SII-SWORD/CoKE huggingface dataset:
Pfam PF00265: Thymidine kinase (family)
Thymidine kinase (TK) (2.7.1.21) is an ubiquitous enzyme that catalyzes the ATP-dependent phosphorylation of thymidine.
Wikipedia: Thymidine kinase is an enzyme, a phosphotransferase : 2'-deoxythymidine kinase, ATP-thymidine 5'-phosphotransferase, EC 2.7.1.21. It can be found in most living cells. It is present in two forms in mammalian cells, TK1 and TK2. Certain viruses also have genetic information for expression of viral thymidine kinases.
Thymidine kinase catalyzes the reaction:Thd + ATP → TMP + ADP
Pfam PF00653: Inhibitor of Apoptosis domain (domain)
BIR stands for 'Baculovirus Inhibitor of apoptosis protein Repeat'. It is found repeated in inhibitor of apoptosis proteins (IAPs), and in fact it is also known as IAP repeat. These domains characteristically have a number of invariant residues, including 3 conserved cysteines and one conserved histidine that coordinate a zinc ion. They are usually made up of 4-5 alpha helices and a three-stranded beta-sheet. BIR is also found in other proteins known as BIR-domain-containing proteins (BIRPs), such as Survivin ([swissprot:O15392]).
Wikipedia: The inhibitor of apoptosis domain -- also known as IAP repeat, Baculovirus Inhibitor of apoptosis protein Repeat, or BIR -- is a structural motif found in proteins with roles in apoptosis, cytokine production, and chromosome segregation. Proteins containing BIR are known as inhibitor of apoptosis proteins (IAPs), or BIR-containing proteins, and include BIRC1 (NAIP), BIRC2 (cIAP1), BIRC3 (cIAP2), BIRC4 (xIAP), BIRC5 (survivin) and BIRC6.
Pfam PF17846: Xrn1 helical domain (domain)
This helical domain is part of the Xrn1 catalytic core. Xrn1 is a cytoplasmic 5'-3' exonuclease that degrades decapped mRNAs.
Pfam PF13090: Polyphosphate kinase C-terminal domain 2 (domain)
Polyphosphate kinase (Ppk) catalyses the formation of polyphosphate from ATP, with chain lengths of up to a thousand or more orthophosphate molecules. This C2-terminal domain has a structure similar to phospholipase D. It is one of two closely related carboxy-terminal domains (C1 and C2 domains). Both the C1 and C2 domains (residues 322-502 and 503-687, respectively) consist of a sevenstranded mixed beta-sheet flanked by five alpha-helices. However, the structural topology and relative orientations of the helices to the beta-sheet in these two domains are different. The C1 and C2 domains are highly conserved in the PPK family. Some of the residues previously shown to be crucial for the enzyme catalytic activity are located in these two domains.
Pfam PF12900: Pyridoxamine 5'-phosphate oxidase (family)
Pyridoxamine 5'-phosphate oxidase is a FMN flavoprotein that catalyses the oxidation of pyridoxamine-5-P (PMP) and pyridoxine-5-P (PNP) to pyridoxal-5-P (PLP).  This entry contains several pyridoxamine 5'-phosphate oxidases, and related proteins.
Pfam PF03442: Carbohydrate binding domain X2 (domain)
This domain binds to cellulose and to bacterial cell walls. It is found in glycosyl hydrolases and in scaffolding proteins of cellulosomes (multiprotein glycosyl hydrolase complexes). In the cellulosome it may aid cellulose degradation by anchoring the cellulosome to the bacterial cell wall and by binding it to its substrate. This domain has an Ig-like fold.
Pfam PF10544: T5orf172 domain (domain)
This domain was identified by Iyer and colleagues.
Pfam PF22421: Tyrosine--tRNA ligase SYY-like C-terminal domain (domain)
This entry represents the C-terminal domain of Tyrosine--tRNA ligases which contains the S4 motif  that binds RNA.
Pfam PF13945: Salt tolerance down-regulator (family)
NST1 is a family of proteins that seem to be involved, directly or indirectly, in the salt sensitivity of some cellular functions in yeast. It does this without affecting sodium accumulation. It negatively affects salt-tolerance through an interaction with the splicing factor Msl1p. This interaction stresses the importance of efficient RNA processing under salt stress conditions.
Pfam PF17627: Inclusion membrane protein E (family)
The chlamydial inclusion membrane is extensively modified by the insertion of type III secreted effector proteins. These inclusion membrane proteins (Incs) have two major characteristics: an N-terminal type III secretion signal that is necessary for their secretion out of the bacterium and a hydrophobic region consisting of at least two trans-membrane helices that allows insertion into the inclusion membrane. Generally, both the N- and C-terminal regions of the Inc are exposed to the host cell cytosol. This family has members such as the IncE (also known as CT116) proteins found in Chlamydia trachomatis. IncE Interacts with Retromer-Associated Sorting Nexins (SNXs) directly binding the PX-domains of SNX5/6. It is expressed within the first 2 hours of C. trachomatis infection. IncE region 101-132 is the binding site for SNX5/6 causing re-localization of SNX5/6 from endosomes to the inclusion membrane. IncE101-132 expression was shown to be sufficient to maintain CI-MPR (Cation-Independent Mannose-6-Phosphate Receptor) in retromer-containing compartments, thereby disrupting efficient CI-MPR trafficking to the trans-Golgi. It has been suggested that SNX5/6 bind directly to IncE independently of phosphoinositides and that the predicted IncE C-terminal beta-hairpin is required. IncE-mediated sequestration of retromer SNX-BAR proteins may promote Golgi fragmentation, a process that facilitates lipid acquisition by C. trachomatis and enhances progeny production.
Pfam PF24195: Family of unknown function (DUF7420) (family)
This entry represents an uncharacterised family of phage integral membrane proteins. The proteins are found in phage of S. aureus and B. subtilis. These proteins contain three potential transmembrane helices.  There is a conserved GXXPL motif that is highly conserved between helices 1 and 2.
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 PF05091: Eukaryotic translation initiation factor 3 subunit 7 (eIF-3) (family)
This family is made up of eukaryotic translation initiation factor 3 subunit 7 (eIF-3 zeta/eIF3 p66/eIF3d). Eukaryotic initiation factor 3 is a multi-subunit complex that is required for binding of mRNA to 40 S ribosomal subunits, stabilisation of ternary complex binding to 40 S subunits, and dissociation of 40 and 60 S subunits. These functions and the complex nature of eIF3 suggest multiple interactions with many components of the translational machinery. The gene coding for the protein has been implicated in cancer in mammals.
Pfam PF03594: Benzoate membrane transport protein (domain)
Several proteins in this entry have been identified as benzoate transporters . They exhibit about 30% identity to each other and show limited sequence similarity to members of the aromatic acid:H+symporter (AAHS) family of the major facilitator superfamily (MFS). Interestingly, they have different protein structures comparing to the MFS members. For instance, Corynebacterium glutamicum BenE (NCgl2326) is predicted to have 11 transmembrane Î±-helices, instead of 12 transmembrane Î±-helices found in the MFS members. BenE is also lacking some conserved domains/amino acids usually found in the MFS members . Therefore, BenE is thought to be a novel type of benzoate transporter. This family is classified as TC number 2.A.46 under the transporter classification (TC) system .
Pfam PF13640: 2OG-Fe(II) oxygenase superfamily (domain)
This family contains members of the 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily.
Pfam PF14449: Pre-toxin TG (family)
PT-TG is a conserved region found in many bacterial toxin proteins. It could function as a linker that links N-terminal secretion-related domain and C-terminal toxin domain. It contains a TG motif.
Pfam PF05972: APC 15 residue motif (conserved_site)
This motif, known as the 15 aa repeat, is found in the APC protein family. They are involved in binding beta-catenin along with the [pfam:PF05923] repeats. Many human cancer mutations map to the region around these motifs, and may be involved in disrupting their binding of beta-catenin.
Pfam PF22354: Hydrophobin (family)
This protein family includes Hydrophobin from Neurospora crassa (Eas) and similar fungal sequences. Eas contributes to surface hydrophobicity, which is important for processes such as association of hyphae in reproductive structures. Eas adopts a beta-barrel structure with several disordered regions, displaying a complete segregation of charged and hydrophobic residues on its surface, which is consistent with its ability to form an amphipathic polymer.
Pfam PF05092: Per os infectivity (family)
This is a family of dsDNA Baculovirus proteins. It is required for the infectivity of the OBs or occlusion bodies. It is a structural protein of the ODV envelope required only in the first steps of per os larva infection, as viruses being produced in cells expressing the gene for this protein but not containing it in their genomes are able to produce successful infections. Baculoviruses are large DNA viruses that infect arthropods, mainly members of the order Lepidoptera. In their life cycle, they produce two kinds of particles, a budded, non-occluded virus (BV), which buds out of the infected cell and is responsible for the cell-to-cell transmission of the virus, and an occluded form, the occlusion body (OB), which is responsible for protecting the virus between encounters with larvae. A variable number of virions are included in the para-crystalline structure of the OB, mainly constituted by the virus-encoded polyhedrin protein; these virions are called occlusion body-derived virions or ODVs.
Pfam PF06362: Protein of unknown function (DUF1067) (family)
This family consists of several hypothetical Mycobacterium leprae specific proteins. 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 PF19812: Family of unknown function (DUF6295) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0001922) is described by MIBiG as an example of the following biosynthetic class, polyketide, in particular the isoindolinomycin biosynthetic gene cluster from Streptomyces sp. SoC090715LN-16. This family 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 PF12575: Poxvirus entry protein complex L1 and I2 (family)
Pox_EPC_I2-L1 family of proteins is found in poxviruses. Proteins in this family are approximately 70 amino acids in length. There is a conserved YLK sequence motif.
Pfam PF21222: Lysosome-associated membrane glycoprotein 2, transmembrane segment (domain)
This domain is found in Lysosome-associated membrane glycoprotein 2 from humans (Lamp2) and similar proteins from vertebrates. Lamp2 is an integral membrane protein that plays an important role in chaperone-mediated autophagy (CMA), targeting pertinent proteins for lysosomal degradation. This protein is organised into two conserved luminal domains, a single transmembrane domain (this entry) and a short C-terminal cytosolic tail. It adopts a trimeric configuration, and the transmembrane domains of the three monomers form a three-helix bundle structure.
Pfam PF21407: Shedu protein SduA, N-terminal (domain)
This domain is found mostly in bacteria. It is found at the N-terminal of Shedu protein SduA, the only component of antiviral defense system Shedu. Expression of Shedu in B.subtilis (strain BEST7003) confers resistance to phages phi105, phi29, rho14 and to a lesser extent to SPP1.
Pfam PF00878: Cation-independent mannose-6-phosphate receptor repeat (family)
The cation-independent mannose-6-phosphate receptor contains 15 copies of a repeat.
Wikipedia: The mannose 6-phosphate receptors (MPRs) are transmembrane glycoproteins that target enzymes to lysosomes in vertebrates.
Pfam PF21499: DYN1, AAA+ ATPase lid domain (domain)
This entry includes dynein heavy chain (DYN1) from yeast, which is a cytoplasmic dynein that acts as a motor for intracellular retrograde motility of vesicles and organelles along microtubules. This entry represents the AAA+ ATPase lid domain.
Pfam PF20866: Phosphoribosyl-dephospho-CoA transferase MdcG N-terminal domain (domain)
This entry represents the N-terminal SH3-like domain from MdcG which is a phosphoribosyl-dephospho-CoA transferase that is involved in the biosynthesis of the prosthetic group of malonate decarboxylase.  Malonate decarboxylase from Klebsiella pneumoniae contains an acyl carrier protein (MdcC) to which a 2'-(5' '-phosphoribosyl)-3'-dephospho-CoA prosthetic group is attached via phosphodiester linkage. MdcG catalyses the following reaction: 2'-(5''-triphosphoribosyl)-3'-dephospho-CoA + apo-[acyl-carrier-protein] = holo-[acyl-carrier-protein] + diphosphate.
Pfam PF22781: Vertebrate Splicing regulator sde2, N-terminal ubiquitin domain (domain)
This entry represents the ubiquitin-fold domain found at the N -terminal of human Sde2 (Splicing regulator sde2, also known as silencing defective 2) and similar proteins from vertebrates. Sde2 in a splicing regulator that supports splicing of selected pre-mRNAs in an intron-specific manner.
Pfam PF16206: C-terminal region of Mon2 protein (family)
Mon2 proteins are found from fungi to plants, to human and is a scaffold protein involved in multiple aspects of endo membrane trafficking. This C-terminal region is essential for Mon2 activity.
Pfam PF17411: Type II site-specific deoxyribonuclease (family)
Family members of this domain are Type II site-specific deoxyribonuclease EC=3.1.21.4. The endonuclease SmaI [swissprot:P14229], recognizes and cleaves the sequence CCCGGGG on DNA, yielding a blunt end scission. It has been used for the diagnosis of neurogenic muscle weakness, ataxia and retinitis pigmentosa disease or Leigh's disease. Due to its specificity in recognizing the cleavage site, it is used in Leigh's disease to specifically eliminate the mutant mitochondrial DNA (mtDNA), which coexists with the wild-type mtDNA (heteroplasmy). Only the mutant mtDNA, but not the wild-type mtDNA, is selectively restricted by the enzyme. By delivering the SmaI gene fused to a mitochondrial targeting sequence, specific elimination of the mutant mtDNA was demonstrated, resulting in restoration of both the normal intracellular ATP level and normal mitochondrial membrane potential. The same strategy has also been demonstrated retinitis pigmentosa (NARP), where a mutant mitochondrial DNA carrying a T8993G transversion has been targeted by using SmaI enzymes.
Pfam PF16856: Cell division control protein 4 dimerisation domain (domain)
This is the dimerisation domain (D domain) of fungal cell division control protein 4.
Pfam PF21774: Hyaluronidase post-catalytic domain-like (domain)
This domain is located at the C-terminus of proteins that are members of family 84 glycoside hydrolases.These enzymes directly hydrolyse O-GlcNAcylated peptides/proteins. This domain folds into a five helical bundle with up-and-down topology. It may function in substrate binding or recognition.
Pfam PF07207: Light regulated protein Lir1 (family)
This family consists of several plant specific light regulated Lir1 proteins.     Lir1 mRNA accumulates in the light, reaching maximum and minimum steady-state levels at the end of the light and dark period, respectively. Plants germinated in the dark have very low levels of lir1 mRNA, whereas plants germinated in continuous light express lir1 at an intermediate but constant level. It is thought that lir1 expression is controlled by light and a circadian clock.  The exact function of this family is unclear.
Pfam PF00310: Glutamine amidotransferases class-II (domain)
A large group of biosynthetic enzymes are able to catalyse the removal of the ammonia group from glutamine and then to transfer this group to a substrate to form a new carbon-nitrogen group. This catalytic activity is known as glutamine amidotransferase (GATase) . The GATase domain exists either as a separate polypeptidic subunit or as part of a larger polypeptide fused in different ways to a synthase domain. On the basis of sequence similarities two classes of GATase domains have been identified : class-I (also known as trpG-type or triad) and class-II (also known as purF-type or Ntn). Class-II (or type 2) GATase domains have been found in the following enzymes:


 * Amido phosphoribosyltransferase (glutamine phosphoribosylpyrophosphate amidotransferase). An enzyme which catalyses the first step in purine biosynthesis, the transfer of the ammonia group of glutamine to PRPP to form 5-phosphoribosylamine (gene purF in bacteria, ADE4 in yeast).
 * Glucosamine--fructose-6-phosphate aminotransferase. This enzyme catalyses a key reaction in amino sugar synthesis, the formation of glucosamine 6-phosphate from fructose 6-phosphate and glutamine (gene glmS in Escherichia coli, nodM in Rhizobium, GFA1 in yeast).
 * Asparagine synthetase (glutamine-hydrolyzing). This enzyme is responsible for the synthesis of asparagine from aspartate and glutamine.
 * Glutamate synthase (gltS), an enzyme which participates in the ammonia assimilation process by catalysing the formation of glutamate from glutamine and 2-oxoglutarate. Glutamate synthase is a multicomponent iron-sulphur flavoprotein and three types occur which use a different electron donor: NADPH-dependent gltS (large chain), ferredoxin-dependent gltS and NADH-dependent gltS .


The active site is formed by a cysteine present at the N-terminal extremity of the mature form of all these enzymes . Two other conserved residues, Asn and Gly, form an oxyanion hole for stabilisation of the formed tetrahedral intermediate. An insert of ~120 residues can occur between the conserved regions . In some class-II GATases (for example in Bacillus subtilis or chicken amido phosphoribosyltransferase) the enzyme is synthesised with a short propeptide which is cleaved off post-translationally by a proposed autocatalytic mechanism. Nuclear-encoded Fd-dependent gltS have a longer propeptide which may contain a chloroplast-targeting peptide in addition to the propeptide that is excised on enzyme activation.

The 3-D structure of the GATase type 2 domain forms a four layer Î±/Î²/Î²/Î± architecture which consists of a fold similar to the N-terminal nucleophile (Ntn) hydrolases. These have the capacity for nucleophilic attack and the possibility of autocatalytic processing. The N-terminal position and the folding of the catalytic Cys differ strongly from the Cys-His-Glu triad which forms the active site of GATases of type 1.
Pfam PF10265: Mitoguardin (family)
Mitoguardin (Miga) was first identified in flies as a mitochondrial outer-membrane protein that promotes mitochondrial fusion. Later, the mammalian Miga homologues, Miga1 and Miga2, were identified. They are found to promote mitochondrial fusion by regulating mitochondrial phospholipid metabolism via MitoPLD.
Pfam PF06998: Protein of unknown function (DUF1307) (family)
This family consists of several hypothetical bacterial proteins of around 150 residues in length. Some family members are described as putative lipoproteins but the function of the 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 PF16598: Linker region of enhancer of mRNA-decapping protein 3 (family)
This region is located between the LSM14 [pfam:PF12701] (Lsm) and FDF [pfam:PF09532] domains of the enhancer of mRNA-decapping protein 3. This region is predicted to be natively unstructured. Its precise functional role is not known.
Pfam PF20935: Family of unknown function (DUF6847) (family)
This family represents bacterial uncharacterised proteins such as Uncharacterized conserved protein Dip1984 from Corynebacterium diphtheriae, which shows an all-alpha structure. Some members of this family are annotated as septicolysin, such as [swissprot:H6NMB2], a cholesterol-dependent pore-forming cytolysin that acts to facilitate the infection of certain pathogenic gram-positive 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 PF11144: Protein of unknown function (DUF2920) (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 PF19649: Family of unknown function (DUF6152) (family)
This family of proteins is functionally uncharacterised. This family of proteins is found in bacteria. Proteins in this family are typically between 122 and 152 amino acids in length. There are two conserved sequence motifs: AHH and NPH.
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 PF07708: Tash protein PEST motif (conserved_site)
This motif is found in the Tash AT-hook proteins of Theileria annulata. These proteins are transported to the hosts nucleus and are likely to be involved in pathogenesis. It is also often found in conjunction with [pfam:PF04385]. It is suggested that they may be 'part of PEST motifs' (a signal for rapid proteolytic degradation) in,  though this is not definite. This motif is also found in other T. annulata proteins, which have no other known domains in (unpublished data: C Yeats).