SII-SWORD/CoKE huggingface dataset:
Pfam PF18090: Centromere-binding protein HTH domain (domain)
This domain is found in centromere-binding protein (SopB). SopB displays an intriguing range of DNA-binding properties essential for partition; it binds the centromere to form a partition complex, which recruits NTPase (SopA), and it also inhibits SopA polymerization. The domain has a helix-turn-helix (HTH) structure and is thought to be the specific DNA-binding domain mainly through residues from the recognition helix, alpha 3, of the HTH. The domain has show structural similarity to the DNA-binding domains of P1 ParB and KorB.
Pfam PF07771: Tick salivary peptide group 1 (family)
This contains a group of peptides derived from a salivary gland cDNA library of the tick Ixodes scapularis. Also present are peptides from a related tick species, Ixodes  ricinus. They are characterised by a putative signal peptide indicative of secretion and conserved cysteine residues.
Pfam PF13081: Domain of unknown function (DUF3941) (family)
This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 30 amino acids in length. There is a conserved YSK sequence motif.
Pfam PF13064: Protein of unknown function (DUF3927) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria and viruses. Proteins in this family are approximately 50 amino acids in length. There is a conserved SVL sequence motif. There is a single completely conserved residue D that may be functionally important.
Pfam PF09493: Tryptophan-rich protein (DUF2389) (family)
Members of this family are small hypothetical proteins of 60 to 100 residues from Cyanobacteria and some Proteobacteria. Prochlorococcus marinus strains have two members, other species one only. Interestingly, of the eight most conserved residues, four are aromatic and three are invariant tryptophans. It appears all species that encode this protein can synthesise tryptophan de novo.
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 PF18808: Importin repeat (repeat)
The importin subunit beta-3 has a superhelical structure composed of tandem repeats structurally similar to HEAT repeats. This Pfam  entry includes a single repeat unit.
Pfam PF18747: 5-hmdU DNA kinase 2 (family)
5-hmdU DNA kinase 2 from phages which phosphorylates 5-hydroxymethyluracil (5hmdU) into 5-phosphomethyl-2'-deoxyuridine (5-PmdU) on DNA as a step in the pathway leading to thymidine hypermodifications in the viral genome, probably prevent degradation of viral by the host restriction-modification antiviral defense system.
Pfam PF02938: GAD domain (domain)
This domain is found in some members of the GatB and aspartyl tRNA synthetases.
Pfam PF19303: Anticodon binding domain of methionyl tRNA ligase (domain)
This domain is found in methionyl tRNA ligase. The domain binds to the anticodon of the tRNA ligase.
Wikipedia: An aminoacyl-tRNA synthetase, also called tRNA-ligase, is an enzyme that attaches the appropriate amino acid onto its corresponding tRNA. It does so by catalyzing the transesterification of a specific cognate amino acid or its precursor to one of all its compatible cognate tRNAs to form an aminoacyl-tRNA. In humans, the 20 different types of aa-tRNA are made by the 20 different aminoacyl-tRNA synthetases, one for each amino acid of the genetic code.
Pfam PF19094: EMC6-arch (family)
This family represents the ER membrane protein complex subunit 6 (EMC6) homologue from archaea. They contain three transmembrane regions.
Pfam PF17232: Elicitor peptide 1-7 (family)
This entry include a group of elicitor peptides from plants, including Arabidopsis AtPEP1-7. AtPEP1 activates transcription of the defensive gene defensin (PDF1.2) and activates the synthesis of H(2)O(2), both being components of the innate immune response.
Pfam PF01786: Alternative oxidase (domain)
The alternative oxidase is used as a second terminal oxidase  in the mitochondria, electrons are transfered directly from reduced ubiquinol to oxygen forming water. This is not coupled to ATP synthesis and is not inhibited by cyanide, this pathway is a single step process. In rice the transcript levels of the alternative oxidase are increased by low temperature.
Wikipedia: The alternative oxidase (AOX) is an enzyme that forms part of the electron transport chain in mitochondria of different organisms. Proteins homologous to the mitochondrial oxidase and the related plastid terminal oxidase have also been identified in bacterial genomes.
Pfam PF07553: Host cell surface-exposed lipoprotein (domain)
This domain is found as 1 to 5 copies in lipoproteins that are involved in superinfection exclusion. Proteins in this group have been shown to act at the stage of DNA release from the phage head into the cell. This domain shows a three-helix bundle belonging to the HTH superfamily.
Pfam PF23266: VPS11-like, N-terminal beta-propeller (repeat)
This is the N-terminal beta-propeller domain of human Vacuolar protein sorting-associated protein 11 homolog (VPS11), which plays a role in vesicle-mediated protein trafficking to lysosomal compartments including the endocytic membrane transport and autophagic pathways.
Pfam PF18875: AF4 interaction motif (conserved_site)
This short motif found in the AF4 protein interacts with AF9.
Pfam PF11398: Protein of unknown function (DUF2813) (family)
This entry contains YjbD from Escherichia coli ([swissprot:P75828]), which is annotated as a nucleotide triphosphate hydrolase.
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 PF19443: DAHL domain (domain)
The DAHL (Double All-Helical Ligand-binding) domain is a novel periplasmic sensory domain, which is found in major types of bacterial signal transduction proteins: histidine kinases and diguanylate cyclases/phosphodiesterases, and, occasionally in chemoreceptors. The majority of the DAHL domain-containing proteins were found in alpha-, beta-, gamma- and epsilonproteobacteria. It is also present in some cyanobacterial species. Secondary structure prediction suggested that DAHL consists predominantly of alpha-helical regions. The DAHL domain was identified in the Tlp10 chemoreceptor from the human pathogen Campylobacter jejuni and in the VirA sensor histidine kinase from a plant pathogen Agrobacterium tumefaciens. This domain recognises Asp, Ile, purine, fumarate, malate, alpha-ketoglutarate, mannose, rhamnose, fucose, sialic acid, Arg, thiamine and galactose (Matilla et al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1 https://doi.org/10.1093/femsre/fuab043).
Pfam PF13791: Sigma factor regulator C-terminal (family)
This family is the C-terminal domain of a sigma factor regulator, this may represent a sensory domain.
Pfam PF14919: MDM2-binding (family)
MTBP, or MDM2-binding protein, binds to MDM2. The MDM2 protein, through its interaction with p53, plays an important role in the regulation of the G1 checkpoint of the cell cycle. MTBP promotes MDM2-mediated ubiquitination and degradation of p53 and also MDM2 stabilisation in an MDM2 RING finger-dependent manner. MTBP differentially regulates the E3 ubiquitin ligase activity of MDM2 towards two of its most critical targets (itself and p53) and in doing so significantly contributes to MDM2-dependent p53 homeostasis in unstressed cells. MTBP inhibits cancer cell migration by interacting with a protein involved in cell motility. This motility protein is alpha-actinin-4 (ACTN4). It is unclear which regions of MTBP interact with which binding-partner.  See PF14918, PF14920.
Pfam PF03519: Invasion protein B family (family)
The surface presentation of antigens protein SpaK (also known as InvB) from Salmonella typhimurium is involved in a secretory pathway responsible for the surface presentation of determinants needed for the entry of Salmonella species into mammalian cells . Other Spa genes in the cluster are related to invasion (Inv) genes in similar Salmonella and Shigella species , and to flagella biosynthesis genes in Helicobacter pylori . A further analogous gene in Yersinia (Spa15 homologue) has also been found .
Pfam PF13399: LytR cell envelope-related transcriptional attenuator (domain)
This family appears at the C-terminus of members of the LytR_cpsA_psr, [pfam:PF03816], family
Wikipedia: The LCP family or TagU family of proteins is a conserved family of phosphotransferases that are involved in the attachment of teichoic acid (TA) molecules to gram-positive cell wall or cell membrane. It was initially thought as the LytR component of a LytABC operon encoding autolysins, but the mechanism of regulation was later realized to be the production of TA molecules. It was accordingly renamed TagU.
Pfam PF09285: Elongation factor P, C-terminal (domain)
Members of this family of nucleic acid binding domains are predominantly found in elongation factor P, where they adopt an OB-fold, with five beta-strands forming a beta-barrel in a Greek-key topology.
Wikipedia: EF-P is an essential protein that in bacteria stimulates the formation of the first peptide bonds in protein synthesis. Studies show that EF-P prevents ribosomes from stalling during the synthesis of proteins containing consecutive prolines. EF-P binds to a site located between the binding site for the peptidyl tRNA and the exiting tRNA. It spans both ribosomal subunits with its amino-terminal domain positioned adjacent to the aminoacyl acceptor stem and its carboxyl-terminal domain positioned next to the anticodon stem-loop of the P site-bound initiator tRNA. The EF-P protein shape and size is very similar to a tRNA and interacts with the ribosome via the exit “E” site on the 30S subunit and the peptidyl-transferase center (PTC) of the 50S subunit. EF-P is a translation aspect of an unknown function, therefore It probably functions indirectly by altering the affinity of the ribosome for aminoacyl-tRNA, thus increasing their reactivity as acceptors for peptidyl transferase.
Pfam PF23886: Family of unknown function (DUF7239) (family)
This entry reprepsents a family of uncharacterised proteins found in mycobacterial phage.
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 PF19398: Lantibiotic duramycin B-like (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001577) is described by MIBiG as an example of the following biosynthetic class, RiPP (ribosomally synthesised and post-translationally modified peptide). It includes lantibiotic duramycin, duramycin B and cinnamycin. Duramycin B is a potent inhibitor of human phospholipase A2.
Pfam PF10189: Integrator complex subunit 3 N-terminal (repeat)
The Integrator complex is involved in small nuclear RNA (snRNA) U1 and U2 transcription, and in their 3'-box-dependent processing. This complex associates with the C-terminal domain of RNA polymerase II largest subunit and is  recruited to the U1 and U2 snRNAs genes. This entry  represents the N-terminal domain of the Integrator complex subunit 3 (Ints3), also known as SOSS complex subunit A (SOSSA). It is a component of the sensor of single-stranded DNA complex (SOSS), which associates with single-stranded DNA, important for DNA repair and efficient homologous recombination. This subunit serves as a central adaptor for SOSS complex assembly and stability, and facilitates the accumulation of the complex to the sites of DNA damage. This region acts as a scaffold for SOSSB1 and SOSSC interaction and it is not essential for ssDNA binding.
Pfam PF20326: Family of unknown function (DUF6621) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 200 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 PF19922: MoxR-vWA-beta-propeller ternary system domain bpX6 (domain)
Uncharacterized domain found in the MoxR-vWA-beta-propeller ternary system, a class of NTP-dependent biological conflict systems.
Pfam PF04941: Late expression factor 8 (LEF-8) (family)
Late expression factor 8 (LEF-8) is one of the primary components of RNA polymerase produced by polyhedrosis viruses. LEF-8 shows homology to the  second largest subunit of prokaryotic DNA-directed RNA polymerase.
Pfam PF11524: Selenium binding protein (family)
Selenium is an important nutrient that needs to be regulated since lack of the nutrient leads to cell abnormalities and high concentrations are toxic.  SeBP regulates the level of free selenium in the cell by sequestering the nutrient during transport. SeBP acts as a pentamer and delivers the selenium to the selenophosphate synthetase enzyme. Each subunit is composed of an alpha helix on top of a four stranded twisted ss sheet, stabilised by hydrogen bonds.
Pfam PF21003: Endonuclease NucS N-terminal PH-like domain (domain)
Endonuclease NucS cleaves both 3' and 5' ssDNA extremities of branched DNA structures and it binds to ssDNA. This entry represents the N-terminal PH-like domain of NucS.
Pfam PF00460: Flagella basal body rod protein (family)
Many bacterial species swim actively by means of flagella. The flagella organelle is made of three parts: the basal body, the hook and the filament. The basal body consists of four rings (L,P,S, and M) mounted on a central rod .

In Salmonella typhimurium and related organisms the rod has been shown to consist of four different, yet evolutionary related proteins: in the distal portion of the rod there are about 26 subunits of protein flgG and in the proximal portion there are about six subunits each of proteins flgB, flgC, and flgF. These four proteins contain a highly conserved asparagine-rich domain at their N terminus.
Pfam PF00128: Alpha amylase, catalytic domain (domain)
Alpha amylase is classified as family 13 of the glycosyl hydrolases. The structure is an 8 stranded alpha/beta barrel containing the  active site, interrupted by a ~70 a.a. calcium-binding domain  protruding between beta strand 3 and alpha helix 3, and a  carboxyl-terminal Greek key beta-barrel domain.
Wikipedia: α-Amylase is an enzyme that hydrolyses α bonds of large, α-linked polysaccharides, such as starch and glycogen, yielding shorter chains thereof, dextrins, and maltose, through the following biochemical process:Endohydrolysis of (1→4)-α-D-glucosidic linkages in polysaccharides containing three or more (1→4)-α-linked D-glucose units
Pfam PF21780: Domain of unknown function (DUF6875) (domain)
This entry represents family of uncharacterised proteins. They share an N-terminal CPF/Y motif that is characteristic of the NCPF superfamily of proteins.
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 PF08599: DNA damage repair protein Nbs1 (family)
This C terminal region of the DNA damage repair protein Nbs1 has been identified to be necessary for the binding of Mre11 and Tel1.
Pfam PF09288: Fungal ubiquitin-associated domain (domain)
Members of this family of ubiquitin binding domains adopt a structure consisting of a three alpha-helix bundle. They are predominantly found in fungal ubiquitin-protein ligases.
Pfam PF01257: Thioredoxin-like [2Fe-2S] ferredoxin (family)
Wikipedia: Respiratory complex I, EC 7.1.1.2 is the first large protein complex of the respiratory chains of many organisms from bacteria to humans. It catalyzes the transfer of electrons from NADH to coenzyme Q10 (CoQ10) and translocates protons across the inner mitochondrial membrane in eukaryotes or the plasma membrane of bacteria.
Pfam PF05564: Dormancy/auxin associated protein (family)
This family contains several plant dormancy-associated and auxin-repressed proteins the function of which are poorly understood.
Pfam PF07128: Protein of unknown function (DUF1380) (family)
This family consists of several hypothetical bacterial proteins of around 140 residues in length. Members of this family seem to be specific to Enterobacteria. 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 PF16247: Domain of unknown function (DUF4904) (domain)
This domain, approximately 130 residues in length, is mainly found in several uncharacterized proteins around 340 residues in Actinobacteria, Cyanobacteria and Metazoa species. It is mainly composed of antiparallel beta sheets and has a cystatin-like fold,  but the specific function of this family is unknown.
Pfam PF18643: BsaWI restriction endonuclease type 2 (domain)
Type II restriction endonucleases recognize short 4-8 bp nucleotide sequences and cleave phosphodiester bonds within or close to their target site. BsaWI restriction endonuclease from the thermophilic bacterium Bacillus stearothermophilus W1718 belongs to a group of restriction endonucleases that share CCGG motif within their target sites, termed 'CCGG-family'. However, the R-(D/E)R motif residues, which are supposed to recognize CCGG from the major groove side, are poorly ordered and located far away from the DNA bases. BsaWI contacts with the CCGG tetranucleotide from the minor groove side. It is folded into two domains an N-terminal helical domain and a C-terminal catalytic domain. Furthermore, it carries a PDXKXE motif at the putative active site.
Pfam PF01750: Hydrogenase maturation protease (domain)
The family consists of hydrogenase maturation proteases. In E. coli HypI the hydrogenase maturation protease is involved in processing of HypE the large subunit of hydrogenases 3, by cleavage of its C-terminal.
Wikipedia: In molecular biology, the hydrogenase maturation protease family is a family of aspartic endopeptidases belonging to MEROPS family A31.
Pfam PF24174: Bacterial deaminase MsddA-like domain (domain)
This domain is found in bacterial deaminases. Some members of this family also contain RHS repeats.
Pfam PF13514: AAA domain (domain)
This domain is found in a number of double-strand DNA break proteins. This domain contains a P-loop motif.
Wikipedia: AAA proteins are a large group of protein family sharing a common conserved module of approximately 230 amino acid residues. This is a large, functionally diverse protein family belonging to the AAA+ protein superfamily of ring-shaped P-loop NTPases, which exert their activity through the energy-dependent remodeling or translocation of macromolecules.
Pfam PF19806: Family of unknown function (DUF6289) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000385) is described by MIBiG as an example of the following biosynthetic class, NRP (non-ribosomal peptide), in  particular the lysobactin biosynthetic gene cluster from  Lysobacter sp. ATCC 53042.
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 PF13282: Domain of unknown function (DUF4070) (domain)
This is a bacterial domain often found at the C-terminus of Radical_SAM methylases.
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 PF09605: Hypothetical bacterial integral membrane protein (Trep_Strep) (family)
This family consists of strongly hydrophobic proteins about 190 amino acids in length with a strongly basic motif near the C-terminus. It is found in rather few species, but in paralogous families of 12 members in the oral pathogenic spirochaete Treponema denticola and 2 in Streptococcus pneumoniae R6.
Pfam PF03938: Outer membrane protein (OmpH-like) (domain)
This family includes outer membrane proteins such as OmpH among others. Skp (OmpH) has been characterised as a molecular chaperone that interacts with unfolded proteins as they emerge in the periplasm from the Sec translocation machinery.
Pfam PF04595: Poxvirus I6-like family (family)
This family includes I6 proteins as well as the related F5L proteins.
Pfam PF21043: Rv3651-like, C-terminal domain (domain)
This domain is found in Rv3651 from Mycobacterium tuberculosis (Swiss: I6YCP0) and similar proteins from Actinobacteria. Rv3651 adopts a three-domain configuration. This entry represents the C-terminal domain, a PAS domain that shows a central antiparallel beta-sheet of five beta-strands.
Pfam PF08612: TATA-binding related factor (TRF) of subunit 20 of Mediator complex (family)
This family of proteins is related to TATA-binding protein (TBP). TBP is a highly conserved RNA polymerase II general transcription factor that binds to the core promoter and initiates assembly of the preinitiation complex.  Human TRF has been shown to associate with an RNA polymerase II-SRB complex. This Med20 subunit of Mediator is found in the non-essential part of the head.
Wikipedia: Mediator is a multiprotein complex that functions as a transcriptional coactivator in all eukaryotes. It was discovered in 1990 in the lab of Roger D. Kornberg, recipient of the 2006 Nobel Prize in Chemistry. Mediator complexes interact with transcription factors and RNA polymerase II. The main function of mediator complexes is to transmit signals from the transcription factors to the polymerase.