SII-SWORD/CoKE huggingface dataset:
Pfam PF08829: Alpha C protein N terminal (domain)
The alpha C protein (ACP) is found in Streptococcus and acts as an invasin which plays a role in the internalisation and translocation of the organism across human epithelial surfaces. Group B Streptococcus is the leading cause of diseases including bacterial pneumonia, sepsis and meningitis. The N terminal of ACP is associated with virulence and forms a beta sandwich and a three helix bundle. ACP consists of an N-terminal domain (170 amino acids) followed by a variable number of tandem repeats (82 amino acids each) and a C-terminal domain (45 amino acids) containing an LPXTG peptidoglycan-anchoring motif. This entry is the N-terminal domain of ACP (NtACP). NtACP can be further divided into two structurally distinct domains, D1 and D2. D1, the more distal (amino-terminal) portion, consists of a beta sandwich with strong structural homology to fibronectin's integrin-binding region (FnIII10). D2 consists of three antiparallel alpha helix coils containing a portion of the glycosaminoglycan (GAG)-binding domain adjacent to the repeat region. NtACP binds to heparin and GAGs only when it is covalently associated with the adjacent repeat region. NtACP's D1 region contains a K144- T145-D146 (KTD) motif, located within a loop region that is structurally analogous to the loop containing the RGD integrin-binding motif in FnIII10. Single mutation within the KTD motif (D146A), present in the D1 domain, reduces NtACP binding to a1b integrion. The a1b1-integrin is one of four collagen-binding I-domain-containing integrins. Structural analysis of the D1 domain, in particular the region containing the putative integrin-binding loop and KTD motif, shares a strong structural homology with the FnIII10's integrin-binding region. Amino acid sequence alignment of Alps indicates that KTD is highly conserved.
Pfam PF15143: Domain of unknown function (DUF4575) (family)
This family of uncharacterised proteins is found in eukaryotes.
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 PF12320: Type 5 capsule protein repressor C-terminal domain (domain)
This domain is found in bacteria and archaea. This domain is about 90 amino acids in length. This domain is found associated with [pfam:PF00149]. SbcD works in complex with SbdC (SbcDC) which is a transcription regulator. It down-regulates transcription of arl and mgr to inhibit type 5 capsule protein production. It acts as part of the SOS pathway of bacteria.
Pfam PF12514: Protein of unknown function (DUF3718) (family)
This domain family is found in bacteria and viruses, and is approximately 70 amino acids in length. There is a single completely conserved residue C that may be functionally important.
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 PF14174: YycC-like protein (family)
The YycC-like protein family includes the B. subtilis YycC protein [swissprot:P37481], which is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are approximately 50 amino acids in length. There is a conserved HIL sequence motif.
Pfam PF17827: PrmC N-terminal domain (domain)
This entry corresponds to the N-terminal alpha helical domain of the HemK protein. HemK is a methyltransferase enzyme that carries out the methylation of the N5 nitrogen of the glutamine found in the conserved GGQ motif of class-1 release factors.
Pfam PF21939: Baseplate structural protein Gp10, C-terminal domain (domain)
This entry represents the C-terminal domain (CTD) of baseplate structural protein Gp10 that assembles into trimeric structures. The core structure and assembly of Gp10 has structural similarity to that of the head domain of Gp11 and the receptor binding domain of Gp12. The monomeric CTD of Gp10 consists of an alpha-helix followed by a three-stranded, antiparallel beta-sheet, which is almost perpendicular to the helix. The three symmetry related beta-sheets interact with their first beta-strands in the trimer, thus creating a flower-like arrangement with the alpha-helices being the flower stem and the three beta-sheets being the petals.
Pfam PF06597: Clostridium P-47 protein (family)
This family consists of several P-47 proteins from various Clostridium species as well as two related sequences from Pseudomonas putida. The function of this family is unknown.
Pfam PF02902: Ulp1 protease family, C-terminal catalytic domain (domain)
This domain contains the catalytic triad Cys-His-Asn.
Pfam PF00528: Binding-protein-dependent transport system inner membrane component (family)
The alignments cover the most conserved region of the proteins, which is thought to be located in a cytoplasmic loop between two transmembrane domains. The members of this family have a variable number of transmembrane helices.
Wikipedia: Bacterial binding protein-dependent transport systems, are multicomponent systems typically composed of a periplasmic substrate-binding protein, one or two reciprocally homologous integral inner-membrane proteins and one or two peripheral membrane ATP-binding proteins that couple energy to the active transport system. The integral inner-membrane proteins translocate the substrate across the membrane. It has been shown, that most of these proteins contain a conserved region located about 80 to 100 residues from their C-terminal extremity. This region seems to be located in a cytoplasmic loop between two transmembrane domains. Apart from the conserved region, the sequence of these proteins is quite divergent, and they have a variable number of transmembrane helices, however they can be classified into seven families which have been respectively termed: araH, cysTW, fecCD, hisMQ, livHM, malFG and oppBC.
Pfam PF15059: Speriolin C-terminus (family)
This family represents the C-terminus of the sperm centrosome protein speriolin.
Pfam PF24123: Myosin VII N-terminal beta barrel domain (domain)
This entry represents a small 5 stranded beta barrel domain found at the N-terminus of some myosin VII proteins.  Myosin-VII proteins are actin-based motor molecules with ATPase activity, playing crucial roles in intracellular movements and cellular projections. They function as single-molecule cargo transporters, maintaining tension in actin filaments. In the retina, they are involved in the renewal of photoreceptor disks and the regulation of opsin transport. In the inner ear, they contribute to the differentiation, morphogenesis, and organization of cochlear hair cell bundles, essential for normal hearing. Additionally, they play roles in epithelial brush border differentiation and microvilli organization.
Pfam PF17058: Mitochondrial biogenesis regulation protein 1 (family)
In yeast this protein participates in mitochondrial biogenesis and stress response. And also seems that may affect the NAM7 function, possibly at the level of mRNA turnover.
Pfam PF03838: Recombination protein U (domain)
This entry includes the Bacillus subtilis RecU protein and similar proteins predominantly found in Firmicutes. RecU has been shown to be required for DNA recombination and repair .
Pfam PF10057: Na+-translocating membrane potential-generating system (MpsC) (family)
This entry corresponds to the Na+-translocating membrane potential-generating system subunit MpsC.
Pfam PF07268: Exported protein precursor (EppA/BapA) (family)
This family consists of a number of exported protein precursor (EppA and BapA) sequences which seem to be specific to Borrelia burgdorferi (Lyme disease spirochete). bapA gene sequences are quite stable but the encoded proteins do not provoke a strong immune response in most individuals. Conversely, EppA proteins are much more antigenic but are more variable in sequence. It is thought that BapA and EppA play important roles during the Borrelia burgdorferi infectious cycle.
Pfam PF23144: Receptor-type tyrosine-protein phosphatase U Fn3 domain (domain)
This entry represents the fourth divergent fibronectin type 3 domain found in Receptor-type tyrosine-protein phosphatase U (PTPRU) and related proteins. This domain is closest to the transmembrane alpha helix.
Pfam PF14050: N-terminal conserved domain of Nudc. (family)
The N-terminus of nuclear distribution gene C homolog (NUDC) proteins contains a highly conserved region consisting of a predicted three helix bundle. In the human homolog this segment has been targeted for structure determination by the Joint Center for Structural Genomics.  NUDC forms a complex with other NUD proteins and is involved in several cellular division activities. Recently it was shown that NUDC regulates platelet-activating factor (PAF) acetylhydrolase with PAF being a pro-inflammatory secondary lipidic messenger.
Pfam PF20209: Domain of unknown function (DUF6570) (domain)
This entry represents a presumed domain of unknown function that is found in a wide range of proteins that includes eukaryotic transposon 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 PF11917: Protein of unknown function (DUF3435) (family)
This family of proteins are functionally uncharacterised. This protein is found in eukaryotes. Proteins in this family are typically between 435 to 791 amino acids in length. This family is related to [pfam:PF00589] suggesting it may be an integrase enzyme.
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 PF00575: S1 RNA binding domain (domain)
The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.
Wikipedia: The S1 domain is a protein domain that was originally identified in ribosomal protein S1 but is found in a large number of RNA-associated proteins. The structure of the S1 RNA-binding domain from the Escherichia coli polynucleotide phosphorylase has been determined using NMR methods and consists of a five-stranded antiparallel beta barrel. Conserved residues on one face of the barrel and adjacent loops form the putative RNA-binding site.
Pfam PF11463: R.HinP1I restriction endonuclease (family)
Hinp1I is a type II restriction endonuclease, recognising and cleaving a palindromic tetranucleotide sequence (G/CGC) resulting in 2 nt 5' overhanging ends. HINP1I has a conserved catalytic core domain containing an active site motif SDC18QXK and a DNA-binding domain.
Pfam PF20667: Exocyst complex component Sec10, N-terminal (repeat)
This entry contains the Sec10 component (approximately 650 residues long) of the eukaryotic exocyst complex, which mediates the tethering of post-Golgi secretory vesicles to the plasma membrane and promotes the assembly of the SNARE complex for membrane fusion. It is also involved in cell polarisation, primary ciliogenesis, cytokinesis, pathogen invasion, tumourigenesis and metastasis. The exocyst is a member of the Complex Associated with Tethering Containing Helical Rods (CATCHRs) which also includes DSL1, COG and GARP complexes, evolutionary related. They share structural features comprising alpha-helical bundles towards the C-terminal and coiled-coil regions at the N-terminal. This entry represents the N-terminal coiled-coil region (also referred to as CorEx motif) of Sec10 and its homologues from animals ECOC5 (Exocyst complex component 5), which participates in the central pair-wise interactions by forming an intact antiparallel 'zipper' which Sec15 subunit. Sec10-Sec15 CorEx motifs interact with Exo70-Exo84 dimers and form a four-helical bundle.
Pfam PF13930: DNA/RNA non-specific endonuclease (domain)
This entry includes EssD, which is a component of the type VII secretion system (Ess) and acts as a secretion factor for the Ess pathway in Staphylococcus aureus . Proteins containing this domain are part of the DNA/RNA non-specific endonuclease family that contains the His-Me finger fold, which is thought to be suited for efficient, nonspecific DNA cleavage .
Pfam PF06476: Protein of unknown function (DUF1090) (family)
This family consists of several bacterial proteins of unknown function and is known as YqjC in E. coli.
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 PF16351: Domain of unknown function (DUF4979) (family)
This family consists of uncharacterized proteins around 450 residues in length and is mainly found in various Bacteroides species. The function of this protein is unknown.
Pfam PF14320: Phosphoprotein P region PNT disordered (domain)
The N-terminal half of the phosphoprotein P of the Paramyxovirinae viruses.  The very first 60 residues have been built as the family Soyouz-module, [pfam:PF14313]. The remaining part of the region, here, is disordered, and is liable to induced folding under the right physiological conditions. The region undergoes an unstructured-to-structured transition upon binding to Measles virus tail, C, unstructured region.
Pfam PF13333: Integrase core domain (family)
The retroviral integrase is the enzyme responsible for the insertion of a DNA copy of the viral genome into host DNA, an essential step in the replication cycle of viruses . Integrases comprise three functional and structural domains: the central core domain, which contains the catalytic residues, an N-terminal zinc finger and a C-terminal DNA binding domain .

The integrase catalytic domain catalyses a series of reactions to integrate the viral genome into a host chromosome. In the first step, it removes two 3' end nucleotides from each strand of the linear viral DNA, leaving overhanging CA-OH ends. In the second step, the processed 3' ends are covalently joined to the 5' ends of the target DNA. In the third step, which probably involves additional cellular enzymes, unpaired nucleotides at the viral 5' ends are removed and the ends are joined to the target site 3' ends, generating an integrated provirus flanked by five base-pair direct repeats of the target site DNA .

The crystal structure of the catalytic domain shows a dimeric structure, with each monomer containing a five-stranded Î²-sheet and six Î±-helices . This fold is characteristic of the polynucleotidyltransferase superfamily whose members include RNase H, the bacteriophage Mu transposase, and the E. coli Holliday junction resolving enzyme, RuvC . The catalytic domain of integrase contains the DD35E triad motif. As in other DNA-binding proteins containing this motif, these acidic residues coordinate a divalent Mg2+ in the resting enzyme. Substituting any one of these residues abolishes both processing and integration activities of integrase.

The integrase catalytic domain is also found in various transposase proteins.
Pfam PF17299: Family of unknown function (DUF5350) (family)
This family is found in Euryarchaeota, predominantly in Methanomicrobia and Archaeoglobi. No known function for this family has been demonstrated.
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 PF12970: Domain of Unknown Function with PDB structure (DUF3858) (family)
This family is based on the third domain of the PDB structure 3KD4(residues 410-525).  It is structurally similar to part of neuropilin-2 (Z=4.6, rmsd 3.6A for 83 CA, 7% seq id).  This domain and the second domain appears to be part of peptide-n-glycanase (1x3w, 2g9f).
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 PF01339: CheB methylesterase (domain)
This entry represents the signal transduction response regulator CheB involved in chemotaxis. CheB methylesterase is responsible for removing the methyl group from the gamma-glutamyl methyl ester residues in the methyl-accepting chemotaxis proteins (MCP). The enzyme catalyses the reaction: protein L-glutamate O-methyl ester and water is converted to protein L-glutamate and methanol. CheB is regulated through phosphorylation by CheA. The N-terminal region of the protein is similar to that of other regulatory components of sensory transduction systems. The Myxococcus xanthus FrzG protein also belongs to this family, and is required for the normal aggregation of cells during fruiting body formation.
Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions . Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk . These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more . Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) . The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK.

A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response .
Wikipedia: The enzyme protein-glutamate methylesterase (EC 3.1.1.61) catalyzes the reactionprotein L-glutamate O 5-methyl ester + H2O  protein L-glutamate + methanol
Pfam PF21401: Cas3 inhibitor AcrF3 (domain)
AcrF3, a protein encoded by gene 35 from phage JBD5, has been reported to specifically inhibit the Cas3 protein of the P. aeruginosa PA14 strain (PaCas3) and to counteract the type I-F CRISPR-Cas system. AcrF3 eluted as a dimer in gel-filtration chromatography. In the complex structure, AcrF3 binds to PaCas3 at a ratio of 2:1, suggesting that AcrF3 functions as a homodimer that inhibits PaCas3. A single AcrF3 molecule has a two-layer architecture with six alpha-helices.
Pfam PF11306: Protein of unknown function (DUF3108) (domain)
This is a bacterial family of putative lipoproteins. The structure for [swissprot:Q64U78], PDB:3fzx, the first structural template for this large family including several homologues in the human gut microbiome and in metagenomic datasets, folds into a beta barrel that topologically looks like a small-scale porin (such as FepA). [swissprot:Q64U78] is a putative exported protein, and this fold is of the YmcC-like type, with a predicted signal peptide SpI cleavage site AGAMA|QNQDC, and a Phobius server prediction of non-cytoplasmic localisation for amino acids 21-236. The possibility of it being a membrane protein can be ruled out by the hydrophilic nature of the solvent exposed surface outside the barrels. Analysis of sequence conservation suggests that an area near Glu172/Trp206 is potentially interesting. These two residues are also conserved in Dali hit PDB:2in5, a hypothetical lipoprotein classified as a new YmcC-like fold in SCOP (SCOP:159271, with a 12-stranded meander beta-sheet folded into a deformed beta-barrel) despite large structural differences between the two structures, suggesting similarity in 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 PF17069: Arginine/Serine-Rich protein 1 (family)
RSRP1 is an eukaryotic protein family. Its function is unknown.
Pfam PF11312: Putative SAM-dependent methyltransferase (family)
This family of largely fungal proteins are likely to be a methyltransferase. This was determined through multiple motif screening in yeast.
Pfam PF00838: Translationally controlled tumour protein (domain)
Mammalian translationally controlled tumour protein (TCTP) (or P23) is a protein which has been found to be preferentially synthesised in cells during the early growth phase of some types of tumour , but which is also expressed in normal cells. The physiological function of TCTP is still not known. It was first identified as a histamine-releasing factor, acting in IgE +-dependent allergic reactions. In addition, TCTP has been shown to bind to tubulin in the cytoskeleton, has a high affinity for calcium, is the binding target for the antimalarial compound artemisinin, and is induced in vitamin D-dependent apoptosis. TCTP production is thought to be controlled at the translational as well as the transcriptional level .
Wikipedia: Translationally controlled tumor protein (TCTP) is a protein that in humans is encoded by the TPT1 gene. TPT1 is mapped to 13q12-q14 on chromosome 13. The human gene contains five introns and six exons, TPT1 contains a promoter with a canonical TATA-box and several promoter elements, which are well-conserved in mammals. The assay with reporter gene exhibits a strong promoter activity comparable to viral promoters.