SII-SWORD/CoKE huggingface dataset:
Pfam PF21982: RecX, first three-helix domain (domain)
This entry represents the first three-helix domain (HTH-like) found in RecX family of proteins. RecX functions as a regulator of DNA recombination and repair pathways in bacterial cells. RecX protein is known to inhibit the activity of RecA protein in DNA recombination.
Pfam PF20217: Family of unknown function (DUF6577) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria, mainly Bacteroidetes and Firmicutes. Proteins in this family are typically between 239 and 255 amino acids in length. There are some conserved sequences, GxY, EKxxVD and YAxxRR and a conserved His.
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 PF23385: IFT140 second beta-propeller (repeat)
IFT140 is one of the core components (together with WDR19/IFT144 and IFT122) of the IFT-A complex which is required for retrograde ciliary transport and entry into cilia of G protein-coupled receptors (GPCRs), being involved in cilia function and/or assembly. IFT-A polymerises interacts with IFT-B, and uses an array of beta-propeller and TPR domains to create 'carriages' of the IFT train that engage TULP adaptor proteins. The beta-propeller domains of IFT140 contact the beta-propeller domains of IFT121 from the adjacent complex. This entry represents the second beta-propeller of IFT140.
Pfam PF09081: Glucan 1,4-alpha-maltotetraohydrolase, domain C (domain)
This entry represents Domain C from Glucan 1,4-alpha- maltotetraohydrolase, which consists of five antiparallel beta-strands.
Pfam PF15993: Fuseless (family)
This family includes Drosophila fuseless protein and contains four WXGXW motifs. Fuseless is a transmembrane protein which regulates pre-synaptic calcium channels.
Pfam PF19730: Family of unknown function (DUF6221) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001065) is described by MIBiG as an example of the following biosynthetic class, polyketide. It includes a member from the herboxidiene biosynthetic gene cluster from Streptomyces  chromofuscus. This family appears to be predominantly found in  Actinobacteria.
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 PF10101: Predicted membrane protein (DUF2339) (family)
This domain, found in various hypothetical bacterial 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 PF06649: Protein of unknown function (DUF1161) (family)
This family consists of several short, hypothetical bacterial proteins of unknown 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 PF08353: MurT ligase C-terminal (domain)
This entry represents the C-terminal domain of MurT ligase from Gram-positive bacteria. MurT is part of the bi-enzymatic complex MurT-GatD involved in the amidation of the alpha-carboxyl group of the D-isoglutamate residue in Lipid II in the peptidoglycan layer to produce D-isoglutamine. This domain contains an aspartate at position 349, the third residue in the catalytic triad GatD-C94, GatD-H189, MurT-D349. This C-terminal domain is built around a central six-stranded, predominantly parallel beta-sheet that is sandwiched between four alpha-helices on one side and two alpha-helices on the other. The MurT-GatD heterodimer adopts a boomerang-shaped conformation, with GatD packing against the C-terminal domain of MurT.
Pfam PF20009: GEVED domain (domain)
Ths presumed domain is found in the CshA protein from Streptococcus gordonii.  The domain is named after the sequence found in CshA in the conserved C-terminal region. The conserved negatively charged residues suggests that this domain may bind to calcium ions. This domain is part of the non-repetitive region NR3.
Pfam PF01312: FlhB HrpN YscU SpaS Family (family)
This family includes the following members:   FlhB, HrpN, YscU, SpaS, HrcU SsaU and YopU. All of these proteins export peptides using the type III secretion system.  The peptides exported are quite diverse.
Pfam PF12549: Tyrosine hydroxylase N terminal (family)
This domain family is found in eukaryotes, and is approximately 30 amino acids in length. There is a single completely conserved residue G that may be functionally important. Tyrosine hydroxylase converts L-tyrosine to L-DOPA in the catecholamine synthesis pathway.
Pfam PF03135: CagE, TrbE, VirB family, component of type IV transporter system (family)
This family includes the Helicobacter pylori protein CagE [swissprot:Q48252], which together with other proteins from the cag pathogenicity island (PAI), encodes a type IV transporter secretion system.  The precise role of CagE is not known, but studies in animal models have shown that it is essential for pathogenesis in Helicobacter pylori induced gastritis and peptic ulceration. Indeed, the expression of the cag PAI has been shown to be essential for stimulating human gastric epithelial cell apoptosis in vitro. Similar type IV transport systems are also found in other bacteria. This family includes the TrbE [swissprot:P54910] and VirB [swissprot:P05353]  proteins from the respective trb and Vir conjugal transfer systems in Agrobacterium tumefaciens. Homologues of VirB proteins from other species are also members of this family, e.g. VirB from Brucella suis [swissprot:Q9RPY1].
Pfam PF23275: ESX-1 secretion-associated protein EspA-like, TPR repeats (repeat)
These predicted tetratrico peptide repeats (TPR) are found in ESX-1 secretion-associated protein EspA from Mycobacterium marinum and similar proteins from actinomycetes. This entry is found C-terminal to [pfam:PF22905] in some sequences.
Pfam PF02753: Pili assembly chaperone PapD, C-terminal domain (domain)
Ig-like beta-sandwich fold. This domain is the C-terminal part of the pilus and flagellar-assembly chaperone protein PapD.
Pfam PF22008: Restriction endonuclease BpuSI, specificity domain (domain)
This domain is found at the C-terminal end of the restriction endonuclease BpuSI from Bacillus pumilus ([swissprot:G1K3S1]) and similar bacterial sequences. BpuSI is a Type IIG restriction endonuclease that consists of three functional domains: an N-terminal domain [pfam:PF15516], a N-6 DNA Methylase domain [pfam:PF02384] and a C-terminal specificity domain (TRD, this entry), which includes a final domain with a mixed alpha/beta structure and unknown function.
Pfam PF20182: Family of unknown function (DUF6545) (family)
This entry represents an integral membrane protein of unknown function. Proteins in this family are found in a range of bacterial species.
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 PF14231: GXWXG protein (family)
This domain is found in bacteria and eukaryotes, and is approximately 60 amino acids in length. There is a conserved GXWXG motif. This domain is frequently found at the N-terminus of [pfam:PF14232].
Pfam PF15947: Domain of unknown function (DUF4755) (family)
This family of proteins is found in bacteria. Proteins in this family are approximately 160 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 PF15597: Immunity protein 59 (family)
A predicted immunity protein with an alpha+beta fold and a conserved [DE]R motif. Proteins containing this domain are present in bacterial polymorphic toxin systems as an immediate gene neighbour of the toxin gene, which usually contains toxin domains of the Ntox13 or Ntox40 families. In some proteins this domain is fused to the Imm38, [pfam:PF15599] immunity domain.
Pfam PF10182: Flo11 domain (domain)
This presumed domain is found at the N-terminus of the S. cerevisiae Flo11 protein. Flo11 is required for diploid pseudohyphal formation and haploid invasive growth. It belongs to a family of proteins involved in invasive growth, cell-cell adhesion, and mating, many of which can substitute for each other under abnormal conditions.
Pfam PF10475: Vacuolar-sorting protein 54, of GARP complex (repeat)
This is a family of vacuolar-sorting proteins 54, from eukaryotes. Along with VPS52 and VPS53 this forms the Golgi-associated retrograde protein complex GARP. VPS54 is separated into N- and C-terminal regions each of which has a different function. This N-terminal family of is important for GARP complex assembly and stability, whereas the C-terminal domain, [pfam:PF07928], brings about localisation to an early endocytic compartment.
Pfam PF04919: Protein of unknown function (DUF655) (family)
This family includes several uncharacterised archaeal proteins. This protein appears to contain two HHH motifs.
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 PF04556: DpnII restriction endonuclease (family)
Members of this family are type II restriction enzymes ([ec:3.1.21.4]).  They recognise the double-stranded unmethylated sequence GATC and cleave before G-1. http://rebase.neb.com/rebase/enz/DpnII.html
Wikipedia: In molecular biology, the DpnII restriction endonuclease family is a family of restriction endonucleases which includes DpnII from Diplococcus pneumoniae. These enzymes recognise the double-stranded DNA unmethylated sequence GATC and cleave before G-1, where it encompasses the full length of the protein.
Pfam PF01789: PsbP (domain)
This entry consists of the 23 kDa subunit of oxygen evolving system of photosystem II or PsbP from various plants (where it is encoded by the  nuclear genome) and Cyanobacteria (known as CyanoP). The 23 KDa PsbP protein is required for PSII to be fully operational in vivo, it increases the affinity of the water oxidation site for Cl- and  provides the conditions required for high affinity binding of Ca2+. Structure of CyanoP from Synechocystis sp. revealed that it has an alpha-beta-alpha fold containing 10 beta strands organized into two anti-parallel beta-sheets, packed against alpha-helices. This entry covers the first seven beta-stands (beta1-beta7) and the N-terminal alpha-helix.
Pfam PF07799: Protein of unknown function (DUF1643) (family)
The members of this family are all sequences found within hypothetical proteins expressed  by various bacterial species. The region  concerned is approximately 150 residues long.
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 PF21363: TNF receptor-associated factor 2/3/5, RING domain (domain)
This is the RING domain of TNF receptor-associated factors 2/3/5 (TRAFs2/3/5). The RING domain is common among ubiquitin E3 ligases and it is found at the N-terminal of TRAFs, followed by a series of zinc fingers and a C-terminal MATH/TRAF domain. This domain, together with the zinc fingers, is required for ligase activity.
Pfam PF14718: Soluble lytic murein transglycosylase L domain (repeat)
Soluble lytic murein transglycosylase (SLT) consists of three domains, an N-terminal U domain, an L domain (linker domain) and a C-terminal domain (C). The L domain may be involved in the interaction of the enzyme with peptidoglycan.
Pfam PF23289: Guanine nucleotide exchange factor DBS-like, spectrin-like (domain)
This spectrin-like domain is found in human Guanine nucleotide exchange factor DBS (MCF2L) and similar sequences mainly found in animals. MCF2L catalyses guanine nucleotide exchange on RHOA and CDC42, and thereby contributes to the regulation of RHOA and CDC42 signalling pathways. The spectrin domain-repeat forms a three helix bundle.
Pfam PF20026: Domain of unknown function (DUF6434) (domain)
This domain of unknown function is found in uncharacterised proteins mainly from bacteria, but it is also found in eukaryotes. Some proteins containing this domain also contain zinc finger C2H2-type domains. There are three conserved motifs: TxI/V, RxFF and FxF, and a conserved W/Y residue at the C-terminal.
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 PF20736: Beta-L-arabinofuranosidase, GH127 middle domain (domain)
This entry represents the first of two beta sandwich domains found in the beta-L-arabinofuranosidase enzyme, [ec:3.2.1.185]. This domain shows a similarity to C-terminal domains of GH44, GH27, and GH39 enzymes.
Pfam PF25088: GPKOW C-terminal domain (domain)
GPKOW (also known as T54 protein or MOS2 homologue) is a nuclear protein that is regulated by catalytic (C) subunit of Protein Kinase A (PKA) and binds RNA, being involved in pre-mRNA splicing. It is part of the minor spliceosome, involved in the splicing of U12-type introns in pre-mRNAs. This entry represents two tandem SH3-like domains found at the C-terminal of these proteins. The second SH3-like domain contains the second KOW motif of GPKOW (the first is represented in [pfam:PF00467]), which mediates RNA-binding.
Pfam PF00625: Guanylate kinase (domain)
This entry represents a domain found in guanylate kinase (2.7.4.8) and in L-type calcium channel.

Guanylate kinase (2.7.4.8) (GK)  catalyzes the ATP-dependent phosphorylation of GMP into GDP. It is essential for recycling GMP and indirectly, cGMP. In prokaryotes (such as Escherichia coli), lower eukaryotes (such as yeast) and in vertebrates, GK is a highly conserved monomeric protein of about 200 amino acids. GK has been shown  to be structurally similar to protein A57R (or SalG2R) from various strains of Vaccinia virus.

L-type calcium channnels are formed from different alpha-1 subunit isoforms that determine the pharmacological properties of the channel, since they form the drug binding domain. Other properties, such as gating voltage-dependence, G protein modulation and kinase susceptibility, are influenced by alpha-2, delta and beta subunits.
Wikipedia: In enzymology, a guanylate kinase is an enzyme that catalyzes the chemical reactionATP + GMP  ADP + GDP
Pfam PF03914: CBF/Mak21 family (repeat)
This domain is present in the CAATT-binding protein which is essential for growth and necessary for 60S ribosomal subunit biogenesis. Other proteins containing this domain stimulate transcription from the HSP70 promoter.
Pfam PF04549: CD47 transmembrane region (family)
This family represents the transmembrane region of CD47 leukocyte antigen.
Pfam PF04104: Eukaryotic and archaeal DNA primase, large subunit (family)
DNA primase is the polymerase that synthesises small RNA primers for the Okazaki fragments made during discontinuous DNA replication.  DNA primase is a heterodimer of two subunits, the small subunit Pri1 (48 kDa in yeast), and the large subunit Pri2 (58 kDa in the yeast S. cerevisiae).  The large subunit of DNA primase forms interactions with the small subunit and the structure implicates that it is not directly involved in catalysis, but plays roles in correctly positioning the primase/DNA complex, and in the transfer of RNA to DNA polymerase.
Wikipedia: DNA primase is an enzyme involved in the replication of DNA and is a type of RNA polymerase. Primase catalyzes the synthesis of a short RNA segment called a primer complementary to a ssDNA template. After this elongation, the RNA piece is removed by a 5' to 3' exonuclease and refilled with DNA.
Pfam PF18893: Family of unknown function (DUF5652) (domain)
This entry represents a protein containing two transmembrane helices. Many of these proteins are found in organisms in the Candidate Phyla Radiation.
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 PF21911: N-terminal domain in putative methyltransferase PG_1098 (domain)
This small alpha-helical domain is found at the N-terminus of putative methyltransferase proteins.
Pfam PF01877: RNA binding (family)
PH1010 [swissprot:O58738] is composed of five alpha-helices (1-5) and eight beta-strands (1-8) with the following topology: beta-1, alpha-1, beta-2, beta-3, alpha-2, alpha-3, beta-4, beta-5, alpha-4, beta-6, alpha-5, beta-7, beta-8. The first six beta-strands (1-6) form a slightly twisted antiparallel beta-sheet and face five alpha-helices on one side. The last two beta-strands form an antiparallel beta-sheet in the C-terminus. PH1010 forms a characteristic homodimer structure in the crystal.                 Dimerisation of the molecule is crucial for function. The structure resembles that of some ribosomal proteins such as the 50S ribosomal protein L5. Although the structure resembles that of the RRM-type RNA-binding domain of the ribosomal L5 protein, the residues involved in RNA-binding in the L5 protein are not conserved in this family. Despite this, these proteins bind to double-stranded RNA in a non-sequence specific manner.
Pfam PF15013: CCSMST1 family (family)
This family of proteins was discovered in a screen of Bos taurus placental ESTs. The B. taurus member of this family was named cattle cerebrum and skeletal muscle-specific transcript 1. This family of proteins is found in eukaryotes. Proteins in this family are typically between 97 and 157 amino acids in length. There is a single completely conserved residue D that may be functionally important. The function of this family is unknown.
Pfam PF20858: Immunodominant antigen Pgp3, N-terminal domain (domain)
This domain is found in Immunodominant antigen Pgp3, a virulence protein from Chlamydia trachomatis involved in stimulating host immune responses and thought to be required for growth within mammalian cells. Pgp3 consists of globular N- and C-terminal domains ([pfam:PF05475] is the latter) connected by a triple-helical coiled coil (THCC). The N-terminal domain (this entry), which includes several structural motifs typically found in trimeric viral proteins, folds into a fairly flat surface.
Pfam PF00735: Septin (domain)
Members of this family include CDC3, CDC10, CDC11 and CDC12/Septin.  Members of this family bind GTP. As regards the septins, these are polypeptides of 30-65kDa with three characteristic GTPase motifs (G-1, G-3 and G-4) that are similar to those of the Ras family. The G-4 motif is strictly conserved with a unique septin consensus of AKAD. Most septins are thought to have at least one coiled-coil region, which in some cases is necessary for intermolecular interactions that allow septins to polymerise to form rod-shaped complexes. In turn, these are arranged into tandem arrays to form filaments. They are multifunctional proteins, with roles in cytokinesis, sporulation, germ cell development, exocytosis and apoptosis.
Wikipedia: Septins are a group of GTP-binding proteins expressed in all eukaryotic cells except plants. Different septins form protein complexes with each other. These complexes can further assemble into filaments, rings and gauzes. Assembled as such, septins function in cells by localizing other proteins, either by providing a scaffold to which proteins can attach, or by forming a barrier preventing the diffusion of molecules from one compartment of the cell to another, or in the cell cortex as a barrier to the diffusion of membrane-bound proteins.
Pfam PF08436: 1-deoxy-D-xylulose 5-phosphate reductoisomerase C-terminal domain (domain)
This domain is found to the C-terminus of [pfam:PF02670] domains in bacterial and plant 1-deoxy-D-xylulose 5-phosphate reductoisomerases which catalyse the formation of 2-C-methyl-D-erythritol 4-phosphate from 1-deoxy-D-xylulose-5-phosphate in the presence of NADPH.
Wikipedia: DXP reductoisomerase is an enzyme that interconverts 1-deoxy-D-xylulose 5-phosphate (DXP) and 2-C-methyl-D-erythritol 4-phosphate (MEP).
Pfam PF00399: Yeast PIR protein repeat (repeat)
A number of yeast cell wall glycoproteins are characterised by the presence of tandem repeats of a region of 18 to 19 residues .
Pfam PF21746: Family of unknown function (DUF6869) (domain)
This short family of bacterial proteins contains a potential alpha helical solenoid structure. The function of these proteins is unknown. Proteins in this family are primarily found in Proteobacteria.
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 PF08569: Mo25-like (repeat)
Mo25-like proteins are involved in both polarised growth and cytokinesis.  In fission yeast Mo25 is localised alternately to the spindle pole body and to the site cell division in a cell cycle dependent manner.