SII-SWORD/CoKE huggingface dataset:
Pfam PF12917: 5'-deoxynucleotidase YfbR-like (family)
This entry contains Escherichia coli (strain K12) YfbR. It a 5'-deoxynucleotidase that functions as a dCMP phosphohydrolase in a salvage pathway for the synthesis of dUMP in a dcd/deoA mutant. YfbR contains a conserved HD domain. YfbR has phosphatase activity with deoxyribonucleoside 5'-monophosphates and does not hydrolyze ribonucleotides or deoxyribonucloside 3'-monophosphates. Crystal structures of YfbR have been solved, it was suggested that the biological unit is a dimer. This family also includes phage HD domain-containing hydrolase-like enzymes, such as A0A2H5BHG9 and A0A2L0V156 from Acinetobacter phage SH-Ab15497, which are associated with PurZ,  an enzyme that catalyses the synthesis of diaminopurine (Z), a DNA modification that gives phages an advantage for evading host restriction enzymes activity. They have 2'-deoxyadenine 5'-triphosphate triphosphohydrolase (dATPase) activity and catalyse the hydrolysis of 2'-deoxyadenine 5'-triphosphate dATP to 2'-deoxyadenine (dA) and triphosphate. These enzymes are highly specific for dATP and also catalyse the hydrolysis of dADP and dAMP into dA, releasing pyrophosphate and phosphate, respectively. Thus, these dATPases facilitate the synthesis of Z-genome synthesis removing dATP and dADP from the nucleotide pool of the host.
Pfam PF23323: Kalirin-like, spectrin repeats (domain)
This entry represents a region of spectrin repeats found in human Kalirin (KALRN) and similar proteins mainly found in animals. KALRN activates specific Rho GTPase family members, thereby inducing various signalling mechanisms that regulate neuronal shape, growth, and plasticity, through their effects on the actin cytoskeleton.
Pfam PF00290: Tryptophan synthase alpha chain (domain)
Tryptophan synthase (4.2.1.20) catalyses the last step in the biosynthesis of tryptophan :

L-serine + 1-(indol-3-yl)glycerol 3-phosphate = L-tryptophan + glyceraldehyde 3-phosphate + H2O

It has two functional domains, each found in bacteria and plants on a separate subunit. In Escherichia coli, the two subunits, A and B, are encoded by the trpA and trpB genes respectively. The alpha chain is for the aldol cleavage of indoleglycerol phosphate to indole and glyceraldehyde 3-phosphate and the beta chain IPR006653 is for the synthesis of tryptophan from indole and serine. In fungi the two domains are fused together in a single multifunctional protein, in the order: (NH2-A-B-COOH) . The two domains of the Neurospora crassa polypeptide are linked by a connector of 54-amino acid residues that has less than 25% identity to the 45-residue connector of the Saccharomyces cerevisiae (Baker's yeast) polypeptide. Two acidic residues are believed to serve as proton donors/acceptors in the enzyme's catalytic mechanism.
Pfam PF18426: Tle cognate immunity protein 4 C-terminal domain (domain)
T6SS bacteria employ toxic effectors to inhibit rival cells and concurrently use effector cognate immunity proteins to protect their sibling cells. The effector and immunity pairs (E-I pairs) endow the bacteria with a great advantage in niche competition. This is the C-terminal domain of Tli4. The Tle cognate immunity proteins (Tlis) can directly disable the transported Tle protein and thereby mediate the self-protection process. The Tle-Tli effector-immunity (E-I) pairs confer substantial advantage to the donor cell during interbacterial competition. Tli4 displays a two-domain structure, in which a large lobe and a small lobe form a crab claw-like conformation. Tli4 uses this crab claw to grasp the cap domain of Tle4, especially the lid2 region, which prevents the interfacial activation of Tle4 and thus causes enzymatic dysfunction of Tle4. Structural comparison indicates similarity between this C-terminal domain of Tli4 and Tsi3, which is the cognate immunity protein of the effector protein Tse3 in P. aeruginosa PDB:4n7s.
Pfam PF04101: Glycosyltransferase family 28 C-terminal domain (domain)
The glycosyltransferase family 28 includes monogalactosyldiacylglycerol synthase ([swissprot:P93115], EC 2.4.1.46) and UDP-N-acetylglucosamine transferase ([swissprot:P74657], EC 2.4.1.-). Structural analysis suggests the C-terminal domain contains the UDP-GlcNAc binding site.
Pfam PF09455: CRISPR system endoribonuclease Csx1, HEPN domain (domain)
CRISPR system endoribonuclease Csx1 is a metal-independent, endoribonuclease that acts selectively on ssRNA and cleaves specifically after adenosines, as part of the type III-B CRISP-Cas system and it is homologous to Csm6, sharing the same domain domain architecture consisting of a CARF domain at the N-terminal that is relatively well conserved, and a HEPN nuclease domain at the C-terminal. This entry represents the HEPN domain, which is has less conservation except for the typical R-X4-H motif.
Pfam PF23622: At1g61320/AtMIF1, LRR domain (repeat)
This entry represents the leucine-rich repeats (LRR) found in plant proteins, such as At1g61320 and At1g61330  from Arabidopsis thaliana, F-box/LRR-repeat containing proteins involved in the ubiquitin-proteasome pathway. They function as components of SCF (SKP1-CUL1-F-box protein) E3 ubiquitin ligase complexes. They have a F-box domain at the N-terminal ([pfam:PF00646]). AtMIF1 (also known as F-box protein AT3G62230) from Arabidopsis, physically interacts with MYB domain protein 5 (MYB5), which results in MYB5 degradation representing a new regulatory pathway, 26S proteasome-AtMIF1-MYB5 that regulates oil content of seeds, increasing their oil content without affecting plant growth.
Pfam PF08197: pORF2a truncated protein (family)
Most isolated ORF2 of TT virus (TTV) encode a 49 amino acids protein  (pORF2a) because of an in-frame stop codon. ORF2s isolated from G1 TTV  encode 202 amino acids protein (pORF2ab).
Pfam PF10901: Protein of unknown function (DUF2690) (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 PF09055: Nickel-containing superoxide dismutase (domain)
Nickel containing superoxide dismutase (NiSOD) is a metalloenzyme containing a hexameric assembly of right-handed 4-helix bundles of up-down-up-down topology with an N-terminal His-Cys-X-X-Pro-Cys-Gly-X-Tyr motif that chelates the active site Ni ions. NiSOD catalyses the disproportionation of superoxide to peroxide and molecular oxygen through alternate oxidation and reduction of Ni, protecting cells from the toxic products of aerobic metabolism.
Wikipedia: Nickel superoxide dismutase (Ni-SOD) is a metalloenzyme that, like the other superoxide dismutases, protects cells from oxidative damage by catalyzing the disproportionation of the cytotoxic superoxide radical to hydrogen peroxide and molecular oxygen. Superoxide is a reactive oxygen species that is produced in large amounts during photosynthesis and aerobic cellular respiration. The equation for the disproportionation of superoxide is shown below:
Pfam PF12815: Spt5 C-terminal nonapeptide repeat binding Spt4 (repeat)
The C-terminal domain of the transcription elongation factor protein Spt5 is necessary for binding to Spt4 to form the functional complex that regulates early transcription elongation by RNA polymerase II. The complex may be involved in pre-mRNA processing through its association with mRNA capping enzymes. This CTD domain carries a regular nonapeptide repeat that can be present in up to 18 copies, as in S. pombe. The repeat has a characteristic TPA motif.
Pfam PF09816: RNA polymerase II transcription elongation factor (domain)
Members of this family act as transcriptional transactivators of ELL and ELL2 elongation activities. Eaf proteins form a stable heterodimer complex with ELL proteins to facilitate the binding of RNA polymerase II to activate transcription elongation. The N-terminus of approx 120 residues is globular and highly conserved.
Wikipedia: In molecular biology, the EAF family of proteins act as transcriptional transactivators of ELL and ELL2 RNA Polymerase II transcriptional elongation factors. EAF proteins form a stable heterodimer complex with ELL proteins to facilitate the binding of RNA polymerase II to activate transcription elongation. ELL and EAF1 are components of Cajal bodies, which have a role in leukemogenesis. EAF1 also has the capacity to interact with ELL1 and ELL2. The N terminus of approx 120 of EAF1 has a region of high serine, aspartic acid, and glutamic acid residues.
Pfam PF23985: Domain of unknown function (DUF7308) (domain)
This domain is found in uncharacterised archaeal proteins most of which likely associated with proteins located in pilBC operon. It is frequently found inserted in [[pfam:PF23960]]. This domain is predicted to fold into a globular structure with a beta-sandwich topology.
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 PF00175: Oxidoreductase NAD-binding domain (domain)
Xanthine dehydrogenases, that also bind FAD/NAD, have essentially no similarity.
Wikipedia: Oxidoreductase NAD-binding domain is an evolutionary conserved protein domain present in a variety of proteins that include, bacterial flavohemoprotein, mammalian NADH-cytochrome b5 reductase, eukaryotic NADPH-cytochrome P450 reductase, nitrate reductase from plants, nitric-oxide synthase, bacterial vanillate demethylase and others.
Pfam PF09566: SacI restriction endonuclease (family)
This family includes the SacI (recognises and cleaves GAGCT^C) restriction endonuclease.
Pfam PF02810: SEC-C motif (domain)
This SEC-C motif is found in the C-terminus of the SecA protein, in the middle of some SWI2 ATPases and also solo in several proteins. The motif chelates zinc with the CXC and C[HC] pairs that constitute the most conserved feature of the motif. In SecA, this zinc binding domain is involved in binding to SecB. This domain has been also predicted to be a potential nucleic acid binding domain.
Pfam PF22854: VEGFR1-3, N-terminal Ig-like domain (domain)
This entry represents the N-terminal Ig-like domain of Vascular endothelial growth factor receptor 1-3 from vertebrates. Members are tyrosine kinase receptors with seven Ig-like domains in its extracellular portion.
Pfam PF01189: 16S rRNA methyltransferase RsmB/F (family)
This is the catalytic core of this SAM-dependent 16S ribosomal methyltransferase RsmB/F enzyme. There is a catalytic cysteine residue at 180 in UniProtKB:Q5SII2, with another highly conserved cysteine at residue 230. It methylates the C(5) position of cytosine 2870 (m5C2870) in 25S rRNA.
Pfam PF08987: Protein of unknown function (DUF1892) (family)
Members of this family, that are synthesised by Saccharomycetes, adopt a structure consisting of a four-stranded beta-sheet, with strand order beta2-beta1-beta4-beta3, and two alpha-helices, with an overall topology of beta-beta-alpha-beta-beta-alpha. They have 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 PF19610: Family of unknown function (DUF6115) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 237 and 288 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 PF22541: Family of unknown function (DUF7005) (family)
This is a family of uncharacterised bacterial proteins. These proteins share partial sequence similarity to the collagenase catalytic core with invariant HExxH motif.
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 PF11110: Baseplate hub distal subunit (family)
These baseplate proteins are also referred to as Gp28. Gp28 is the structural component of the central part of the bacteriophage T4 baseplate, which possesses a hydrophobic region and is membrane bound. Gp28 forms a complex with gp27 which is another structural component of the baseplate.
Pfam PF00494: Squalene/phytoene synthase (domain)
Squalene synthase 2.5.1.21 (farnesyl-diphosphate farnesyltransferase)(SQS) and phytoene synthase 2.5.1.32 (PSY) share a number of functional similarities. These similarities are also reflected at the level of their primary structure . In particular three well conserved regions are shared by SQS and PSY; they could be involved in substrate binding and/or the catalytic mechanism. SQS catalyses the conversion of two molecules of farnesyl diphosphate (FPP) into squalene. It is the first committed step in the cholesterol biosynthetic pathway. The reaction carried out by SQS is catalysed in two separate steps: the first is a head-to-head condensation of the two molecules of FPP to form presqualene diphosphate; this intermediate is then rearranged in a NADP-dependent reduction, to form squalene:

2 FPP ->presqualene diphosphate + NADP ->squalene

SQS is found in eukaryotes. In yeast it is encoded by the ERG9 gene, in mammals by the FDFT1 gene. SQS seems to be membrane-bound.

PSY catalyses the conversion of two molecules of geranylgeranyl diphosphate (GGPP)into phytoene. It is the second step in the biosynthesis of carotenoids from isopentenyl diphosphate. The reaction carried out by PSY is catalysed in two separate steps: the first is a head-to-head condensation of the two molecules of GGPP to form prephytoene diphosphate; this intermediate is then rearranged to form phytoene:

2 GGPP ->prephytoene diphosphate ->phytoene

PSY is found in all organisms that synthesise carotenoids: plants and photosynthetic bacteria as well as some non-photosynthetic bacteria and fungi. In bacteria PSY is encoded by the gene crtB. In plants PSY is localised in the chloroplast.
Wikipedia: The squalene/phytoene synthase family represents proteins that catalyze the head-to-head condensation of C15 and C20 prenyl units (i.e. farnesyl diphosphate and genranylgeranyl diphosphate). This enzymatic step constitutes part of steroid and carotenoid biosynthesis pathway. Squalene synthase EC (SQS) and Phytoene synthase EC (PSY) are two well-known examples of this protein family and share a number of functional similarities. These similarities are also reflected in their primary structure. In particular three well conserved regions are shared by SQS and PSY; they could be involved in substrate binding and/or the catalytic mechanism. SQS catalyzes the conversion of two molecules of farnesyl diphosphate (FPP) into squalene. It is the first committed step in the cholesterol biosynthetic pathway. The reaction carried out by SQS is catalyzed in two separate steps: the first is a head-to-head condensation of the two molecules of FPP to form presqualene diphosphate; this intermediate is then rearranged in a NADP-dependent reduction, to form squalene:
Pfam PF18272: single-stranded DNA binding TraI N-terminal subdomain (domain)
This is a subdomain found in TraI present in E. coli. Tra1 is a conjugative relaxase that forms part of the Type IV secretion system. This subdomain, referred to as 2A, is located in N-terminal region of the translocation signal (TSA) domain. TSA is known to reside in a larger ssDNA-binding domain.
Pfam PF16256: Domain of unknown function (DUF4911) (family)
This family consists of uncharacterized proteins around 75 residues in length and is mainly found in various Thermotogav species. The  function of this family is unknown.
Pfam PF22126: C2c1 CRISPR-Cas endonuclease, RuvC-like domain (domain)
This entry represents the RuvC-like domain of C2c1 CRISPR-Cas endonuclease (also known as Cas12b). C2c1 is a class 2 type V-B effector protein that site-specifically targets and cleaves both strands of target DNA.
Pfam PF03377: TAL effector repeat (repeat)
The proteins in this family bind to DNA.  Each repeat binds to a base pair in a predictable way. The structure shows that each repeat is composed of two alpha helices.
Wikipedia: Transcription Activator-Like Effector-Likes (TALE-likes) are a group of bacterial DNA binding proteins named for the first and still best-studied group, the TALEs of Xanthomonas bacteria. TALEs are important factors in the plant diseases caused by Xanthomonas bacteria, but are known primarily for their role in biotechnology as programmable DNA binding proteins, particularly in the context of TALE nucleases. TALE-likes have additionally been found in many strains of the Ralstonia solanacearum bacterial species complex, in Paraburkholderia rhizoxinica strain HKI 454, and in two unknown marine bacteria. Whether or not all these proteins form a single phylogenetic grouping is as yet unclear.
Pfam PF12804: MobA-like NTP transferase domain (domain)
This family includes the MobA protein (Molybdopterin-guanine dinucleotide biosynthesis protein A). The family also includes a wide range of other NTP transferase domain.
Pfam PF24209: Domain of unknown function (DUF7431) (domain)
This entry represents the domain of unknown function found towards the C-terminal of some MACPF domain-containing proteins from fungi, such as SwissProt:A0A2P4PCT2. It is found associated with MACPF_1 ([pfam:PF22693]) domain.
Wikipedia: A domain of unknown function (DUF) is a protein domain that has no characterised function. These families have been collected together in the Pfam database using the prefix DUF followed by a number, with examples being DUF2992 and DUF1220. As of 2019, there are almost 4,000 DUF families within the Pfam database representing over 22% of known families. Some DUFs are not named using the nomenclature due to popular usage but are nevertheless DUFs.
Pfam PF02084: Bindin (family)
Bindin, the major protein component of the acrosome granule of sea urchin sperm, mediates species-specific adhesion of sperm to the egg surface during fertilisation . The protein coats the acrosomal process after externalisation by the acrosome reaction; it binds to sulphated, fucose-containing polysaccharides on the vitelline-layer receptor proteoglycans that cover the egg plasma membrane. Bindins from different genera show high levels of sequence similarity in both the mature bindin domain and in the probindin precursor region. The most highly conserved region is a 42-residue segment in the central portion of the mature bindin protein. This domain may be responsible for conserved functions of bindin, while the more highly divergent flanking regions may be responsible for its species-specific properties .
Pfam PF20976: Ribonucleases P/MRP protein subunit Pop8 (domain)
Pop8 is a component of ribonuclease P, a protein complex that generates mature tRNA molecules by cleaving their 5'-ends. It is also a component of Ribonuclease MRP, which cleaves pre-rRNA sequences. Ribonuclease P consists of an RNA moiety and at least 9 protein subunits including POP1, POP3, POP4, POP5, POP6, POP7, POP8, RPP1 and RPR2. Ribonuclease MRP complex consists of an RNA moiety and at least 10 protein subunits including POP1, POP3, POP4, POP5, POP6, POP7, POP8, RMP1, RPP1 and SNM1, many of which are shared with the Ribonuclease P complex. Pop8 interacts with Pop5 and Rpp1 to form the Pop5-Pop8-(Rpp1)2 heterotetramer, which is part of the arm module of the p[protein hook.
Pfam PF19634: Family of unknown function (DUF6137) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000709) is described by MIBiG as an example of the following biosynthetic class, saccharide. It includes a member from  the neomycin biosynthetic gene cluster from Streptomyces fradiae  ATCC 10745 = DSM 40063 and appears to be predominantly found in  bacteria.
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 PF01132: Elongation factor P (EF-P) OB domain (domain)
Elongation factor P (EF-P) is a prokaryotic protein translation factor required for efficient peptide bond synthesis on 70S ribosomes from fMet-tRNAfMet . EF-P enhances the synthesis of certain dipeptides with N-formylmethionyl-tRNA and puromycine in vitro. EF-P binds to both the 30S and 50S ribosomal subunits. EF-P binds near the streptomycine binding site of the 16S rRNA in the 30S subunit. EF-P interacts with domains 2 and 5 of the 23S rRNA. The L16 ribosomal protein of the 50S or its N-terminal fragment are required for EF-P mediated peptide bond synthesis, whereas L11, L15, and L7/L12 are not required in this reaction, suggesting that EF-P may function at a different ribosomal site than most other translation factors. EF-P is essential for cell viability and is required for protein synthesis. EF-P is mainly present in bacteria. The EF-P homologs in archaea and eukaryotes are the initiation factors aIF5A and eIF5A, respectively.
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 PF05717: IS66 Orf2 like protein (family)
This protein is found in insertion sequences related to IS66. The function of these proteins is uncertain, but they are probably essential for transposition.