SII-SWORD/CoKE huggingface dataset:
Pfam PF16963: PelD GGDEF domain (domain)
This degenerate GGDEF domain is found at the C-terminus of PelD, a membrane-bound c-di-GMP-specific receptor. It contains an RXXD motif resembling the allosteric inhibition site found in diguanylate cyclases . In PelD this RXXD motif binds to dimeric c-di-GMP.
Pfam PF20977: Glutamyl-tRNA(Gln) amidotransferase subunit F (family)
GatFAB is a trimeric tRNA-dependent amidotransferase (AdT) that allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in the mitochondria. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu-tRNA(Gln). This family represents GatF (also known as GFT1), an essential subunit of the yeast tRNA-dependent amidotransferase. GatF is a fungi-specific orthologue of the GatC subunit found in all other known heterotrimeric AdTs (GatCAB). GatF C-terminal encircles the GatA-GatB interface in the same manner as GatC to maintain GatA-GatB assembly, whereas the N-terminal region mediates additional hydrophobic and hydrophilic interactions with GatA, which may modulate GatA folding and stability.
Pfam PF19792: Family of unknown function (DUF6276) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in archaea. Proteins in this family are approximately 130 amino acids in length. They contain an N-terminal zinc binding domain.
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 PF16178: Anoctamin, dimerisation domain (domain)
This entry represents the dimerisation domain of anoctamin family of proteins. Seven members can be divided into two subfamilies; Ca2-dependent Cl(-) channels (TMEM16A and 16B) and Ca2-dependent lipid scramblases (TMEM16C, 16D, 16F, 16G, and 16J). This domain is responsible for creating the homodimeric architecture of the chloride-channel proteins.
Pfam PF14896: EmbC C-terminal domain (domain)
Arabinosyltransferase is involved in arabinogalactan (AG) biosynthesis pathway in mycobacteria. AG is a component of the macromolecular assembly of the mycolyl-AG-peptidoglycan complex of the cell wall. This enzyme has important clinical applications as it is believed to be the target of the antimycobacterial drug Ethambutol. This domain represents the C-terminal extracellular domain that is likely to bind to carbohydrate.
Wikipedia: An arabinosyltransferase is a transferase enzyme acting upon arabinose.
This enzyme is involved in polymerisation of arabinogalactan. Mycobacterially, the more precise term is arabinofuranosyltransferase, since the arabinose residues occur only in a furanose form.
Pfam PF02291: Transcription initiation factor IID, 31kD subunit (domain)
This family represents the N-terminus of the 31kD subunit (42kD in  drosophila) of transcription initiation factor IID (TAFII31). TAFII31 binds to p53, and is an essential requirement for p53 mediated transcription activation.
Wikipedia: The TBP-associated factors (TAF) are proteins that associate with the TATA-binding protein in transcription initiation. It is a part of the transcription initiation factor TFIID multimeric protein complex. It also makes up many other factors, including SL1. They mediate the formation of the transcription preinitiation complex, a step preceding transcription of DNA to RNA by RNA polymerase II.
Pfam PF07840: FadR C-terminal domain (family)
This family contains sequences that are similar to the fatty acid metabolism regulator protein (FadR, [swissprot:P09371]). This functions as a dimer, with each monomer being composed of an N-terminal DNA-binding domain and a regulatory C-terminal domain. A linker comprising two short alpha helices joins the two domains. In the C-terminal domain, an antiparallel array of six alpha helices forms a barrel-like structure, while a seventh alpha helix forms a 'lid' at the end closest to the N-terminal domain. This structure was found to be similar to that of the C-terminal domain of the Tet repressor. Long-chain acyl-CoA thioesters interact directly and reversibly with the C-terminal domain, and this interaction affects the structure and therefore the DNA binding properties of the N-terminal domain.
Wikipedia: In molecular biology, the fatty acid metabolism regulator protein FadR, is a bacterial transcription factor.
Pfam PF00353: RTX calcium-binding nonapeptide repeat (4 copies) (repeat)
Gram-negative bacteria produce a number of proteins that are secreted into the growth medium by a mechanism by the type I secretion system that does not require a cleaved N-terminal signal sequence. These proteins, while having different functions, share two properties: they bind calcium and they contain a multiple tandem repeat of a nonapeptide . The nonapeptide is found in a group of bacterial exported proteins that includes haemolysin, cyclolysin, leukotoxin and metallopeptidases belonging to MEROPS peptidase family M10 (clan MA(M)), subfamily 10B (serralysin).

It has been suggested that the internally repeated domain of haemolysin may be involved in Ca-mediated binding to erythrocytes. It has been shown that such a domain is involved in the binding of calcium ions in a parallel Î² roll structure .
The Bordetella pertussis adenylate cyclase toxin tertiary structure has been solved. The C-terminal RTX repeats are Asp-rich, which bind calcium ions as the protein moves from the low calcium intercellular environment to a higher extracellular concentration of calcium ions. The C-terminal assembly containing the RTX repeats has been shown to form Î²-rolls, which prevent backsliding of the protein in the type I secretion system conduits and accelerating secretion of the large toxin .
Pfam PF23510: Apicomplexa microprotein (family)
This protein family includes uncharacterised microproteins encoded by small open reading frames (smORFs) from apicomplexa, including [swissprot:A7AQF6] from the parasite Babesia bovis.
Pfam PF23263: Mucin-4-like C8-3 domain (domain)
This domain is found in human Mucin-4 (MUC4) and related proteins including SUSD2, MESH etc. It is usually found next to VWD domain ([pfam:PF00094]). Despite lack of sequence similarity it is predicted to adopt similar structure to the C8-3 domain of MUC2 consisting of three alpha-helical bundle. This domain contains two highly conserved cysteine residues and these may engage in disulfide bond formation. MUC4 is a membrane-bound mucin which belongs to a family of highly glycosylated proteins that constitute the major component of the mucus.
Pfam PF14513: Diacylglycerol kinase N-terminus (domain)
This domain is found at the N-terminus of diacylglycerol kinases.
Pfam PF18173: Bacterial HORMA domain 2 (domain)
Family of bacterial HORMA domains found in conserved genome contexts with Pch2/TRIP13 P-loop NTPases. Acts as a 'third component' in broad class of conflict systems reliant on the production of second messenger nucleotide or nucleotide derivatives. Together with Pch2/TRIP13, could act as co-effectors or in regulation of other effectors of the systems. This domain found in bacterial proteins from the cyclic-oligonucleotide-based anti-phage signalling system (CBASS), such us CD-NTase-associated protein 7 from P. aeruginosa (Cap7), which is part of the type III-CBASS. CBSSs are a family of defence systems against bacteriophages.
Pfam PF16049: Frog antimicrobial peptide (family)
This family includes antimicrobial peptides such as Aurein-5 and Caerin 2 which are secreted from frog skin.
Pfam PF24670: Domain of unknown function (DUF7653) (domain)
This domain is found in uncharacterised proteins mainly from plants.
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 PF06678: Protein of unknown function (DUF1179) (family)
This family consists of several hypothetical Caenorhabditis elegans proteins of around 106 residues in length. The function of the 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 PF22150: Type IV pilin Tt1218 (domain)
The founding member of this family is Tt1218 that is a type IV pilin. This protein is likely involved in the formation of polymers that extend from the surface of the bacterial cell and could mediate a wide variety of functions such as adhesion, motility and natural competence. This domain is closely related to type II secretion pseudopilin EpsI. It consists of the canonical type IV pilin structural core comprising an alpha-helix packed against a four-stranded antiparallel beta-sheet.
Pfam PF04917: Bacterial shufflon protein, N-terminal constant region (family)
This family represents the high-similarity N-terminal 'constant region' shared by shufflon proteins.
Pfam PF21128: MCM4, winged helix domain (domain)
DNA replication licensing factor MCM4 is a component of the MCM2-MCM7 complex which consists of six sequence-related AAA+ type ATPases/helicases that form a heterohexameric ring essential for 'once per cell cycle' DNA replication initiation and elongation in eukaryotic cells. This is the winged helix domain (WHD) found at the C-terminal of MCM4. Upon ssDNA binding the MCM5-WHD moves out of the central channel and becomes disordered, the MCM6-WHD moves backward and away from the channel, and the MCM4-WHD now partially occludes the channel opening. These changes enable CMG (Cdc45, Mcm2-7, GINS, the eukaryotic replicative helicase) to encircle dsDNA, and is consistent with reports that showed the MCM2-7 matures into two fully assembled CMGs on dsDNA before origin DNA unwinding occurs.
Pfam PF07903: PaRep2a protein (family)
This is a family of proteins expressed by the  crenarchaeon Pyrobaculum aerophilum. The members  are highly variable in length and level of conservation.  The presence of numerous frameshifts and internal stop  codons in multiple alignments are thought to indicate  that most family members are no longer functional.
Pfam PF13863: Domain of unknown function (DUF4200) (family)
This family is found in eukaryotes. It is a coiled-coil domain of unknwon 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 PF24312: Nucleoporin POM152, Ig-like domain (domain)
This entry includes the Ig-like domains found in Nucleoporin POM152 from yeast, a component of the nuclear pore complex (NPC). POM152 is a glycoprotein subunit of transmembrane ring of NPC and is important for the assembly of the NPC.
Pfam PF21058: Stereocilin (repeat)
Stereocilin is expressed in the sensory hair cells and is associated with the stereocilia, the stiff microvilli forming the structure for mechanoreception of sound stimulation. It is essential for the formation of horizontal top connectors in hair cells, which leads to deafness when it is defective. This is a large secreted protein containing a large leucine-rich region.
Pfam PF15363: BTB/POZ domain-containing protein 8, C-terminal (domain)
This domain is found at the C terminus of BTB/POZ domain-containing protein 8 (BTBD8, also known as AP2-interacting clathrin-endocytosis protein). BTBD8  is involved in clathrin-mediated endocytosis at the synapse and plays a role in neuronal development and in synaptic vesicle recycling in mature neurons, a process required for normal synaptic transmission. There is a conserved ELET sequence motif. There are two completely conserved residues (S and E) that may be functionally important.
Pfam PF06175: tRNA-(MS[2]IO[6]A)-hydroxylase (MiaE) (domain)
This family consists of several bacterial tRNA-(MS(2)IO(6)A)-hydroxylase (MiaE) proteins. The modified nucleoside 2-methylthio-N-6-isopentenyl adenosine (ms2i6A) is present at position 37 (3' of the anticodon) of tRNAs that read codons beginning with U except tRNA(I,V Ser) in Escherichia coli. Salmonella typhimurium 2-methylthio-cis-ribozeatin (ms2io6A) is found in tRNA, probably in the corresponding species that have ms2i6A in E. coli. The miaE gene is absent in E. coli, a finding consistent with the absence of the hydroxylated derivative of ms2i6A in this species.
Pfam PF07653: Variant SH3 domain (domain)
SH3 (Src homology 3) domains are often indicative of a protein involved in  signal transduction related to cytoskeletal organisation. First described in the Src cytoplasmic tyrosine kinase [swissprot:P12931]. The structure is a partly opened beta barrel.
Wikipedia: The SRC Homology 3 Domain is a small protein domain of about 60 amino acid residues. Initially, SH3 was described as a conserved sequence in the viral adaptor protein v-Crk. This domain is also present in the molecules of phospholipase and several cytoplasmic tyrosine kinases such as Abl and Src. It has also been identified in several other protein families such as: PI3 Kinase, Ras GTPase-activating protein, CDC24 and cdc25. SH3 domains are found in proteins of signaling pathways regulating the cytoskeleton, the Ras protein, and the Src kinase and many others. The SH3 proteins interact with adaptor proteins and tyrosine kinases. Interacting with tyrosine kinases, SH3 proteins usually bind far away from the active site. Approximately 300 SH3 domains are found in proteins encoded in the human genome. In addition to that, the SH3 domain was responsible for controlling protein-protein interactions in the signal transduction pathways and regulating the interactions of proteins involved in the cytoplasmic signaling.
Pfam PF04554: Extensin-like region (disordered)
Extensins shares protein sequence similarity with hydroxyproline-rich glycoproteins (HRGPs) found in the plant extracellular matrix. They form a structural component which strengthens the primary cell wall; they can account for up to 20% of the dry weight of the cell wall. The key to the role of HRGPs in cell wall self-assembly and cell extension lies in their chemistry, which is dependent on extensive post-translational modifications (PTMs): hydroxylation, glycosylation, and cross-linking. Repetitive peptide motifs characterise HRGPs .
Pfam PF24525: TTC3, helical domain (domain)
This domain is found in human E3 ubiquitin-protein ligase TTC3 and in similar protein sequences predominantly found in vertebrates. TTC3 catalyzes the formation of 'Lys-48'- polyubiquitin chains and regulates Akt signalling, TGFB1- induced epithelial-mesenchymal transition and myofibroblast differentiation, neuronal differentiation and cell proliferation. This domain is predicted to adopt a helical configuration.
Pfam PF18494: Pullulanase Ins domain (domain)
Pullulanases (pullulan 6-glucanohydrolase, EC 3.2.1.41) are debranching enzymes that are able to hydrolyze the alpha-1,6-glycosidic linkage in pullulan, starch, amylopectin, and related oligosaccharides. Type I pullulanases specifically cleave the alpha-1,6-glycosidic linkages in pullulan and branched oligosaccharides to produce maltotriose and linear oligosaccharides, respectively. Structural analysis of Klebsiella lipoprotein pullulanase (PulA) illustrates that the catalytic core is composed of two major regions: the TIM-barrel domain A and beta-sandwich fold domain C. PulA contains an extra domain, a highly mobile Ins subdomain of unknown function which is inserted into the catalytic TIM-barrel domain A of Klebsiella pullulanases. The Ins subdomain is rich in helical and loop secondary structure. A disulfide bond between Cys491 and Cys506 and two Ca2+ ions presumably stabilizes this domain.This insertion is also found in pullulanases from other Gram-negative genera that have a functional T2SS, such as Vibrio, Aeromonas, and Photorhabdus. Functional analysis indicate that this domain is required for PulA secretion via the T2SS.
Pfam PF08873: Bacteriophage Mu, Gp37 (domain)
This family is represented by Bacteriophage Mu, Gp37 (also known as Probable tail terminator protein) which may stop tail tube polymerization by capping the rapidly polymerising tail tube once it has reached its requisite length and prevent its depolymerization. This family also has prophages matches, such as the Gp37 protein from the FluMu prophage.
Pfam PF05110: AF-4 proto-oncoprotein N-terminal region (family)
This family consists of AF4 (Proto-oncogene AF4) and FMR2 (Fragile X syndrome) nuclear proteins. These proteins have been linked to human diseases such as acute lymphoblastic leukaemia and mental disabilities. The family also contains a Drosophila AF4 protein homologue Lilliputian which contains an AT-hook domain.  Lilliputian represents a novel pair-rule gene that acts in cytoskeleton regulation, segmentation and morphogenesis in Drosophila.
Wikipedia: AF4/FMR2 (AFF) is a family of nuclear transcriptional activators that encourage RNA elongation. There are four genes in this family, all of which reside in the nucleus of the cells. The gene family includes AFF1/AF4, AFF2/FMR2, AFF3/LAF4 and AFF4/AF5q31. Within the family, the AFF2/FMR2 is silenced in FRAXE intellectual disability; while the other three gene families will form fusion genes as a consequence of chromosome translocations with the myeloid/lymphoid or mixed lineage leukemia gene in acute lymphoblastic leukemias. While different members of the AF4/FMR2 family are known for playing various roles in cells, they all commonly participate in the regulation of splicing and transcription.
Pfam PF01931: Protein of unknown function DUF84 (domain)
NTPase_I-T is a family of NTPases with supreme activity against ITP and XTP. Active site analysis and structure comparison of YjjX strongly suggested that it is an NTP binding protein with nucleoside triphosphatase activity. YjjX exhibits a mixed alpha-beta fold.
Pfam PF13788: Domain of unknown function (DUF4180) (family)
This presumed domain is functionally uncharacterised.
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 PF00280: Potato inhibitor I family (domain)
This family of proteinase inhibitors belong to MEROPS inhibitor family I13, clan IG. They inhibit peptidases of the S1 (IPR001254) and S8 (IPR000209) families . Potato inhibitor type I sequences are not solely restricted to potatoes but are found in other plant species for example: barley endosperm chymotrypsin inhibitor , and pumpkin trypsin inhibitor. Apart from leeches, e.g.Hirudo medicinalis (Medicinal leech), homologues are not found in metazoa . In general, the proteins have retained a specificity towards chymotrypsin-like and elastase-like proteases. Structurally these inhibitors are small (60 to 90 residues) and in contrast with other families of protease inhibitors, they lack disulphide bonds. The inhibitor is a wedge-shaped molecule, its pointed edge formed by the protease-binding loop, which contains the scissile bond. The loop binds tightly to the protease active site, subsequent cleavage of the scissile bond causing inhibition of the enzyme .

The inhibitors (designated type I and II) are synthesised in potato tubers, increasing in concentration as the tuber develops. Synthesis of the inhibitors throughout the plant is also induced by leaf damage; this systemic response being triggered by the release of a putative plant hormone.

Examples found in the bacteria and archaea are probable false positives.
Pfam PF14936: Tumour protein p53-inducible protein 11 (family)
TP53 is a tumour suppressor gene, when switched on it suppresses tumour development by inducing stable growth arrest or cell apoptosis. The tumour protein TP53 inducible protein 11 encoded for by the gene TP53I11, has a protein sequence of 189 amino acids in length and 21 kDa in mass. The role of this protein is thought to negatively regulate cell proliferation in response to stress, and therefore suppress tumour formation.
Pfam PF09830: ATP adenylyltransferase C-terminal domain (domain)
Members of this family of proteins catabolise Ap4N nucleotides (where N is A,C,G or U). Additionally they catalyse the conversion of adenosine-5-phosphosulfate (AMPs) plus Pi to ADP plus sulphate, the exchange of NDP and phosphate and the synthesis of Ap4A from AMPs plus ATP.
Pfam PF02740: Colipase, C-terminal domain (domain)
SCOP reports duplication of common fold with Colipase N-terminal domain.
Wikipedia: Colipase, abbreviated CLPS, is a protein co-enzyme that counteracts the inhibitory effect of intestinal bile acid on the enzymatic activity of pancreatic lipase. It is secreted by the pancreas in an inactive form, procolipase, which is activated in the intestinal lumen by trypsin.
Pfam PF01774: UreD urease accessory protein (family)
UreD is a urease accessory protein. Urease [pfam:PF00449] hydrolyses  urea into ammonia and carbamic acid. UreD is involved in  activation of the urease enzyme via the UreD-UreF-UreG-urease complex and is required for urease nickel metallocenter assembly.  See also UreF [pfam:PF01730], UreG [pfam:PF01495].
Pfam PF10563: Delta carbonic anhydrase (family)
Delta carbonic anhydrases are one of the at least five independently evolved families of carbonic anhydrases. Their activities, low CO2-induction, and localizations have been well studied in diatoms. The catalytic mechanism of delta CAs is currently unknown. Proteins of this family are also common in bacteria, but due to more distant relationship (identities less than 30% to the diatom delta CAs) and to the lack of experimental data the carbonic anhydrase activity is only putative in prokaryotic delta CAs.
Pfam PF09930: Predicted transporter (DUF2162) (family)
Members of this family of bacterial proteins are thought to be membrane transporters, but their exact function has not, as yet, been elucidated.
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.