SII-SWORD/CoKE huggingface dataset:
Pfam PF17297: Phosphoenolpyruvate carboxykinase N-terminal domain (domain)
Catalyses the formation of phosphoenolpyruvate by decarboxylation of  oxaloacetate.
Wikipedia: Phosphoenolpyruvate carboxykinase is an enzyme in the lyase family used in the metabolic pathway of gluconeogenesis. It converts oxaloacetate into phosphoenolpyruvate and carbon dioxide.
Pfam PF19789: Domain of unknown function (DUF6273) (domain)
This domain is predominantly found in Firmicute bacterial proteins and is functionally uncharacterised. It is found in proteins that are likely to be surface exposed. It is predicted to fold into a globular structure with C-type lectin topology. This domain is frequently found in combination with other carbohydrate-binding domains implying that it may be involved in carbohydrate recognition/binding.
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 PF03345: OST48, N-terminal domain (domain)
Members of this entry are involved in asparagine-linked protein glycosylation. In particular, dolichyl-diphosphooligosaccharide-protein glycosyltransferase (DDOST), also known as oligosaccharyltransferase, transfers the high-mannose sugar GlcNAc(2)-Man(9)-Glc(3) from a dolichol-linked donor to an asparagine acceptor in a consensus Asn-X-Ser/Thr motif. In most eukaryotes, the DDOST complex is composed of three subunits, which in humans are described as a 48kD subunit, ribophorin I, and ribophorin II. However, the yeast DDOST appears to consist of six subunits (alpha, beta, gamma, delta, epsilon, zeta). The yeast beta subunit is a 45kD polypeptide, previously discovered as the Wbp1 protein, with known sequence similarity to the human 48kD subunit and the other orthologues. This is the N-terminal domain of OST48 subunits from animals and plants and the orthologue from yeast Wbp1. This domain is distantly related to the IFT52 N-terminal domain ([pfam:PF23355]).
Pfam PF24436: Integrator complex subunit 7, N-terminal (repeat)
Integrator complex subunit 7 (INTS7) is a component of the integrator complex, a complex that is recruited to the U1 and U2 snRNA genes and mediates the snRNAs' 3' end processing. The integrator complex interacts with the C-terminal tail of the largest subunit of RNA-polymerase II to promote 3'-snRNA processing. This entry represents the superhelical alpha-solenoid found at the N-terminal of INTS7. INTS7 interacts with INTS1 and INTS2 making extensive contacts with each other, nucleating the assembly of the whole INTAC complex.
Pfam PF21661: Domain of unknown function (DUF6860) (domain)
This is the N-terminal domain of uncharacterised proteins such as YhiJ from E.coli. According to AlphaFold model, this domain may have an alpha/beta structure consisting of five beta-sheets and three short alpha-helices.
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 PF17613: Modifier of transcription (family)
Family members are transcription regulation-related proteins found in Myoviridae such as Enterobacteria phage T4.
Pfam PF01481: Arterivirus nucleocapsid protein (family)
Arterivirus are ssRNA positive-strand viruses with no DNA stage in their replication cycle. This family contains the viral nucleocapsid protein, which encapsidates the viral ssRNA.

Porcine reproductive and respiratory syndrome virus (PRRSV) is the causative agent of both severe and persistent respiratory disease and reproductive failure in pigs worldwide. The PRRSV virion contains a core made of the 123 amino acid nucleocapsid (N or VP1) protein, a product of the ORF7 gene. The crystal structure of the capsid-forming domain of the nucleocapsid protein has been determined to 2.6 A resolution. The protein exists as a tight dimer forming a four-stranded Î² sheet floor superposed by two long Î± helices and flanked by two N- and two C-terminal Î± helices. The structure represents a new class of viral capsid-forming domains, distinctly different from those of other known enveloped viruses, but reminiscent of the coat protein of bacteriophage MS2 .
Pfam PF07295: Zinc-ribbon containing domain (family)
This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein.
Pfam PF11333: Protein of unknown function (DUF3135) (family)
This family of proteins with unkown function appears to be restricted to 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 PF10639: Putative transmembrane family 234 (family)
TMEM234 is a family of putative inner membrane proteins.  Many bacterial members are annotated as putative L-Ara4N-phosphoundecaprenol flippase subunit ArnE, and as inner membrane proteins. They may be transporters of the multi-drug-resistant superfamily.
Pfam PF23036: Trafficking protein particle complex subunit 10-like, N-terminal (domain)
This domain is found at the N-terminal end of human Trafficking protein particle complex subunit 10 (TRAPPC10), a specific subunit of the TRAPP (transport protein particle) II complex, a highly conserved vesicle tethering complex that functions in late Golgi trafficking as a membrane tether. It is predicted to adopt an alpha-beta configuration.
Pfam PF16811: TRAP transporter T-component (repeat)
TAtT is a family of one component, the T-component, of a sub-set of TRAP-Ts or Tripartite ATP-independent periplasmic transporters. TRAP-Ts are bacterial transport systems implicated in the import of small molecules into the cytoplasm in bacteria. They are all periplasmic lipoproteins. TatT consists of a 13-alpha-helical fold containing cryptic tetratricopeptide repeat motifs (cTPRs) and encompassing a pore, ie is a water-soluble trimer whose protomers are each perforated by a pore. It forms a complex with a P component, and a putative ligand-binding cleft of TatPT aligns with the pore of TatT. Family TatPT is represented by some members of [pfam:PF03480].
Pfam PF01682: DB module (family)
This domain has no known function. It is found in several C. elegans proteins. The domain contains 12 conserved cysteines that probably form six disulphide bridges. This domain is found associated with ig [pfam:PF00047] and fn3 [pfam:PF00041] domains, as well as in some lipases [pfam:PF00657].
Pfam PF08933: Monodechloroaminopyrrolnitrin synthase PrnB (family)
This protein family includes Monodechloroaminopyrrolnitrin synthase PrnB from Pseudomonas fluorescens and similar bacterial proteins. PrnB is involved in the biosynthesis of the antifungal compound pyrrolnitrin. It is organised into two domains: a small N-terminal capping domain that consists of 7 alpha-helices and the core helical domain, which is related to myoglobin. PrnB shows structural homology to the heme b-dependent two-domain indoleamine 2,3-dioxygenase enzyme (IDO, [pfam:PF01231]) and to the tryptophan 2,3-dioxygenase (TDO, [pfam:PF03301]) family.
Pfam PF21243: ECT2, BRCT0 domain (domain)
ECT2 (Epithelial Cell Transforming Sequence 2) is a guanine nucleotide exchange factor (GEF) that catalyses the exchange of GDP for GTP. It is a cell cycle regulator that plays key roles in cytokinesis. ECT2 contains triple copies of the BRCT domain (BRCT0, BRCT1 ([pfam:PF12738]) and BRCT2 ([pfam:PF00533]) at the N-terminal, separated from the C-terminal DH ([pfam:PF00621]) and PH ([pfam:PF21242]) domains by a linker of about 100 residues. This entry represents the first BRCT domain, BRCT0. The BRCT and DH-PH domains mediate intra-molecular interactions that restrains ETC2 activity during interphase.
Pfam PF12247: Temperature dependent protein affecting M2 dsRNA replication (family)
This domain family is found in eukaryotes, and is typically between 231 and 255 amino acids in length. There is a single completely conserved residue P that may be functionally important. MKT1 is required for maintenance of K2 toxin above 30 degrees C in strains with the L-A-HN variant of the L-A double-stranded RNA virus of Saccharomyces cerevisiae. MKT1 is a 93 kDa protein with serine-rich regions and the retroviral protease signature, DTG. This family is the N terminal region of MKT1.
Pfam PF04800: NADH dehydrogenase ubiquinone Fe-S protein 4 (family)
This entry represents NADH dehydrogenase [ubiquinone] iron-sulfur protein 4, an accessory subunit of the mitochondrial membrane respiratory chain NADH dehydrogenase (Complex I), initially identified in Neurospora crassa as a 21 kDa protein. It is believed that members of this family are not to be involved in catalysis.
Wikipedia: Respiratory complex I, EC 7.1.1.2 is the first large protein complex of the respiratory chains of many organisms from bacteria to humans. It catalyzes the transfer of electrons from NADH to coenzyme Q10 (CoQ10) and translocates protons across the inner mitochondrial membrane in eukaryotes or the plasma membrane of bacteria.
Pfam PF05797: Yeast trans-acting factor (REP1/REP2) (family)
This family consists of the yeast trans-acting factor B and C (REP1 and 2) proteins. The yeast plasmid stability system consists of two plasmid-coded proteins, Rep1 and Rep2, and a cis-acting locus, STB. The Rep proteins show both self- and cross-interactions in vivo and in vitro, and bind to the STB DNA with assistance from host factor(s). Within the yeast nucleus, the Rep1 and Rep2 proteins tightly associate with STB-containing plasmids into well organised plasmid foci that form a cohesive unit in partitioning. It is generally accepted that the protein-protein and DNA-protein interactions engendered by the Rep-STB system are central to plasmid partitioning. Point mutations in Rep1 that knock out interaction with Rep2 or with STB simultaneously block the ability of these Rep1 variants to support plasmid stability.
Pfam PF06143: Baculovirus 11 kDa family (family)
Family of uncharacterised Baculovirus proteins that are all about 11 kDa in size.
Pfam PF14579: Helix-hairpin-helix motif (domain)
The HHH domain is a short DNA-binding domain.
Pfam PF18018: DNA polymerase delta subunit OB-fold domain (domain)
The eukaryotic DNA polymerase delta (Pol delta) participates in genome replication, homologous recombination, DNA repair and damage tolerance. Human Pol delta consists of four subunits: p125, p50, p66 and p12. The first three subunits correspond to the three subunits of S. cerevisiae Pol delta. p50 serves as a scaffold for the assembly of Pol delta by interacting simultaneously with all of the other three subunits.  This entry corresponds to the OB fold domain found in the p50 subunit.
Pfam PF04691: Apolipoprotein C-I (ApoC-1) (family)
Apolipoprotein C-I (ApoC-1) is a water-soluble protein component of plasma lipoprotein.  It solubalises lipids and regulates lipid metabolism.  ApoC-1 transfers among HDL (high density lipoprotein), VLDL (very low-density lipoprotein) and chylomicrons.  ApoC-1 activates lecithin:choline acetyltransferase (LCAT), inhibits cholesteryl ester transfer protein, can inhibit hepatic lipase and phospholipase 2 and can stimulate cell growth. ApoC-1 delays the clearance of beta-VLDL by inhibiting its uptake via the LDL receptor-related pathway. ApoC-1 has been implicated in hypertriglyceridemia, and Alzheimer's disease.
Wikipedia: Apolipoprotein C-I is a protein component of lipoproteins that in humans is encoded by the APOC1 gene.
Pfam PF01122: Eukaryotic cobalamin-binding protein (repeat)
Cobalamin (Cbl or vitamin B12) is only accessible through diet in mammals. Absorption, plasma transport and cellular uptake of Cbl in mammals involves three Cbl-transporting proteins, which are listed below in order of increasing Cbl-specificity:


 * Haptocorrin (cobalophilin), which binds Cbl and Cbl-derivatives such as cobinamide; it may play a role in preventing the absorption of cobalamin analogues produced by bacteria.
 * Transcobalamin (TC), which transport Cbl from blood to cells.
 * Intrinsic factor (IF), which promotes Cbl absorption in the ileum by specific receptor-mediated endocytosis.


The structure of TC reveals a two-domain structure, an N-terminal Î±(6)-Î±(6) barrel, and a smaller C-terminal domain . Many interactions between Cbl and its binding site in the interface of the two domains are conserved among the other Cbl transporters. Specificity for Cbl between the different transporters may reside in a Î²-hairpin motif found in the smaller C-terminal domain .
Pfam PF06275: Protein of unknown function (DUF1031) (family)
This family consists of several Lactococcus lactis bacteriophage and Lactococcus lactis 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 PF19912: Domain of unknown function (DUF6385) (domain)
This presumed domain is functionally uncharacterised. This domain family is found in bacteria, and is approximately 80 amino acids in length. There is a conserved sequence motif SG.
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 PF22004: Small regulatory polypeptide of amino acid response (family)
This family represents human Small regulatory polypeptide of amino acid response (SPAR) and similar sequences from vertebrates. SPAR interacts with the lysosomal v-ATPase to negatively regulate the activation of the signalling complex mTORC1 upon stimulation with amino acids. It also acts as a regulator of muscle regeneration following injury.
Pfam PF23274: Domain of unknown function (DUF7077) (domain)
This domain is found in a group of uncharacterised proteins mainly from fungi. It shares a weak sequence similarity with the Ig-like domains found in Trs130, particularly the second Ig-like domain, and it is predicted to adopt a structure with a similar 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 PF22978: Peroxisome biogenesis protein 22, Haloacid dehydrogenase-like domain (domain)
This entry represents a HAD-like domain found in Pex22 proteins. Pex22 anchors Pex4 to the peroxisome membrane. PEX4 is a ubiquitin-conjugating enzyme (UBC) that ubiquitinates proteins associated with the peroxisomal membrane.
Pfam PF22461: SLBB domain (domain)
This entry represents a set of SLBB domains.
Pfam PF05202: Recombinase Flp protein (family)
Yeast Flp-like recombinases mediate the amplification of the 2 micron circular plasmid copy number by catalyzing the intra-molecular recombination between two inverted repeats during replication. They belong to the DNA breaking-rejoining enzyme superfamily, which also includes prokaryotic tyrosine recombinases and type IB topoisomerases. These enzymes share the same fold in their catalytic domain containing six conserved active site residues and the overall reaction mechanism. Flp-like recombinases are almost exclusively found in yeast and are highly diverged in sequence from the prokaryotic tyrosine recombinases. They cleave their target DNA in trans with a composite active site in which the catalytic tyrosine is provided by a promoter bound to a site other than the one being cleaved. Thus each active site within Flp complexes is assembled by domain swapping and contains catalytic residues from two different monomers. Two DNA segments are synapsed by the tetrameric enzyme, carrying the nucleophilic tyrosine in each active site with only two of the four monomers active at a given time. The catalytic domain is linked through a flexible loop to the N-terminal domain, which is largely responsible for non-specific DNA binding and isomerization. Its overall fold is similar to the SAM domain fold also found in the N-terminal domains of lambda integrase and XerD recombinase .
Pfam PF13972: Bacterial transcriptional repressor (family)
This family of bacterial transcriptional repressors is characterised by the short approximately 50 amino acid stretch of residues constituting the helix-turn-helix DNA binding motif, around the YRFhY motif. The target proteins that are repressed are involved in the transcriptional control of multi-drug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity.  The regulatory network in which TetR itself is involved is in being released in the presence of tetracycline, binding to the target operator, and repressing tetA transcription.
Pfam PF14292: SusE outer membrane protein (domain)
This family includes the SusE outer membrane protein from Bacteroides thetaiotaomicron, [swissprot:Q45769]. This protein has a role in starch utilisation, but is not essential for growth on starch.
Pfam PF21507: Sputnik minor capsid protein V18/19 (domain)
This entry includes Sputnik virus minor capsid proteins, such V19. Sputnik  is a dsDNA virus, referred to as a virophage, that is coassembled with Mimivirus in the host amoeba. It is an icosahedral virus and its capsid contains a major protein (V20) and two minor proteins (V18/19). Proteins in this entry have a single jelly-roll structure.
Pfam PF19392: Family of unknown function (DUF5967) (family)
This entry represents a member of a biosynthetic gene cluster (BGC). This BGC (BGC0000571) is described by MIBiG as an example of the following biosynthetic class, RiPP (ribosomally synthesised and post-translationally modified peptide).
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 PF22754: Plant bHLH transcription factor, ACT-like domain (domain)
This entry represents an ACT-like domain found at the C-terminal of plant transcription factors, such as transcription factor GLABRA 3 from Arabidopsis and the bHLH transcription factor (swissprot:A0A060CUZ2) from maize, which is associated with bHLH domains. This domain association is unique to the plantae kingdom. Phylogenetic analysis show that the association of ACT-like and bHLH domains occurred early in Plantae by recruitment of an ACT-like domain in a common ancestor with widely distributed ACT DOMAIN REPEAT (ACR) genes by an ancestral bHLH gene. The functional significance of this association relies on the homodimer formation of ACT-like domains that negatively affects DNA binding of the associated bHLH domains. For some bHLH transcription factors with the C-terminal ACT-like domain, such as Arabidopsis SPEECHLESS and MUTE, the ACT-like domain serves as heterodimerisation selectivity interface.
Pfam PF17979: Cysteine rich domain with multizinc binding regions (domain)
This is a cysteine rich domain which contains four zinc-binding regions (binding five zinc ions). Family members include human CHFR which interacts with Poly(ADP-ribose) (PAR) through a 20-amino acid PAR binding zinc finger region (PBZ) found at the C-terminal end of this cysteine-rich domain (i.e. the 4th region towards the C-terminal). CHFR lacking PBZ does not co-localize with nuclear PAR foci in interphase cells and cannot rescue antephase checkpoint function despite retaining autoubiquitination activity. Hence it has been suggested that the CHFR-PAR interaction is an important part of the antephase checkpoint and could form part of the checkpoint sensor for cellular stress and microtubule poisons or be required for proper localization of CHFR. The PBZ region of CHFR contains two adenine binding sites.
Pfam PF22351: TraH VirB8-like domain (domain)
This entry represents the VirB8-like domain present in TraH protein. TraH is part of the type IV secretion system (T4SS). This domain shows structural similarity to the VirB8 domain ([pfam:PF04335]).
Pfam PF12371: Transmembrane protein 131-like N-terminal (domain)
TMEM131_like is a family of bacterial, plant and other metazoa transmembrane proteins. Many of the members are multi-pass transmembrane proteins. This domain represents the N-terminal region which contains a conserved homology domain (CHD1).
Pfam PF14321: Domain of unknown function (DUF4382) (family)
This family is found in bacteria and archaea, and is typically between 142 and 161 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 PF19964: Effector-associated domain 11 (repeat)
Effector-associated domains (EADs) are predicted to function as adaptor domains mediating protein-protein interactions. The EADs show a characteristic architectural pattern. One copy is always fused, typically to the N- or C-terminus, of a core component of a biological conflict system; examples include VMAP, iSTAND, or GAP1. Further copies of the same EAD are fused to either effector or signal-transducing domains, or additional EADs. EAD pairs are frequently observed together on the genome in conserved gene neighborhoods, but can also be severed from such neighborhoods and located in distant regions, indicating EAD-EAD protein domain coupling attenuates collinear transcription requirements.