cycle that catalyzes the cleavage of isocitrate to succinate and glyoxylate. Together with malate synthase, it bypasses the two decarboxylation steps of the tricarboxylic acid cycle and is used by bacteria, fungi, and plants.
Pfam PF11032: ApoM domain (domain)
ApoM is a 25 kDa plasma protein associated with high-density lipoproteins (HDLs). ApoM is important in the formation of pre-ss-HDL and also in increasing cholesterol efflux from macrophage foam cells. Lipoproteins consist of lipids solubilized by apolipoproteins. ApoM lacks an external amphipathic motif and is uniquely secreted to plasma without cleavage of its terminal signal peptide.
Wikipedia: Apolipoprotein M is an apolipoprotein and member of the lipocalin protein family that in humans is encoded by the APOM gene. It is found associated with high density lipoproteins and to a lesser extent with low density lipoproteins and triglyceride-rich lipoproteins. The encoded protein is secreted through the plasma membrane but remains membrane-bound, where it is involved in lipid transport. Two transcript variants encoding two different isoforms have been found for this gene, but only one of them has been fully characterized. It lacks an external amphipathic motif and is uniquely secreted to plasma without cleavage of its terminal signal peptide. The average molecular weight is 21253 Da, and the monoisotopic molecular weight is 21239 Da.
Pfam PF03235: GmrSD restriction endonuclease, N-terminal domain (domain)
This entry (previously known as DUF262) represents a domain found N-terminal in the GmrSD family of modification-dependent restriction endonuclease, including BrxU and SspE proteins. BrxU is a type IV DNA modification-dependent restriction enzyme, which is promiscuous and uses a range of nucleotide and metal co-factors to recognise and cleave DNA that contains any of at least three different modifications, and this activity is dependent on the initial nucleotide-driven dissociation of BrxU dimers, and subsequent nucleotide hydrolysis. SspE is a dual-function protein that exerts both N-terminal NTPase and C-terminal DNA nicking nuclease activities to defend against phage infection. BrxU targets and cleaves DNA containing one of at least three DNA modifications, 5mC, 5hmC or glc-5hmC whereas SspE has a phosphorothioate (PT) modification-binding preference and utilizes epigenetic PT modification to accomplish self-nonself discrimination and to coordinate its NTPase and DNA nicking activities to fight against phages. The domain represented in this entry is involved in nucleotide binding, recognition and hydrolysis.
Pfam PF20479: TMEM128 protein (family)
This entry represents the uncharacterised TMEM128 protein which contains four transmembrane helices. This protein is resident in the endoplasmic reticulum.
Pfam PF20439: Sporulation stage IV protein A, C-terminal (domain)
SpoIVA (Sporulation stage IV protein A) acts in the mother cell compartment and plays a role in spore coat morphogenesis. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species. This entry represents the C-terminal domain of SpoIVA, which plays a key role in targeting the protein to the outer forespore membrane, in particular the five hydrophobic residues at the extreme C-terminal are essential for this function. Structure predictions suggest that it has three conserved alpha helices followed by a beta-hairpin.
Pfam PF02585: GlcNAc-PI de-N-acetylase (family)
Members of this family are related to PIG-L an N-acetylglucosaminylphosphatidylinositol de-N-acetylase ([ec:3.5.1.89]) that catalyses the second step in GPI biosynthesis.
Pfam PF19863: Family of unknown function (DUF6337) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000791) is described by MIBiG as an example of the following biosynthetic class, saccharide, in particular the O-antigen biosynthetic gene cluster from Cronobacter sakazakii.
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 PF14058: PcfK-like protein (family)
The PcfK-like protein family includes the Enterococcus faecalis PcfK protein [swissprot:Q82YK9] which is functionally uncharacterised. This family of proteins is found in bacteria and viruses. Proteins in this family are typically between 137 and 257 amino acids in length. There are two completely conserved residues (D and L) that may be functionally important.
Pfam PF07356: Protein of unknown function (DUF1481) (family)
This family consists of several hypothetical bacterial proteins of around 230 residues in length. Members of this family are often referred to as YjaH and are found in the Orders Vibrionales and Enterobacteriales. 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 PF01724: Domain of unknown function DUF29 (family)
This family consists of various hypothetical proteins from cyanobacteria, none of which are functionally described. The aligned region is approximately 120-140 amino acids long corresponding to almost the entire length of the proteins in the family. [swissprot:Q2RPE2], PDB:3fcn, is a small protein that has a novel all-alpha fold. The N-terminal helical hairpin is likely to function as a dimerisation module. This protein is a member of PFam family PF01724. The function of this protein is unknown. One protein sequence contains a fusion of this protein and a DnaB domain, suggesting a possible role in DNA helicase activity (hypothetical). Dali hits have low Z and high rmsd, suggesting probably only topological similarities (not functional relevance) (details derived from TOPSAN). The family has several highly conserved sequence motifs, including YD/ExD, DxxNVxEEIE, and CPY/F/W, as well as conserved tryptophans.
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 PF21565: Immune protein Tsi1 (family)
This protein family includes Immune protein Tsi1 from Pseudomonas aeruginosa and similar proteins predominantly from bacteria. Tsi1 plays a role in preventing early activation of toxin Tse1. Tsi1 binds to a large surface of Tse1 and thereby occludes the active site to specifically inhibits enzyme activity by forming a hydrogen bond with the catalytic diad. It adopts an all-beta fold consisting of 14 beta-strands, which constitute three antiparallel blade-shaped beta-sheets.
Pfam PF22952: Eukaryotic type KH-domain (KH-domain type I) (domain)
This entry represents a KH domain, which is typically found in RNA-binding proteins along with many other KH domains belonging to [pfam:PF00013].
Pfam PF10961: Selenoprotein SelK_SelG (family)
This entry inclues a group of eukaryotic selenoproteins,  such as SelK and SelG. SelK seems to play an important  role in protecting cells from endoplasmic reticulum  stress induced apoptosis. SelG may be involved in  regulating the redox state of the cell.
Pfam PF16494: C-terminal extension of sodium/calcium exchanger domain (family)
Na_Ca_ex_C is a region of the higher eukaryote sodium/calcium exchanger domain that extends toward the C-terminal, and is cytoplasmic.
Pfam PF19010: Family of unknown function (DUF5739) (family)
A highly conserved domain of unknown function found in various Platyhelminthes.
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 PF05899: EutQ-like cupin domain (domain)
This entry represents the cupin domain, with a conserved jelly roll-like beta-barrel fold capable of homodimerisation found in bacteria, plant and fungi. It is present in EutQ family from the eut operon, involved in ethanolamine degradation. EutQ is essential during anoxic growth and has acetate kinase activity. The cupin domain from EutQ does not possess the His residues responsible for metal coordination in other classes of cupins. This domain is also found in (S)-ureidoglycine aminohydrolase (UGlyAH) from E.coli, which is involved in the anaerobic nitrogen utilisation via the assimilation of allantoin. It catalyses the deamination of allantoin to produce S-ureidoglycolate and ammonia from S-ureidoglycine.
Wikipedia: The cupin superfamily is a diverse superfamily of proteins named after its conserved barrel domain. The superfamily includes a wide variety of enzymes as well as non-enzymatic seed storage proteins.
Pfam PF17835: NOG1 N-terminal helical domain (domain)
This domain is found at the N-terminus of NOG1 GTPase proteins.
Pfam PF17924: Tetracyclin repressor-like, C-terminal domain (domain)
TetR family regulators are involved in the transcriptional control of multidrug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity. The TetR proteins identified in overm ultiple genera of bacteria and archaea share a common helix-turn-helix (HTH) structure in their DNA-binding domain. However, TetR proteins can work in different ways: they can bind a target operator directly to exert their effect (e.g. TetR binds Tet(A) gene to repress it in the absence of tetracycline), or they can be involved in complex regulatory cascades in which the TetR protein can either be modulated by another regulator or TetR can trigger the cellular response. TetR regulates the expression of the membrane-associated tetracycline resistance protein, TetA, which exports the tetracycline antibiotic out of the cell before it can attach to the ribosomes and inhibit protein synthesis. TetR blocks transcription from the genes encoding both TetA and TetR in the absence of antibiotic. The C-terminal domain is multi-helical and is interlocked in the homodimer with the helix-turn-helix (HTH) DNA-binding domain. This entry represents the C-terminal domain present the transcriptional regulator heme-regulated transporter regulator (HrtR), which senses and binds a heme molecule as its physiological effector to regulate the expression of the heme-efflux system responsible for heme homeostasis in L. lactis.
Pfam PF13279: Thioesterase-like superfamily (domain)
This family contains a wide variety of enzymes, principally thioesterases. These enzymes are part of the Hotdog fold superfamily.
Pfam PF09494: Slx4 endonuclease (domain)
The Slx4 protein is a heteromeric structure-specific endonuclease found from fungi to mammals.  Slx4 with Slx1 acts as a nuclease on branched DNA substrates, particularly simple-Y, 5'-flap, or replication fork structures by cleaving the strand bearing the 5' non-homologous arm at the branch junction and thus generating ligatable nicked products from 5'-flap or replication fork substrates.