SII-SWORD/CoKE huggingface dataset:
Pfam PF13443: Cro/C1-type HTH DNA-binding domain (domain)
This is a helix-turn-helix domain that probably binds to DNA.
Wikipedia: Helix-turn-helix is a DNA-binding domain (DBD). The helix-turn-helix (HTH) is a major structural motif capable of binding DNA. Each monomer incorporates two α helices, joined by a short strand of amino acids, that bind to the major groove of DNA. The HTH motif occurs in many proteins that regulate gene expression. It should not be confused with the helix–loop–helix motif.
Pfam PF10141: Single-strand DNA-specific exonuclease, C terminal domain (family)
Members of this set of prokaryotic domains are found in a set of single-strand DNA-specific exonucleases, including RecJ. Their exact function has not, as yet, been determined.
Pfam PF21443: G3P, pilus binding domain (domain)
Attachment protein G3P from filamentous phages plays essential roles both in the penetration of the viral genome into the bacterial host via pilus retraction and in the extrusion process. In the initial stages of infection, G3P mediates adsorption of the phage to its primary receptor, the tip of host F-pilus. Subsequent interaction with the host entry receptor tolA induces penetration of the viral DNA into the host cytoplasm. This entry represents the N-terminal (N1) pilus-binding domain from Salmonella phage IKe and Enterobacteria phage I2-2 GP3. It clamps together with the adjacent N2 domain (referred to as TolA binding domain in) by the hinge region to form a bilobal, horseshoe-like structure.
Pfam PF07184: Citrus tristeza virus P33 protein (family)
This family consists of several Citrus tristeza virus (CTV) P33 proteins. The function of P33 is unclear although it is known that the protein is not needed for virion formation.
Pfam PF02791: DDT domain (family)
The DDT domain is named after (DNA binding homeobox and Different  Transcription factors) and is approximately 60 residues in length. Along with the WHIM motifs, it comprises an entirely alpha  helical module found in diverse eukaryotic chromatin proteins.  Based on the structure of Ioc3, this module is inferred to  interact with nucleosomal linker DNA and the SLIDE domain of ISWI  proteins. The resulting complex forms a protein ruler that  measures out the spacing between two adjacent nucleosomes.  In particular, the DDT domain, in combination with the WHIM1 and WHIM2 motifs form the SLIDE domain binding pocket.
Pfam PF07530: Associated with zinc fingers (domain)
This function of this domain is unknown and is often found associated with [pfam:PF00096].
Pfam PF03949: Malic enzyme, NAD binding domain (domain)
This entry represents the NAD-binding domain of malic enzymes.
Malic enzymes (malate oxidoreductases) catalyse the oxidative decarboxylation of malate to form pyruvate, a reaction important in a number of metabolic pathways - e.g. carbon dioxide released from the reaction may be used in sugar production during the Calvin cycle of photosynthesis . There are 3 forms of the enzyme : an NAD-dependent form that decarboxylates oxaloacetate; an NAD-dependent form that does not decarboxylate oxalo-acetate; and an NADPH-dependent form . Other proteins known to be similar to malic enzymes are the Escherichia coli scfA protein; an enzyme from Zea mays (Maize), formerly thought to be cinnamyl-alcohol dehydrogenase ; and the hypothetical Saccharomyces cerevisiae protein YKL029c.

Studies on the duck liver malic enzyme reveals that it can be alkylated by bromopyruvate, resulting in the loss of oxidative decarboxylation and the subsequent enhancement of pyruvate reductase activity . The alkylated form is able to bind NADPH but not L-malate, indicating impaired substrate or divalent metal ion-binding in the active site . Sequence analysis has highlighted a cysteine residue as the point of alkylation, suggesting that it may play an important role in the activity of the enzyme , although it is absent in the sequences from some species.

Malic enzyme is a tetramer comprised of subunits with four domains each .
Pfam PF04356: Protein of unknown function (DUF489) (family)
Protein of unknown function, cotranscribed with purB in Escherichia coli, but with function unrelated to purine biosynthesis.
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 PF06639: Basal layer antifungal peptide (BAP) (family)
This family consists of several basal layer antifungal peptide (BAP) sequences specific to Zea mays. The BAP2 peptide exhibits potent broad-range activity against a range of filamentous fungi, including several plant pathogens.
Pfam PF23523: Apicomplexa microprotein (family)
This protein family includes uncharacterised microproteins encoded by small open reading frames (smORFs) from apicomplexa, including [swissprot:A7ARX4] from the parasite Babesia bovis.
Pfam PF02108: Flagellar assembly protein FliH (family)
This entry represents a region found in the flagellar assembly protein FliH, as well as in type III secretion system protein HrpE.

Many flagellar proteins are exported by a flagellum-specific export pathway. Attempts have been made to characterise the apparatus responsible for this process, by designing assays to screen for mutants with export defects. Experiments involving filament removal from temperature-sensitive flagellar mutants of Salmonella typhimurium have shown that, while most mutants were able to regrow filaments, flhA, fliH, fliI and fliN mutants showed no or greatly reduced regrowth. This suggests that the corresponding gene products are involved in the process of flagellum-specific export . The sequence of fliH has been deduced and shown to encode a protein of molecular mass of 25,782 Da.

Bacterial HrpE proteins are belived to function on the type III secretion system, specifically the secretion of HrpZ (harpinPss) .
Pfam PF24233: Family of unknown function (DUF7446) (family)
This entry represents a highly conserved domain found in various bacteriophages, particularly those infecting Salmonella and related bacteria. The domain is also present in some bacterial species, suggesting possible horizontal gene transfer. The function is unknown, but the high degree of conservation implies an important role in phage biology. A conserved motif DVT is present centrally in many family members. The aspartate and threonine form side chain hydrogen bonds that help stabilise the dimeric interaction.  Structure prediction suggests these proteins form a confident homodimer (iPTM=0.83).
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 PF16301: Domain of unknown function (DUF4943) (family)
This small family consists of several uncharacterized proteins around 170 residues in length and is mainly found in various Bacteroides species. The function of this family is unknown.
Pfam PF23046: UBE2O, tandem tSH3-B domain (domain)
This domain is found in the human E3-independent E2 ubiquitin-conjugating enzyme UBE2O and related proteins. UBE2O is involved in the monoubiquitination of diverse targets to mediate important processes such as targeting proteins for quality control, regulation of nuclear trafficking of chromatin-associated proteins and clearing ribosomes during erythropoiesis. UBE2O is a multidomain protein composed of several SH3-like domains, UBC domain and a CR3 helix. The domain represented by this entry folds into two tandem intertwined beta-barrels each of which with typical SH3 topology. This tandem SH3-like domain is involved in binding to NAP1L1, one of the major regulators of the UBE2O target selection.
Pfam PF08084: PROCT (NUC072) domain (domain)
The PROCT domain is the C-terminal domain in pre-mRNA splicing factors of PRO8 family.
Pfam PF03552: Cellulose synthase (family)
Cellulose, an aggregate of unbranched polymers of beta-1,4-linked glucose residues, is the major component of wood and thus paper, and is synthesised by plants, most algae, some bacteria and fungi, and even some animals. The genes that synthesise cellulose in higher plants differ greatly from the well-characterised genes found in Acetobacter and Agrobacterium sp. More correctly designated as 'cellulose synthase catalytic subunits', plant cellulose synthase (CesA) proteins are integral membrane proteins, approximately 1,000 amino acids in length. There are a number of highly conserved residues, including several motifs shown to be necessary for processive glycosyltransferase activity.
Wikipedia: The UDP-forming form of cellulose synthase is the main enzyme that produces cellulose. Systematically, it is known as UDP-glucose:(1→4)-β-D-glucan 4-β-D-glucosyltransferase in enzymology. It catalyzes the chemical reaction:UDP-glucose + [(1→4)-β-D-glucosyl]n = UDP + [(1→4)-β-D-glucosyl]n+1
Pfam PF01065: Hexon, adenovirus major coat protein, N-terminal domain (domain)
Hexon is the major coat protein from adenovirus type 2. Hexon forms a homo-trimer.  The 240 copies of the hexon trimer are organised so that 12 lie on each of the 20 facets. The central 9 hexons in a facet are cemented together by 12 copies of polypeptide IX.  The penton complex, formed by the peripentonal hexons and base hexon (holding in place a fibre), lie at each of the 12 vertices. The N and C-terminal domains adopt the same PNGase F-like fold although they are significantly different in length.
Wikipedia: In molecular biology, the hexon protein is a major coat protein found in adenoviruses. Hexon coat proteins are synthesised during late infection and form homo-trimers. The 240 copies of the hexon trimer that are produced are organised so that 12 lie on each of the 20 facets. The central 9 hexons in a facet are cemented together by 12 copies of polypeptide IX. The penton complex, formed by the peripentonal hexons and penton base, lie at each of the 12 vertices. The hexon coat protein is a duplication consisting of two domains with a similar fold packed together like the nucleoplasmin subunits. Within a hexon trimer, the domains are arranged around a pseudo 6-fold axis. The domains have a beta-sandwich structure consisting of 8 strands in two sheets with a jelly-roll topology; each domain is heavily decorated with many insertions. Some hexon proteins contain a distinct C-terminal domain.
Pfam PF21120: Archaeal MCM, winged-helix (domain)
This entry represents the conserved truncated winged helix domain of minichromosome maintenance complex (MCM, a replicative DNA helicase) from archaea, which lacks the two typical 'wings' of canonical WH domains.
Pfam PF23804: Family of unknown function (DUF7179) (family)
This entry represents an uncharacterized protein domain found in phage, predominantly those infecting bacteria in the Enterobacteriaceae family such as Escherichia, Salmonella, Klebsiella and Vibrio. The protein is typically around 80 to 100 amino acids in length. In some phage the protein contains a predicted central coiled-coil region.  The function of this protein family is currently 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 PF01926: 50S ribosome-binding GTPase (family)
The full-length GTPase protein is required for the complete activity of the protein of interacting with the 50S ribosome and binding of both adenine and guanine nucleotides, with a preference for guanine nucleotide.
Pfam PF04193: PQ loop repeat (repeat)
Members of this family are all membrane bound proteins possessing a pair of repeats each spanning two transmembrane helices connected by a loop. The PQ motif found on loop 2 is critical for the localisation of cystinosin to lysosomes. However, the PQ motif appears not to be a general lysosome-targeting motif. It is thought likely to possess a more general function. Most probably this involves a glutamine residue. Family members are membrane transporters since two members, cystinosin and PQLC2, transport cystine and cationic amino acids, respectively, across the lysosomal membrane. The 2nd PQ-loop of cystinosin hosts the substrate-coupled H+ binding site underlying its H+ symport mechanism, suggesting that PQ-loop repeats have functional significance. It is thus likely that PQ-loop-containing proteins act as a family of membrane transporters. Some transport cystine and cationic amino acids, respectively, across the lysosomal membrane. Others transport lysine and or arginine across the lysosomal membrane in order to maintain the acidic homoeostasis.
Pfam PF06550: Signal-peptide peptidase, presenilin aspartyl protease (family)
SPP is a family of signal-peptide aspartyl proteases. The family carries the characteristic catalytic aspartate GXGD motif, and members are integral membrane peptidases of the presenilin-type with nine transmembrane regions. UniProtKB:Q18K19 is part of the TCDB family 1.A.54.3.4, the presenilin er Ca(2+) leak channel (presenilin).
Pfam PF04981: NMD3 family (family)
The NMD3 protein is involved in nonsense mediated mRNA decay. This amino terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway.
Pfam PF08765: Mor transcription activator family (domain)
Mor (Middle operon regulator) is a sequence specific DNA binding protein.  It mediates transcription activation through its interactions with the C-terminal domains of the alpha and sigma subunits of bacterial RNA polymerase.  The N terminal region of Mor is the dimerisation region, and the C terminal contains a helix-turn-helix motif which binds DNA.
Pfam PF23841: Phage tail termination protein (domain)
This entry represents a protein domain found in some bacteriophages that infect Actinobacteria. It is located in the tail region and acts as a terminator or cap the end of the tail. The domain is around 130-170 amino acids in length.
Pfam PF09668: Aspartyl protease (family)
This family of eukaryotic aspartyl proteases have a fold similar to retroviral proteases which implies they function proteolytically during regulated protein turnover.
Wikipedia: Aspartic proteases are a catalytic type of protease enzymes that use an activated water molecule bound to one or more aspartate residues for catalysis of their peptide substrates. In general, they have two highly conserved aspartates in the active site and are optimally active at acidic pH. Nearly all known aspartyl proteases are inhibited by pepstatin.
Pfam PF10847: Protein of unknown function (DUF2656) (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 PF24381: Family of unknown function (DUF7537) (family)
This family includes a group of proteins from archaea. Members are predicted to adopt a mainly beta structure.
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 PF23967: Family of unknown function (DUF7295) (family)
This entry represents an uncharacterized protein found in various bacteriophages that infect Salmonella, Escherichia, Shigella, Pantoea and Serratia species. This family includes a member in bacteriophage T5. The function of this protein is currently unknown. Structure prediction does not predict a globular compact fold for this protein.
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 PF16343: Domain of unknown function (DUF4973) (domain)
This family consists of uncharacterized proteins around 340 residues in length and is mainly found in various Bacteroides and  Prevotella species. The function of this protein is unknown.
Pfam PF07550: Heme-binding protein Shr-like, Hb-interacting domain (domain)
The Hb-interacting domain (HID) is found duplicated in Heme-binding protein Shr from Streptococcus pyogenes, a potentially lethal human pathogen, and in one to six copies in other uncharacterised bacterial proteins. Shr is a virulence factor that captures Hb and binds to the oxidized form of heme through an N-terminal region that contains two copies of this domain. HID shows a beta-sandwich-type fold in which two antiparallel beta-sheets are flanked by an alpha-helix.
Pfam PF13062: Protein of unknown function (DUF3924) (domain)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 60 amino acids in length.
Pfam PF11821: Alternative complex III, ActD subunit (family)
Alternative complex III (ACIII) is a multisubunit quinol:electron acceptor oxidoreductase that couples quinol oxidation with transmembrane proton translocation similar to bc1 complex (or complex III). It is a key component of the respiratory and photosynthetic electron transport chains in many bacteria. It has six subunits (ActA-F), ActD subunit represented in this entry. The transmembrane regions of this subunit form part of the TM arm of the complex. Although the function of this subunit is not clear, it may play a role in stabilizing the TM region of ACIII which contributes to a stable menaquinol binding pocket and proton translocation passage.
Pfam PF07081: Protein of unknown function (DUF1349) (domain)
This family consists of several hypothetical bacterial proteins but contains one sequence ([swissprot:P40893]) from Saccharomyces cerevisiae. Members of this family are typically around 200 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 PF13922: PHD domain of transcriptional enhancer, Asx (domain)
This is the DNA-binding domain on the additional sex combs-like 1 proteins. The Asx protein acts as an enhancer of trithorax and polycomb in displaying bidirectional homoeotic phenotypes in Drosophila, suggesting that it is required for maintenance of both activation and silencing of Hox genes. Asx is required for normal adult haematopoiesis and its function depends on its cellular context.
Pfam PF03016: Exostosin GT47 domain (domain)
The EXT family is a family of tumour suppressor genes. Mutations of EXT1 [swissprot:Q16394] on 8q24.1, EXT2 [swissprot:Q93063] on 11p11-13, and EXT3 on 19p have been associated with the autosomal dominant disorder known as hereditary multiple exostoses (HME). This is the most common known skeletal dysplasia. The chromosomal locations of other EXT genes suggest association with other forms of neoplasia.  EXT1 and EXT2 have both been shown to encode a heparan sulphate polymerase with both D-glucuronyl (GlcA) and N-acetyl-D-glucosaminoglycan (GlcNAC) transferase activities. The nature of the defect in heparan sulphate biosynthesis in HME is unclear. This entry represents the b-glucuronyltransferase domain found at the N-terminal of EXTs.
Pfam PF10177: Uncharacterised conserved protein (DUF2371) (family)
This is a family of proteins conserved from nematodes to humans. The function is not known.
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 PF22253: Domain of unknown function (DUF6948) (domain)
This domain is found either as standalone or in combination with other domains in a group of uncharacterised proteins. It is distantly related to EDC3 mRNA-decapping protein 3 and it could be involved in RNA-binding. It is predicted to adopt a barrel-like structure with a typical Sm-like fold. The pair of glycines responsible for maintaining the Sm-barrel curvature are also conserved in the members of this family.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF17651: RACo middle region (domain)
This family includes reductive activator of CoFeSP (RACo) proteins, [swissprot:Q3ACS2]. Structure analysis of RACo indicate that it contains 4 regions: N-terminal region [pfam:PF00111] (residues 3-94) binding the [2Fe-2S] cluster, a linker region (residues 95-125), the middle region (residues 126-206), and the large C-terminal domain [pfam:PF14574] (residues 207-630). This entry pertains to the middle region. This region contains residues in their alpha-helices  (H6 and H7) that mediate dimerization with subdomain I of the  C-terminal domain.
Pfam PF18894: Putative phage metallopeptidase (domain)
This entry represents a probable metallopeptidase found in a variety of phage and bacterial proteomes.
Pfam PF21601: GldM second domain (domain)
This immunoglobulin-like domain is found in bacteria in the GldM protein.  GldM, is named for the member from Cytophaga johnsonae (Flavobacterium johnsoniae), which is required for a type of rapid gliding motility found in certain members of the Bacteriodetes.
Pfam PF06505: Activator of aromatic catabolism (family)
This domain is found at the N terminus of a subset of sigma54-dependent transcriptional activators in several proteobacteria, including activators of phenol degradation such as XylR. It is found adjacent to [pfam:PF02830].